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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:24:48 UTC
[01/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Repository: incubator-taverna-workbench-common-activities
Updated Branches:
refs/heads/master b4725724c -> 54050685c
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeNode.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeNode.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeNode.java
new file mode 100644
index 0000000..d1e98f7
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeNode.java
@@ -0,0 +1,81 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import org.dom4j.QName;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public abstract class XPathActivityXMLTreeNode extends DefaultMutableTreeNode
+{
+ protected static final int DISPLAY_LABEL_MAX_LENGTH = 200;
+
+ private final boolean isAttribute;
+
+ public XPathActivityXMLTreeNode(Object userObject, boolean isAttribute)
+ {
+ super(userObject);
+ this.isAttribute = isAttribute;
+ }
+
+ public boolean isAttribute() {
+ return (isAttribute);
+ }
+
+
+ public QName getNodeQName() {
+ if (this.isAttribute()) {
+ return (((XPathActivityXMLTreeAttributeNode)this).getAssociatedAttribute().getQName());
+ }
+ else {
+ return (((XPathActivityXMLTreeElementNode)this).getAssociatedElement().getQName());
+ }
+ }
+
+
+ public String getTreeNodeDisplayLabel(boolean bIncludeValue, boolean bIncludeElementNamespace, boolean bUseStyling)
+ {
+ if (this.isAttribute()) {
+ return (((XPathActivityXMLTreeAttributeNode)this).getTreeNodeDisplayLabel(bIncludeValue, bUseStyling));
+ }
+ else {
+ return (((XPathActivityXMLTreeElementNode)this).getTreeNodeDisplayLabel(bIncludeValue, bIncludeElementNamespace, bUseStyling));
+ }
+ }
+
+
+ protected String truncateElementTextValue(String textValue)
+ {
+ if (textValue != null && textValue.length() > DISPLAY_LABEL_MAX_LENGTH) {
+ textValue = textValue.substring(0, DISPLAY_LABEL_MAX_LENGTH) + "(...)";
+ }
+ return (textValue);
+ }
+
+
+ /**
+ * Tiny helper to strip out all HTML tags. This will not leave any HTML tags
+ * at all (so that the content can be displayed in DialogTextArea - and the
+ * like - components. This helps to present HTML content inside JAVA easier.
+ */
+ public static String stripAllHTML(String source) {
+ // don't do anything if not string is provided
+ if (source == null)
+ return ("");
+
+ // need to preserve at least all line breaks
+ // (ending and starting paragraph also make a line break)
+ source = source.replaceAll("</p>[\r\n]*<p>", "<br>");
+ source = source.replaceAll("\\<br/?\\>", "\n\n");
+
+ // strip all HTML
+ source = source.replaceAll("\\<.*?\\>", ""); // any HTML tags
+ source = source.replaceAll("&\\w{1,4};", ""); // this is for things like " ", ">", etc
+
+ return (source);
+ }
+
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeSelectionHandler.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeSelectionHandler.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeSelectionHandler.java
new file mode 100644
index 0000000..389bf1a
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeSelectionHandler.java
@@ -0,0 +1,251 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreeNode;
+import javax.swing.tree.TreePath;
+
+import net.sf.taverna.t2.activities.xpath.ui.config.XPathActivityConfigurationPanel;
+
+import org.dom4j.DocumentHelper;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityXMLTreeSelectionHandler implements TreeSelectionListener
+{
+ private final XPathActivityXMLTree theTree;
+ private final XPathActivityConfigurationPanel parentConfigPanel;
+
+
+ public XPathActivityXMLTreeSelectionHandler(XPathActivityConfigurationPanel parentConfigPanel,
+ XPathActivityXMLTree tree)
+ {
+ this.parentConfigPanel = parentConfigPanel;
+ this.theTree = tree;
+ }
+
+
+ public void valueChanged(TreeSelectionEvent e)
+ {
+ // get the newly made selection
+ TreePath newSelectedPath = e.getNewLeadSelectionPath();
+
+ // NB! Safety check - sometimes the container of the XML tree will remove all selections,
+ // in such case this listener is not supposed to perform any action -> terminate
+ if (newSelectedPath == null) return;
+
+
+ // --- XPath GENERATION ---
+
+ // get the XPath expression for the new selection + taking into consideration all previous ones
+ List<String> wildcardedXPath = generateWildcardedXPathExpression(newSelectedPath);
+
+ // assemble the xpath expression as one string
+ StringBuilder xpath = new StringBuilder();
+ for (String leg : wildcardedXPath) {
+ xpath.append(leg);
+ }
+ theTree.setCurrentXPathExpression(DocumentHelper.createXPath(xpath.toString()));
+ theTree.getCurrentXPathExpression().setNamespaceURIs(theTree.getCurrentXPathNamespaces());
+
+
+ // --- UPDATE CONFIG PANEL ---
+ // (with new values for XPath expression and namespace mappings)
+
+ // inform the parent activity configuration panel to update the XPath expression in the UI
+ /* We do not update the XPath expression after changes in selection in the XML tree - we
+ * now have a button to explicitly do that.
+ * theTree.getParentConfigPanel().updateXPathEditingPanelValues();
+ */
+
+ // --- SELECTION ---
+ selectAllNodesThatMatchTheCurrentXPath(wildcardedXPath, newSelectedPath);
+ }
+
+
+ /**
+ * Selects all nodes that match the <code>wildcardedXPath</code> expression.
+ *
+ * Keyboard focus is set to remain on the "deepest" (e.g. furthest from root)
+ * element of the <code>lastSelectedPath</code>.
+ *
+ * @param wildcardedXPath List of strings, where each string contains one "leg" of the XPath expression
+ * (e.g. a string starting with a "/" and containing the name of one node of the tree).
+ *
+ * @param lastSelectedPath The path that was last selected in the tree (normally,
+ * because of this selection {@link XPathActivityXMLTreeSelectionHandler#valueChanged(TreeSelectionEvent)}
+ * was executed and this method was started as a part of that.
+ */
+ public void selectAllNodesThatMatchTheCurrentXPath(List<String> wildcardedXPath, TreePath lastSelectedPath)
+ {
+ // first of all - calculate the number of nodes that match this XPath
+ // expression in the XML tree
+ int numberOfMatchingNodes = parentConfigPanel.runXPath(false);
+
+
+ // store all tree selection listeners in order to temporarily remove them;
+ // this is necessary as selection modifications will be made here -- don't
+ // want any listeners to respond to these new events
+ theTree.removeAllSelectionListeners();
+
+
+ // remove all previous selections - safest way to get the new ones correctly
+ theTree.clearSelection();
+
+
+ if (numberOfMatchingNodes <= XPathActivityConfigurationPanel.MAX_NUMBER_OF_MATCHING_NODES_TO_HIGHLIGHT_IN_THE_TREE)
+ {
+ // find all nodes that match the XPath expression
+ List<XPathActivityXMLTreeNode> matchingNodes = new ArrayList<XPathActivityXMLTreeNode>();
+ findAllNodesThatMatchWildcardedXPath(
+ (XPathActivityXMLTreeNode)theTree.getModel().getRoot(),
+ wildcardedXPath.subList(1, wildcardedXPath.size()),
+ matchingNodes);
+
+ // obtain and select TreePaths for each of the matching nodes
+ for (XPathActivityXMLTreeNode matchingNode : matchingNodes) {
+ TreeNode[] pathAsObjects = ((DefaultTreeModel)theTree.getModel()).getPathToRoot(matchingNode);
+ TreePath path = new TreePath(pathAsObjects);
+ selectTreePathAndAllItsAncestors(path);
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog(parentConfigPanel,
+ "Current XPath expression matches " + numberOfMatchingNodes + " nodes in the XML tree.\n" +
+ "The XPath Activity is unable to highlight all these nodes in the tree due to\n" +
+ "performance reasons.\n\n" +
+ "The XPath Activity will still work correctly - both during the workflow execution\n" +
+ "and if 'Run XPath' button is clicked to run this expression against the example XML.",
+ "XPath Activity", JOptionPane.INFORMATION_MESSAGE);
+ }
+
+
+ // make sure the keyboard focus stays on the actual node that was clicked on -
+ // no direct way to do this, so simply de-select and re-select again
+ if (lastSelectedPath != null) {
+ theTree.removeSelectionPath(lastSelectedPath);
+ theTree.addSelectionPath(lastSelectedPath);
+ }
+
+ // restore all previously stored selection listeners
+ theTree.restoreAllSelectionListeners();
+ }
+
+
+
+ /**
+ * This cannot work for XPath expressions that were modified manually -
+ * only works for the type generated by the click in the XML tree.
+ *
+ * @param nodeToStartAt
+ * @param xpathLegs From <code>nodeToStartAt</code>.
+ * @param matchingNodes
+ */
+ private void findAllNodesThatMatchWildcardedXPath(XPathActivityXMLTreeNode nodeToStartAt,
+ List<String> xpathLegs, List<XPathActivityXMLTreeNode> matchingNodes)
+ {
+ // some of the input data is missing, just return...
+ if (nodeToStartAt == null || xpathLegs == null || matchingNodes == null) {
+ return;
+ }
+
+ // no XPath expression to match against the 'nodeToStartAt', therefore
+ // we've "found" the macthing node: 'nodeToStartAt'
+ if (xpathLegs.size() == 0) {
+ matchingNodes.add(nodeToStartAt);
+ return;
+ }
+
+ // standard case - there is something to match, proceed as normal
+ Enumeration<XPathActivityXMLTreeNode> startNodeChildren = nodeToStartAt.children();
+ while (startNodeChildren.hasMoreElements()) {
+ XPathActivityXMLTreeNode child = startNodeChildren.nextElement();
+
+ if (xpathLegs.get(0).equals("/*") ||
+ xpathLegs.get(0).equals(this.theTree.getXMLTreeNodeEffectiveQualifiedNameAsXPathLeg(child)))
+ {
+ // this node matches current section of the XPath expression
+ if (xpathLegs.size() == 1) {
+ // no more sections in the XPath leg list to match, so this child
+ // node is the one we were looking for - add to the result
+ matchingNodes.add(child);
+ }
+ else {
+ // ...or process its children recursively
+ findAllNodesThatMatchWildcardedXPath(child, xpathLegs.subList(1, xpathLegs.size()), matchingNodes);
+ }
+ }
+ }
+ }
+
+
+ private List<String> generateWildcardedXPathExpression(TreePath newSelectedPath)
+ {
+ // look through previous selection to find paths of the same length, as the newly selected one
+ List<TreePath> pathsOfSameLength = new ArrayList<TreePath>();
+ TreePath[] previouslySelectedPaths = theTree.getSelectionPaths();
+ for (TreePath path : previouslySelectedPaths) {
+ if (path.getPathCount() == newSelectedPath.getPathCount()) {
+ pathsOfSameLength.add(path);
+ }
+ }
+
+ // if there were found any paths of the same length, we have a "wildcard" situation
+ List<String> wildcardXPathLegs = theTree.generateXPathFromTreePathAsLegList(newSelectedPath);
+
+ if (pathsOfSameLength.size() > 0)
+ {
+ // it's okay to use just the first path - TODO: explain that this is because of previous comparisons
+ List<String> firstMatchingLengthPathLegs = theTree.generateXPathFromTreePathAsLegList(pathsOfSameLength.get(0));
+
+ int pathLength = wildcardXPathLegs.size();
+
+ // only use wildcards if the last segments of both paths are identical
+ if (wildcardXPathLegs.get(pathLength - 1).equals(firstMatchingLengthPathLegs.get(pathLength - 1)))
+ {
+ // continue all the way to the last segment, but don't touch it
+ for (int i = 0; i < wildcardXPathLegs.size() - 1; i++)
+ {
+ if (!wildcardXPathLegs.get(i).equals(firstMatchingLengthPathLegs.get(i))) {
+ // set wildcard
+ // TODO - make wildcard a constant
+ // TODO - may need to make the wildcard to have a namespace? (e.g. "/default:*" instead of simply "/*")
+ wildcardXPathLegs.set(i, "/*"); // definitely an element, not an attribute (as not the last segment in the path)
+ }
+ }
+ }
+ }
+
+ return (wildcardXPathLegs);
+ }
+
+
+
+ private void selectTreePathAndAllItsAncestors(TreePath path)
+ {
+ // select all ancestors of that path
+ TreePath pathToSelect = path;
+ for (int i = 0; i < path.getPathCount(); i++)
+ {
+ pathToSelect = pathToSelect.getParentPath();
+ theTree.addSelectionPath(pathToSelect);
+ }
+
+ // select the specified path itself
+ //
+ // NB! important to do this after the ancestors, so that the supplied
+ // path is the one that retains the keyboard focus after this method terminates
+ theTree.addSelectionPath(path);
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/ConfigureXPathActivityMenuAction.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/ConfigureXPathActivityMenuAction.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/ConfigureXPathActivityMenuAction.java
new file mode 100644
index 0000000..6695dc9
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/ConfigureXPathActivityMenuAction.java
@@ -0,0 +1,65 @@
+package net.sf.taverna.t2.activities.xpath.ui.contextualview;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.xpath.ui.config.XPathActivityConfigureAction;
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+/**
+ * This action is responsible for enabling the contextual menu entry on processors that perform
+ * XPathActivity'ies.
+ * NB! As a side-effect this also enables the pop-up with for configuration of the processor when it
+ * is added to the workflow from the Service Panel.
+ *
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class ConfigureXPathActivityMenuAction extends AbstractConfigureActivityMenuAction {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public ConfigureXPathActivityMenuAction() {
+ super(XPathTemplateService.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ XPathActivityConfigureAction configAction = new XPathActivityConfigureAction(
+ findActivity(), getParentFrame(), editManager, fileManager, activityIconManager,
+ serviceDescriptionRegistry, serviceRegistry);
+ configAction.putValue(Action.NAME, "Configure XPath service");
+ addMenuDots(configAction);
+ return configAction;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextViewFactory.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextViewFactory.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextViewFactory.java
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index 0000000..355ab8d
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+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextViewFactory.java
@@ -0,0 +1,59 @@
+package net.sf.taverna.t2.activities.xpath.ui.contextualview;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityMainContextViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public boolean canHandle(Object selection) {
+ return selection instanceof Activity
+ && ((Activity) selection).getType()
+ .equals(XPathTemplateService.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity selection) {
+ return Arrays.<ContextualView> asList(new XPathActivityMainContextualView(selection,
+ editManager, fileManager, activityIconManager, serviceDescriptionRegistry,
+ serviceRegistry));
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextualView.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextualView.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextualView.java
new file mode 100644
index 0000000..d872228
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/contextualview/XPathActivityMainContextualView.java
@@ -0,0 +1,209 @@
+package net.sf.taverna.t2.activities.xpath.ui.contextualview;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.Action;
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.table.DefaultTableModel;
+
+import net.sf.taverna.t2.activities.xpath.ui.config.XPathActivityConfigureAction;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class XPathActivityMainContextualView extends ContextualView {
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private XPathActivityMainContextualView thisContextualView;
+
+ private final Activity activity;
+
+ private JPanel jpMainPanel;
+ private JTextField tfXPathExpression;
+
+ private DefaultTableModel xpathNamespaceMappingsTableModel;
+ private JTable jtXPathNamespaceMappings;
+ private JScrollPane spXPathNamespaceMappings;
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final ServiceRegistry serviceRegistry;
+
+ public XPathActivityMainContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.serviceRegistry = serviceRegistry;
+ this.thisContextualView = this;
+ this.activity = activity;
+ initView();
+ }
+
+ @Override
+ public JComponent getMainFrame() {
+ jpMainPanel = new JPanel(new GridBagLayout());
+ jpMainPanel.setBorder(BorderFactory.createCompoundBorder(
+ BorderFactory.createEmptyBorder(4, 2, 4, 2), BorderFactory.createEmptyBorder()));
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.WEST;
+ c.weighty = 0;
+
+ // --- XPath Expression ---
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.insets = new Insets(5, 5, 5, 5);
+ JLabel jlXPathExpression = new JLabel("XPath Expression:");
+ jlXPathExpression.setFont(jlXPathExpression.getFont().deriveFont(Font.BOLD));
+ jpMainPanel.add(jlXPathExpression, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ tfXPathExpression = new JTextField();
+ tfXPathExpression.setEditable(false);
+ jpMainPanel.add(tfXPathExpression, c);
+
+ // --- Label to Show/Hide Mapping Table ---
+
+ final JLabel jlShowHideNamespaceMappings = new JLabel("Show namespace mappings...");
+ jlShowHideNamespaceMappings.setForeground(Color.BLUE);
+ jlShowHideNamespaceMappings.setCursor(new Cursor(Cursor.HAND_CURSOR));
+ jlShowHideNamespaceMappings.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ spXPathNamespaceMappings.setVisible(!spXPathNamespaceMappings.isVisible());
+ jlShowHideNamespaceMappings.setText((spXPathNamespaceMappings.isVisible() ? "Hide"
+ : "Show") + " namespace mappings...");
+ thisContextualView.revalidate();
+ }
+ });
+
+ c.gridx = 0;
+ c.gridy++;
+ c.gridwidth = 2;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ jpMainPanel.add(jlShowHideNamespaceMappings, c);
+
+ // --- Namespace Mapping Table ---
+
+ xpathNamespaceMappingsTableModel = new DefaultTableModel() {
+ /**
+ * No cells should be editable
+ */
+ public boolean isCellEditable(int rowIndex, int columnIndex) {
+ return (false);
+ }
+ };
+ xpathNamespaceMappingsTableModel.addColumn("Namespace Prefix");
+ xpathNamespaceMappingsTableModel.addColumn("Namespace URI");
+
+ jtXPathNamespaceMappings = new JTable();
+ jtXPathNamespaceMappings.setModel(xpathNamespaceMappingsTableModel);
+ jtXPathNamespaceMappings.setPreferredScrollableViewportSize(new Dimension(200, 90));
+ // TODO - next line is to be enabled when Taverna is migrated to Java
+ // 1.6; for now it's fine to run without this
+ // jtXPathNamespaceMappings.setFillsViewportHeight(true); // makes sure
+ // that when the dedicated area is larger than the table, the latter is
+ // stretched vertically to fill the empty space
+
+ jtXPathNamespaceMappings.getColumnModel().getColumn(0).setPreferredWidth(20); // set
+ // relative
+ // sizes of
+ // columns
+ jtXPathNamespaceMappings.getColumnModel().getColumn(1).setPreferredWidth(300);
+
+ c.gridy++;
+ spXPathNamespaceMappings = new JScrollPane(jtXPathNamespaceMappings);
+ spXPathNamespaceMappings.setVisible(false);
+ jpMainPanel.add(spXPathNamespaceMappings, c);
+
+ // populate the view with values
+ refreshView();
+
+ return jpMainPanel;
+ }
+
+ @Override
+ /**
+ * This is the title of the contextual view - shown in the list of other available
+ * views (even when this contextual view is collapsed).
+ */
+ public String getViewTitle() {
+ return "XPath Service Details";
+ }
+
+ /**
+ * Typically called when the activity configuration has changed.
+ */
+ @Override
+ public void refreshView() {
+ Configuration configuration = scufl2Tools.configurationFor(activity, activity.getParent());
+ JsonNode json = configuration.getJson();
+
+ // Set XPath Expression
+ tfXPathExpression.setText(json.get("xpathExpression").asText());
+
+ // Populate Namespace Mappings
+ xpathNamespaceMappingsTableModel.getDataVector().removeAllElements();
+ if (json.has("xpathNamespaceMap")) {
+ for (JsonNode mapping : json.get("xpathNamespaceMap")) {
+ xpathNamespaceMappingsTableModel.addRow(new Object[] {
+ mapping.get("prefix").asText(), mapping.get("uri").asText() });
+ }
+ }
+ }
+
+ /**
+ * View position hint
+ */
+ @Override
+ public int getPreferredPosition() {
+ // want to be on top, as it's the main contextual view for this activity
+ return 100;
+ }
+
+ @Override
+ public Action getConfigureAction(final Frame owner) {
+ // "Configure" button appears because of this action being returned
+ return new XPathActivityConfigureAction(activity, owner, editManager, fileManager,
+ activityIconManager, serviceDescriptionRegistry, serviceRegistry);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateAction.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateAction.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateAction.java
new file mode 100644
index 0000000..a80696d
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateAction.java
@@ -0,0 +1,110 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.xpath.ui.menu;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+/**
+ * An action to add a REST activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class AddXPathTemplateAction extends AbstractContextualMenuAction {
+
+ private static final String ADD_XPATH = "XPath";
+
+ private static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+
+ private EditManager editManager;
+
+ private MenuManager menuManager;
+
+ private SelectionManager selectionManager;
+
+ private ActivityIconManager activityIconManager;
+
+ private ServiceRegistry serviceRegistry;
+
+ public AddXPathTemplateAction() {
+ super(insertSection, 1000);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+
+ return new AddXPathAction();
+ }
+
+ protected class AddXPathAction extends AbstractAction {
+ AddXPathAction() {
+ super(ADD_XPATH, activityIconManager
+ .iconForActivity(XPathTemplateService.ACTIVITY_TYPE));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+
+ WorkflowView.importServiceDescription(XPathTemplateService.getServiceDescription(),
+ false, editManager, menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateMenuAction.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateMenuAction.java
new file mode 100644
index 0000000..9132110
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/menu/AddXPathTemplateMenuAction.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.xpath.ui.menu;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService;
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+/**
+ * An action to add a REST activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author alanrw
+ */
+@SuppressWarnings("serial")
+public class AddXPathTemplateMenuAction extends AbstractMenuAction {
+
+ private static final String ADD_XPATH = "XPath";
+
+ private static final URI INSERT = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#insert");
+
+ private static final URI ADD_XPATH_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuAddXPath");
+
+ private EditManager editManager;
+
+ private MenuManager menuManager;
+
+ private SelectionManager selectionManager;
+
+ private ActivityIconManager activityIconManager;
+
+ private ServiceRegistry serviceRegistry;
+
+ public AddXPathTemplateMenuAction() {
+ super(INSERT, 1000, ADD_XPATH_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddXPathMenuAction();
+ }
+
+ protected class AddXPathMenuAction extends AbstractAction implements DesignOnlyAction {
+ AddXPathMenuAction() {
+ super();
+ putValue(SMALL_ICON,
+ activityIconManager.iconForActivity(XPathTemplateService.ACTIVITY_TYPE));
+ putValue(NAME, ADD_XPATH);
+ putValue(SHORT_DESCRIPTION, "XPath service");
+ putValue(
+ Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_P, InputEvent.SHIFT_DOWN_MASK
+ | InputEvent.ALT_DOWN_MASK));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(XPathTemplateService.getServiceDescription(),
+ false, editManager, menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathActivityIcon.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathActivityIcon.java
new file mode 100644
index 0000000..2251efb
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathActivityIcon.java
@@ -0,0 +1,86 @@
+package net.sf.taverna.t2.activities.xpath.ui.servicedescription;
+
+import java.awt.Color;
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityIcon implements ActivityIconSPI {
+ private static final Color PROCESSOR_COLOUR = Color.decode("#E6FF5E");
+
+ // --- LOCATIONS OF ICONS USED IN THE XPath ACTIVITY ---
+
+ private static final String FAMFAMFAM_SILK_PATH = "famfamfam_silk/";
+ private static final String FOLDS_PATH = "folds/";
+
+ public static final String XPATH_ACTIVITY_ICON = FAMFAMFAM_SILK_PATH + "page_white_code.png";
+ public static final String XPATH_ACTIVITY_CONFIGURATION_PARSE_XML_ICON = "arrow_right.png";
+
+ public static final String XML_TREE_ROOT_ICON = FAMFAMFAM_SILK_PATH + "page_white_code.png";
+ public static final String XML_TREE_NODE_ICON = FAMFAMFAM_SILK_PATH + "tag.png";
+ public static final String XML_TREE_ATTRIBUTE_ICON = "xpath_attribute.png";
+
+ public static final String XML_TREE_EXPAND_ALL_ICON = FAMFAMFAM_SILK_PATH
+ + "text_linespacing.png";
+ public static final String XML_TREE_COLLAPSE_ALL_ICON = FAMFAMFAM_SILK_PATH
+ + "text_linespacing (collapse).png";
+
+ public static final String XPATH_STATUS_OK_ICON = FAMFAMFAM_SILK_PATH + "accept.png";
+ public static final String XPATH_STATUS_ERROR_ICON = FAMFAMFAM_SILK_PATH + "exclamation.png";
+ public static final String XPATH_STATUS_UNKNOWN_ICON = FAMFAMFAM_SILK_PATH + "help.png";
+
+ public static final String FOLD_ICON = FOLDS_PATH + "fold.png";
+ public static final String UNFOLD_ICON = FOLDS_PATH + "unfold.png";
+
+ // ------
+
+ private static ImageIcon icon;
+
+ public int canProvideIconScore(URI activityType) {
+ if (XPathTemplateService.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getXPathActivityIcon();
+ }
+
+ public static Icon getXPathActivityIcon() {
+ if (icon == null) {
+ synchronized (XPathActivityIcon.class) {
+ if (icon == null) {
+ try {
+ icon = new ImageIcon(
+ XPathActivityIcon.class.getResource(XPATH_ACTIVITY_ICON));
+ } catch (NullPointerException e) {
+ /* icon wasn't found - do nothing, but no icon will be available */
+ }
+ }
+ }
+ }
+ return (icon);
+ }
+
+ public static Icon getIconById(String iconID) {
+ try {
+ return (new ImageIcon(XPathActivityIcon.class.getResource(iconID)));
+ } catch (NullPointerException e) {
+ // requested icon wasn't found - just return null
+ return (null);
+ }
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ colourManager.setPreferredColour(XPathTemplateService.ACTIVITY_TYPE.toString(), PROCESSOR_COLOUR);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathTemplateService.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathTemplateService.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathTemplateService.java
new file mode 100644
index 0000000..d55235d
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/servicedescription/XPathTemplateService.java
@@ -0,0 +1,57 @@
+package net.sf.taverna.t2.activities.xpath.ui.servicedescription;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.servicedescriptions.AbstractTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class XPathTemplateService extends AbstractTemplateService {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/xpath");
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ ObjectNode json = (ObjectNode) configuration.getJson();
+ json.put("xpathExpression", "/");
+ return configuration;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return XPathActivityIcon.getXPathActivityIcon();
+ }
+
+ public String getName() {
+ return "XPath";
+ }
+
+ public String getDescription() {
+ return "Service for point-and-click creation of XPath expressions for XML data";
+ }
+
+ public static ServiceDescription getServiceDescription() {
+ XPathTemplateService gts = new XPathTemplateService();
+ return gts.templateService;
+ }
+
+ public String getId() {
+ return "http://www.taverna.org.uk/2010/services/xpath";
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..be7da5f
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..7700abb
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.activities.xpath.ui.contextualview.ConfigureXPathActivityMenuAction
+net.sf.taverna.t2.activities.xpath.ui.menu.AddXPathTemplateAction
+net.sf.taverna.t2.activities.xpath.ui.menu.AddXPathTemplateMenuAction
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..b759c2e
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..e248981
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+ net.sf.taverna.t2.activities.xpath.ui.contextualview.XPathActivityMainContextViewFactory
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/resources/META-INF/spring/xpath-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/resources/META-INF/spring/xpath-activity-ui-context-osgi.xml b/taverna-xpath-activity-ui/src/main/resources/META-INF/spring/xpath-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..1e53ea6
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/resources/META-INF/spring/xpath-activity-ui-context-osgi.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="XPathActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="XPathTemplateService" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="ConfigureXPathActivityMenuAction" auto-export="interfaces" />
+ <service ref="AddXPathTemplateAction" auto-export="interfaces" />
+ <service ref="AddXPathTemplateMenuAction" auto-export="interfaces" />
+
+ <service ref="XPathActivityMainContextViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+
+</beans:beans>
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+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="XPathActivityIcon"
+ class="net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathActivityIcon">
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+ <bean id="XPathTemplateService"
+ class="net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathTemplateService" />
+
+ <bean id="ConfigureXPathActivityMenuAction"
+ class="net.sf.taverna.t2.activities.xpath.ui.contextualview.ConfigureXPathActivityMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="AddXPathTemplateAction"
+ class="net.sf.taverna.t2.activities.xpath.ui.menu.AddXPathTemplateAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="AddXPathTemplateMenuAction"
+ class="net.sf.taverna.t2.activities.xpath.ui.menu.AddXPathTemplateMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+ <bean id="XPathActivityMainContextViewFactory"
+ class="net.sf.taverna.t2.activities.xpath.ui.contextualview.XPathActivityMainContextViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+</beans>
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/test/java/Dom4JTest.java
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+++ b/taverna-xpath-activity-ui/src/test/java/Dom4JTest.java
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+import java.util.List;
+
+import org.dom4j.Document;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Node;
+import org.dom4j.XPath;
+
+
+public class Dom4JTest
+{
+ private static void testDom4j() throws Exception
+ {
+ String strDoc =
+ "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" +
+ "<services>" +
+ "<parameters>" +
+ "<filters>" +
+ "</filters>" +
+ "<query urlKey=\"q\"></query>" +
+ "<sortBy urlKey=\"sort_by\" urlValue=\"created\">Created at date</sortBy>" +
+ "<sortOrder urlKey=\"sort_order\" urlValue=\"desc\">Descending</sortOrder>" +
+ "<page urlKey=\"page\">1</page>" +
+ "<pageSize urlKey=\"per_page\">10</pageSize>" +
+ "</parameters>" +
+ "<statistics>" +
+ "<pages>170</pages>" +
+ "<results>1695</results>" +
+ "<total>1695</total>" +
+ "</statistics>" +
+ "<results>" +
+ "<services>" +
+ "<service name=\"1\" />" +
+ "<service name=\"2\" />" +
+ "<service name=\"3\" />" +
+ "<service name=\"4\" />" +
+ "</services>" +
+ "</results>" +
+ "</services>";
+
+
+ Document doc = DocumentHelper.parseText(strDoc);
+
+// // Pretty print the document to System.out
+// OutputFormat format = OutputFormat.createPrettyPrint();
+// XMLWriter writer = new XMLWriter( System.out, format );
+// writer.write( doc );
+
+
+ XPath expr = DocumentHelper.createXPath("//pages");
+
+ List<Node> matchingNodes = expr.selectNodes(doc);
+
+// List<Node> matchingNodes = doc.selectNodes("/services/parameters");
+
+
+// System.out.println("\n\n");
+ System.out.println(matchingNodes.size());
+ for (Node n : matchingNodes) {
+ System.out.println(n.asXML());
+ }
+ }
+
+ /**
+ * @param args
+ * @throws Exception
+ */
+ public static void main(String[] args) throws Exception {
+ testDom4j();
+ }
+
+}
[14/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProviderConfig.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProviderConfig.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProviderConfig.java
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+/*******************************************************************************
+ * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+
+/**
+ * ExternalToolServiceProviderConfig stores the URL of the use case repository XML file
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolServiceProviderConfig extends PropertyAnnotated {
+ private String repositoryUrl;
+
+ public ExternalToolServiceProviderConfig() {
+ }
+
+ public ExternalToolServiceProviderConfig(String repositoryUrl) {
+ this.repositoryUrl = repositoryUrl;
+ }
+
+ @PropertyAnnotation(displayName = "Tool registry location", preferred = true)
+ public String getRepositoryUrl() {
+ return repositoryUrl;
+ }
+
+ public void setRepositoryUrl(String repositoryUrl) {
+ this.repositoryUrl = repositoryUrl;
+ }
+
+ @Override
+ public String toString() {
+ return repositoryUrl;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolTemplateServiceDescription.java
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+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import java.net.URI;
+import java.util.UUID;
+
+import javax.swing.Icon;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManager;
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.servicedescriptions.AbstractTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolTemplateServiceDescription extends
+ AbstractTemplateService<ExternalToolActivityConfigurationBean> {
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/external-tool");
+
+ private static final String EXTERNAL_TOOL = "Tool";
+
+ private static InvocationGroupManager manager = InvocationGroupManagerImpl.getInstance();
+
+ @Override
+ public Class<? extends Activity<ExternalToolActivityConfigurationBean>> getActivityClass() {
+ return ExternalToolActivity.class;
+ }
+
+ @Override
+ public ExternalToolActivityConfigurationBean getActivityConfiguration() {
+ ExternalToolActivityConfigurationBean result = new ExternalToolActivityConfigurationBean();
+ result.setExternaltoolid(UUID.randomUUID().toString());
+ result.setUseCaseDescription(new UseCaseDescription(""));
+ result.setMechanism(manager.getDefaultMechanism());
+ return result;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return ExternalToolActivityIcon.getExternalToolIcon();
+ }
+
+ @Override
+ public String getDescription() {
+ return "A service that allows tools to be used as services";
+ }
+
+ @SuppressWarnings("unchecked")
+ public static ServiceDescription getServiceDescription() {
+ ExternalToolTemplateServiceDescription bts = new ExternalToolTemplateServiceDescription();
+ return bts.templateService;
+ }
+
+
+
+ @Override
+ public String getId() {
+ return providerId.toString();
+ }
+
+ @Override
+ public String getName() {
+ return EXTERNAL_TOOL;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/utils/Tools.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/utils/Tools.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/utils/Tools.java
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+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.utils;
+
+import java.awt.Color;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.border.CompoundBorder;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+
+/**
+ * @author alanrw
+ *
+ */
+public class Tools {
+
+ private static CompoundBorder border = BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(5,5,5,5), BorderFactory.createLineBorder(Color.BLACK, 1));
+
+ private static Insets insets = new Insets(5,5,5,5);
+
+ public static void addViewer(final JPanel innerPanel, String[] labels, JComponent[] elements,
+ final List viewerList, final Object viewer, final JPanel outerPanel) {
+ final JPanel subPanel = new JPanel();
+ subPanel.setLayout(new GridBagLayout());
+ subPanel.setBorder(border);
+
+ final GridBagConstraints labelConstraint = new GridBagConstraints();
+ labelConstraint.insets = insets;
+ labelConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ labelConstraint.fill = GridBagConstraints.BOTH;
+ labelConstraint.gridy = 0;
+ labelConstraint.gridx = 0;
+ labelConstraint.weightx = 0;
+
+ final GridBagConstraints elementConstraint = new GridBagConstraints();
+ elementConstraint.insets = insets;
+ elementConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ elementConstraint.fill = GridBagConstraints.BOTH;
+ elementConstraint.gridy = 0;
+ elementConstraint.gridx = 1;
+ elementConstraint.weightx = 1.0;
+
+ final GridBagConstraints removeConstraint = new GridBagConstraints();
+ removeConstraint.insets = insets;
+ removeConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ removeConstraint.fill = GridBagConstraints.BOTH;
+ removeConstraint.gridx = 1;
+ removeConstraint.weightx = 0;
+ removeConstraint.fill = GridBagConstraints.NONE;
+ removeConstraint.anchor = GridBagConstraints.EAST;
+
+ final GridBagConstraints subPanelConstraint = new GridBagConstraints();
+ subPanelConstraint.insets = insets;
+ subPanelConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ subPanelConstraint.fill = GridBagConstraints.BOTH;
+ subPanelConstraint.gridx = 1;
+// subPanelConstraint.gridy = ++stringReplacementGridy;
+ subPanelConstraint.weightx = 1.00;
+ subPanelConstraint.fill = GridBagConstraints.HORIZONTAL;
+ subPanelConstraint.anchor = GridBagConstraints.WEST;
+
+ for (int i = 0; i < labels.length; i++) {
+ subPanel.add(new JLabel(labels[i] + ":"), labelConstraint);
+ subPanel.add(elements[i], elementConstraint);
+ labelConstraint.gridy++;
+ elementConstraint.gridy++;
+ }
+
+ removeConstraint.gridy = labelConstraint.gridy + 1;
+ final JButton removeButton = new DeselectingButton("Remove",
+ new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ synchronized (viewerList) {
+ viewerList.remove(viewer);
+ }
+ innerPanel.remove(subPanel);
+ innerPanel.revalidate();
+ innerPanel.repaint();
+ outerPanel.revalidate();
+ outerPanel.repaint();
+ }
+
+ });
+ subPanel.add(removeButton, removeConstraint);
+ innerPanel.add(subPanel, subPanelConstraint);
+ }
+
+ public static boolean isStringReplacement(ScriptInputUser si) {
+ return !si.isList() && !si.isFile() && !si.isTempFile();
+ }
+
+ public static boolean isInputFile(ScriptInputUser si) {
+ return !si.isList() && si.isFile();
+ }
+
+ public static boolean isFileList(ScriptInputUser si) {
+ return si.isList() && si.isFile();
+ }
+
+ public static boolean isUnderstood(ScriptInputUser si) {
+ return isStringReplacement(si) || isInputFile(si) || isFileList(si);
+ }
+
+ public static boolean areAllUnderstood(Map<String, ScriptInput> inputs) {
+ for (ScriptInput si : inputs.values()) {
+ if ((si instanceof ScriptInputUser) && !isUnderstood((ScriptInputUser) si)) {
+ return false;
+ }
+ }
+ return true;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/AnnotationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/AnnotationPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/AnnotationPanel.java
new file mode 100644
index 0000000..83e75e8
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/AnnotationPanel.java
@@ -0,0 +1,41 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.FlowLayout;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+/**
+ * @author alanrw
+ *
+ */
+public class AnnotationPanel extends JPanel {
+
+ public AnnotationPanel(Component nameField, Component descriptionArea, Component groupField) {
+ super();
+ this.setLayout(new BorderLayout());
+ JPanel subPanel = new JPanel(new BorderLayout());
+ JPanel namePanel = new JPanel();
+ namePanel.setLayout(new FlowLayout(FlowLayout.LEFT));
+ namePanel.add(new JLabel("Name: "));
+ namePanel.add(nameField);
+ subPanel.add(namePanel, BorderLayout.NORTH);
+ JPanel groupPanel = new JPanel();
+ groupPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
+ groupPanel.add(new JLabel("Group: "));
+ groupPanel.add(groupField);
+ subPanel.add(groupPanel, BorderLayout.SOUTH);
+ this.add(subPanel, BorderLayout.NORTH);
+ JPanel descriptionPanel = new JPanel();
+ descriptionPanel.setLayout(new BorderLayout());
+ descriptionPanel.add(new JLabel("Description:"), BorderLayout.NORTH);
+ descriptionPanel.add(descriptionArea, BorderLayout.CENTER);
+ this.add(descriptionPanel, BorderLayout.CENTER);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/EditablePanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/EditablePanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/EditablePanel.java
new file mode 100644
index 0000000..b395983
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/EditablePanel.java
@@ -0,0 +1,76 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseEnumeration;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolServiceDescription;
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+
+/**
+ * @author alanrw
+ *
+ */
+public class EditablePanel extends JPanel {
+ public EditablePanel(final ExternalToolConfigView view) {
+ super(new FlowLayout());
+
+ JButton update = new DeselectingButton("Update tool description",
+ new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ExternalToolActivityConfigurationBean bean = view.getConfiguration();
+ String repositoryUrl = bean.getRepositoryUrl();
+ String id = bean.getExternaltoolid();
+ UseCaseDescription usecase = null;
+ try {
+ usecase = UseCaseEnumeration.readDescriptionFromUrl(
+ repositoryUrl, id);
+ }
+ catch (IOException ex) {
+ // Already logged
+ }
+ if (usecase != null) {
+ bean.setUseCaseDescription(usecase);
+ view.refreshConfiguration(bean);
+ } else {
+ JOptionPane.showMessageDialog(view, "Unable to find tool description " + id, "Missing tool description", JOptionPane.ERROR_MESSAGE);
+ }
+ }});
+ this.add(update);
+
+ JButton makeEditable = new DeselectingButton("Edit tool description",
+ new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0) {
+ ExternalToolActivityConfigurationBean config = view.makeConfiguration();
+ view.setEditable(true, config);
+
+ }
+ });
+ makeEditable.setToolTipText("Edit the tool description");
+ if (Tools.areAllUnderstood(view.getConfiguration().getUseCaseDescription().getInputs())) {
+ this.add(makeEditable);
+ }
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityContextualView.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityContextualView.java
new file mode 100644
index 0000000..46c14be
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityContextualView.java
@@ -0,0 +1,181 @@
+/*******************************************************************************
+ * Copyright (C) 2010 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.Frame;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.actions.ExternalToolActivityConfigureAction;
+import net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolActivityIcon;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+
+/**
+ * ExternalToolActivityContextualView displays the use case information in a HTML table. Currently,
+ * this is only the use case ID.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolActivityContextualView extends
+ HTMLBasedActivityContextualView<ExternalToolActivityConfigurationBean> {
+ private static final long serialVersionUID = 1L;
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+
+ public ExternalToolActivityContextualView(Activity<?> activity, EditManager editManager,
+ FileManager fileManager, ColourManager colourManager, ActivityIconManager activityIconManager) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ String html = "";
+ ExternalToolActivityConfigurationBean bean = getConfigBean();
+ String repositoryUrl = bean.getRepositoryUrl();
+ if ((repositoryUrl == null) || repositoryUrl.isEmpty()) {
+ repositoryUrl = "<b>Not specified</b>";
+ }
+ html += "<tr><td>Repository URL</td><td>" + repositoryUrl + "</td></tr>";
+
+ String id = bean.getExternaltoolid();
+ if ((id == null) || id.isEmpty()) {
+ id = "<b>Not specified</b>";
+ }
+ html += "<tr><td>Id</td><td>" + id + "</td></tr>";
+
+ UseCaseDescription useCaseDescription = bean.getUseCaseDescription();
+ String name = useCaseDescription.getUsecaseid();
+ if ((name == null) || name.isEmpty()) {
+ name = "<b>Not specified</b>";
+ }
+ html += "<tr><td>Name</td><td>" + name + "</td></tr>";
+
+ Map<String, ScriptInput> stringReplacements = new TreeMap<String, ScriptInput>();
+ Map<String, ScriptInput> fileInputs = new TreeMap<String, ScriptInput>();
+
+ for (Entry<String, ScriptInput> entry : useCaseDescription.getInputs().entrySet()) {
+ String key = entry.getKey();
+ ScriptInput value = entry.getValue();
+ if (value.isFile()) {
+ fileInputs.put(key, value);
+ } else if (value.isTempFile()) {
+ // Nothing
+ } else {
+ stringReplacements.put(key, value);
+ }
+ }
+
+ if (!stringReplacements.isEmpty()) {
+ html += "<tr><td colspan=2 align=center><b>String replacements</b></td></tr>";
+ html += "<tr><td><b>Port name</b></td><td><b>Replaces</b></td></tr>";
+ for (String siName : stringReplacements.keySet()) {
+ html += "<tr><td>" + siName + "</td>";
+ ScriptInput si = stringReplacements.get(siName);
+ html += "<td>%%" + si.getTag() + "%%</td>";
+
+ html += "</tr>";
+ }
+ }
+
+ if (!fileInputs.isEmpty()) {
+ html += "<tr><td colspan=2 align=center><b>File inputs</b></td></tr>";
+ html += "<tr><td><b>Port name</b></td><td><b>To file</b></td></tr>";
+ for (String siName : fileInputs.keySet()) {
+ html += "<tr><td>" + siName + "</td>";
+ ScriptInput si = fileInputs.get(siName);
+ html += "<td>" + si.getTag() + "</td>";
+
+ html += "</tr>";
+ }
+ }
+
+ List<ScriptInputStatic> staticInputs = useCaseDescription.getStatic_inputs();
+ if (!staticInputs.isEmpty()) {
+ html += "<tr><td colspan=2 align=center><b>Static inputs</b></td></tr>";
+ html += "<tr><td><b>Type</b></td><td><b>To file</b></td></tr>";
+ for (ScriptInputStatic si : staticInputs) {
+ if (si.getUrl() != null) {
+ html += "<td><b>URL</b></td>";
+ } else {
+ html += "<td><b>Explicit content</b></td>";
+ }
+ if (si.isFile()) {
+ html += "<td>" + si.getTag() + "</td>";
+ }
+ html += "</tr>";
+ }
+ }
+ Map<String, ScriptOutput> outputs = useCaseDescription.getOutputs();
+ if (!outputs.isEmpty()) {
+ html += "<tr><td colspan=2 align=center><b>File outputs</b></td></tr>";
+ html += "<tr><td><b>Port name</b></td><td><b>From file</b></td></tr>";
+ for (String soName : outputs.keySet()) {
+ html += "<tr><td>" + soName + "</td>";
+ ScriptOutput so = outputs.get(soName);
+ html += "<td>" + so.getPath() + "</td>";
+ html += "</tr>";
+ }
+ }
+ return html;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Tool service";
+ }
+
+ @Override
+ public Action getConfigureAction(final Frame owner) {
+ return new ExternalToolActivityConfigureAction((ExternalToolActivity) getActivity(), owner,
+ editManager, fileManager, activityIconManager);
+ }
+
+ public String getBackgroundColour() {
+
+ return ExternalToolActivityIcon.getColourString();
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityViewFactory.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityViewFactory.java
new file mode 100644
index 0000000..902c736
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolActivityViewFactory.java
@@ -0,0 +1,76 @@
+/*******************************************************************************
+ * Copyright (C) 2010 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+
+/**
+ * ExternalToolActivityViewFactory produces an ExternalToolActivityContextualView to show
+ * information for a use case activity.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolActivityViewFactory implements ContextualViewFactory<ExternalToolActivity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+
+ public boolean canHandle(Object object) {
+ if (object instanceof ExternalToolActivity) {
+ return true;
+ }
+ return false;
+ }
+
+ public List<ContextualView> getViews(ExternalToolActivity selection) {
+ return Arrays.asList(new ContextualView[] { new ExternalToolActivityContextualView(
+ selection, editManager, fileManager, colourManager, activityIconManager) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolConfigView.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolConfigView.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolConfigView.java
new file mode 100644
index 0000000..4723a78
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolConfigView.java
@@ -0,0 +1,868 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.Map.Entry;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.help.CSH;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JEditorPane;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.JTextPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityHealthChecker;
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.KeywordDocument;
+import net.sf.taverna.t2.lang.ui.LinePainter;
+import net.sf.taverna.t2.lang.ui.NoWrapEditorKit;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+
+import org.apache.log4j.Logger;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+
+/**
+ * Provides the configurable view for a {@link ExternalToolActivity} through
+ * it's {@link ExternalToolActivityConfigurationBean}. Has 3 main tabs - Script,
+ * Ports & Dependencies. The {@link #inputViewList} contains the
+ * {@link ExternalToolInputViewer}s describing the input ports and
+ * {@link #outputViewList} has the {@link ExternalToolFileViewer}s
+ *
+ * @author Ian Dunlop
+ * @author Alex Nenadic
+ * @author Alan R Williams
+ *
+ */
+@SuppressWarnings("serial")
+public class ExternalToolConfigView
+ extends
+ ActivityConfigurationPanel<ExternalToolActivity, ExternalToolActivityConfigurationBean> {
+
+ private static final Color LINE_COLOR = new Color(225,225,225);
+
+ private static final String FILE_INPUT_DESCRIPTION = "You can use a file input to feed data into " +
+ "the service via an input port and have that data written to the specified file.";
+
+ private static final String FILE_OUTPUT_DESCRIPTION = "You can use a file output to take the " +
+ "content of a file produced by the tool and send it to an output port of the service.";
+
+ private static final String FILE_LIST_DESCRIPTION = "If you feed a list of data into a file list " +
+ "input, then each data item is written to a temporary file. A file is produced containing " +
+ "the names of those temporary file. That index file can then be used as part of the tool " +
+ "command.";
+
+ private static final String VALID_NAME_REGEX = "[\\p{L}\\p{Digit}_]+";
+
+ private static Logger logger = Logger
+ .getLogger(ExternalToolConfigView.class);
+
+ /** The activity which this view describes */
+ protected ExternalToolActivity activity;
+
+ /** The configuration bean used to configure the activity */
+ private ExternalToolActivityConfigurationBean configuration;
+
+ private JTabbedPane tabbedPane = null;
+ private JPanel advancedPanel = null;
+ private JTabbedPane advancedTab = null;
+ private AnnotationPanel annotationPanel = null;
+
+ private int stringReplacementGridy = 1;
+ private List<ExternalToolStringReplacementViewer> stringReplacementViewList = new ArrayList<ExternalToolStringReplacementViewer>();
+
+ private List<ExternalToolFileViewer> inputFileViewList = new ArrayList<ExternalToolFileViewer>();
+
+ private List<ExternalToolFileViewer> fileListViewList = new ArrayList<ExternalToolFileViewer>();
+
+ private int inputGridy = 1;
+
+ private int outputGridy = 1;
+ private List<ExternalToolFileViewer> outputViewList = new ArrayList<ExternalToolFileViewer>();
+
+ private int staticGridy = 1;
+ private List<ExternalToolStaticUrlViewer> staticUrlViewList = new ArrayList<ExternalToolStaticUrlViewer>();
+
+ private List<ExternalToolStaticStringViewer> staticStringViewList = new ArrayList<ExternalToolStaticStringViewer>();
+
+/* private List<ExternalToolRuntimeEnvironmentViewer> runtimeEnvironmentViewList = new ArrayList<ExternalToolRuntimeEnvironmentViewer>();
+*/
+
+ private JTextField nameField = new JTextField(20);
+ private JTextField groupField = new JTextField(20);
+ private JTextArea descriptionArea = new JTextArea(6, 40);
+
+ private JEditorPane scriptTextArea;
+
+ private InvocationPanel invocationPanel;
+
+ private JCheckBox stdInCheckBox = new JCheckBox("Show STDIN");
+ private JCheckBox stdOutCheckBox = new JCheckBox("Show STDOUT");
+ private JCheckBox stdErrCheckBox = new JCheckBox("Show STDERR");
+
+ private JTextField returnCodesField = new JTextField(20);
+
+ /**
+ * Stores the {@link ExternalToolActivity}, gets its
+ * {@link ExternalToolActivityConfigurationBean}, sets the layout and calls
+ * {@link #initialise()} to get the view going
+ *
+ * @param activity
+ * the {@link ExternalToolActivity} that the view is over
+ */
+ public ExternalToolConfigView(ExternalToolActivity activity) {
+ this.activity = activity;
+ ExternalToolActivityHealthChecker.updateLocation(activity.getConfiguration());
+ configuration = (ExternalToolActivityConfigurationBean) cloneBean(activity
+ .getConfiguration());
+ setLayout(new GridBagLayout());
+ initialise(configuration);
+ }
+
+ public void noteConfiguration() {
+ configuration = makeConfiguration();
+ }
+
+ public ExternalToolActivityConfigurationBean makeConfiguration() {
+ ExternalToolActivityConfigurationBean newConfiguration = (ExternalToolActivityConfigurationBean) cloneBean(configuration);
+ ExternalToolActivityHealthChecker.updateLocation(newConfiguration);
+
+
+ if (!isFromRepository()) {
+ UseCaseDescription ucd = newConfiguration.getUseCaseDescription();
+
+ ucd.setUsecaseid(nameField.getText());
+ if (groupField.getText().isEmpty()) {
+ ucd.setGroup(null);
+ } else {
+ ucd.setGroup(groupField.getText());
+ }
+ ucd.setDescription(descriptionArea.getText());
+ ucd.setCommand(scriptTextArea.getText());
+ ucd.setReturnCodesAsText(returnCodesField.getText());
+ ucd.setIncludeStdIn(stdInCheckBox.isSelected());
+ ucd.setIncludeStdOut(stdOutCheckBox.isSelected());
+ ucd.setIncludeStdErr(stdErrCheckBox.isSelected());
+
+ ucd.getInputs().clear();
+ ucd.getTags().clear();
+ synchronized (fileListViewList) {
+ for (ExternalToolFileViewer viewer : fileListViewList) {
+ ScriptInputUser si = new ScriptInputUser();
+ si.setBinary(viewer.isBinary());
+ si.setList(true);
+ si.setTag(viewer.getValue());
+ si.setTempFile(false);
+ si.setFile(true);
+ ucd.getInputs().put(viewer.getName(), si);
+ }
+ }
+
+ synchronized (stringReplacementViewList) {
+ for (ExternalToolStringReplacementViewer viewer : stringReplacementViewList) {
+ ScriptInputUser si = new ScriptInputUser();
+ si.setBinary(false);
+ si.setList(false);
+ si.setTag(viewer.getValue());
+ si.setTempFile(false);
+ si.setFile(false);
+ ucd.getTags().add(si.getTag());
+ ucd.getInputs().put(viewer.getName(), si);
+ }
+ }
+
+ synchronized (inputFileViewList) {
+ for (ExternalToolFileViewer viewer : inputFileViewList) {
+ ScriptInputUser si = new ScriptInputUser();
+ si.setBinary(viewer.isBinary());
+ si.setList(false);
+ si.setTag(viewer.getValue());
+ si.setTempFile(false);
+ si.setFile(true);
+ ucd.getInputs().put(viewer.getName(), si);
+ }
+ }
+
+ synchronized (outputViewList) {
+ ucd.getOutputs().clear();
+ for (ExternalToolFileViewer viewer : outputViewList) {
+ ScriptOutput so = new ScriptOutput();
+ so.setBinary(viewer.isBinary());
+ so.setPath(viewer.getValue());
+ ucd.getOutputs().put(viewer.getName(), so);
+ }
+ }
+ ucd.getStatic_inputs().clear();
+ synchronized (staticStringViewList) {
+ for (ExternalToolStaticStringViewer viewer : staticStringViewList) {
+ ScriptInputStatic sis = new ScriptInputStatic();
+ sis.setContent(viewer.getContent());
+ sis.setTag(viewer.getValue());
+ sis.setTempFile(false);
+ sis.setFile(true);
+ ucd.getStatic_inputs().add(sis);
+ }
+ }
+ synchronized (staticUrlViewList) {
+ for (ExternalToolStaticUrlViewer viewer : staticUrlViewList) {
+ ScriptInputStatic sis = new ScriptInputStatic();
+ sis.setUrl(viewer.getContent());
+ sis.setTag(viewer.getValue());
+ sis.setTempFile(false);
+ sis.setFile(true);
+ ucd.getStatic_inputs().add(sis);
+ }
+ }
+
+/* synchronized (runtimeEnvironmentViewList) {
+ ucd.getREs().clear();
+ for (ExternalToolRuntimeEnvironmentViewer viewer : runtimeEnvironmentViewList) {
+ RuntimeEnvironmentConstraint newConstraint = new RuntimeEnvironmentConstraint(
+ viewer.getId(), viewer.getRelation());
+ ucd.getREs().add(newConstraint);
+ }
+ }*/
+ }
+ invocationPanel.fillInConfiguration(newConfiguration);
+
+ return newConfiguration;
+ }
+
+ public boolean isConfigurationChanged() {
+ String configurationString = convertBeanToString(activity
+ .getConfiguration());
+ return (!convertBeanToString(makeConfiguration()).equals(
+ configurationString));
+ }
+
+ /**
+ * Adds a {@link JButton} which handles the reconfiguring of the
+ * {@link ExternalToolActivity} through the altered
+ * {@link ExternalToolActivityConfigurationBean}. Sets up the initial tabs -
+ * Script (also sets the initial value), Ports & Dependencies and their
+ * initial values through {@link #setDependencies()},
+ * {@link #getPortPanel()}
+ */
+ private void initialise(ExternalToolActivityConfigurationBean configuration) {
+ CSH.setHelpIDString(
+ this,
+ "net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ExternalToolConfigView");
+ this.configuration = configuration;
+ setBorder(javax.swing.BorderFactory.createTitledBorder(null, null,
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Lucida Grande", 1, 12)));
+
+ tabbedPane = new JTabbedPane();
+
+ if (invocationPanel != null) {
+ invocationPanel.stopObserving();
+ }
+
+ if (!isFromRepository()) {
+ UseCaseDescription useCaseDescription = configuration
+ .getUseCaseDescription();
+
+ nameField.setText(useCaseDescription.getUsecaseid());
+ if (useCaseDescription.getGroup() != null) {
+ groupField.setText(useCaseDescription.getGroup());
+ }
+ descriptionArea.setText(useCaseDescription.getDescription());
+ stringReplacementViewList = new ArrayList<ExternalToolStringReplacementViewer>();
+ inputFileViewList = new ArrayList<ExternalToolFileViewer>();
+ fileListViewList = new ArrayList<ExternalToolFileViewer>();
+ outputViewList = new ArrayList<ExternalToolFileViewer>();
+ staticUrlViewList = new ArrayList<ExternalToolStaticUrlViewer>();
+ staticStringViewList = new ArrayList<ExternalToolStaticStringViewer>();
+/* runtimeEnvironmentViewList = new ArrayList<ExternalToolRuntimeEnvironmentViewer>();*/
+
+ for (Entry<String, ScriptInput> entry : useCaseDescription
+ .getInputs().entrySet()) {
+ String name = entry.getKey();
+ ScriptInputUser si = (ScriptInputUser) entry.getValue();
+ if (Tools.isStringReplacement(si)) {
+ final ExternalToolStringReplacementViewer inputView = new ExternalToolStringReplacementViewer(
+ name, si);
+ stringReplacementViewList.add(inputView);
+ }
+
+ }
+ Collections.sort(stringReplacementViewList,
+ new Comparator<ExternalToolStringReplacementViewer>() {
+
+ @Override
+ public int compare(
+ ExternalToolStringReplacementViewer o1,
+ ExternalToolStringReplacementViewer o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (Entry<String, ScriptInput> entry : useCaseDescription
+ .getInputs().entrySet()) {
+ String name = entry.getKey();
+ ScriptInputUser si = (ScriptInputUser) entry.getValue();
+ if (Tools.isInputFile(si)) {
+ final ExternalToolFileViewer inputView = new ExternalToolFileViewer(
+ name, si.getTag(), si.isBinary());
+ inputFileViewList.add(inputView);
+ }
+
+ }
+ Collections.sort(inputFileViewList,
+ new Comparator<ExternalToolFileViewer>() {
+
+ @Override
+ public int compare(ExternalToolFileViewer o1,
+ ExternalToolFileViewer o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (Entry<String, ScriptInput> entry : useCaseDescription
+ .getInputs().entrySet()) {
+ String name = entry.getKey();
+ ScriptInputUser si = (ScriptInputUser) entry.getValue();
+ if (Tools.isFileList(si)) {
+ final ExternalToolFileViewer inputView = new ExternalToolFileViewer(
+ name, si.getTag(), si.isBinary());
+ fileListViewList.add(inputView);
+ }
+
+ }
+ Collections.sort(fileListViewList,
+ new Comparator<ExternalToolFileViewer>() {
+
+ @Override
+ public int compare(ExternalToolFileViewer o1,
+ ExternalToolFileViewer o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (Entry<String, ScriptOutput> entry : useCaseDescription
+ .getOutputs().entrySet()) {
+ ScriptOutput so = entry.getValue();
+ final ExternalToolFileViewer outputView = new ExternalToolFileViewer(
+ entry.getKey(), so.getPath(), so.isBinary());
+ outputViewList.add(outputView);
+ }
+ Collections.sort(outputViewList,
+ new Comparator<ExternalToolFileViewer>() {
+
+ @Override
+ public int compare(ExternalToolFileViewer o1,
+ ExternalToolFileViewer o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (ScriptInputStatic siss : useCaseDescription.getStatic_inputs()) {
+ if ((siss.getUrl() == null) && siss.isFile()) {
+ final ExternalToolStaticStringViewer staticView = new ExternalToolStaticStringViewer(
+ siss);
+ staticStringViewList.add(staticView);
+ }
+ }
+ Collections.sort(staticStringViewList,
+ new Comparator<ExternalToolStaticStringViewer>() {
+
+ @Override
+ public int compare(ExternalToolStaticStringViewer o1,
+ ExternalToolStaticStringViewer o2) {
+ return o1.getContent().compareTo(o2.getContent());
+ }
+ });
+
+ for (ScriptInputStatic sis : useCaseDescription.getStatic_inputs()) {
+ if ((sis.getUrl() != null) && sis.isFile()) {
+ final ExternalToolStaticUrlViewer staticView = new ExternalToolStaticUrlViewer(
+ sis);
+ staticUrlViewList.add(staticView);
+ }
+ }
+ Collections.sort(staticUrlViewList,
+ new Comparator<ExternalToolStaticUrlViewer>() {
+
+ @Override
+ public int compare(ExternalToolStaticUrlViewer o1,
+ ExternalToolStaticUrlViewer o2) {
+ return o1.getContent().compareTo(o2.getContent());
+ }
+ });
+
+/* for (RuntimeEnvironmentConstraint rec : useCaseDescription.getREs()) {
+ final ExternalToolRuntimeEnvironmentViewer newView = new ExternalToolRuntimeEnvironmentViewer(
+ rec.getID(), rec.getRelation());
+ runtimeEnvironmentViewList.add(newView);
+ }
+ Collections.sort(runtimeEnvironmentViewList,
+ new Comparator<ExternalToolRuntimeEnvironmentViewer>() {
+
+ @Override
+ public int compare(
+ ExternalToolRuntimeEnvironmentViewer o1,
+ ExternalToolRuntimeEnvironmentViewer o2) {
+ return o1.getId().compareTo(o2.getId());
+ }
+ });*/
+
+ scriptTextArea = new JTextPane();
+ new LinePainter(scriptTextArea, LINE_COLOR);
+
+ final KeywordDocument doc = new KeywordDocument(
+ new HashSet<String>());
+ // NOTE: Due to T2-1145 - always set editor kit BEFORE setDocument
+ scriptTextArea.setEditorKit(new NoWrapEditorKit());
+ scriptTextArea.setFont(new Font("Monospaced", Font.PLAIN, 14));
+ scriptTextArea.setDocument(doc);
+ scriptTextArea.setText(useCaseDescription.getCommand());
+ scriptTextArea.setCaretPosition(0);
+ scriptTextArea.setPreferredSize(new Dimension(200, 100));
+
+ tabbedPane.addTab("Command", new ScriptPanel(this, scriptTextArea, stdInCheckBox, stdOutCheckBox, stdErrCheckBox, returnCodesField));
+ tabbedPane.addTab("String replacements",
+ new StringReplacementPanel(this, stringReplacementViewList));
+ tabbedPane.addTab(
+ "File inputs",
+ new FilePanel(this, inputFileViewList, "To file", "File type",
+ "in", FILE_INPUT_DESCRIPTION, "Add file input"));
+ tabbedPane.addTab(
+ "File outputs",
+ new FilePanel(this, outputViewList, "From file", "File type",
+ "out", FILE_OUTPUT_DESCRIPTION, "Add file output"));
+ advancedPanel = new JPanel();
+ advancedPanel.setLayout(new GridBagLayout());
+ GridBagConstraints advancedConstraint = new GridBagConstraints();
+ advancedConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ advancedConstraint.gridx = 0;
+ advancedConstraint.gridy = 0;
+
+ advancedConstraint.fill = GridBagConstraints.BOTH;
+ advancedConstraint.weighty = 0.1;
+ advancedConstraint.weightx = 0.1;
+ advancedTab = new JTabbedPane();
+ advancedTab.addTab("Strings", new StaticStringPanel(staticStringViewList));
+ advancedTab.addTab("URLs", new StaticUrlPanel(staticUrlViewList));
+ advancedTab.addTab(
+ "File lists",
+ new FilePanel(this, fileListViewList,
+ "To file containing list", "Individual file type",
+ "in", FILE_LIST_DESCRIPTION, "Add file list"));
+ annotationPanel = new AnnotationPanel(nameField, descriptionArea, groupField);
+ advancedTab.addTab("Annotation", annotationPanel);
+ final ToolXMLPanel toolXMLPanel = new ToolXMLPanel(configuration.getUseCaseDescription());
+ advancedTab.addTab("XML", toolXMLPanel);
+ advancedTab.addChangeListener(new ChangeListener() {
+
+ @Override
+ public void stateChanged(ChangeEvent e) {
+ if (advancedTab.getSelectedComponent() == toolXMLPanel) {
+ toolXMLPanel.regenerateTree(makeConfiguration().getUseCaseDescription());
+ }
+ }});
+ tabbedPane.addChangeListener(new ChangeListener() {
+
+ @Override
+ public void stateChanged(ChangeEvent e) {
+ if ((tabbedPane.getSelectedComponent() == advancedPanel) &&
+ (advancedTab.getSelectedComponent() == toolXMLPanel)) {
+ toolXMLPanel.regenerateTree(makeConfiguration().getUseCaseDescription());
+ }
+ }
+
+ });
+/* advancedTab.addTab("Runtime environments",
+ createRuntimeEnvironmentPanel(runtimeEnvironmentViewList));*/
+ advancedPanel.add(advancedTab, advancedConstraint);
+ tabbedPane.addTab("Advanced", advancedPanel);
+ }
+ invocationPanel = new InvocationPanel(configuration);
+
+ tabbedPane.addTab("Location", invocationPanel);
+ if (isFromRepository()) {
+ tabbedPane.addTab("Edit", new EditablePanel(this));
+ }
+ GridBagConstraints outerConstraint = new GridBagConstraints();
+ outerConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ outerConstraint.gridx = 0;
+ outerConstraint.gridy = 0;
+
+ outerConstraint.fill = GridBagConstraints.BOTH;
+ outerConstraint.weighty = 0.1;
+ outerConstraint.weightx = 0.1;
+ add(tabbedPane, outerConstraint);
+
+ setPreferredSize(new Dimension(700, 500));
+ this.validate();
+ }
+
+ public void whenOpened() {
+ if (scriptTextArea != null) {
+ scriptTextArea.requestFocus();
+ }
+ }
+
+ private boolean isFromRepository() {
+ return (!this.configuration.isEdited() && isOriginallyFromRepository());
+ }
+
+ public boolean isOriginallyFromRepository() {
+ String repositoryUrl = this.configuration.getRepositoryUrl();
+ return ((repositoryUrl != null) && !repositoryUrl
+ .isEmpty());
+
+ }
+
+
+ @Override
+ public ExternalToolActivityConfigurationBean getConfiguration() {
+ return configuration;
+ }
+
+ public void refreshConfiguration(
+ ExternalToolActivityConfigurationBean config) {
+ int visibleTab = -1;
+ int secondaryTab = -1;
+ if (tabbedPane != null) {
+ visibleTab = tabbedPane.getSelectedIndex();
+ if (tabbedPane.getSelectedComponent().equals(advancedTab)) {
+ secondaryTab = advancedTab.getSelectedIndex();
+ }
+ }
+ this.removeAll();
+ initialise(config);
+ if (visibleTab != -1) {
+ tabbedPane.setSelectedIndex(visibleTab);
+ }
+ if (secondaryTab != -1) {
+ advancedTab.setSelectedIndex(secondaryTab);
+ }
+ }
+
+ public void showAnnotationPanel() {
+ tabbedPane.setSelectedComponent(advancedPanel);
+ advancedTab.setSelectedComponent(annotationPanel);
+ }
+
+ @Override
+ public void refreshConfiguration() {
+ refreshConfiguration(activity.getConfiguration());
+ }
+
+ static Pattern tagPattern = Pattern.compile("%%([^%]*)%%");
+
+ @Override
+ /**
+ * Need to check that the script contains the string replacements and only them - done
+ *
+ * Need to check the input port names are valid and unique - done
+ * Need to check the output port names are valid and unique - done
+ *
+ * Need to check the input files and static files are unique - done
+ * Need to check the file names are valid
+ * Need to check the URLs are valid
+ * Need to check the replacement tags are unique - done
+ */
+ public boolean checkValues() {
+ if (isFromRepository()) {
+ return true;
+ }
+ boolean result = true;
+ String text = "";
+ Set<String> stringReplacementPortNames = new HashSet<String>();
+ Set<String> stringReplacementTags = new HashSet<String>();
+ for (ExternalToolStringReplacementViewer v : stringReplacementViewList) {
+ String name = v.getName();
+ if (name.equalsIgnoreCase("stdin") || name.equalsIgnoreCase("stdout") || name.equalsIgnoreCase("stderr")) {
+ text += "A string replacement port has a reserved name \"" + name + "\"\n";
+ result = false;
+ }
+ else if (stringReplacementPortNames.contains(name)) {
+ text += "Two string replacement ports have the name \"" + name
+ + "\"\n";
+ result = false;
+ } else if (!name.matches(VALID_NAME_REGEX)) {
+ text += "String replacement port name \"" + name
+ + "\" is invalid\n";
+ result = false;
+ } else {
+ stringReplacementPortNames.add(name);
+ }
+
+ String tag = v.getValue();
+ if (stringReplacementTags.contains(tag)) {
+ text += "Two string replacement ports replace \"%%" + tag
+ + "%%\"\n";
+ result = false;
+ } else if (!tag.matches(VALID_NAME_REGEX)) {
+ text += "String replacement tag \"%%" + tag
+ + "%%\" is invalid\n";
+ result = false;
+ } else {
+ stringReplacementTags.add(tag);
+ }
+ }
+
+ Matcher m = tagPattern.matcher(scriptTextArea.getText());
+ Set<String> tags = new HashSet<String>();
+ while (m.find()) {
+ String tag = m.group(1);
+ if (tag != null) {
+ if (tag.isEmpty()) {
+ text += "The command contains an empty tag i.e. %%%%\n";
+ result = false;
+ } else {
+ if (!tag.matches(VALID_NAME_REGEX)) {
+ text += "The command contains an invalid tag \"%%"
+ + tag + "\"%%\n";
+ result = false;
+ }
+ if (!stringReplacementTags.contains(tag)) {
+ text += "There is no string replacement for %%" + tag
+ + "%%\n";
+ result = false;
+ } else {
+ tags.add(tag);
+ }
+ }
+ }
+ }
+
+ for (String tag : stringReplacementTags) {
+ if (!tags.contains(tag)) {
+ text += "String replacement for %%" + tag
+ + "%% is not used in the command\n";
+ result = false;
+ }
+ }
+
+ Set<String> inputFilePortNames = new HashSet<String>();
+ Set<String> inputFileNames = new HashSet<String>();
+ for (ExternalToolFileViewer v : inputFileViewList) {
+ String name = v.getName();
+ if (name.equalsIgnoreCase("stdin") || name.equalsIgnoreCase("stdout") || name.equalsIgnoreCase("stderr")) {
+ text += "An input file port has a reserved name \"" + name + "\"\n";
+ result = false;
+ }
+ else if (stringReplacementPortNames.contains(name)) {
+ text += "A string replacement port and an input file port have the name \""
+ + name + "\"\n";
+ result = false;
+ } else if (inputFilePortNames.contains(name)) {
+ text += "Two file input ports have the name \"" + name + "\"\n";
+ result = false;
+ } else if (!name.matches(VALID_NAME_REGEX)) {
+ text += "File input port name \"" + name + "\" is invalid\n";
+ result = false;
+ } else {
+ inputFilePortNames.add(name);
+ }
+
+ String fileName = v.getValue();
+ if (inputFileNames.contains(fileName)) {
+ text += "Two file inputs ports write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else {
+ inputFileNames.add(fileName);
+ }
+ }
+
+ Set<String> fileListPortNames = new HashSet<String>();
+ Set<String> fileListFileNames = new HashSet<String>();
+ for (ExternalToolFileViewer v : fileListViewList) {
+ String name = v.getName();
+ if (name.equalsIgnoreCase("stdin") || name.equalsIgnoreCase("stdout") || name.equalsIgnoreCase("stderr")) {
+ text += "A file list port has a reserved name \"" + name + "\"\n";
+ result = false;
+ } else if (stringReplacementPortNames.contains(name)) {
+ text += "A string replacement port and a file list port have the name \""
+ + name + "\"\n";
+ result = false;
+ } else if (inputFilePortNames.contains(name)) {
+ text += "A file input port and a file list port have the name \""
+ + name + "\"\n";
+ result = false;
+ } else if (fileListPortNames.contains(name)) {
+ text += "Two file list ports have the name \"" + name + "\"\n";
+ result = false;
+ } else if (!name.matches(VALID_NAME_REGEX)) {
+ text += "File list port name \"" + name + "\" is invalid\n";
+ result = false;
+ } else {
+ fileListPortNames.add(name);
+ }
+
+ String fileName = v.getValue();
+ if (fileListFileNames.contains(fileName)) {
+ text += "Two file list ports write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else if (inputFileNames.contains(fileName)) {
+ text += "A file input port and a file list port write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else {
+ fileListFileNames.add(fileName);
+ }
+ }
+
+ Set<String> staticStringFileNames = new HashSet<String>();
+ for (ExternalToolStaticStringViewer v : staticStringViewList) {
+ String fileName = v.getValue();
+ if (staticStringFileNames.contains(fileName)) {
+ text += "Two static strings write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else if (inputFileNames.contains(fileName)) {
+ text += "A file input port and a static string write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else if (fileListFileNames.contains(fileName)) {
+ text += "A file list port and a static string write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else {
+ staticStringFileNames.add(fileName);
+ }
+ }
+
+ Set<String> staticUrlFileNames = new HashSet<String>();
+ for (ExternalToolStaticUrlViewer v : staticUrlViewList) {
+ String fileName = v.getValue();
+ if (staticUrlFileNames.contains(fileName)) {
+ text += "Two static URLss write to the same file \"" + fileName
+ + "\"\n";
+ result = false;
+ } else if (inputFileNames.contains(fileName)) {
+ text += "A file input port and a static URL write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else if (fileListFileNames.contains(fileName)) {
+ text += "A file list port and a static URL write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else if (staticStringFileNames.contains(fileName)) {
+ text += "A static string and a static URL write to the same file \""
+ + fileName + "\"\n";
+ result = false;
+ } else {
+ staticUrlFileNames.add(fileName);
+ }
+ }
+ Set<String> outputPortNames = new HashSet<String>();
+ for (ExternalToolFileViewer v : outputViewList) {
+ String name = v.getName();
+ if (name.equalsIgnoreCase("stdin") || name.equalsIgnoreCase("stdout") || name.equalsIgnoreCase("stderr")) {
+ text += "An output port has a reserved name \"" + name + "\"\n";
+ result = false;
+ } else if (outputPortNames.contains(name)) {
+ text += "Two output file ports have the name \"" + name
+ + "\"\n";
+ result = false;
+ } else if (!name.matches(VALID_NAME_REGEX)) {
+ text += "Output file port name \"" + name + "\" is invalid\n";
+ result = false;
+ } else {
+ outputPortNames.add(name);
+ }
+ }
+ if (!result) {
+ JOptionPane.showMessageDialog(this, text, "Problems",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ return result;
+ }
+
+ /**
+ * Check the proposed port name against the set of ports
+ *
+ * @return
+ */
+ public boolean portNameExists(String name) {
+ if (name.equalsIgnoreCase("stdin") || name.equalsIgnoreCase("stdout") || name.equalsIgnoreCase("stderr")) {
+ return true;
+ }
+
+ for (ExternalToolFileViewer v : inputFileViewList) {
+ if (name.equals(v.getName())) {
+ return true;
+ }
+ }
+ for (ExternalToolFileViewer v : fileListViewList) {
+ if (name.equals(v.getName())) {
+ return true;
+ }
+ }
+ for (ExternalToolStringReplacementViewer v : stringReplacementViewList) {
+ if (name.equals(v.getName())) {
+ return true;
+ }
+ }
+ for (ExternalToolFileViewer v : outputViewList) {
+ if (name.equals(v.getName())) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+
+ public void setEditable(boolean editable, ExternalToolActivityConfigurationBean config) {
+ ExternalToolActivityConfigurationBean newConfig = (ExternalToolActivityConfigurationBean) cloneBean(config);
+ ExternalToolActivityHealthChecker.updateLocation(newConfig);
+ newConfig.setEdited(editable);
+ refreshConfiguration(newConfig);
+ }
+
+ public void whenClosed() {
+ if (invocationPanel != null) {
+ invocationPanel.stopObserving();
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolFileViewer.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolFileViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolFileViewer.java
new file mode 100644
index 0000000..11fb0c4
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolFileViewer.java
@@ -0,0 +1,103 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JTextField;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolFileViewer {
+
+ private JTextField nameField;
+ private String name;
+ private JTextField valueField;
+ private JCheckBox valueFromField;
+ private JComboBox typeSelector;
+
+ public ExternalToolFileViewer(String name, String value, boolean isBinary) {
+ this(name);
+ nameField.setText(name);
+ if (!value.equals(name)) {
+ valueFromField.setSelected(false);
+ valueField.setText(value);
+ valueField.setEnabled(true);
+ }
+ if (isBinary) {
+ typeSelector.setSelectedItem("Binary");
+ } else {
+ typeSelector.setSelectedItem("Text");
+ }
+ }
+
+ public ExternalToolFileViewer(final String name) {
+ this.name = name;
+ nameField = new JTextField(20);
+ valueField = new JTextField(20);
+ valueFromField = new JCheckBox(new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (valueFromField.isSelected()) {
+ valueField.setText("");
+ valueField.setEnabled(false);
+ } else {
+ valueField.setText(getName());
+ valueField.setEnabled(true);
+ }
+ }});
+ valueFromField.setSelected(true);
+ valueField.setEnabled(false);
+ typeSelector = new JComboBox(new String[] {"Binary", "Text"});
+ nameField.setText(name);
+ typeSelector.setSelectedItem("Text");
+
+ }
+
+ public JTextField getNameField() {
+ return nameField;
+ }
+
+ public JTextField getValueField() {
+ return valueField;
+ }
+
+ public JComboBox getTypeSelector() {
+ return typeSelector;
+ }
+
+ public String getName() {
+ return nameField.getText();
+ }
+
+ public boolean isBinary() {
+ return (typeSelector.getSelectedItem().equals("Binary"));
+ }
+
+ public String getValue() {
+ if (valueFromField.isSelected()) {
+ return getName();
+ }
+ return valueField.getText();
+ }
+
+ /**
+ * @return the valueFromField
+ */
+ public JCheckBox getValueFromField() {
+ return valueFromField;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolRuntimeEnvironmentViewer.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolRuntimeEnvironmentViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolRuntimeEnvironmentViewer.java
new file mode 100644
index 0000000..1451660
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolRuntimeEnvironmentViewer.java
@@ -0,0 +1,56 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import javax.swing.JComboBox;
+import javax.swing.JTextField;
+
+import de.uni_luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolRuntimeEnvironmentViewer {
+
+ private JTextField idField;
+ private JComboBox relationSelector;
+
+ public ExternalToolRuntimeEnvironmentViewer(String id, String relation) {
+ this(id);
+ idField.setText(id);
+ relationSelector.setSelectedItem(relation);
+ }
+
+ public ExternalToolRuntimeEnvironmentViewer(String id) {
+ this();
+ idField.setText(id);
+ }
+
+ public ExternalToolRuntimeEnvironmentViewer() {
+ idField = new JTextField(20);
+ relationSelector = new JComboBox(RuntimeEnvironmentConstraint.getAcceptedRelations());
+ relationSelector.setSelectedItem(RuntimeEnvironmentConstraint.getDefaultRelation());
+ }
+
+ public JTextField getIdField() {
+ return idField;
+ }
+
+ public JComboBox getRelationSelector() {
+ return relationSelector;
+ }
+
+ public String getId() {
+ return idField.getText();
+ }
+
+ public String getRelation() {
+ return (String) relationSelector.getSelectedItem();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticStringViewer.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticStringViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticStringViewer.java
new file mode 100644
index 0000000..d82d9b7
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticStringViewer.java
@@ -0,0 +1,53 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolStaticStringViewer {
+
+ ScriptInputStatic input;
+ private JTextArea contentField = new JTextArea();
+ private JTextField valueField;
+
+
+ public ExternalToolStaticStringViewer(ScriptInputStatic input) {
+ this();
+ this.input = input;
+ contentField.setText((String) input.getContent());
+ valueField.setText(input.getTag());
+ }
+
+ public ExternalToolStaticStringViewer() {
+ contentField = new JTextArea(5, 40);
+ contentField.setText("");
+ valueField = new JTextField(20);
+ valueField.setText("");
+ }
+
+ public String getContent() {
+ return contentField.getText();
+ }
+
+ public JTextArea getContentField() {
+ return contentField;
+ }
+
+
+ public JTextField getValueField() {
+ return valueField;
+ }
+
+ public String getValue() {
+ return valueField.getText();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticUrlViewer.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticUrlViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticUrlViewer.java
new file mode 100644
index 0000000..f7a1793
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStaticUrlViewer.java
@@ -0,0 +1,56 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import javax.swing.JComboBox;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolStaticUrlViewer {
+
+ ScriptInputStatic input;
+ private JTextField contentField = new JTextField();
+ private JTextField valueField;
+
+
+ public ExternalToolStaticUrlViewer(ScriptInputStatic input) {
+ this();
+ this.input = input;
+ contentField.setText(input.getUrl());
+ valueField.setText(input.getTag());
+ }
+
+ public ExternalToolStaticUrlViewer() {
+ contentField = new JTextField(40);
+ contentField.setText("");
+ valueField = new JTextField(20);
+ valueField.setText("");
+ }
+
+ public String getContent() {
+ return contentField.getText();
+ }
+
+ public JTextField getContentField() {
+ return contentField;
+ }
+
+
+ public JTextField getValueField() {
+ return valueField;
+ }
+
+ public String getValue() {
+ return valueField.getText();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStringReplacementViewer.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStringReplacementViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStringReplacementViewer.java
new file mode 100644
index 0000000..8e24183
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ExternalToolStringReplacementViewer.java
@@ -0,0 +1,97 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.event.ActionEvent;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.swing.AbstractAction;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JTextField;
+
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
+import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolStringReplacementViewer {
+
+ private static Pattern p = Pattern.compile("\\w+");
+ private static final String PERCENTS = "%%";
+ ScriptInput input;
+ private JTextField nameField;
+ private String name;
+ private JTextField valueField;
+ private JCheckBox valueFromField;
+
+ public ExternalToolStringReplacementViewer(String name, ScriptInputUser input) {
+ this(name);
+ this.input = input;
+ nameField.setText(name);
+ if (!input.getTag().equals(name)) {
+ valueFromField.setSelected(false);
+ valueField.setText(PERCENTS + input.getTag() + PERCENTS);
+ valueField.setEnabled(true);
+ }
+ }
+
+ public ExternalToolStringReplacementViewer(String name) {
+ this.name = name;
+ nameField = new JTextField(20);
+ nameField.setText(name);
+ valueField = new JTextField(20);
+ valueFromField = new JCheckBox(new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (valueFromField.isSelected()) {
+ valueField.setText("");
+ valueField.setEnabled(false);
+ } else {
+ valueField.setText(PERCENTS + getName() + PERCENTS);
+ valueField.setEnabled(true);
+ }
+ }});
+ valueFromField.setSelected(true);
+ valueField.setEnabled(false);
+ }
+
+ public JTextField getNameField() {
+ return nameField;
+ }
+
+ public JTextField getValueField() {
+ return valueField;
+ }
+
+ public String getName() {
+ return nameField.getText();
+ }
+
+ public String getValue() {
+ if (valueFromField.isSelected()) {
+ return getName();
+ }
+ String enteredValue = valueField.getText();
+
+ Matcher m = p.matcher(enteredValue);
+ String result = "";
+ if (m.find()) {
+ result = m.group();
+ }
+ return result;
+ }
+
+ /**
+ * @return the valueFromField
+ */
+ public JCheckBox getValueFromField() {
+ return valueFromField;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/FilePanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/FilePanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/FilePanel.java
new file mode 100644
index 0000000..678711c
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/FilePanel.java
@@ -0,0 +1,119 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+
+/**
+ * @author alanrw
+ *
+ */
+public class FilePanel extends JPanel {
+
+ private int outputGridy = 1;
+ private final ExternalToolConfigView view;
+
+ public FilePanel(final ExternalToolConfigView view,
+ final List<ExternalToolFileViewer> viewList,
+ String fileHeader, String typeHeader, final String portPrefix,
+ final String description, String addText) {
+ super();
+ this.view = view;
+ this.setLayout(new BorderLayout());
+ final JPanel fileEditPanel = new JPanel(new GridBagLayout());
+
+ final GridBagConstraints fileConstraint = new GridBagConstraints();
+ fileConstraint.insets = new Insets(5, 5, 5, 5);
+ fileConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ fileConstraint.gridx = 0;
+ fileConstraint.gridy = 0;
+ fileConstraint.weightx = 0.1;
+ fileConstraint.fill = GridBagConstraints.BOTH;
+
+ final String[] elementLabels = new String[] {"Taverna port name",
+ "Use port name for file",
+ fileHeader,
+ typeHeader
+ };
+
+ fileConstraint.gridx = 0;
+ synchronized (viewList) {
+ for (ExternalToolFileViewer outputView : viewList) {
+ addFileViewer(viewList, this, fileEditPanel,
+ outputView, elementLabels);
+ }
+ }
+ JButton addFilePortButton = new DeselectingButton(addText,
+ new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+
+ int portNumber = 1;
+
+ String name2 = portPrefix + portNumber++;
+ boolean nameExists = true;
+ while (nameExists == true) {
+ nameExists = view.portNameExists(name2);
+ if (nameExists) {
+ name2 = portPrefix + portNumber++;
+ }
+ }
+
+ ExternalToolFileViewer newViewer = new ExternalToolFileViewer(
+ name2);
+ synchronized (viewList) {
+ viewList.add(newViewer);
+ addFileViewer(viewList, FilePanel.this, fileEditPanel,
+ newViewer, elementLabels);
+ fileEditPanel.revalidate();
+ fileEditPanel.repaint();
+ }
+ }
+
+ });
+ JTextArea descriptionText = new ReadOnlyTextArea(description);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+
+ this.add(descriptionText, BorderLayout.NORTH);
+
+ this.add(new JScrollPane(fileEditPanel), BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel(new BorderLayout());
+
+ buttonPanel.add(addFilePortButton, BorderLayout.EAST);
+
+ this.add(buttonPanel, BorderLayout.SOUTH);
+
+ }
+
+ private void addFileViewer(final List<ExternalToolFileViewer> viewList,
+ final JPanel outerPanel, final JPanel panel,
+ ExternalToolFileViewer viewer, String[] elementLabels) {
+ Tools.addViewer(panel,
+ elementLabels,
+ new JComponent[] {viewer.getNameField(), viewer.getValueFromField(), viewer.getValueField(), viewer.getTypeSelector()},
+ viewList,
+ viewer,
+ outerPanel);
+ }
+
+}
[10/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
new file mode 100644
index 0000000..d3149d6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
@@ -0,0 +1,55 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>headers</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>header_key</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>header_value</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>if ((headers == void) || (headers == null)) {
+ throw new RuntimeException("Headers must be specified");
+}
+
+if ((header_key == void) || (header_key == null)) {
+ throw new RuntimeException("Header_key must be specified");
+}
+
+String header_value = "";
+if (!header_key.endsWith(":")) {
+ header_key += ":";
+}
+for (String h : headers) {
+ if (h.startsWith(header_key)) {
+ header_value = h.substring(header_key.length());
+ header_value = header_value.trim();
+ break;
+ }
+}</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
new file mode 100644
index 0000000..0e510fa
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((headers == void) || (headers == null)) {\n\tthrow new RuntimeException(\"Headers must be specified\");\n}\n\nif ((header_key == void) || (header_key == null)) {\n\tthrow new RuntimeException(\"Header_key must be specified\");\n}\n\nString header_value = \"\";\nif (!header_key.endsWith(\":\")) {\n\theader_key += \":\";\n}\nfor (String h : headers) {\n\tif (h.startsWith(header_key)) {\n\t\theader_value = h.substring(header_key.length());\n\t\theader_value = header_value.trim();\n\t\tbreak;\n\t}\n}",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
+ "inputPorts" : [ {
+ "name" : "headers",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "header_key",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "header_value",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker
new file mode 100644
index 0000000..f094efa
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker
@@ -0,0 +1,41 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.swing.JOptionPane;
+
+answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);
+
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>message</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>answer</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
new file mode 100644
index 0000000..c2095cc
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nanswer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);\n\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.AskWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
new file mode 100644
index 0000000..5244d77
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
@@ -0,0 +1,80 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
+if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
+ throw new RuntimeException("selectionValues must be specified and non-empty");
+}
+
+ButtonGroup group = new ButtonGroup();
+JPanel messagePanel = new JPanel();
+messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));
+
+messagePanel.add(new JLabel((message == void ? null : message)));
+
+JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
+for (int i = 0; i < buttonArray.length; i++) {
+ buttonArray[i] = new JRadioButton(selectionValues.get(i));
+ if (i==0) buttonArray[i].setSelected(true);
+ group.add(buttonArray[i]);
+ messagePanel.add(buttonArray[i]);
+}
+
+JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
+ JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
+
+String answer="";
+for (JRadioButton button : buttonArray) {
+ if (button.isSelected()) {
+ answer=button.getText();
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>message</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>selectionValues</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>answer</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
new file mode 100644
index 0000000..0410fc7
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.BoxLayout;\nimport javax.swing.ButtonGroup;\nimport javax.swing.JLabel;\nimport javax.swing.JOptionPane;\nimport javax.swing.JPanel;\nimport javax.swing.JRadioButton;\n\nif ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {\n throw new RuntimeException(\"selectionValues must be specified and non-empty\");\n}\n\nButtonGroup group = new ButtonGroup();\nJPanel messagePanel = new JPanel();\nmessagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));\n\nmessagePanel.add(new JLabel((message == void ? null : message)));\n\t\t\nJRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];\nfor (int i = 0; i < buttonArray.length; i++) {\t\t\t\n\tbuttonArray[i] = new JRadioButton(selectionValues.get(i));\n\tif (i==0) buttonArray[i].setSelected(true);\n\tgroup.add(buttonArray[i]);\n\tmessagePanel.add(buttonArray[i]);\n}\t\t\t\t\n\nJOptionPane.showOptionDialog(null, messagePanel, (title == void ? null
: title),\n\t\tJOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{\"OK\"}, null);\n\t\t\nString answer=\"\";\nfor (JRadioButton button : buttonArray) {\n\tif (button.isSelected()) {\n\t\tanswer=button.getText();\n\t}\n}\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.ChooseWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "selectionValues",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
new file mode 100644
index 0000000..e594b7f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
@@ -0,0 +1,116 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import java.awt.CardLayout;
+import java.awt.Image;
+import java.awt.Toolkit;
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.ImageIcon;
+import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.filechooser.FileFilter;
+
+class FileExtFilter extends FileFilter {
+
+ public FileExtFilter(String ext, String label, boolean includeDir) {
+ this.ext = ext;
+ this.label = label;
+ this.includeDir = includeDir;
+ }
+
+ public String getDescription() {
+ return this.label;
+ }
+
+ public boolean accept(File file) {
+ if (file.isDirectory() && includeDir) {
+ return true;
+ } else {
+ return file.getName().endsWith(this.ext);
+ }
+ }
+
+ String ext, label;
+
+ boolean includeDir;
+}
+
+if (title == void) {
+ title = null;
+}
+
+if ((fileExtensions == void) || (fileExtensions == null)) {
+ fileExtensions = "";
+}
+
+if ((fileExtLabels == void) || (fileExtLabels == null)) {
+ fileExtLabels = "";
+}
+
+JFileChooser chooser = new JFileChooser();
+chooser.setDialogTitle(title);
+
+String[] fileTypeList = fileExtensions.split(",");
+String[] filterLabelList = fileExtLabels.split(",");
+
+if (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {
+ throw new RuntimeException("The list of extensions and file filter labels must be the same length");
+}
+
+// create the file filters
+for (int i = 0; i < fileTypeList.length; i++) {
+ FileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);
+ chooser.setFileFilter(filter);
+}
+
+chooser.showOpenDialog(null);
+File file = chooser.getSelectedFile();
+selectedFile = file.getAbsolutePath();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>fileExtensions</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>fileExtLabels</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>selectedFile</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
new file mode 100644
index 0000000..1d71cef
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.awt.CardLayout;\nimport java.awt.Image;\nimport java.awt.Toolkit;\nimport java.io.File;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.swing.ImageIcon;\nimport javax.swing.JEditorPane;\nimport javax.swing.JFileChooser;\nimport javax.swing.JLabel;\nimport javax.swing.JPanel;\nimport javax.swing.filechooser.FileFilter;\n\nclass FileExtFilter extends FileFilter {\n\n\tpublic FileExtFilter(String ext, String label, boolean includeDir) {\n\t\tthis.ext = ext;\n\t\tthis.label = label;\n\t\tthis.includeDir = includeDir;\n\t}\n\n\tpublic String getDescription() {\n\t\treturn this.label;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\tif (file.isDirectory() && includeDir) {\n\t\t\treturn true;\n\t\t} else {\n\t\t\treturn file.getName().endsWith(this.ext);\n\t\t}\n\t}\n\n\tString ext, label;\n\n\tboolean includeDir;\n}\n\nif (title == void) {\n\ttitle = null;\n}\n\nif ((fileExtensions == void) || (fileExtensions == null)) {\n\tfileExtensions = \"\
";\n}\n\nif ((fileExtLabels == void) || (fileExtLabels == null)) {\n\tfileExtLabels = \"\";\n}\n\nJFileChooser chooser = new JFileChooser();\nchooser.setDialogTitle(title);\n\nString[] fileTypeList = fileExtensions.split(\",\");\nString[] filterLabelList = fileExtLabels.split(\",\");\n\nif (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {\n\tthrow new RuntimeException(\"The list of extensions and file filter labels must be the same length\");\n}\n\n// create the file filters\nfor (int i = 0; i < fileTypeList.length; i++) {\n\tFileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);\n\tchooser.setFileFilter(filter);\n}\n\nchooser.showOpenDialog(null);\nFile file = chooser.getSelectedFile();\nselectedFile = file.getAbsolutePath();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "fileExtensions",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "fileExtLabels",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "selectedFile",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
new file mode 100644
index 0000000..1745844
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
@@ -0,0 +1,53 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.swing.JOptionPane;
+
+if ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {
+ throw new RuntimeException("valueList must be specified and non-empty");
+}
+
+answer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>valueList</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>message</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>answer</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
new file mode 100644
index 0000000..6c287b6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nif ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {\n throw new RuntimeException(\"valueList must be specified and non-empty\");\n}\n\nanswer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectWorker",
+ "inputPorts" : [ {
+ "name" : "valueList",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker
new file mode 100644
index 0000000..99ee6ab
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker
@@ -0,0 +1,42 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.swing.JOptionPane;
+
+JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.INFORMATION_MESSAGE);
+
+answer = "answer";
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>message</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>answer</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
new file mode 100644
index 0000000..8037a42
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.INFORMATION_MESSAGE);\n\nanswer = \"answer\";\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.TellWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker
new file mode 100644
index 0000000..b211ba5
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker
@@ -0,0 +1,42 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.swing.JOptionPane;
+
+JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.WARNING_MESSAGE);
+
+answer = "answer";
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>title</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>message</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>answer</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
new file mode 100644
index 0000000..eaa8c93
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.WARNING_MESSAGE);\n\nanswer = \"answer\";\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.WarnWorker",
+ "inputPorts" : [ {
+ "name" : "title",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "message",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "answer",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
new file mode 100644
index 0000000..0395225
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
@@ -0,0 +1,75 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.dom4j.Document;
+import org.dom4j.Node;
+import org.dom4j.io.SAXReader;
+
+SAXReader reader = new SAXReader(false);
+reader.setIncludeInternalDTDDeclarations(false);
+reader.setIncludeExternalDTDDeclarations(false);
+
+Document document = reader.read(new StringReader(xmltext));
+List nodelist = document.selectNodes(xpath);
+
+// Process the elements in the nodelist
+ArrayList outputList = new ArrayList();
+ArrayList outputXmlList = new ArrayList();
+
+String val = null;
+String xmlVal = null;
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
+ Node element = (Node) iter.next();
+ xmlVal = element.asXML();
+ val = element.getStringValue();
+ if (val != null && !val.equals("")) {
+ outputList.add(val);
+ outputXmlList.add(xmlVal);
+ }
+
+}
+
+List nodelist=outputList;
+List nodelistAsXML=outputXmlList;</script>
+ <dependencies>
+ <string>dom4j:dom4j:1.6</string>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>xpath</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>xml-text</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/xml'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>nodelist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>nodelistAsXML</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
new file mode 100644
index 0000000..3fa2385
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.dom4j.Document;\nimport org.dom4j.Node;\nimport org.dom4j.io.SAXReader;\n\nSAXReader reader = new SAXReader(false);\nreader.setIncludeInternalDTDDeclarations(false);\nreader.setIncludeExternalDTDDeclarations(false);\n\nDocument document = reader.read(new StringReader(xmltext));\nList nodelist = document.selectNodes(xpath);\n\n// Process the elements in the nodelist\nArrayList outputList = new ArrayList();\nArrayList outputXmlList = new ArrayList();\n\nString val = null;\nString xmlVal = null;\nfor (Iterator iter = nodelist.iterator(); iter.hasNext();) {\n\tNode element = (Node) iter.next();\n\txmlVal = element.asXML();\n\tval = element.getStringValue();\n\tif (val != null && !val.equals(\"\")) {\n\t\toutputList.add(val);\n\t\toutputXmlList.add(xmlVal);\n\t}\n\n}\n\nList nodelist=outputList;\nList nodelistAsXML=outputXmlList;",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
+ "inputPorts" : [ {
+ "name" : "xpath",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "xml-text",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "nodelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ }, {
+ "name" : "nodelistAsXML",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
new file mode 100644
index 0000000..1532b63
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
@@ -0,0 +1,152 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.StringWriter;
+import java.io.Writer;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.xml.transform.Result;
+import javax.xml.transform.Source;
+import javax.xml.transform.SourceLocator;
+import javax.xml.transform.Templates;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+BufferedReader getReader (String fileUrl) throws IOException {
+ InputStreamReader reader;
+ try {
+ reader = new FileReader(fileUrl);
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ reader = new InputStreamReader (url.openStream());
+ }
+ return new BufferedReader(reader);
+ }
+
+BufferedWriter getWriter (String fileUrl) throws IOException {
+ Writer writer;
+ try {
+ writer = new FileWriter(fileUrl);
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ writer = new OutputStreamWriter (url.openConnection().getOutputStream());
+ }
+ return new BufferedWriter(writer);
+ }
+
+String xslFilename = xslFileURL;
+String outFilename;
+if (outFileURL != void) {
+ outFilename = outFileURL;
+}
+
+String ext;
+if (outputExt != void) {
+ ext = outputExt;
+}
+
+if (((outFilename == null) || outFilename.equals("")) && (ext != null)) {
+ outFilename = inFileURL.substring(0, inFileURL.indexOf(".")+1) + ext;
+}
+
+// Create transformer factory
+TransformerFactory factory = TransformerFactory.newInstance();
+
+// Use the factory to create a template containing the xsl file
+Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));
+
+// Use the template to create a transformer
+Transformer xformer = template.newTransformer();
+
+// Prepare the input and output files
+Reader sourceReader = getReader(inFileURL);
+Source source = new StreamSource(sourceReader);
+StringWriter resultStr = new StringWriter();
+Result result = new StreamResult(resultStr);
+
+// Apply the xsl file to the source file and write the result to the
+// output file
+xformer.transform(source, result);
+
+outputStr = resultStr.toString();
+
+if ((outFilename != null) && !outFilename.equals("")) {
+
+ BufferedWriter out = getWriter(outFilename);
+
+ out.write(outputStr);
+ out.close();
+}
+sourceReader.close();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>xslFileURL</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>outFileURL</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>inFileURL</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>outputExt</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputStr</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/xml'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
new file mode 100644
index 0000000..09aff0d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
@@ -0,0 +1,28 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.io.BufferedReader;\nimport java.io.BufferedWriter;\nimport java.io.FileInputStream;\nimport java.io.FileNotFoundException;\nimport java.io.FileReader;\nimport java.io.FileWriter;\nimport java.io.IOException;\nimport java.io.InputStreamReader;\nimport java.io.OutputStreamWriter;\nimport java.io.StringWriter;\nimport java.io.Writer;\nimport java.net.URL;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.xml.transform.Result;\nimport javax.xml.transform.Source;\nimport javax.xml.transform.SourceLocator;\nimport javax.xml.transform.Templates;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerConfigurationException;\nimport javax.xml.transform.TransformerException;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\
t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nBufferedWriter getWriter (String fileUrl) throws IOException {\n\t\tWriter writer;\n\t\ttry {\n\t\t\twriter = new FileWriter(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\twriter = new OutputStreamWriter (url.openConnection().getOutputStream());\n\t\t}\n\t\treturn new BufferedWriter(writer);\n\t}\n\t\nString xslFilename = xslFileURL;\nString outFilename;\nif (outFileURL != void) {\n outFilename = outFileURL;\n}\n\nString ext;\nif (outputExt != void) {\n ext = outputExt;\n}\n\nif (((outFilename == null) || outFilename.equals(\"\")) && (ext != null)) {\n\t\toutFilename = inFileURL.substring(0, inFileURL.indexOf(\".\")+1) + ext;\n}\n\
n// Create transformer factory\nTransformerFactory factory = TransformerFactory.newInstance();\n\n// Use the factory to create a template containing the xsl file\nTemplates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\n\n// Use the template to create a transformer\nTransformer xformer = template.newTransformer();\n\n// Prepare the input and output files\nReader sourceReader = getReader(inFileURL);\nSource source = new StreamSource(sourceReader);\nStringWriter resultStr = new StringWriter();\nResult result = new StreamResult(resultStr);\n\n// Apply the xsl file to the source file and write the result to the\n// output file\nxformer.transform(source, result);\n\noutputStr = resultStr.toString();\n\nif ((outFilename != null) && !outFilename.equals(\"\")) {\n\n\tBufferedWriter out = getWriter(outFilename);\n\n\tout.write(outputStr);\n\tout.close();\n}\nsourceReader.close();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
+ "inputPorts" : [ {
+ "name" : "xslFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "outFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "inFileURL",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "outputExt",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputStr",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
new file mode 100644
index 0000000..768c8f9
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
@@ -0,0 +1,100 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
+ <class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
+ <inputMap>
+ <map from="xsltString" to="xsltString" />
+ <map from="paramList" to="paramList" />
+ <map from="sourceString" to="sourceString" />
+ </inputMap>
+ <outputMap>
+ <map from="outputString" to="outputString" />
+ </outputMap>
+ <configBean encoding="xstream">
+ <net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>sourceString</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>xsltString</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>paramList</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <name>outputString</name>
+ <depth>0</depth>
+ <mimeTypes />
+ <granularDepth>0</granularDepth>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>//From a proposal by Mikolaj Rybinski
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+param(paramstr) {
+ nameAndValue = paramstr.split("=");
+ if (nameAndValue.length != 2) {
+ throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");
+ }
+ name = nameAndValue[0].trim();
+ value = nameAndValue[1].trim();
+ return this;
+}
+
+if ((sourceString == void) || (sourceString == null)) {
+ throw new RuntimeException("sourceString must be specified");
+}
+
+if ((xsltString == void) || (xsltString == null)) {
+ throw new RuntimeException("xsltString must be specified");
+}
+
+Source inSource = new StreamSource(new StringReader(sourceString));
+Source xslSource = new StreamSource(new StringReader(xsltString));
+
+// the factory pattern supports different XSLT processors
+// e.g. set the "javax.xml.transform.TransformerFactory" system property
+TransformerFactory tnfFact = TransformerFactory.newInstance();
+Transformer tnf = tnfFact.newTransformer(xslSource);
+
+if (paramList != void) {
+ for (String paramstr : paramList) {
+ p = param(paramstr);
+ tnf.setParameter(p.name, p.value);
+ }
+}
+
+Writer outputWriter = new StringWriter();
+tnf.transform(inSource, new StreamResult(outputWriter));
+outputString = outputWriter.toString();</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
new file mode 100644
index 0000000..0800c76
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "//From a proposal by Mikolaj Rybinski\nimport javax.xml.transform.Source;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\n\nparam(paramstr) {\n nameAndValue = paramstr.split(\"=\");\n if (nameAndValue.length != 2) {\n throw new RuntimeException(\"Wrong parameter format: \\\"\" + paramstr + \"\\\".\");\n }\n name = nameAndValue[0].trim();\n value = nameAndValue[1].trim();\n return this;\n}\n\nif ((sourceString == void) || (sourceString == null)) {\n throw new RuntimeException(\"sourceString must be specified\");\n}\n\nif ((xsltString == void) || (xsltString == null)) {\n throw new RuntimeException(\"xsltString must be specified\");\n}\n\nSource inSource = new StreamSource(new StringReader(sourceString));\nSource xslSource = new StreamSource(new StringReader(xsltString));\n\n// the factory patte
rn supports different XSLT processors\n// e.g. set the \"javax.xml.transform.TransformerFactory\" system property\nTransformerFactory tnfFact = TransformerFactory.newInstance();\nTransformer tnf = tnfFact.newTransformer(xslSource);\n\nif (paramList != void) {\n for (String paramstr : paramList) {\n p = param(paramstr);\n tnf.setParameter(p.name, p.value);\n }\n}\n\nWriter outputWriter = new StringWriter();\ntnf.transform(inSource, new StreamResult(outputWriter));\noutputString = outputWriter.toString();",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
+ "inputPorts" : [ {
+ "name" : "sourceString",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "xsltString",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "paramList",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputString",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
new file mode 100644
index 0000000..35b50d0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
@@ -0,0 +1,44 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((bytes == void) || (bytes == null)) {
+ throw new RuntimeException("The 'bytes' parameter must be specified");
+}
+if (encoding == void) {
+ string = new String(bytes);
+} else {
+ string = new String(bytes, encoding);
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>[B</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>bytes</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'application/octet-stream'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>string</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
new file mode 100644
index 0000000..ae7f934
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((bytes == void) || (bytes == null)) {\n\tthrow new RuntimeException(\"The 'bytes' parameter must be specified\");\n}\nif (encoding == void) {\n\tstring = new String(bytes);\n} else {\n\tstring = new String(bytes, encoding);\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
+ "inputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "type" : "byte[]"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "string",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64 b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64
new file mode 100644
index 0000000..62c01bd
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64
@@ -0,0 +1,31 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.apache.commons.codec.binary.Base64;
+
+bytes = Base64.decodeBase64(base64.getBytes());
+</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">commons-codec:commons-codec:1.3</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>base64</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>bytes</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'application/octet-stream'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json
new file mode 100644
index 0000000..1cb0f62
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.DecodeBase64.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.apache.commons.codec.binary.Base64;\n\nbytes = Base64.decodeBase64(base64.getBytes());\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
+ "inputPorts" : [ {
+ "name" : "base64",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList
new file mode 100644
index 0000000..615c762
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList
@@ -0,0 +1,26 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>outputlist = inputlist;</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>[B</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>inputlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>outputlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json
new file mode 100644
index 0000000..aa0d198
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EchoList.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "outputlist = inputlist;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EchoList",
+ "inputPorts" : [ {
+ "name" : "inputlist",
+ "depth" : 1,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
new file mode 100644
index 0000000..6045d0a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
@@ -0,0 +1,19 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>List strings = new ArrayList();
+for (int i = 0; i < 40; i++) {
+ strings.add("String" + i);
+}
+</script>
+ <dependencies />
+ <inputs />
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>strings</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json
new file mode 100644
index 0000000..4afc1f8
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List strings = new ArrayList();\nfor (int i = 0; i < 40; i++) {\n\tstrings.add(\"String\" + i);\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
+ "outputPorts" : [ {
+ "name" : "strings",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64 b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64
new file mode 100644
index 0000000..8f6bcd0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64
@@ -0,0 +1,30 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.apache.commons.codec.binary.Base64;
+
+base64 = new String(Base64.encodeBase64(bytes));</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">commons-codec:commons-codec:1.3</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>[B</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>bytes</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'application/octet-stream'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>base64</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json
new file mode 100644
index 0000000..5cbd786
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.EncodeBase64.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.apache.commons.codec.binary.Base64;\n\nbase64 = new String(Base64.encodeBase64(bytes));",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
+ "inputPorts" : [ {
+ "name" : "bytes",
+ "depth" : 0,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "base64",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
new file mode 100644
index 0000000..05946b1
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
@@ -0,0 +1,41 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>String lowerCaseContent = document.toLowerCase();
+int index = 0;
+List imagelinks = new ArrayList();
+while ((index = lowerCaseContent.indexOf("<img", index)) != -1) {
+ if ((index = lowerCaseContent.indexOf("src", index)) == -1)
+ break;
+ if ((index = lowerCaseContent.indexOf("=", index)) == -1)
+ break;
+ index++;
+ String remaining = document.substring(index);
+ StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#");
+ String strLink = st.nextToken();
+ imagelinks.add(strLink);
+}
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>document</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/html'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>imagelinks</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/x-taverna-web-url')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json
new file mode 100644
index 0000000..2a23a47
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "String lowerCaseContent = document.toLowerCase();\nint index = 0;\nList imagelinks = new ArrayList();\nwhile ((index = lowerCaseContent.indexOf(\"<img\", index)) != -1) {\n\tif ((index = lowerCaseContent.indexOf(\"src\", index)) == -1)\n\t\tbreak;\n\tif ((index = lowerCaseContent.indexOf(\"=\", index)) == -1)\n\t\tbreak;\n\tindex++;\n\tString remaining = document.substring(index);\n\tStringTokenizer st = new StringTokenizer(remaining, \"\\t\\n\\r\\\">#\");\n\tString strLink = st.nextToken();\n\timagelinks.add(strLink);\n}\n\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
+ "inputPorts" : [ {
+ "name" : "document",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "imagelinks",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList
new file mode 100644
index 0000000..7b107e6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList
@@ -0,0 +1,43 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>filteredlist = new ArrayList();
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ if (item.matches(regex)) {
+ filteredlist.add(item);
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>regex</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>filteredlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json
new file mode 100644
index 0000000..0f26e3e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FilterStringList.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "filteredlist = new ArrayList();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tif (item.matches(regex)) {\n\t\tfilteredlist.add(item);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.FilterStringList",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filteredlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList
new file mode 100644
index 0000000..558cc99
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList
@@ -0,0 +1,39 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>flatten(inputs, outputs, depth) {
+ for (i = inputs.iterator(); i.hasNext();) {
+ element = i.next();
+ if (element instanceof Collection && depth > 0) {
+ flatten(element, outputs, depth - 1);
+ } else {
+ outputs.add(element);
+ }
+ }
+}
+
+outputlist = new ArrayList();
+
+flatten(inputlist, outputlist, 1);</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>[B</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>inputlist</name>
+ <depth>2</depth>
+ <mimeTypes>
+ <string>l(l(''))</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>outputlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
[15/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/configuration/ToolInvocationConfiguration.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/configuration/ToolInvocationConfiguration.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/configuration/ToolInvocationConfiguration.java
new file mode 100644
index 0000000..0877045
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/configuration/ToolInvocationConfiguration.java
@@ -0,0 +1,57 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.configuration;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import uk.org.taverna.configuration.AbstractConfigurable;
+
+
+/**
+ * @author alanrw
+ *
+ */
+public class ToolInvocationConfiguration extends AbstractConfigurable {
+
+ private static ToolInvocationConfiguration instance;
+
+ private Map<String, String> defaultPropertyMap;
+
+ public static ToolInvocationConfiguration getInstance() {
+ if (instance == null) {
+ instance = new ToolInvocationConfiguration();
+ }
+ return instance;
+ }
+
+ @Override
+ public String getCategory() {
+ return "general";
+ }
+
+ @Override
+ public Map<String, String> getDefaultPropertyMap() {
+ if (defaultPropertyMap == null) {
+ defaultPropertyMap = new HashMap<String, String>();
+ }
+ return defaultPropertyMap;
+ }
+
+ @Override
+ public String getDisplayName() {
+ return "Tool invocation";
+ }
+
+ @Override
+ public String getFilePrefix() {
+ return "ToolInvocation";
+ }
+
+ @Override
+ public String getUUID() {
+ return "B611F5C2-EB49-479E-B01A-7F3F56E6918A";
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/GroupPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/GroupPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/GroupPanel.java
new file mode 100644
index 0000000..8f62787
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/GroupPanel.java
@@ -0,0 +1,113 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+
+/**
+ * UI for creating/editing dataflow input ports.
+ *
+ * @author David Withers
+ */
+public class GroupPanel extends JPanel {
+
+ private static final long serialVersionUID = 1L;
+
+ private JTextField groupNameField;
+
+ private JComboBox mechanismComboBox;
+
+ private static InvocationGroupManager manager = InvocationGroupManagerImpl.getInstance();
+
+ public GroupPanel(Object[] mechanisms) {
+ super(new GridBagLayout());
+
+ groupNameField = new JTextField();
+
+
+ setBorder(new EmptyBorder(10, 10, 10, 10));
+
+ GridBagConstraints constraints = new GridBagConstraints();
+
+ constraints.anchor = GridBagConstraints.WEST;
+ constraints.gridx = 0;
+ constraints.gridy = 0;
+ constraints.ipadx = 10;
+ add(new JLabel("Name:"), constraints);
+
+ constraints.gridx = 1;
+ constraints.gridwidth = 2;
+ constraints.ipadx = 0;
+ constraints.weightx = 1d;
+ constraints.fill = GridBagConstraints.HORIZONTAL;
+ add(groupNameField, constraints);
+
+ constraints.gridx = 0;
+ constraints.gridy = 1;
+ constraints.gridwidth = 1;
+ constraints.weightx = 0d;
+ constraints.fill = GridBagConstraints.NONE;
+ constraints.ipadx = 10;
+ constraints.insets = new Insets(10, 0, 0, 0);
+ add(new JLabel("Explicit location:"), constraints);
+
+ mechanismComboBox = new JComboBox(mechanisms);
+ mechanismComboBox.setSelectedItem(manager.getDefaultMechanism());
+
+ constraints.gridx = 1;
+ constraints.gridwidth = 2;
+ constraints.ipadx = 0;
+ add(mechanismComboBox, constraints);
+ }
+
+ /**
+ * Returns the portNameField.
+ *
+ * @return the portNameField
+ */
+ public JTextField getGroupNameField() {
+ return groupNameField;
+ }
+
+ /**
+ * Returns the group name.
+ *
+ * @return the group name
+ */
+ public String getGroupName() {
+ return groupNameField.getText();
+ }
+
+ public InvocationMechanism getSelectedMechanism() {
+ return (InvocationMechanism) mechanismComboBox.getSelectedItem();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerShutdownHook.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerShutdownHook.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerShutdownHook.java
new file mode 100644
index 0000000..3d54b26
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerShutdownHook.java
@@ -0,0 +1,34 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.workbench.ShutdownSPI;
+
+/**
+ * @author alanrw
+ *
+ */
+public class InvocationGroupManagerShutdownHook implements ShutdownSPI {
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.workbench.ShutdownSPI#positionHint()
+ */
+ @Override
+ public int positionHint() {
+ return 710;
+ }
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.workbench.ShutdownSPI#shutdown()
+ */
+ @Override
+ public boolean shutdown() {
+ InvocationGroupManager manager = InvocationGroupManagerImpl.getInstance();
+ manager.saveConfiguration();
+ manager.persistInvocations();
+ return true;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerStartupHook.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerStartupHook.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerStartupHook.java
new file mode 100644
index 0000000..43cf4df
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationGroupManagerStartupHook.java
@@ -0,0 +1,47 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.workbench.StartupSPI;
+
+/**
+ * Load previously saved workflow ids that were scheduled to be deleted before
+ * previous Taverna shutdown, and initiate deletion of them now.
+ *
+ * @see StoreRunIdsToDeleteLaterShutdownHook
+ * @see DatabaseCleanup
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+public class InvocationGroupManagerStartupHook implements StartupSPI {
+
+ public int positionHint() {
+ return 900;
+ }
+
+ public boolean startup() {
+ InvocationGroupManagerImpl.getInstance().loadInvocations();
+ return true;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationMechanismEditor.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationMechanismEditor.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationMechanismEditor.java
new file mode 100644
index 0000000..495d22b
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/InvocationMechanismEditor.java
@@ -0,0 +1,28 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import javax.swing.JPanel;
+
+/**
+ * @author alanrw
+ *
+ */
+public abstract class InvocationMechanismEditor<T extends InvocationMechanism> extends JPanel {
+
+ public abstract String getName();
+
+ public abstract boolean canShow(Class<?> c);
+
+ public abstract void show(T invocationMechanism);
+
+ public abstract T updateInvocationMechanism();
+
+ public abstract InvocationMechanism createMechanism(String mechanismName);
+
+ public boolean isSingleton() {
+ return false;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/MechanismPanel.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/MechanismPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/MechanismPanel.java
new file mode 100644
index 0000000..c068d56
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/MechanismPanel.java
@@ -0,0 +1,121 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.util.List;
+
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+/**
+ * UI for creating/editing dataflow input ports.
+ *
+ * @author David Withers
+ */
+public class MechanismPanel extends JPanel {
+
+ private static final long serialVersionUID = 1L;
+
+ private JTextField mechanismNameField;
+
+ private JComboBox mechanismTypeSelector;
+
+ public MechanismPanel(List<InvocationMechanismEditor<?>> invocationMechanismEditors) {
+ super(new GridBagLayout());
+
+ mechanismNameField = new JTextField();
+
+
+ setBorder(new EmptyBorder(10, 10, 10, 10));
+
+ GridBagConstraints constraints = new GridBagConstraints();
+
+ constraints.anchor = GridBagConstraints.WEST;
+ constraints.gridx = 0;
+ constraints.gridy = 0;
+ constraints.ipadx = 10;
+ add(new JLabel("Name:"), constraints);
+
+ constraints.gridx = 1;
+ constraints.gridwidth = 2;
+ constraints.ipadx = 0;
+ constraints.weightx = 1d;
+ constraints.fill = GridBagConstraints.HORIZONTAL;
+ add(mechanismNameField, constraints);
+
+ constraints.gridx = 0;
+ constraints.gridy = 1;
+ constraints.gridwidth = 1;
+ constraints.weightx = 0d;
+ constraints.fill = GridBagConstraints.NONE;
+ constraints.ipadx = 10;
+ constraints.insets = new Insets(10, 0, 0, 0);
+ add(new JLabel("Type:"), constraints);
+
+ mechanismTypeSelector = new JComboBox();
+ for (InvocationMechanismEditor<?> ime : invocationMechanismEditors) {
+ if (!ime.isSingleton()) {
+ mechanismTypeSelector.addItem(ime.getName());
+ }
+ }
+ constraints.gridx = 1;
+ constraints.gridwidth = 2;
+ constraints.ipadx = 0;
+ add(mechanismTypeSelector, constraints);
+
+
+ }
+
+ /**
+ * Returns the portNameField.
+ *
+ * @return the portNameField
+ */
+ public JTextField getMechanismNameField() {
+ return mechanismNameField;
+ }
+
+ /**
+ * Returns the port name.
+ *
+ * @return the port name
+ */
+ public String getMechanismName() {
+ return mechanismNameField.getText();
+ }
+
+ public String getMechanismTypeName() {
+ return (String) mechanismTypeSelector.getSelectedItem();
+ }
+
+ public Component getMechanismTypeSelector() {
+ return mechanismTypeSelector;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationPanel.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationPanel.java
new file mode 100644
index 0000000..22500cd
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationPanel.java
@@ -0,0 +1,379 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.DefaultListModel;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingUtilities;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.lang.observer.Observable;
+import net.sf.taverna.t2.lang.observer.Observer;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.ValidatingUserInputDialog;
+import net.sf.taverna.t2.workbench.helper.Helper;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ToolInvocationConfigurationPanel extends JPanel implements
+ Observer<InvocationManagerEvent> {
+
+ public static final String HEADER_TEXT = "A tool can be set to run at an explicit location (e.g. on a specificic machine or one of a set of machines). Alternatively, it can be set to run at a symbolic location, which means the tool will then be run at the explicit location pointed to by the symbolic location.";
+
+ private static InvocationGroupManagerImpl manager = InvocationGroupManagerImpl.getInstance();
+
+ private final List<InvocationMechanismEditor<?>> invocationMechanismEditors;
+
+ private JTextArea headerText;
+
+ private static String EXPLICIT_LOCATIONS = "explicit locations";
+ private static String SYMBOLIC_LOCATIONS = "symbolic locations";
+
+ private List<MechanismCreator> mechanismCreators;
+
+ JList locationList = new JList();
+
+ DefaultListModel groupListModel = new DefaultListModel();
+ DefaultListModel mechanismListModel = new DefaultListModel();
+ JComboBox locationTypeCombo = new JComboBox(new String[] { EXPLICIT_LOCATIONS,
+ SYMBOLIC_LOCATIONS });
+
+ public ToolInvocationConfigurationPanel(List<MechanismCreator> mechanismCreators,
+ List<InvocationMechanismEditor<?>> invocationMechanismEditors) {
+ super();
+ this.mechanismCreators = mechanismCreators;
+ this.invocationMechanismEditors = invocationMechanismEditors;
+ manager.addObserver(this);
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+
+ headerText = new JTextArea(HEADER_TEXT);
+ headerText.setLineWrap(true);
+ headerText.setWrapStyleWord(true);
+ headerText.setEditable(false);
+ headerText.setFocusable(false);
+ headerText.setBorder(new EmptyBorder(10, 10, 10, 10));
+
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(0, 0, 10, 0);
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.gridwidth = 1;
+ gbc.weightx = 1.0;
+ gbc.weighty = 0.0;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ add(headerText, gbc);
+
+ JPanel locationPanel = new JPanel(new BorderLayout());
+ JPanel subPanel = new JPanel(new FlowLayout());
+ JLabel modify = new JLabel("Modify:");
+
+ locationTypeCombo.setSelectedItem(EXPLICIT_LOCATIONS);
+ locationTypeCombo.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ switchList();
+ }
+ });
+ subPanel.add(modify);
+ subPanel.add(locationTypeCombo);
+
+ populateLists();
+ switchList();
+ locationList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ locationList.setCellRenderer(new DefaultListCellRenderer() {
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ Object toShow = value;
+ if (value instanceof InvocationGroup) {
+ InvocationGroup invocationGroup = (InvocationGroup) value;
+ toShow = invocationGroup.getName() + " --> "
+ + invocationGroup.getMechanismName();
+ }
+ return super.getListCellRendererComponent(list, toShow, index, isSelected,
+ cellHasFocus);
+ }
+ });
+ locationPanel.add(new JScrollPane(locationList), BorderLayout.CENTER);
+ locationPanel.add(subPanel, BorderLayout.NORTH);
+
+ JPanel buttonPanel = new JPanel(new FlowLayout());
+ JButton helpButton = new DeselectingButton("Help", new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ Helper.showHelp(ToolInvocationConfigurationPanel.this);
+ }
+ });
+
+ buttonPanel.add(helpButton);
+
+ buttonPanel.add(addLocationButton());
+ buttonPanel.add(removeLocationButton());
+ buttonPanel.add(editLocationButton());
+ locationPanel.add(buttonPanel, BorderLayout.SOUTH);
+
+ gbc.gridy++;
+ gbc.weighty = 1;
+
+ gbc.fill = GridBagConstraints.BOTH;
+ gbc.anchor = GridBagConstraints.SOUTH;
+ gbc.insets = new Insets(10, 0, 0, 0);
+ this.add(locationPanel, gbc);
+ }
+
+ private void switchList() {
+ if (isShowingGroups()) {
+ locationList.setModel(groupListModel);
+ } else {
+ locationList.setModel(mechanismListModel);
+ }
+ }
+
+ private void populateLists() {
+ poopulateGroupList();
+ populateMechanismList();
+ }
+
+ private void populateMechanismList() {
+ Object currentSelection = locationList.getSelectedValue();
+ ArrayList<InvocationMechanism> mechanisms = new ArrayList<InvocationMechanism>();
+ mechanisms.addAll(manager.getMechanisms());
+ Collections.sort(mechanisms, new Comparator<InvocationMechanism>() {
+
+ @Override
+ public int compare(InvocationMechanism o1, InvocationMechanism o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+ mechanismListModel.clear();
+ for (InvocationMechanism m : mechanisms) {
+ mechanismListModel.addElement(m);
+ }
+ if ((currentSelection != null) && !isShowingGroups()) {
+ locationList.setSelectedValue(currentSelection, true);
+ }
+ }
+
+ private void poopulateGroupList() {
+ Object currentSelection = locationList.getSelectedValue();
+ ArrayList<InvocationGroup> groups = new ArrayList<InvocationGroup>();
+ groups.addAll(manager.getInvocationGroups());
+ Collections.sort(groups, new Comparator<InvocationGroup>() {
+
+ @Override
+ public int compare(InvocationGroup o1, InvocationGroup o2) {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+ groupListModel.clear();
+ for (InvocationGroup g : groups) {
+ groupListModel.addElement(g);
+ }
+ if ((currentSelection != null) && isShowingGroups()) {
+ locationList.setSelectedValue(currentSelection, true);
+ }
+ }
+
+ private boolean isShowingGroups() {
+ return (locationTypeCombo.getSelectedItem().equals(SYMBOLIC_LOCATIONS));
+ }
+
+ private JButton addLocationButton() {
+ final JButton result = new DeselectingButton("Add", new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (isShowingGroups()) {
+ Set<String> usedGroupNames = new HashSet<String>();
+ for (InvocationGroup g : manager.getInvocationGroups()) {
+ usedGroupNames.add(g.getName());
+ }
+
+ GroupPanel inputPanel = new GroupPanel(mechanismListModel.toArray());
+
+ ValidatingUserInputDialog vuid = new ValidatingUserInputDialog(
+ "Add symbolic location", inputPanel);
+ vuid.addTextComponentValidation(inputPanel.getGroupNameField(),
+ "Set the symbolic location name.", usedGroupNames,
+ "Duplicate symbolic location name.", "[\\p{L}\\p{Digit}_.]+",
+ "Invalid symbolic location name.");
+ vuid.setSize(new Dimension(400, 250));
+
+ if (vuid.show(ToolInvocationConfigurationPanel.this)) {
+ String groupName = inputPanel.getGroupName();
+ InvocationGroup newGroup = new InvocationGroup(mechanismCreators);
+ newGroup.setName(groupName);
+ newGroup.setMechanism(inputPanel.getSelectedMechanism());
+ manager.addInvocationGroup(newGroup);
+ locationList.setSelectedValue(newGroup, true);
+ }
+ } else {
+ Set<String> usedNames = new HashSet<String>();
+ for (InvocationMechanism m : manager.getMechanisms()) {
+ usedNames.add(m.getName());
+ }
+
+ MechanismPanel inputPanel = new MechanismPanel(invocationMechanismEditors);
+
+ ValidatingUserInputDialog vuid = new ValidatingUserInputDialog(
+ "Add explicit location", inputPanel);
+ vuid.addTextComponentValidation(inputPanel.getMechanismNameField(),
+ "Set the explicit location name.", usedNames,
+ "Duplicate explicit location name.", "[\\p{L}\\p{Digit}_.]+",
+ "Invalid explicit location name.");
+ vuid.addMessageComponent(inputPanel.getMechanismTypeSelector(),
+ "Set the location name and type.");
+ vuid.setSize(new Dimension(400, 250));
+
+ if (vuid.show(ToolInvocationConfigurationPanel.this)) {
+ String mechanismName = inputPanel.getMechanismName();
+ String mechanismTypeName = inputPanel.getMechanismTypeName();
+ InvocationMechanismEditor ime = findEditor(mechanismTypeName);
+ InvocationMechanism newMechanism = ime.createMechanism(mechanismName);
+ manager.addMechanism(newMechanism);
+ ime.show(newMechanism);
+ ime.setPreferredSize(new Dimension(550, 500));
+ int answer = JOptionPane.showConfirmDialog(
+ ToolInvocationConfigurationPanel.this, ime,
+ "New explicit location", JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.PLAIN_MESSAGE, null);
+ if (answer == JOptionPane.OK_OPTION) {
+ ime.updateInvocationMechanism();
+ InvocationGroupManagerImpl.getInstance().mechanismChanged(newMechanism);
+ }
+ locationList.setSelectedValue(newMechanism, true);
+ }
+ }
+ }
+ });
+ return result;
+ }
+
+ private JButton removeLocationButton() {
+ JButton result = new DeselectingButton("Remove", new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (isShowingGroups()) {
+ InvocationGroup toRemove = (InvocationGroup) locationList.getSelectedValue();
+ if ((toRemove != null) && !toRemove.equals(manager.getDefaultGroup())) {
+ manager.removeInvocationGroup(toRemove);
+ }
+ locationList.setSelectedValue(manager.getDefaultGroup(), true);
+ } else {
+ InvocationMechanism toRemove = (InvocationMechanism) locationList
+ .getSelectedValue();
+ if ((toRemove != null) && !toRemove.equals(manager.getDefaultMechanism())) {
+ manager.removeMechanism(toRemove);
+ locationList.setSelectedValue(manager.getDefaultMechanism(), true);
+ }
+ }
+ }
+ });
+ return result;
+ }
+
+ private JButton editLocationButton() {
+ final JButton result = new DeselectingButton("Edit", new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (isShowingGroups()) {
+ InvocationGroup toEdit = (InvocationGroup) locationList.getSelectedValue();
+ if (toEdit != null) {
+ InvocationMechanism chosenMechanism = (InvocationMechanism) JOptionPane
+ .showInputDialog(ToolInvocationConfigurationPanel.this,
+ "Select an explicit location", "Edit symbolic location",
+ JOptionPane.PLAIN_MESSAGE, null,
+ mechanismListModel.toArray(), toEdit.getMechanism());
+ if (chosenMechanism != null) {
+ toEdit.setMechanism(chosenMechanism);
+ manager.groupChanged(toEdit);
+ }
+ }
+ } else {
+ InvocationMechanism toEdit = (InvocationMechanism) locationList
+ .getSelectedValue();
+ if (toEdit != null) {
+ InvocationMechanismEditor ime = findEditor(toEdit.getClass());
+ ime.show(toEdit);
+ ime.setPreferredSize(new Dimension(550, 500));
+ int answer = JOptionPane.showConfirmDialog(
+ ToolInvocationConfigurationPanel.this, ime,
+ "Edit explicit location", JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.PLAIN_MESSAGE, null);
+ if (answer == JOptionPane.OK_OPTION) {
+ ime.updateInvocationMechanism();
+ InvocationGroupManagerImpl.getInstance().mechanismChanged(toEdit);
+ }
+ }
+ }
+ }
+ });
+ return result;
+ }
+
+ protected InvocationMechanismEditor findEditor(String name) {
+ for (InvocationMechanismEditor ime : invocationMechanismEditors) {
+ if (ime.getName().equalsIgnoreCase(name)) {
+ return ime;
+ }
+ }
+ return null;
+ }
+
+ protected InvocationMechanismEditor findEditor(Class c) {
+ for (InvocationMechanismEditor ime : invocationMechanismEditors) {
+ if (ime.canShow(c)) {
+ return ime;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void notify(Observable<InvocationManagerEvent> arg0, InvocationManagerEvent arg1)
+ throws Exception {
+ if (SwingUtilities.isEventDispatchThread()) {
+ populateLists();
+ } else {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ populateLists();
+ }
+ });
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationUIFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationUIFactory.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationUIFactory.java
new file mode 100644
index 0000000..82dd443
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ToolInvocationConfigurationUIFactory.java
@@ -0,0 +1,54 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager;
+
+import java.util.List;
+
+import javax.swing.JPanel;
+
+import uk.org.taverna.configuration.Configurable;
+import uk.org.taverna.configuration.ConfigurationUIFactory;
+
+import net.sf.taverna.t2.activities.externaltool.configuration.ToolInvocationConfiguration;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ToolInvocationConfigurationUIFactory implements ConfigurationUIFactory {
+
+ private List<MechanismCreator> mechanismCreators;
+ private List<InvocationMechanismEditor<?>> invocationMechanismEditors;
+
+ private ToolInvocationConfigurationPanel configPanel;
+
+ @Override
+ public boolean canHandle(String uuid) {
+ return uuid.equals(getConfigurable().getUUID());
+ }
+
+ @Override
+ public Configurable getConfigurable() {
+ return ToolInvocationConfiguration.getInstance();
+ }
+
+ @Override
+ public JPanel getConfigurationPanel() {
+ if (configPanel == null) {
+ configPanel = new ToolInvocationConfigurationPanel(mechanismCreators,
+ invocationMechanismEditors);
+ }
+ return configPanel;
+ }
+
+ public void setMechanismCreators(List<MechanismCreator> mechanismCreators) {
+ this.mechanismCreators = mechanismCreators;
+ }
+
+ public void setInvocationMechanismEditors(
+ List<InvocationMechanismEditor<?>> invocationMechanismEditors) {
+ this.invocationMechanismEditors = invocationMechanismEditors;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/local/LocalInvocationMechanismEditor.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/local/LocalInvocationMechanismEditor.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/local/LocalInvocationMechanismEditor.java
new file mode 100644
index 0000000..64fcc36
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/local/LocalInvocationMechanismEditor.java
@@ -0,0 +1,122 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager.local;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import net.sf.taverna.t2.activities.externaltool.local.ExternalToolLocalInvocationMechanism;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor;
+
+/**
+ * @author alanrw
+ *
+ */
+public final class LocalInvocationMechanismEditor extends
+ InvocationMechanismEditor<ExternalToolLocalInvocationMechanism> {
+
+ private ExternalToolLocalInvocationMechanism invocationMechanism;
+
+ private JTextField directoryField = new JTextField(30);
+
+ private JTextField shellPrefixField = new JTextField(30);
+
+ private JTextField linkCommandField = new JTextField(30);
+
+ private JCheckBox retrieveDataField = new JCheckBox();
+
+
+ @Override
+ public boolean canShow(Class<?> c) {
+ return ExternalToolLocalInvocationMechanism.class.isAssignableFrom(c);
+ }
+
+ @Override
+ public String getName() {
+ return ("Local");
+ }
+
+ @Override
+ public void show(ExternalToolLocalInvocationMechanism invocationMechanism) {
+ this.invocationMechanism = invocationMechanism;
+ this.removeAll();
+ final JPanel innerPanel = new JPanel(new GridBagLayout());
+ final GridBagConstraints inputConstraint = new GridBagConstraints();
+// inputConstraint.insets = new Insets(5,5,5,5);
+ inputConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy = 0;
+ inputConstraint.weightx = 0.1;
+ inputConstraint.fill = GridBagConstraints.BOTH;
+ innerPanel.add(new JLabel("Working directory: "), inputConstraint);
+ inputConstraint.gridx++;
+ directoryField.setText(invocationMechanism.getDirectory());
+ innerPanel.add(directoryField, inputConstraint);
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy++;
+ innerPanel.add(new JLabel("Shell: "), inputConstraint);
+ inputConstraint.gridx++;
+ shellPrefixField.setText(invocationMechanism.getShellPrefix());
+ innerPanel.add(shellPrefixField, inputConstraint);
+
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy++;
+ innerPanel.add(new JLabel("Link command: "), inputConstraint);
+ inputConstraint.gridx++;
+ linkCommandField.setText(invocationMechanism.getLinkCommand());
+ innerPanel.add(linkCommandField, inputConstraint);
+
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy++;
+ innerPanel.add(new JLabel("Fetch data: "), inputConstraint);
+ inputConstraint.gridx++;
+ retrieveDataField.setSelected(invocationMechanism.isRetrieveData());
+ innerPanel.add(retrieveDataField, inputConstraint);
+
+ this.add(innerPanel);
+ }
+
+ @Override
+ public ExternalToolLocalInvocationMechanism updateInvocationMechanism() {
+ if ((directoryField.getText() == null) || (directoryField.getText().length() == 0)) {
+ invocationMechanism.setDirectory(null);
+ } else {
+ invocationMechanism.setDirectory(directoryField.getText());
+ }
+ if ((shellPrefixField.getText() == null) || (shellPrefixField.getText().length() == 0)) {
+ invocationMechanism.setShellPrefix(null);
+ } else {
+ invocationMechanism.setShellPrefix(shellPrefixField.getText());
+ }
+ if ((shellPrefixField.getText() == null) || (shellPrefixField.getText().length() == 0)) {
+ invocationMechanism.setShellPrefix(null);
+ } else {
+ invocationMechanism.setShellPrefix(shellPrefixField.getText());
+ }
+ if ((linkCommandField.getText() == null) || (linkCommandField.getText().length() == 0)) {
+ invocationMechanism.setLinkCommand(null);
+ } else {
+ invocationMechanism.setLinkCommand(linkCommandField.getText());
+ }
+ invocationMechanism.setRetrieveData(retrieveDataField.isSelected());
+ return invocationMechanism;
+ }
+
+ @Override
+ public InvocationMechanism createMechanism(String mechanismName) {
+ ExternalToolLocalInvocationMechanism result = new ExternalToolLocalInvocationMechanism();
+ result.setName(mechanismName);
+ return(result);
+ }
+
+ public boolean isSingleton() {
+ return true;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/ExternalToolSshNodeViewer.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/ExternalToolSshNodeViewer.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/ExternalToolSshNodeViewer.java
new file mode 100644
index 0000000..fb837c5
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/ExternalToolSshNodeViewer.java
@@ -0,0 +1,110 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager.ssh;
+
+import javax.swing.JCheckBox;
+import javax.swing.JTextField;
+
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
+
+import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
+
+
+
+/**
+ * @author alanrw
+ *
+ */
+public class ExternalToolSshNodeViewer {
+
+ private JTextField hostnameField;
+ private JTextField portField;
+ private JTextField directoryField;
+ private JTextField linkCommandField;
+ private JTextField copyCommandField;
+ private JCheckBox retrieveDataField;
+
+ public ExternalToolSshNodeViewer(SshNode node) {
+ this();
+ hostnameField.setText(node.getHost());
+ portField.setText(Integer.toString(node.getPort()));
+ if (node.getDirectory() != null) {
+ directoryField.setText(node.getDirectory());
+ } else {
+ directoryField.setText("");
+ }
+ if (node.getLinkCommand() != null) {
+ linkCommandField.setText(node.getLinkCommand());
+ } else {
+ linkCommandField.setText("");
+ }
+ if (node.getCopyCommand() != null) {
+ copyCommandField.setText(node.getCopyCommand());
+ } else {
+ copyCommandField.setText("");
+ }
+ retrieveDataField.setSelected(node.isRetrieveData());
+ }
+
+ public ExternalToolSshNodeViewer() {
+ hostnameField = new JTextField(30);
+ hostnameField.setText(SshNode.DEFAULT_HOST);
+ portField = new JTextField(3);
+ portField.setText("" + SshNode.DEFAULT_PORT);
+ directoryField = new JTextField(30);
+ directoryField.setText(SshNode.DEFAULT_DIRECTORY);
+ linkCommandField = new JTextField(30);
+ linkCommandField.setText(InvocationMechanism.UNIX_LINK);
+ copyCommandField = new JTextField(30);
+ copyCommandField.setText(InvocationMechanism.UNIX_COPY);
+ retrieveDataField = new JCheckBox();
+ }
+
+ public JTextField getHostnameField() {
+ return hostnameField;
+ }
+
+ public JTextField getPortField() {
+ return portField;
+ }
+
+ public JTextField getDirectoryField() {
+ return directoryField;
+ }
+
+ public JTextField getLinkCommandField() {
+ return linkCommandField;
+ }
+
+ public JTextField getCopyCommandField() {
+ return copyCommandField;
+ }
+
+ public String getHostname() {
+ return hostnameField.getText();
+ }
+
+ public int getPort() {
+ return Integer.parseInt(portField.getText());
+ }
+
+ public String getDirectory() {
+ return directoryField.getText();
+ }
+
+ public String getLinkCommand() {
+ return linkCommandField.getText();
+ }
+
+ public String getCopyCommand() {
+ return copyCommandField.getText();
+ }
+
+ /**
+ * @return the retrieveDataField
+ */
+ public JCheckBox getRetrieveDataField() {
+ return retrieveDataField;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/SshInvocationMechanismEditor.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/SshInvocationMechanismEditor.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/SshInvocationMechanismEditor.java
new file mode 100644
index 0000000..e8291ed
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/manager/ssh/SshInvocationMechanismEditor.java
@@ -0,0 +1,234 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.manager.ssh;
+
+import java.awt.Color;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.border.CompoundBorder;
+
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor;
+import net.sf.taverna.t2.activities.externaltool.ssh.ExternalToolSshInvocationMechanism;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
+import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
+
+/**
+ * @author alanrw
+ *
+ */
+public final class SshInvocationMechanismEditor extends
+ InvocationMechanismEditor<ExternalToolSshInvocationMechanism> {
+
+ private ArrayList<ExternalToolSshNodeViewer> nodeViewers = new ArrayList<ExternalToolSshNodeViewer>();
+ private int inputGridy = 0;
+
+ private ExternalToolSshInvocationMechanism mechanism = null;
+
+ private static Insets insets = new Insets(1,5,1,5);
+
+ private static CompoundBorder border = BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(5,5,5,5), BorderFactory.createLineBorder(Color.BLACK, 1));
+
+ @Override
+ public boolean canShow(Class<?> c) {
+ return ExternalToolSshInvocationMechanism.class.isAssignableFrom(c);
+ }
+
+ @Override
+ public void show(ExternalToolSshInvocationMechanism invocationMechanism) {
+ mechanism = invocationMechanism;
+ this.removeAll();
+ inputGridy = 1;
+ final JPanel innerPanel = new JPanel(new GridBagLayout());
+
+ final GridBagConstraints inputConstraint = new GridBagConstraints();
+ inputConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy = 0;
+ inputConstraint.weightx = 0.1;
+ inputConstraint.fill = GridBagConstraints.BOTH;
+
+ inputConstraint.gridx = 0;
+ nodeViewers.clear();
+ for (SshNode node : invocationMechanism.getNodes()) {
+ ExternalToolSshNodeViewer nodeViewer = new ExternalToolSshNodeViewer(node);
+ addNodeViewer(this, innerPanel, nodeViewer);
+ }
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints outerPanelConstraint = new GridBagConstraints();
+ outerPanelConstraint.gridx = 0;
+ outerPanelConstraint.gridy = 0;
+ outerPanelConstraint.weightx = 0.1;
+ outerPanelConstraint.weighty = 0.1;
+ outerPanelConstraint.fill = GridBagConstraints.BOTH;
+ this.add(new JScrollPane(innerPanel),
+ outerPanelConstraint);
+ outerPanelConstraint.weighty = 0;
+ final JButton addHostButton = new DeselectingButton("Add host",
+ new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+
+ ExternalToolSshNodeViewer newViewer = new ExternalToolSshNodeViewer();
+
+ addNodeViewer(SshInvocationMechanismEditor.this, innerPanel, newViewer);
+ innerPanel.revalidate();
+ innerPanel.repaint();
+ }
+
+ });
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new GridBagLayout());
+
+ JPanel filler = new JPanel();
+ outerPanelConstraint.weightx = 0.1;
+ outerPanelConstraint.weighty = 0;
+ outerPanelConstraint.gridx = 0;
+ outerPanelConstraint.gridy = 0;
+
+ buttonPanel.add(filler, outerPanelConstraint);
+
+ outerPanelConstraint.weightx = 0;
+ outerPanelConstraint.weighty = 0;
+ outerPanelConstraint.gridx = 1;
+ outerPanelConstraint.gridy = 0;
+
+ buttonPanel.add(addHostButton, outerPanelConstraint);
+
+ outerPanelConstraint.weightx = 0;
+ outerPanelConstraint.weighty = 0;
+ outerPanelConstraint.gridx = 0;
+ outerPanelConstraint.gridy = 1;
+ outerPanelConstraint.fill = GridBagConstraints.BOTH;
+ this.add(buttonPanel, outerPanelConstraint);
+ }
+
+ protected void addNodeViewer(final JPanel result, final JPanel innerPanel,
+ ExternalToolSshNodeViewer viewer) {
+ final JPanel subPanel = new JPanel();
+ subPanel.setLayout(new GridBagLayout());
+ subPanel.setBorder(border);
+ final GridBagConstraints inputConstraint = new GridBagConstraints();
+ inputConstraint.insets = insets;
+ inputConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ inputConstraint.weightx = 0.1;
+ inputConstraint.fill = GridBagConstraints.BOTH;
+
+ inputConstraint.gridy = 0 ;
+ inputConstraint.gridx = 0;
+
+ subPanel.add(new JLabel("Host: "), inputConstraint);
+ final JTextField hostnameField = viewer.getHostnameField();
+ inputConstraint.gridx++;
+ subPanel.add(hostnameField, inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 0;
+ subPanel.add(new JLabel("Port: "), inputConstraint);
+ final JTextField portField = viewer.getPortField();
+ inputConstraint.gridx++;
+ subPanel.add(portField ,inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 0;
+ subPanel.add(new JLabel("Working directory: "), inputConstraint);
+ final JTextField directoryField = viewer.getDirectoryField();
+ inputConstraint.gridx++;
+ subPanel.add(directoryField ,inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 0;
+ subPanel.add(new JLabel("Link command: "), inputConstraint);
+ final JTextField linkCommandField = viewer.getLinkCommandField();
+ inputConstraint.gridx++;
+ subPanel.add(linkCommandField ,inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 0;
+ subPanel.add(new JLabel("Copy command: "), inputConstraint);
+ final JTextField copyCommandField = viewer.getCopyCommandField();
+ inputConstraint.gridx++;
+ subPanel.add(copyCommandField ,inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 0;
+ subPanel.add(new JLabel("Fetch data: "), inputConstraint);
+ inputConstraint.gridx++;
+ final JCheckBox retrieveDataField = viewer.getRetrieveDataField();
+ subPanel.add(retrieveDataField ,inputConstraint);
+
+ inputConstraint.gridy++ ;
+ inputConstraint.gridx = 1;
+ inputConstraint.fill = GridBagConstraints.NONE;
+ inputConstraint.anchor = GridBagConstraints.EAST;
+ final ExternalToolSshNodeViewer v = viewer;
+ final JButton removeButton = new DeselectingButton("Remove",
+ new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ synchronized(nodeViewers) {
+ nodeViewers.remove(v);
+ }
+ innerPanel.remove(subPanel);
+ innerPanel.revalidate();
+ innerPanel.repaint();
+ result.revalidate();
+ result.repaint();
+ }
+
+ });
+ subPanel.add(removeButton, inputConstraint);
+
+ inputConstraint.gridy = ++inputGridy;
+ innerPanel.add(subPanel, inputConstraint);
+
+ nodeViewers.add(viewer);
+ inputGridy++;
+ }
+
+ private List<SshNode> getNodeList() {
+ List<SshNode> result = new ArrayList<SshNode>();
+ for (ExternalToolSshNodeViewer viewer : nodeViewers) {
+ SshNode node = SshNodeFactory.getInstance().getSshNode(viewer.getHostname(), viewer.getPort(), viewer.getDirectory());
+ node.setLinkCommand(viewer.getLinkCommand());
+ node.setCopyCommand(viewer.getCopyCommand());
+ node.setRetrieveData(viewer.getRetrieveDataField().isSelected());
+ result.add(node);
+ }
+ return result;
+ }
+
+ @Override
+ public ExternalToolSshInvocationMechanism updateInvocationMechanism() {
+ mechanism.setNodes(getNodeList());
+ return mechanism;
+ }
+
+ @Override
+ public InvocationMechanism createMechanism(String mechanismName) {
+ ExternalToolSshInvocationMechanism result = new ExternalToolSshInvocationMechanism();
+ result.setName(mechanismName);
+ return result;
+ }
+
+ @Override
+ public String getName() {
+ return ("SSH");
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolContextualMenuAction.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolContextualMenuAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolContextualMenuAction.java
new file mode 100644
index 0000000..505546d
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolContextualMenuAction.java
@@ -0,0 +1,111 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.menu;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolTemplateServiceDescription;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+
+import org.apache.log4j.Logger;
+
+/**
+ * An action to add an external tool + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author Alan Williamns
+ *
+ */
+@SuppressWarnings("serial")
+public class AddExternalToolContextualMenuAction extends AbstractContextualMenuAction {
+
+ private static final String ADD_EXTERNAL_TOOL = "Tool";
+
+ private static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+
+ private static Logger logger = Logger.getLogger(AddExternalToolMenuAction.class);
+
+ private EditManager editManager;
+
+ private MenuManager menuManager;
+
+ private SelectionManager selectionManager;
+
+ private ActivityIconManager activityIconManager;
+
+ public AddExternalToolContextualMenuAction() {
+ super(insertSection, 900);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && getContextualSelection().getSelection() instanceof Dataflow;
+ }
+
+ @Override
+ protected Action createAction() {
+
+ return new AddExternalToolAction();
+ }
+
+ protected class AddExternalToolAction extends AbstractAction {
+ AddExternalToolAction() {
+ super(ADD_EXTERNAL_TOOL, activityIconManager.iconForActivity(
+ new ExternalToolActivity()));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(
+ ExternalToolTemplateServiceDescription.getServiceDescription(), false,
+ editManager, menuManager, selectionManager);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolMenuAction.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolMenuAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolMenuAction.java
new file mode 100644
index 0000000..ff1f11e
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/AddExternalToolMenuAction.java
@@ -0,0 +1,111 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.menu;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolTemplateServiceDescription;
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import net.sf.taverna.t2.workbench.views.graph.menu.InsertMenu;
+
+import org.apache.log4j.Logger;
+
+/**
+ * An action to add a externaltool activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author alanrw
+ *
+ */
+@SuppressWarnings("serial")
+public class AddExternalToolMenuAction extends AbstractMenuAction {
+
+ private static final String ADD_EXTERNAL_TOOL = "Tool";
+
+ private static final URI ADD_EXTERNAL_TOOL_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuAddExternalTool");
+
+ private static Logger logger = Logger
+ .getLogger(AddExternalToolMenuAction.class);
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+
+ private ActivityIconManager activityIconManager;
+
+ public AddExternalToolMenuAction() {
+ super(InsertMenu.INSERT, 900, ADD_EXTERNAL_TOOL_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+
+ return new AddExternalToolAction();
+ }
+
+ protected class AddExternalToolAction extends DesignOnlyAction {
+ AddExternalToolAction () {
+ super ();
+ putValue(SMALL_ICON, activityIconManager.iconForActivity(
+ new ExternalToolActivity()));
+ putValue(NAME, ADD_EXTERNAL_TOOL);
+ putValue(SHORT_DESCRIPTION, "Tool");
+ putValue(Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_T, InputEvent.SHIFT_DOWN_MASK | InputEvent.ALT_DOWN_MASK));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(ExternalToolTemplateServiceDescription.getServiceDescription(),
+ false, editManager, menuManager, selectionManager);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/ConfigureExternalToolMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/ConfigureExternalToolMenuAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/ConfigureExternalToolMenuAction.java
new file mode 100644
index 0000000..f57b25c
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/ConfigureExternalToolMenuAction.java
@@ -0,0 +1,69 @@
+/*******************************************************************************
+ * Copyright (C) 2010 Hajo Nils Krabbenhoeft, spratpix GmbH & Co. KG
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.menu;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.actions.ExternalToolActivityConfigureAction;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+/**
+ * This class adds the plugin configuration action to the context menu of every use case activity.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ConfigureExternalToolMenuAction extends
+ AbstractConfigureActivityMenuAction<ExternalToolActivity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+
+ public ConfigureExternalToolMenuAction() {
+ super(ExternalToolActivity.class);
+ }
+
+ @Override
+ protected Action createAction() {
+ ExternalToolActivityConfigureAction configAction = new ExternalToolActivityConfigureAction(
+ findActivity(), getParentFrame(), editManager, fileManager, activityIconManager);
+ addMenuDots(configAction);
+ return configAction;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/FeedbackMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/FeedbackMenuAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/FeedbackMenuAction.java
new file mode 100644
index 0000000..8c7a284
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/menu/FeedbackMenuAction.java
@@ -0,0 +1,82 @@
+/*******************************************************************************
+ * Copyright (C) 2010 Hajo Nils Krabbenhoeft, spratpix GmbH & Co. KG
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.menu;
+
+import java.awt.Desktop;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.Icon;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class adds the feedback item to the context menu of every use case
+ * activity.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class FeedbackMenuAction extends AbstractMenuAction {
+
+ private static Logger logger = Logger.getLogger(FeedbackMenuAction.class);
+
+
+ private static final URI feedbackSection = URI.create("http://taverna.sf.net/2009/contextMenu/configure");
+
+ public FeedbackMenuAction() {
+ super(feedbackSection, 51);
+ }
+
+ protected Action createAction() {
+ // final ImageIcon icon = KnowARCConfigurationFactory.getConfiguration().getIcon();
+ return new SendFeedbackAction("Send Feedback...", null);
+ }
+
+ private final class SendFeedbackAction extends AbstractAction {
+ private static final long serialVersionUID = 1L;
+
+ private static final String errTitle = "Could not open web browser for feedback:";
+ private static final String feedbackUrl = "http://www.taverna.org.uk/about/contact-us/feedback?product=ExternalToolService";
+
+ private SendFeedbackAction(String name, Icon icon) {
+ super(name, icon);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (Desktop.isDesktopSupported()) {
+ try {
+ Desktop.getDesktop().browse(URI.create(feedbackUrl));
+ } catch (IOException e1) {
+ JOptionPane.showMessageDialog(null, feedbackUrl + "\n" + e1.getLocalizedMessage(), errTitle, JOptionPane.ERROR_MESSAGE);
+ }
+ } else {
+ JOptionPane.showMessageDialog(null, "Go to " + feedbackUrl, errTitle, JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/AddExternalToolServiceDialog.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/AddExternalToolServiceDialog.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/AddExternalToolServiceDialog.java
new file mode 100644
index 0000000..86b0882
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/AddExternalToolServiceDialog.java
@@ -0,0 +1,189 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLConnection;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.workbench.MainWindow;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Dialog that lets user specify a URL of a Tool service they want
+ * to add to the Service Panel. In the case the Tool URL is behind
+ * HTTPS or service's endpoints require HTTPS it will ask user to confirm
+ * if they want to trust it.
+ *
+ * @author Alex Nenadic
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class AddExternalToolServiceDialog extends HelpEnabledDialog {
+
+ private JTextField toolLocationField;
+ private Logger logger = Logger.getLogger(AddExternalToolServiceDialog.class);
+
+ public AddExternalToolServiceDialog() {
+ super(MainWindow.getMainWindow(), "Add tool service", true, null); // create a non-modal dialog
+ initComponents();
+ setLocationRelativeTo(getParent());
+ }
+
+ private void initComponents() {
+ JPanel mainPanel = new JPanel(new GridBagLayout());
+ mainPanel.setBorder(new EmptyBorder(10,10,10,10));
+
+ JLabel toolLocatitionLabel = new JLabel("Tool registry location",ExternalToolActivityIcon.getExternalToolIcon(), JLabel.LEFT);
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weighty = 0.0;
+
+ gbc.weightx = 0.0;
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 0);
+ mainPanel.add(toolLocatitionLabel, gbc);
+
+ toolLocationField = new JTextField("http://taverna.nordugrid.org/sharedRepository/xml.php");
+ gbc.weightx = 1.0;
+ gbc.gridx = 1;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 5);
+ mainPanel.add(toolLocationField, gbc);
+
+ final JButton addServiceButton = new JButton("Add");
+ addServiceButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ addPressed();
+ }
+ });
+
+ // When user presses "Return" key fire the action on the "Add" button
+ addServiceButton.addKeyListener(new java.awt.event.KeyAdapter() {
+ public void keyPressed(java.awt.event.KeyEvent evt) {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER) {
+ addPressed();
+ }
+ }
+ });
+ getRootPane().setDefaultButton(addServiceButton);
+
+ JPanel buttonsPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ buttonsPanel.add(addServiceButton);
+
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(mainPanel, BorderLayout.CENTER);
+ getContentPane().add(buttonsPanel, BorderLayout.SOUTH);
+
+ setSize(getPreferredSize());
+ pack();
+ }
+
+ /**
+ * 'Add service' button pressed or otherwise activated.
+ */
+ private void addPressed()
+ {
+ final String toolURLString = toolLocationField.getText().trim();
+ new Thread("Adding tool " + toolURLString) {
+ public void run() {
+ // Only add the service provider for this service if service URL
+ // starts with 'http'
+ // or if it starts with 'https' and user explicitly said they
+ // wanted to trust this service.
+ /*
+ * if (shouldTrust(toolURLString)){ addRegistry(toolURLString);
+ * }
+ */
+ try {
+ URL url = new URL(toolURLString);
+ URLConnection connection = url.openConnection();
+ try {
+ // If the url starts with 'https' - security hook for
+ // https connection's trust manager
+ // will be engaged and user will be asked automatically
+ // if they want
+ // to trust the connection (if it is not already
+ // trusted). If the urls starts with 'http' -
+ // this will not have any effect apart from checking if
+ // we can open a connection.
+ connection.connect(); // if this does not fail - add the
+ // tool
+ // service provider for this service to
+ // the registry
+ } finally {
+ try {
+ connection.getInputStream().close();
+ } catch (IOException ex) {
+ }
+ }
+ addRegistry(toolURLString);
+ } catch (Exception ex) { // anything failed
+ JOptionPane.showMessageDialog(null,
+ "Could not read the tool descriptions from "
+ + toolURLString + ":\n" + ex,
+ "Could not add tool service",
+ JOptionPane.ERROR_MESSAGE);
+
+ logger.error(
+ "Failed to add tool description provider for service: "
+ + toolURLString, ex);
+
+ }
+ };
+ }.start();
+ closeDialog();
+ }
+
+ protected abstract void addRegistry(String tool);
+
+ /**
+ * Closes the dialog.
+ */
+ private void closeDialog() {
+ setVisible(false);
+ dispose();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolActivityIcon.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolActivityIcon.java
new file mode 100644
index 0000000..f91755f
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolActivityIcon.java
@@ -0,0 +1,73 @@
+/*******************************************************************************
+ * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import java.awt.Color;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+/**
+ * This class provides an icon for the use case activity.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolActivityIcon implements ActivityIconSPI {
+
+ private static final String PROCESSOR_COLOUR_STRING = "#F28C55";
+
+ private static Icon icon;
+
+ public int canProvideIconScore(Activity<?> activity) {
+ if (activity.getClass().getName().equals(ExternalToolActivity.class.getName()))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(Activity<?> activity) {
+ return getExternalToolIcon();
+ }
+
+ public static Icon getExternalToolIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(ExternalToolActivityIcon.class.getResource("/externaltool.png"));
+ }
+ return icon;
+ }
+
+ public static String getColourString() {
+ return PROCESSOR_COLOUR_STRING;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ // set colour for XPath processors in the workflow diagram
+ colourManager.setPreferredColour(ExternalToolActivity.class.getCanonicalName(),
+ Color.decode(PROCESSOR_COLOUR_STRING));
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceDescription.java
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diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceDescription.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceDescription.java
new file mode 100644
index 0000000..02c2bf6
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceDescription.java
@@ -0,0 +1,149 @@
+/*******************************************************************************
+ * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import org.apache.log4j.Logger;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManager;
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.activities.externaltool.views.ExternalToolConfigView;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+
+/**
+ * ExternalToolServiceDescription stores the repository URL and the use case id so
+ * that it can create an ExternalToolActivityConfigurationBean
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolServiceDescription extends ServiceDescription<ExternalToolActivityConfigurationBean> {
+
+ private static Logger logger = Logger
+ .getLogger(ExternalToolServiceDescription.class);
+
+
+ private static InvocationGroupManager manager = InvocationGroupManagerImpl.getInstance();
+
+ private String repositoryUrl;
+ private String externaltoolid;
+ private UseCaseDescription useCaseDescription;
+
+ public String getRepositoryUrl() {
+ return repositoryUrl;
+ }
+
+ public void setRepositoryUrl(String repositoryUrl) {
+ this.repositoryUrl = repositoryUrl;
+ }
+
+ public String getExternaltoolid() {
+ return externaltoolid;
+ }
+
+ public void setExternaltoolid(String externaltoolid) {
+ this.externaltoolid = externaltoolid;
+ }
+
+ public Icon getIcon() {
+ if (useCaseDescription != null) {
+ String icon_url = useCaseDescription.getIcon_url();
+ if ((icon_url != null) && !icon_url.isEmpty() && !icon_url.endsWith(".ico"))
+ try {
+ ImageIcon result = new ImageIcon(new URL(icon_url));
+ if ((result != null) && (result.getIconHeight() != 0) && (result.getIconWidth() != 0)){
+ return result;
+ }
+ } catch (MalformedURLException e) {
+ logger.error("Problematic URL" + icon_url, e);
+ }
+ }
+ return ExternalToolActivityIcon.getExternalToolIcon();
+ }
+
+ public Class<? extends Activity<ExternalToolActivityConfigurationBean>> getActivityClass() {
+ return ExternalToolActivity.class;
+ }
+
+ public ExternalToolActivityConfigurationBean getActivityConfiguration() {
+ ExternalToolActivityConfigurationBean bean = new ExternalToolActivityConfigurationBean();
+ bean.setRepositoryUrl(repositoryUrl);
+ bean.setExternaltoolid(externaltoolid);
+ bean.setUseCaseDescription(useCaseDescription);
+ bean.setMechanism(manager.getDefaultMechanism());
+
+ return bean;
+ }
+
+ public String getName() {
+ return externaltoolid;
+ }
+
+ @SuppressWarnings("unchecked")
+ public List<? extends Comparable> getPath() {
+ List<String> result = new ArrayList<String>();
+ result.add("Tools decribed @ " + repositoryUrl);
+ String group = useCaseDescription.getGroup();
+ if ((group != null) && !group.isEmpty()) {
+ String[] groups = group.split(":");
+ for (String g : groups) {
+ result.add(g);
+ }
+ }
+ return result;
+ }
+
+ protected List<Object> getIdentifyingData() {
+ // we require use cases inside one XML file to have unique IDs, which
+ // means every externaltool is uniquely identified by its repository URL and
+ // its use case ID.
+ return Arrays.<Object> asList(repositoryUrl, externaltoolid);
+ }
+
+ public String getDescription() {
+ if (useCaseDescription != null) {
+ String description = useCaseDescription.getDescription();
+ if (description == null) {
+ return "";
+ }
+ return description;
+ }
+ return "";
+ }
+
+ public void setUseCaseDescription(UseCaseDescription usecase) {
+ this.useCaseDescription = usecase;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProvider.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProvider.java
new file mode 100644
index 0000000..4f3cbf2
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/servicedescriptions/ExternalToolServiceProvider.java
@@ -0,0 +1,132 @@
+/*******************************************************************************
+ * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.servicedescriptions;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.CustomizedConfigurePanelProvider;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseEnumeration;
+
+/**
+ * ExternalToolServiceProvider searches an use case repository XML for use case
+ * descriptions.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+public class ExternalToolServiceProvider extends AbstractConfigurableServiceProvider<ExternalToolServiceProviderConfig> implements
+CustomizedConfigurePanelProvider<ExternalToolServiceProviderConfig>{
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/externaltool");
+
+ public ExternalToolServiceProvider() {
+ super(new ExternalToolServiceProviderConfig("http://taverna.nordugrid.org/sharedRepository/xml.php"));
+ }
+
+ public String getName() {
+ return "Tool service";
+ }
+
+ public List<ExternalToolServiceProviderConfig> getDefaultConfigurations() {
+ List<ExternalToolServiceProviderConfig> defaults = new ArrayList<ExternalToolServiceProviderConfig>();
+ // Disabled until sensible set
+// defaults.add(new ExternalToolServiceProviderConfig("http://taverna.nordugrid.org/sharedRepository/xml.php"));
+ return defaults;
+ }
+
+ public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
+ String repositoryUrl = serviceProviderConfig.getRepositoryUrl();
+ callBack.status("Parsing use case repository:" + repositoryUrl);
+ // prepare a list of all use case descriptions which are stored in
+ // the given repository URL
+ List<UseCaseDescription> usecases = new ArrayList<UseCaseDescription> ();
+ try {
+ usecases = UseCaseEnumeration.readDescriptionsFromUrl(
+ repositoryUrl);
+ } catch (IOException e) {
+ callBack.fail("Unable to read tool descriptions", e);
+ }
+ callBack.status("Found " + usecases.size() + " use cases:" + repositoryUrl);
+ // convert all the UseCaseDescriptions in the XML file into
+ // ExternalToolServiceDescription items
+ List<ExternalToolServiceDescription> items = new ArrayList<ExternalToolServiceDescription>();
+ for (UseCaseDescription usecase : usecases) {
+ ExternalToolServiceDescription item = new ExternalToolServiceDescription();
+ item.setRepositoryUrl(repositoryUrl);
+ item.setExternaltoolid(usecase.getUsecaseid());
+ item.setUseCaseDescription(usecase);
+ items.add(item);
+ }
+ // we dont have streaming data loading or partial results, so return
+ // results and finish
+ callBack.partialResults(items);
+ callBack.finished();
+ }
+
+ @Override
+ public String toString() {
+ return getName() + " " + getConfiguration().getRepositoryUrl();
+ }
+
+ public Icon getIcon() {
+ return ExternalToolActivityIcon.getExternalToolIcon();
+ }
+
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ List<String> result;
+ // one can fully identify an use case repository by its URL
+ result = Arrays.asList(getConfiguration().getRepositoryUrl());
+ return result;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry registry) {
+ }
+
+ @SuppressWarnings("serial")
+ public void createCustomizedConfigurePanel(final CustomizedConfigureCallBack<ExternalToolServiceProviderConfig> callBack) {
+
+ AddExternalToolServiceDialog addWSDLServiceDialog = new AddExternalToolServiceDialog() {
+ @Override
+ protected void addRegistry(String externalToolURL) {
+
+ ExternalToolServiceProviderConfig providerConfig = new ExternalToolServiceProviderConfig(externalToolURL);
+ callBack.newProviderConfiguration(providerConfig);
+ }
+ };
+ addWSDLServiceDialog.setVisible(true);
+ }
+
+
+ public String getId() {
+ return providerId.toString();
+ }
+}
[04/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..17d19e3
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLActivityIcon
+net.sf.taverna.t2.activities.wsdl.servicedescriptions.XMLInputSplitterActivityIcon
+net.sf.taverna.t2.activities.wsdl.servicedescriptions.XMLOutputSplitterActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..04d48eb
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1,2 @@
+net.sf.taverna.t2.activities.wsdl.views.WSDLActivityViewFactory
+net.sf.taverna.t2.activities.wsdl.views.XMLSplitterViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context-osgi.xml b/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..ac79064
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context-osgi.xml
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="WSDLActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+ <service ref="XMLInputSplitterActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+ <service ref="XMLOutputSplitterActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="WSDLServiceProvider">
+ <interfaces>
+ <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
+ <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
+ </interfaces>
+ </service>
+
+ <service ref="AddXMLInputSplitterForWSDLActivityMenuAction" auto-export="interfaces" />
+ <service ref="AddXMLInputSplitterForXMLInputSplitterMenuAction" auto-export="interfaces" />
+ <service ref="AddXMLOutputSplitterForWSDLActivityMenuAction" auto-export="interfaces" />
+ <service ref="AddXMLOutputSplitterForXMLOutputSplitterMenuAction" auto-export="interfaces" />
+ <service ref="ConfigureWSDLMenuAction" auto-export="interfaces" />
+
+ <service ref="WSDLActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+ <service ref="XMLSplitterViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="credentialManager" interface="net.sf.taverna.t2.security.credentialmanager.CredentialManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context.xml b/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context.xml
new file mode 100644
index 0000000..fede275
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/spring/wsdl-activity-ui-context.xml
@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="WSDLActivityIcon" class="net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLActivityIcon" />
+ <bean id="XMLInputSplitterActivityIcon" class="net.sf.taverna.t2.activities.wsdl.servicedescriptions.XMLInputSplitterActivityIcon" />
+ <bean id="XMLOutputSplitterActivityIcon" class="net.sf.taverna.t2.activities.wsdl.servicedescriptions.XMLOutputSplitterActivityIcon" />
+
+ <bean id="WSDLServiceProvider" class="net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider">
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="credentialManager" ref="credentialManager" />
+ </bean>
+
+ <bean id="AddXMLInputSplitterForWSDLActivityMenuAction" class="net.sf.taverna.t2.activities.wsdl.menu.AddXMLInputSplitterForWSDLActivityMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="AddXMLInputSplitterForXMLInputSplitterMenuAction" class="net.sf.taverna.t2.activities.wsdl.menu.AddXMLInputSplitterForXMLInputSplitterMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="AddXMLOutputSplitterForWSDLActivityMenuAction" class="net.sf.taverna.t2.activities.wsdl.menu.AddXMLOutputSplitterForWSDLActivityMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="AddXMLOutputSplitterForXMLOutputSplitterMenuAction" class="net.sf.taverna.t2.activities.wsdl.menu.AddXMLOutputSplitterForXMLOutputSplitterMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ </bean>
+ <bean id="ConfigureWSDLMenuAction" class="net.sf.taverna.t2.activities.wsdl.menu.ConfigureWSDLMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="credentialManager" ref="credentialManager" />
+ </bean>
+
+ <bean id="WSDLActivityViewFactory" class="net.sf.taverna.t2.activities.wsdl.views.WSDLActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="credentialManager" ref="credentialManager" />
+ </bean>
+ <bean id="XMLSplitterViewFactory" class="net.sf.taverna.t2.activities.wsdl.views.XMLSplitterViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/wsdl.png
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diff --git a/taverna-wsdl-activity-ui/src/main/resources/wsdl.png b/taverna-wsdl-activity-ui/src/main/resources/wsdl.png
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diff --git a/taverna-wsdl-activity-ui/src/main/resources/xml-input-splitter.png b/taverna-wsdl-activity-ui/src/main/resources/xml-input-splitter.png
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diff --git a/taverna-wsdl-activity-ui/src/main/resources/xml-output-splitter.png b/taverna-wsdl-activity-ui/src/main/resources/xml-output-splitter.png
new file mode 100644
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diff --git a/taverna-wsdl-activity-ui/src/main/resources/xml-splitter.png b/taverna-wsdl-activity-ui/src/main/resources/xml-splitter.png
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/test/java/net/sf/taverna/t2/activities/wsdl/views/TestWSDLActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/test/java/net/sf/taverna/t2/activities/wsdl/views/TestWSDLActivityContextualView.java b/taverna-wsdl-activity-ui/src/test/java/net/sf/taverna/t2/activities/wsdl/views/TestWSDLActivityContextualView.java
new file mode 100644
index 0000000..0fa054b
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/test/java/net/sf/taverna/t2/activities/wsdl/views/TestWSDLActivityContextualView.java
@@ -0,0 +1,53 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import static org.junit.Assert.assertNull;
+
+import org.junit.Before;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class TestWSDLActivityContextualView {
+
+ Activity a;
+
+ @Before
+ public void setUp() throws Exception {
+ a=new Activity();
+ Configuration configuration = new Configuration();
+ ObjectNode json = (ObjectNode) configuration.getJson();
+ ObjectNode operation = json.objectNode();
+ operation.put("name", "getReport");
+ json.set("operation", operation);
+ String wsdlUrl=TestWSDLActivityContextualView.class.getResource("/GMService.wsdl").toExternalForm();
+ operation.put("wsdl", wsdlUrl);
+ configuration.setConfigures(a);
+ }
+
+ public void testConfigurationAction() {
+ WSDLActivityContextualView view = new WSDLActivityContextualView(a, null, null, null, null, null, null, null);
+ assertNull("WSDL has no configure action, so should be null",view.getConfigureAction(null));
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/test/resources/GMService.wsdl
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/test/resources/GMService.wsdl b/taverna-wsdl-activity-ui/src/test/resources/GMService.wsdl
new file mode 100644
index 0000000..cf128ba
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/test/resources/GMService.wsdl
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<wsdl:definitions xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" xmlns:tns="http://webservice.gominer.lmp.nci.nih.gov" xmlns:wsdlsoap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="http://webservice.gominer.lmp.nci.nih.gov">
+ <wsdl:types>
+ <xsd:schema targetNamespace="http://webservice.gominer.lmp.nci.nih.gov" elementFormDefault="qualified" attributeFormDefault="qualified">
+ <xsd:complexType name="ArrayOfString">
+ <xsd:sequence>
+ <xsd:element name="string" type="xsd:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ </xsd:complexType>
+ <xsd:element name="getReport">
+
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="in0" type="tns:ArrayOfString" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in1" type="tns:ArrayOfString" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in2" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in3" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in4" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in5" type="xsd:boolean" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="in6" type="xsd:boolean" minOccurs="1" maxOccurs="1"/>
+
+ <xsd:element name="in7" type="xsd:boolean" minOccurs="1" maxOccurs="1"/>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="getReportResponse">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="out" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ </xsd:sequence>
+
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:schema>
+ </wsdl:types>
+ <wsdl:message name="getReportResponse">
+ <wsdl:part element="tns:getReportResponse" name="parameters"/>
+ </wsdl:message>
+ <wsdl:message name="getReportRequest">
+ <wsdl:part element="tns:getReport" name="parameters"/>
+
+ </wsdl:message>
+ <wsdl:portType name="GOMinerWSPortType">
+ <wsdl:operation name="getReport">
+ <wsdl:input message="tns:getReportRequest" name="getReportRequest"/>
+ <wsdl:output message="tns:getReportResponse" name="getReportResponse"/>
+ </wsdl:operation>
+ </wsdl:portType>
+ <wsdl:binding name="GOMinerWSHttpBinding" type="tns:GOMinerWSPortType">
+ <wsdlsoap:binding style="document" transport="http://schemas.xmlsoap.org/soap/http"/>
+
+ <wsdl:operation name="getReport">
+ <wsdlsoap:operation soapAction=""/>
+ <wsdl:input name="getReportRequest">
+ <wsdlsoap:body use="literal"/>
+ </wsdl:input>
+ <wsdl:output name="getReportResponse">
+ <wsdlsoap:body use="literal"/>
+ </wsdl:output>
+ </wsdl:operation>
+
+ </wsdl:binding>
+ <wsdl:service name="GOMinerWS">
+ <wsdl:port binding="tns:GOMinerWSHttpBinding" name="GOMinerWSHttpPort">
+ <wsdlsoap:address location="http://discover.nci.nih.gov/gominer/xfire/GMService"/>
+ </wsdl:port>
+ </wsdl:service>
+</wsdl:definitions>
\ No newline at end of file
[03/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/test/resources/kegg.wsdl
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/test/resources/kegg.wsdl b/taverna-wsdl-activity-ui/src/test/resources/kegg.wsdl
new file mode 100644
index 0000000..a62b707
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/test/resources/kegg.wsdl
@@ -0,0 +1,1889 @@
+<?xml version="1.0"?>
+<definitions
+ name="KEGG_v6.1"
+ xmlns:typens="SOAP/KEGG"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+ xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/"
+ xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
+ xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
+ xmlns="http://schemas.xmlsoap.org/wsdl/"
+ targetNamespace="SOAP/KEGG">
+
+ <types>
+ <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
+ <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
+ <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
+<!-- common variable -->
+ <xsd:complexType name="ArrayOfint">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="xsd:int[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfstring">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="xsd:string[]"/>
+ </xsd:restriction>
+
+ </xsd:complexContent>
+ </xsd:complexType>
+<!-- SSDB -->
+ <xsd:complexType name="SSDBRelation">
+ <xsd:all>
+ <xsd:element name="genes_id1" type="xsd:string"/>
+ <xsd:element name="genes_id2" type="xsd:string"/>
+ <xsd:element name="sw_score" type="xsd:int"/>
+ <xsd:element name="bit_score" type="xsd:float"/>
+
+ <xsd:element name="identity" type="xsd:float"/>
+ <xsd:element name="overlap" type="xsd:int"/>
+ <xsd:element name="start_position1" type="xsd:int"/>
+ <xsd:element name="end_position1" type="xsd:int"/>
+ <xsd:element name="start_position2" type="xsd:int"/>
+ <xsd:element name="end_position2" type="xsd:int"/>
+ <xsd:element name="best_flag_1to2" type="xsd:boolean"/>
+ <xsd:element name="best_flag_2to1" type="xsd:boolean"/>
+ <xsd:element name="definition1" type="xsd:string"/>
+
+ <xsd:element name="definition2" type="xsd:string"/>
+ <xsd:element name="length1" type="xsd:int"/>
+ <xsd:element name="length2" type="xsd:int"/>
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfSSDBRelation">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:SSDBRelation[]"/>
+
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+<!-- MOTIF -->
+ <xsd:complexType name="MotifResult">
+ <xsd:all>
+ <xsd:element name="motif_id" type="xsd:string"/>
+ <xsd:element name="definition" type="xsd:string"/>
+ <xsd:element name="genes_id" type="xsd:string"/>
+
+ <xsd:element name="start_position" type="xsd:int"/>
+ <xsd:element name="end_position" type="xsd:int"/>
+ <xsd:element name="score" type="xsd:float"/>
+ <xsd:element name="evalue" type="xsd:double"/>
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfMotifResult">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:MotifResult[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+<!-- DEFINITION -->
+ <xsd:complexType name="Definition">
+ <xsd:all>
+ <xsd:element name="entry_id" type="xsd:string"/>
+ <xsd:element name="definition" type="xsd:string"/>
+
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfDefinition">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Definition[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+<!-- LinkDB -->
+ <xsd:complexType name="LinkDBRelation">
+ <xsd:all>
+ <xsd:element name="entry_id1" type="xsd:string"/>
+ <xsd:element name="entry_id2" type="xsd:string"/>
+ <xsd:element name="type" type="xsd:string"/>
+ <xsd:element name="path" type="xsd:string"/>
+ </xsd:all>
+ </xsd:complexType>
+
+ <xsd:complexType name="ArrayOfLinkDBRelation">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:LinkDBRelation[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+<!-- Pathway -->
+ <xsd:complexType name="PathwayElement">
+
+ <xsd:all>
+ <xsd:element name="element_id" type="xsd:int"/>
+ <xsd:element name="type" type="xsd:string"/>
+ <xsd:element name="names" type="typens:ArrayOfstring"/>
+ <xsd:element name="components" type="typens:ArrayOfint"/>
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfPathwayElement">
+ <xsd:complexContent>
+
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:PathwayElement[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+ <xsd:complexType name="PathwayElementRelation">
+ <xsd:all>
+ <xsd:element name="element_id1" type="xsd:int"/>
+ <xsd:element name="element_id2" type="xsd:int"/>
+
+ <xsd:element name="type" type="xsd:string"/>
+ <!--xsd:element name="name" type="xsd:string"/-->
+ <xsd:element name="subtypes" type="typens:ArrayOfSubtype"/>
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfPathwayElementRelation">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:PathwayElementRelation[]"/>
+
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+ <xsd:complexType name="Subtype">
+ <xsd:all>
+ <xsd:element name="relation" type="xsd:string"/>
+ <xsd:element name="element_id" type="xsd:int"/>
+ <xsd:element name="type" type="xsd:string"/>
+ </xsd:all>
+
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfSubtype">
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Subtype[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+<!-- v6.0 -->
+
+ <xsd:complexType name="StructureAlignment">
+ <xsd:all>
+ <xsd:element name="target_id" type="xsd:string"/>
+ <xsd:element name="score" type="xsd:float"/>
+ <xsd:element name="query_nodes" type="typens:ArrayOfint"/>
+ <xsd:element name="target_nodes" type="typens:ArrayOfint"/>
+ </xsd:all>
+ </xsd:complexType>
+ <xsd:complexType name="ArrayOfStructureAlignment">
+
+ <xsd:complexContent>
+ <xsd:restriction base="soapenc:Array">
+ <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:StructureAlignment[]"/>
+ </xsd:restriction>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ </xsd:schema>
+ </types>
+
+<!-- KEGG information -->
+<!-- list_databases -->
+ <message name="list_databasesRequest"/>
+ <message name="list_databasesResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- list_organisms -->
+ <message name="list_organismsRequest"/>
+ <message name="list_organismsResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+
+ </message>
+<!-- list_pathways -->
+ <message name="list_pathwaysRequest">
+ <part name="org" type="xsd:string"/>
+ </message>
+ <message name="list_pathwaysResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- list_ko_classes -->
+ <message name="list_ko_classesRequest">
+
+ <part name="class_id" type="xsd:string"/>
+ </message>
+ <message name="list_ko_classesResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- DBGET -->
+<!-- binfo -->
+ <message name="binfoRequest">
+ <part name="db" type="xsd:string"/>
+ </message>
+
+ <message name="binfoResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- bget -->
+ <message name="bgetRequest">
+ <part name="string" type="xsd:string"/>
+ </message>
+ <message name="bgetResponse">
+ <part name="return" type="xsd:string"/>
+
+ </message>
+<!-- bfind -->
+ <message name="bfindRequest">
+ <part name="string" type="xsd:string"/>
+ </message>
+ <message name="bfindResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- btit -->
+ <message name="btitRequest">
+
+ <part name="string" type="xsd:string"/>
+ </message>
+ <message name="btitResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- bconv -->
+ <message name="bconvRequest">
+ <part name="string" type="xsd:string"/>
+ </message>
+
+ <message name="bconvResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- LinkDB -->
+ <message name="get_linkdb_by_entryRequest">
+ <part name="entry_id" type="xsd:string"/>
+ <part name="db" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_linkdb_by_entryResponse">
+ <part name="return" type="typens:ArrayOfLinkDBRelation"/>
+ </message>
+<!-- SSDB -->
+<!-- get_best_neighbors_by_gene -->
+ <message name="get_best_neighbors_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_best_neighbors_by_geneResponse">
+ <part name="return" type="typens:ArrayOfSSDBRelation"/>
+ </message>
+<!-- get_best_best_neighbors_by_gene -->
+ <message name="get_best_best_neighbors_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_best_best_neighbors_by_geneResponse">
+ <part name="return" type="typens:ArrayOfSSDBRelation"/>
+ </message>
+<!-- get_reverse_best_neighbors_by_gene -->
+ <message name="get_reverse_best_neighbors_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_reverse_best_neighbors_by_geneResponse">
+ <part name="return" type="typens:ArrayOfSSDBRelation"/>
+ </message>
+<!-- get_paralogs_by_geneRequest -->
+ <message name="get_paralogs_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_paralogs_by_geneResponse">
+ <part name="return" type="typens:ArrayOfSSDBRelation"/>
+ </message>
+<!-- MOTIF -->
+<!-- get_motifs_by_gene -->
+ <message name="get_motifs_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="db" type="xsd:string"/>
+ </message>
+
+ <message name="get_motifs_by_geneResponse">
+ <part name="return" type="typens:ArrayOfMotifResult"/>
+ </message>
+<!-- get_genes_by_motifs -->
+ <message name="get_genes_by_motifsRequest">
+ <part name="motif_id_list" type="typens:ArrayOfstring"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+
+ <message name="get_genes_by_motifsResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- KO,OC,PC -->
+<!-- get_ko_by_gene -->
+ <message name="get_ko_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ </message>
+ <message name="get_ko_by_geneResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+
+ </message>
+<!-- get_ko_by_ko_class -->
+ <message name="get_ko_by_ko_classRequest">
+ <part name="class_id" type="xsd:string"/>
+ </message>
+ <message name="get_ko_by_ko_classResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- get_genes_by_ko -->
+ <message name="get_genes_by_koRequest">
+
+ <part name="ko_id" type="xsd:string"/>
+ <part name="org" type="xsd:string"/>
+ </message>
+ <message name="get_genes_by_koResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- get_genes_by_ko_class -->
+ <message name="get_genes_by_ko_classRequest">
+ <part name="class_id" type="xsd:string"/>
+
+ <part name="org" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+ <message name="get_genes_by_ko_classResponse">
+ <part name="return" type="typens:ArrayOfDefinition"/>
+ </message>
+<!-- get_oc_members_by_gene -->
+<!--
+ <message name="get_oc_members_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+ <message name="get_oc_members_by_geneResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+-->
+<!-- get_pc_members_by_gene -->
+
+<!--
+ <message name="get_pc_members_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+ <message name="get_pc_members_by_geneResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+-->
+<!-- PATHWAY -->
+<!-- Coloring pathways -->
+<!-- mark_pathway_by_objects -->
+ <message name="get_elements_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_elements_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfPathwayElement"/>
+ </message>
+ <message name="get_element_relations_by_pathwayRequest">
+
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_element_relations_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfPathwayElementRelation"/>
+ </message>
+ <message name="color_pathway_by_elementsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="element_list" type="typens:ArrayOfint"/>
+ <part name="fg_color_list" type="typens:ArrayOfstring"/>
+
+ <part name="bg_color_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="color_pathway_by_elementsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+ <message name="get_html_of_colored_pathway_by_elementsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="element_list" type="typens:ArrayOfint"/>
+ <part name="fg_color_list" type="typens:ArrayOfstring"/>
+
+ <part name="bg_color_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_html_of_colored_pathway_by_elementsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+
+ <message name="mark_pathway_by_objectsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="object_id_list" type="typens:ArrayOfstring"/>
+
+ </message>
+ <message name="mark_pathway_by_objectsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- color_pathway_by_objects -->
+ <message name="color_pathway_by_objectsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="object_id_list" type="typens:ArrayOfstring"/>
+ <part name="fg_color_list" type="typens:ArrayOfstring"/>
+
+ <part name="bg_color_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="color_pathway_by_objectsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- get_html_org_marked_pathway_by_objects -->
+ <message name="get_html_of_marked_pathway_by_objectsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="object_id_list" type="typens:ArrayOfstring"/>
+
+ </message>
+ <message name="get_html_of_marked_pathway_by_objectsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- get_html_of_colored_pathway_by_objects -->
+ <message name="get_html_of_colored_pathway_by_objectsRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ <part name="object_id_list" type="typens:ArrayOfstring"/>
+ <part name="fg_color_list" type="typens:ArrayOfstring"/>
+
+ <part name="bg_color_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_html_of_colored_pathway_by_objectsResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+<!-- Objects on the pathway -->
+<!-- get_genes_by_pathway -->
+ <message name="get_genes_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+
+ <message name="get_genes_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- get_enzymes_by_pathway -->
+ <message name="get_enzymes_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_enzymes_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+
+ </message>
+<!-- get_reactions_by_pathway -->
+ <message name="get_reactions_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_reactions_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- Pathways by objects -->
+<!-- get_pathways_by_genes -->
+
+ <message name="get_pathways_by_genesRequest">
+ <part name="genes_id_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_genesResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- get_pathways_by_enzymes -->
+ <message name="get_pathways_by_enzymesRequest">
+ <part name="enzyme_id_list" type="typens:ArrayOfstring"/>
+
+ </message>
+ <message name="get_pathways_by_enzymesResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- get_pathways_by_reactions -->
+ <message name="get_pathways_by_reactionsRequest">
+ <part name="reaction_id_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_reactionsResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- Mutual transformation of objects -->
+<!-- Relation among pathways -->
+<!-- get_linked_pathways -->
+ <message name="get_linked_pathwaysRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_linked_pathwaysResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+
+ </message>
+<!-- Relation among genes and enzymes -->
+<!-- get_genes_by_enzyme -->
+ <message name="get_genes_by_enzymeRequest">
+ <part name="enzyme_id" type="xsd:string"/>
+ <part name="org" type="xsd:string"/>
+ </message>
+ <message name="get_genes_by_enzymeResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+<!-- get_enzymes_by_gene -->
+ <message name="get_enzymes_by_geneRequest">
+ <part name="genes_id" type="xsd:string"/>
+ </message>
+ <message name="get_enzymes_by_geneResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- Relation among enzymes, compounds and reactions -->
+<!-- get_enzymes_by_reaction -->
+ <message name="get_enzymes_by_reactionRequest">
+
+ <part name="reaction_id" type="xsd:string"/>
+ </message>
+ <message name="get_enzymes_by_reactionResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- get_reactions_by_enzyme -->
+ <message name="get_reactions_by_enzymeRequest">
+ <part name="enzyme_id" type="xsd:string"/>
+ </message>
+
+ <message name="get_reactions_by_enzymeResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- GENES -->
+<!-- get_genes_by_organism -->
+ <message name="get_genes_by_organismRequest">
+ <part name="org" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+
+ <message name="get_genes_by_organismResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+<!-- GENOME -->
+<!-- get_number_of_genes_by_organism -->
+ <message name="get_number_of_genes_by_organismRequest">
+ <part name="abbr" type="xsd:string"/>
+ </message>
+ <message name="get_number_of_genes_by_organismResponse">
+ <part name="return" type="xsd:int"/>
+
+ </message>
+<!-- LIGAND -->
+ <message name="get_reactions_by_glycanRequest">
+ <part name="glycan_id" type="xsd:string"/>
+ </message>
+ <message name="get_reactions_by_glycanResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_reactions_by_compoundRequest">
+
+ <part name="compound_id" type="xsd:string"/>
+ </message>
+ <message name="get_reactions_by_compoundResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_enzymes_by_glycanRequest">
+ <part name="glycan_id" type="xsd:string"/>
+ </message>
+ <message name="get_enzymes_by_glycanResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_enzymes_by_compoundRequest">
+ <part name="compound_id" type="xsd:string"/>
+ </message>
+ <message name="get_enzymes_by_compoundResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_compoundsRequest">
+
+ <part name="compound_id_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_compoundsResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_glycansRequest">
+ <part name="glycan_id_list" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_glycansResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_compounds_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_compounds_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_compounds_by_enzymeRequest">
+
+ <part name="enzyme_id" type="xsd:string"/>
+ </message>
+ <message name="get_compounds_by_enzymeResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_glycans_by_enzymeRequest">
+ <part name="enzyme_id" type="xsd:string"/>
+ </message>
+ <message name="get_glycans_by_enzymeResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_glycans_by_pathwayRequest">
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_glycans_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_compounds_by_reactionRequest">
+
+ <part name="reaction_id" type="xsd:string"/>
+ </message>
+ <message name="get_compounds_by_reactionResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_glycans_by_reactionRequest">
+ <part name="reaction_id" type="xsd:string"/>
+ </message>
+ <message name="get_glycans_by_reactionResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="convert_mol_to_kcfRequest">
+ <part name="mol_text" type="xsd:string"/>
+ </message>
+ <message name="convert_mol_to_kcfResponse">
+ <part name="return" type="xsd:string"/>
+ </message>
+ <message name="get_kos_by_pathwayRequest">
+
+ <part name="pathway_id" type="xsd:string"/>
+ </message>
+ <message name="get_kos_by_pathwayResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+ <message name="get_pathways_by_kosRequest">
+ <part name="ko_id_list" type="typens:ArrayOfstring"/>
+ <part name="org" type="xsd:string"/>
+ </message>
+
+ <message name="get_pathways_by_kosResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+<!-- v6.0 -->
+ <message name="search_compounds_by_nameRequest">
+ <part name="name" type="xsd:string"/>
+ </message>
+ <message name="search_compounds_by_nameResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+
+ </message>
+
+ <message name="search_glycans_by_nameRequest">
+ <part name="name" type="xsd:string"/>
+ </message>
+ <message name="search_glycans_by_nameResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_compounds_by_compositionRequest">
+
+ <part name="composition" type="xsd:string"/>
+ </message>
+ <message name="search_compounds_by_compositionResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_compounds_by_massRequest">
+ <part name="mass" type="xsd:float"/>
+ <part name="range" type="xsd:float"/>
+
+ </message>
+ <message name="search_compounds_by_massResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_glycans_by_massRequest">
+ <part name="mass" type="xsd:float"/>
+ <part name="range" type="xsd:float"/>
+ </message>
+
+ <message name="search_glycans_by_massResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_glycans_by_compositionRequest">
+ <part name="composition" type="xsd:string"/>
+ </message>
+ <message name="search_glycans_by_compositionResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+
+ </message>
+
+ <message name="search_compounds_by_subcompRequest">
+ <part name="mol" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+ <message name="search_compounds_by_subcompResponse">
+ <part name="return" type="typens:ArrayOfStructureAlignment"/>
+
+ </message>
+
+ <message name="search_glycans_by_kcamRequest">
+ <part name="kcf" type="xsd:string"/>
+ <part name="program" type="xsd:string"/>
+ <part name="option" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+
+ <message name="search_glycans_by_kcamResponse">
+ <part name="return" type="typens:ArrayOfStructureAlignment"/>
+ </message>
+
+ <message name="get_linkdb_between_databasesRequest">
+ <part name="from_db" type="xsd:string"/>
+ <part name="to_db" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+
+ </message>
+ <message name="get_linkdb_between_databasesResponse">
+ <part name="return" type="typens:ArrayOfLinkDBRelation"/>
+ </message>
+
+<!-- v6.1 -->
+ <message name="search_drugs_by_nameRequest">
+ <part name="name" type="xsd:string"/>
+ </message>
+ <message name="search_drugs_by_nameResponse">
+
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_drugs_by_compositionRequest">
+ <part name="composition" type="xsd:string"/>
+ </message>
+ <message name="search_drugs_by_compositionResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_drugs_by_massRequest">
+ <part name="mass" type="xsd:float"/>
+ <part name="range" type="xsd:float"/>
+ </message>
+ <message name="search_drugs_by_massResponse">
+ <part name="return" type="typens:ArrayOfstring"/>
+ </message>
+
+ <message name="search_drugs_by_subcompRequest">
+
+ <part name="mol" type="xsd:string"/>
+ <part name="offset" type="xsd:int"/>
+ <part name="limit" type="xsd:int"/>
+ </message>
+ <message name="search_drugs_by_subcompResponse">
+ <part name="return" type="typens:ArrayOfStructureAlignment"/>
+ </message>
+
+ <portType name="KEGGPortType">
+
+<!-- KEGG information -->
+ <operation name="list_databases">
+ <input message="typens:list_databasesRequest"/>
+ <output message="typens:list_databasesResponse"/>
+ </operation>
+ <operation name="list_organisms">
+ <input message="typens:list_organismsRequest"/>
+ <output message="typens:list_organismsResponse"/>
+ </operation>
+
+ <operation name="list_pathways">
+ <input message="typens:list_pathwaysRequest"/>
+ <output message="typens:list_pathwaysResponse"/>
+ </operation>
+ <operation name="list_ko_classes">
+ <input message="typens:list_ko_classesRequest"/>
+ <output message="typens:list_ko_classesResponse"/>
+ </operation>
+<!-- DBGET -->
+
+ <operation name="binfo">
+ <input message="typens:binfoRequest"/>
+ <output message="typens:binfoResponse"/>
+ </operation>
+ <operation name="bget">
+ <input message="typens:bgetRequest"/>
+ <output message="typens:bgetResponse"/>
+ </operation>
+ <operation name="bfind">
+
+ <input message="typens:bfindRequest"/>
+ <output message="typens:bfindResponse"/>
+ </operation>
+ <operation name="btit">
+ <input message="typens:btitRequest"/>
+ <output message="typens:btitResponse"/>
+ </operation>
+ <operation name="bconv">
+ <input message="typens:bconvRequest"/>
+
+ <output message="typens:bconvResponse"/>
+ </operation>
+<!-- LinkDB -->
+ <operation name="get_linkdb_by_entry">
+ <input message="typens:get_linkdb_by_entryRequest"/>
+ <output message="typens:get_linkdb_by_entryResponse"/>
+ </operation>
+<!-- SSDB -->
+ <operation name="get_best_neighbors_by_gene">
+ <input message="typens:get_best_neighbors_by_geneRequest"/>
+
+ <output message="typens:get_best_neighbors_by_geneResponse"/>
+ </operation>
+ <operation name="get_best_best_neighbors_by_gene">
+ <input message="typens:get_best_best_neighbors_by_geneRequest"/>
+ <output message="typens:get_best_best_neighbors_by_geneResponse"/>
+ </operation>
+ <operation name="get_reverse_best_neighbors_by_gene">
+ <input message="typens:get_reverse_best_neighbors_by_geneRequest"/>
+ <output message="typens:get_reverse_best_neighbors_by_geneResponse"/>
+
+ </operation>
+ <operation name="get_paralogs_by_gene">
+ <input message="typens:get_paralogs_by_geneRequest"/>
+ <output message="typens:get_paralogs_by_geneResponse"/>
+ </operation>
+<!-- MOTIF -->
+ <operation name="get_motifs_by_gene">
+ <input message="typens:get_motifs_by_geneRequest"/>
+ <output message="typens:get_motifs_by_geneResponse"/>
+
+ </operation>
+ <operation name="get_genes_by_motifs">
+ <input message="typens:get_genes_by_motifsRequest"/>
+ <output message="typens:get_genes_by_motifsResponse"/>
+ </operation>
+<!-- KO,OC,PC -->
+ <operation name="get_ko_by_gene">
+ <input message="typens:get_ko_by_geneRequest"/>
+ <output message="typens:get_ko_by_geneResponse"/>
+
+ </operation>
+ <operation name="get_ko_by_ko_class">
+ <input message="typens:get_ko_by_ko_classRequest"/>
+ <output message="typens:get_ko_by_ko_classResponse"/>
+ </operation>
+ <operation name="get_genes_by_ko">
+ <input message="typens:get_genes_by_koRequest"/>
+ <output message="typens:get_genes_by_koResponse"/>
+ </operation>
+
+ <operation name="get_genes_by_ko_class">
+ <input message="typens:get_genes_by_ko_classRequest"/>
+ <output message="typens:get_genes_by_ko_classResponse"/>
+ </operation>
+<!--
+ <operation name="get_oc_members_by_gene">
+ <input message="typens:get_oc_members_by_geneRequest"/>
+ <output message="typens:get_oc_members_by_geneResponse"/>
+ </operation>
+-->
+<!--
+ <operation name="get_pc_members_by_gene">
+ <input message="typens:get_pc_members_by_geneRequest"/>
+ <output message="typens:get_pc_members_by_geneResponse"/>
+ </operation>
+-->
+<!-- PATHWAY -->
+<!-- Coloring pathways -->
+ <operation name="get_elements_by_pathway">
+ <input message="typens:get_elements_by_pathwayRequest"/>
+ <output message="typens:get_elements_by_pathwayResponse"/>
+
+ </operation>
+ <operation name="get_element_relations_by_pathway">
+ <input message="typens:get_element_relations_by_pathwayRequest"/>
+ <output message="typens:get_element_relations_by_pathwayResponse"/>
+ </operation>
+ <operation name="color_pathway_by_elements">
+ <input message="typens:color_pathway_by_elementsRequest"/>
+ <output message="typens:color_pathway_by_elementsResponse"/>
+ </operation>
+
+ <operation name="get_html_of_colored_pathway_by_elements">
+ <input message="typens:get_html_of_colored_pathway_by_elementsRequest"/>
+ <output message="typens:get_html_of_colored_pathway_by_elementsResponse"/>
+ </operation>
+
+ <operation name="mark_pathway_by_objects">
+ <input message="typens:mark_pathway_by_objectsRequest"/>
+ <output message="typens:mark_pathway_by_objectsResponse"/>
+ </operation>
+
+ <operation name="color_pathway_by_objects">
+ <input message="typens:color_pathway_by_objectsRequest"/>
+ <output message="typens:color_pathway_by_objectsResponse"/>
+ </operation>
+ <operation name="get_html_of_marked_pathway_by_objects">
+ <input message="typens:get_html_of_marked_pathway_by_objectsRequest"/>
+ <output message="typens:get_html_of_marked_pathway_by_objectsResponse"/>
+ </operation>
+ <operation name="get_html_of_colored_pathway_by_objects">
+
+ <input message="typens:get_html_of_colored_pathway_by_objectsRequest"/>
+ <output message="typens:get_html_of_colored_pathway_by_objectsResponse"/>
+ </operation>
+<!-- Objects on the pathway -->
+ <operation name="get_genes_by_pathway">
+ <input message="typens:get_genes_by_pathwayRequest"/>
+ <output message="typens:get_genes_by_pathwayResponse"/>
+ </operation>
+ <operation name="get_enzymes_by_pathway">
+
+ <input message="typens:get_enzymes_by_pathwayRequest"/>
+ <output message="typens:get_enzymes_by_pathwayResponse"/>
+ </operation>
+ <operation name="get_reactions_by_pathway">
+ <input message="typens:get_reactions_by_pathwayRequest"/>
+ <output message="typens:get_reactions_by_pathwayResponse"/>
+ </operation>
+<!-- Pathways by objects -->
+ <operation name="get_pathways_by_genes">
+
+ <input message="typens:get_pathways_by_genesRequest"/>
+ <output message="typens:get_pathways_by_genesResponse"/>
+ </operation>
+ <operation name="get_pathways_by_enzymes">
+ <input message="typens:get_pathways_by_enzymesRequest"/>
+ <output message="typens:get_pathways_by_enzymesResponse"/>
+ </operation>
+ <operation name="get_pathways_by_reactions">
+ <input message="typens:get_pathways_by_reactionsRequest"/>
+
+ <output message="typens:get_pathways_by_reactionsResponse"/>
+ </operation>
+<!-- Mutual transformation of objects -->
+<!-- Realtion among pathways -->
+ <operation name="get_linked_pathways">
+ <input message="typens:get_linked_pathwaysRequest"/>
+ <output message="typens:get_linked_pathwaysResponse"/>
+ </operation>
+<!-- Realtion among genes and enzymes -->
+ <operation name="get_genes_by_enzyme">
+
+ <input message="typens:get_genes_by_enzymeRequest"/>
+ <output message="typens:get_genes_by_enzymeResponse"/>
+ </operation>
+ <operation name="get_enzymes_by_gene">
+ <input message="typens:get_enzymes_by_geneRequest"/>
+ <output message="typens:get_enzymes_by_geneResponse"/>
+ </operation>
+<!-- Realtion among enzymes, compounds and reactions -->
+ <operation name="get_enzymes_by_reaction">
+
+ <input message="typens:get_enzymes_by_reactionRequest"/>
+ <output message="typens:get_enzymes_by_reactionResponse"/>
+ </operation>
+ <operation name="get_reactions_by_enzyme">
+ <input message="typens:get_reactions_by_enzymeRequest"/>
+ <output message="typens:get_reactions_by_enzymeResponse"/>
+ </operation>
+<!-- GENES -->
+ <operation name="get_genes_by_organism">
+
+ <input message="typens:get_genes_by_organismRequest"/>
+ <output message="typens:get_genes_by_organismResponse"/>
+ </operation>
+<!-- GENOME -->
+ <operation name="get_number_of_genes_by_organism">
+ <input message="typens:get_number_of_genes_by_organismRequest"/>
+ <output message="typens:get_number_of_genes_by_organismResponse"/>
+ </operation>
+<!-- LIGAND -->
+ <operation name="get_reactions_by_glycan">
+
+ <input message="typens:get_reactions_by_glycanRequest"/>
+ <output message="typens:get_reactions_by_glycanResponse"/>
+ </operation>
+ <operation name="get_reactions_by_compound">
+ <input message="typens:get_reactions_by_compoundRequest"/>
+ <output message="typens:get_reactions_by_compoundResponse"/>
+ </operation>
+ <operation name="get_enzymes_by_glycan">
+ <input message="typens:get_enzymes_by_glycanRequest"/>
+
+ <output message="typens:get_enzymes_by_glycanResponse"/>
+ </operation>
+ <operation name="get_enzymes_by_compound">
+ <input message="typens:get_enzymes_by_compoundRequest"/>
+ <output message="typens:get_enzymes_by_compoundResponse"/>
+ </operation>
+ <operation name="get_pathways_by_compounds">
+ <input message="typens:get_pathways_by_compoundsRequest"/>
+ <output message="typens:get_pathways_by_compoundsResponse"/>
+
+ </operation>
+ <operation name="get_pathways_by_glycans">
+ <input message="typens:get_pathways_by_glycansRequest"/>
+ <output message="typens:get_pathways_by_glycansResponse"/>
+ </operation>
+ <operation name="get_compounds_by_pathway">
+ <input message="typens:get_compounds_by_pathwayRequest"/>
+ <output message="typens:get_compounds_by_pathwayResponse"/>
+ </operation>
+
+ <operation name="get_glycans_by_pathway">
+ <input message="typens:get_glycans_by_pathwayRequest"/>
+ <output message="typens:get_glycans_by_pathwayResponse"/>
+ </operation>
+ <operation name="get_compounds_by_reaction">
+ <input message="typens:get_compounds_by_reactionRequest"/>
+ <output message="typens:get_compounds_by_reactionResponse"/>
+ </operation>
+ <operation name="get_glycans_by_reaction">
+
+ <input message="typens:get_glycans_by_reactionRequest"/>
+ <output message="typens:get_glycans_by_reactionResponse"/>
+ </operation>
+ <operation name="get_compounds_by_enzyme">
+ <input message="typens:get_compounds_by_enzymeRequest"/>
+ <output message="typens:get_compounds_by_enzymeResponse"/>
+ </operation>
+ <operation name="get_glycans_by_enzyme">
+ <input message="typens:get_glycans_by_enzymeRequest"/>
+
+ <output message="typens:get_glycans_by_enzymeResponse"/>
+ </operation>
+ <operation name="convert_mol_to_kcf">
+ <input message="typens:convert_mol_to_kcfRequest"/>
+ <output message="typens:convert_mol_to_kcfResponse"/>
+ </operation>
+ <operation name="get_kos_by_pathway">
+ <input message="typens:get_kos_by_pathwayRequest"/>
+ <output message="typens:get_kos_by_pathwayResponse"/>
+
+ </operation>
+ <operation name="get_pathways_by_kos">
+ <input message="typens:get_pathways_by_kosRequest"/>
+ <output message="typens:get_pathways_by_kosResponse"/>
+ </operation>
+<!-- v6.0 -->
+ <operation name="search_compounds_by_name">
+ <input message="typens:search_compounds_by_nameRequest"/>
+ <output message="typens:search_compounds_by_nameResponse"/>
+
+ </operation>
+ <operation name="search_glycans_by_name">
+ <input message="typens:search_glycans_by_nameRequest"/>
+ <output message="typens:search_glycans_by_nameResponse"/>
+ </operation>
+ <operation name="search_compounds_by_composition">
+ <input message="typens:search_compounds_by_compositionRequest"/>
+ <output message="typens:search_compounds_by_compositionResponse"/>
+ </operation>
+
+ <operation name="search_compounds_by_mass">
+ <input message="typens:search_compounds_by_massRequest"/>
+ <output message="typens:search_compounds_by_massResponse"/>
+ </operation>
+ <operation name="search_glycans_by_mass">
+ <input message="typens:search_glycans_by_massRequest"/>
+ <output message="typens:search_glycans_by_massResponse"/>
+ </operation>
+ <operation name="search_glycans_by_composition">
+
+ <input message="typens:search_glycans_by_compositionRequest"/>
+ <output message="typens:search_glycans_by_compositionResponse"/>
+ </operation>
+ <operation name="search_compounds_by_subcomp">
+ <input message="typens:search_compounds_by_subcompRequest"/>
+ <output message="typens:search_compounds_by_subcompResponse"/>
+ </operation>
+ <operation name="search_glycans_by_kcam">
+ <input message="typens:search_glycans_by_kcamRequest"/>
+
+ <output message="typens:search_glycans_by_kcamResponse"/>
+ </operation>
+ <operation name="get_linkdb_between_databases">
+ <input message="typens:get_linkdb_between_databasesRequest"/>
+ <output message="typens:get_linkdb_between_databasesResponse"/>
+ </operation>
+
+<!-- v6.1 -->
+ <operation name="search_drugs_by_name">
+ <input message="typens:search_drugs_by_nameRequest"/>
+
+ <output message="typens:search_drugs_by_nameResponse"/>
+ </operation>
+ <operation name="search_drugs_by_composition">
+ <input message="typens:search_drugs_by_compositionRequest"/>
+ <output message="typens:search_drugs_by_compositionResponse"/>
+ </operation>
+ <operation name="search_drugs_by_mass">
+ <input message="typens:search_drugs_by_massRequest"/>
+ <output message="typens:search_drugs_by_massResponse"/>
+
+ </operation>
+ <operation name="search_drugs_by_subcomp">
+ <input message="typens:search_drugs_by_subcompRequest"/>
+ <output message="typens:search_drugs_by_subcompResponse"/>
+ </operation>
+
+ </portType>
+
+
+ <binding name="KEGGBinding" type="typens:KEGGPortType">
+
+ <soap:binding style="rpc" transport="http://schemas.xmlsoap.org/soap/http"/>
+<!-- KEGG information -->
+ <operation name="list_databases">
+ <soap:operation soapAction="SOAP/KEGG#list_databases"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="list_organisms">
+ <soap:operation soapAction="SOAP/KEGG#list_organisms"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="list_pathways">
+ <soap:operation soapAction="SOAP/KEGG#list_pathways"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="list_ko_classes">
+ <soap:operation soapAction="SOAP/KEGG#list_ko_classes"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+<!-- DBGET -->
+ <operation name="binfo">
+ <soap:operation soapAction="SOAP/KEGG#binfo"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="bget">
+ <soap:operation soapAction="SOAP/KEGG#bget"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="bfind">
+ <soap:operation soapAction="SOAP/KEGG#bfind"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="btit">
+ <soap:operation soapAction="SOAP/KEGG#btit"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="bconv">
+ <soap:operation soapAction="SOAP/KEGG#bconv"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- LinkDB -->
+ <operation name="get_linkdb_by_entry">
+ <soap:operation soapAction="SOAP/KEGG#get_linkdb_by_entry"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- SSDB -->
+ <operation name="get_best_neighbors_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_best_neighbors_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_best_best_neighbors_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_best_best_neighbors_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_reverse_best_neighbors_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_reverse_best_neighbors_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_paralogs_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_paralogs_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- MOTIF -->
+ <operation name="get_motifs_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_motifs_by_gene"/>
+ <input>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_genes_by_motifs">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_motifs"/>
+ <input>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- KO,OC,PC -->
+ <operation name="get_ko_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_ko_by_gene"/>
+
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_ko_by_ko_class">
+ <soap:operation soapAction="SOAP/KEGG#get_ko_by_ko_class"/>
+
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_genes_by_ko">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_ko"/>
+
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_genes_by_ko_class">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_ko_class"/>
+
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!--
+ <operation name="get_oc_members_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_oc_members_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+-->
+<!--
+ <operation name="get_pc_members_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_pc_members_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+-->
+<!-- PATHWAY -->
+
+<!-- Coloring pathways -->
+ <operation name="get_elements_by_pathway">
+ <soap:operation soapAction="SOAP/KEGG#get_elements_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="get_element_relations_by_pathway">
+ <soap:operation soapAction="SOAP/KEGG#get_element_relations_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="color_pathway_by_elements">
+ <soap:operation soapAction="SOAP/KEGG#color_pathway_by_elements"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="get_html_of_colored_pathway_by_elements">
+ <soap:operation soapAction="SOAP/KEGG#get_html_of_colored_pathway_by_elements"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+
+ <operation name="mark_pathway_by_objects">
+ <soap:operation soapAction="SOAP/KEGG#mark_pathway_by_objects"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="color_pathway_by_objects">
+ <soap:operation soapAction="SOAP/KEGG#color_pathway_by_objects"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="get_html_of_marked_pathway_by_objects">
+ <soap:operation soapAction="SOAP/KEGG#get_html_of_marked_pathway_by_objects"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="get_html_of_colored_pathway_by_objects">
+ <soap:operation soapAction="SOAP/KEGG#get_html_of_colored_pathway_by_objects"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+<!-- Objects on the pathway -->
+ <operation name="get_genes_by_pathway">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_enzymes_by_pathway">
+ <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_reactions_by_pathway">
+ <soap:operation soapAction="SOAP/KEGG#get_reactions_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- Pathways by object -->
+ <operation name="get_pathways_by_genes">
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_genes"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_pathways_by_enzymes">
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_enzymes"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_pathways_by_reactions">
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_reactions"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- Mutual transformation of objects -->
+ <operation name="get_linked_pathways">
+ <soap:operation soapAction="SOAP/KEGG#get_linked_pathways"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_genes_by_enzyme">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_enzyme"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_enzymes_by_gene">
+ <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_gene"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_enzymes_by_reaction">
+ <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_reaction"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_reactions_by_enzyme">
+ <soap:operation soapAction="SOAP/KEGG#get_reactions_by_enzyme"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- GENES -->
+ <operation name="get_genes_by_organism">
+ <soap:operation soapAction="SOAP/KEGG#get_genes_by_organism"/>
+ <input>
+
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- GENOME -->
+ <operation name="get_number_of_genes_by_organism">
+ <soap:operation soapAction="SOAP/KEGG#get_number_of_genes_by_organism"/>
+
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+<!-- LIGAND -->
+ <operation name="get_reactions_by_glycan">
+
+ <soap:operation soapAction="SOAP/KEGG#get_reactions_by_glycan"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_reactions_by_compound">
+
+ <soap:operation soapAction="SOAP/KEGG#get_reactions_by_compound"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_enzymes_by_glycan">
+
+ <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_glycan"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_enzymes_by_compound">
+
+ <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_compound"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_pathways_by_compounds">
+
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_compounds"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_pathways_by_glycans">
+
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_glycans"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_compounds_by_pathway">
+
+ <soap:operation soapAction="SOAP/KEGG#get_compounds_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_glycans_by_pathway">
+
+ <soap:operation soapAction="SOAP/KEGG#get_glycans_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_compounds_by_reaction">
+
+ <soap:operation soapAction="SOAP/KEGG#get_compounds_by_reaction"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_glycans_by_reaction">
+
+ <soap:operation soapAction="SOAP/KEGG#get_glycans_by_reaction"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_compounds_by_enzyme">
+
+ <soap:operation soapAction="SOAP/KEGG#get_compounds_by_enzyme"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_glycans_by_enzyme">
+
+ <soap:operation soapAction="SOAP/KEGG#get_glycans_by_enzyme"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="convert_mol_to_kcf">
+
+ <soap:operation soapAction="SOAP/KEGG#convert_mol_to_kcf"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_kos_by_pathway">
+
+ <soap:operation soapAction="SOAP/KEGG#get_kos_by_pathway"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+ <operation name="get_pathways_by_kos">
+
+ <soap:operation soapAction="SOAP/KEGG#get_pathways_by_kos"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+ </operation>
+
+<!-- v6.0 -->
+ <operation name="search_compounds_by_name">
+ <soap:operation soapAction="SOAP/KEGG#search_compounds_by_name"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_glycans_by_name">
+ <soap:operation soapAction="SOAP/KEGG#search_glycans_by_name"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_compounds_by_composition">
+ <soap:operation soapAction="SOAP/KEGG#search_compounds_by_composition"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_compounds_by_mass">
+ <soap:operation soapAction="SOAP/KEGG#search_compounds_by_mass"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_glycans_by_mass">
+ <soap:operation soapAction="SOAP/KEGG#search_glycans_by_mass"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_glycans_by_composition">
+ <soap:operation soapAction="SOAP/KEGG#search_glycans_by_composition"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_compounds_by_subcomp">
+ <soap:operation soapAction="SOAP/KEGG#search_compounds_by_subcomp"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="search_glycans_by_kcam">
+ <soap:operation soapAction="SOAP/KEGG#search_glycans_by_kcam"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+ <operation name="get_linkdb_between_databases">
+ <soap:operation soapAction="SOAP/KEGG#get_linkdb_between_databases"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </output>
+
+ </operation>
+
+<!-- v6.1 -->
+ <operation name="search_drugs_by_name">
+ <soap:operation soapAction="SOAP/KEGG#search_drugs_by_name"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="search_drugs_by_composition">
+ <soap:operation soapAction="SOAP/KEGG#search_drugs_by_composition"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="search_drugs_by_mass">
+ <soap:operation soapAction="SOAP/KEGG#search_drugs_by_mass"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+ <operation name="search_drugs_by_subcomp">
+ <soap:operation soapAction="SOAP/KEGG#search_drugs_by_subcomp"/>
+ <input>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+ </input>
+ <output>
+ <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
+
+ </output>
+ </operation>
+
+ </binding>
+
+ <service name="KEGG">
+ <port name="KEGGPort" binding="typens:KEGGBinding">
+ <soap:address location="http://soap.genome.jp/keggapi/request_v6.1.cgi"/>
+ </port>
+ </service>
+
+</definitions>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/pom.xml b/taverna-xpath-activity-ui/pom.xml
new file mode 100644
index 0000000..53b81ee
--- /dev/null
+++ b/taverna-xpath-activity-ui/pom.xml
@@ -0,0 +1,68 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>xpath-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>XPath Activity - UI bindings</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>xpath-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>report-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/TwoFieldQueryPanel.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/TwoFieldQueryPanel.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/TwoFieldQueryPanel.java
new file mode 100644
index 0000000..d0f131a
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/TwoFieldQueryPanel.java
@@ -0,0 +1,110 @@
+package net.sf.taverna.t2.activities.xpath.ui.config;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+/**
+ * Auxiliary class that creates a JPanel with two labels and two text fields.
+ *
+ * It can be used to be placed into a dialog made by JOptionPane to get two
+ * input values, not just one.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class TwoFieldQueryPanel extends JPanel {
+ private JTextField tfFirstValue;
+ private JTextField tfSecondValue;
+
+ public TwoFieldQueryPanel(String firstFieldName, String secondFieldName) {
+ this(null, firstFieldName, null, secondFieldName, null);
+ }
+
+ public TwoFieldQueryPanel(String message, String firstFieldName,
+ String secondFieldName) {
+ this(message, firstFieldName, null, secondFieldName, null);
+ }
+
+ public TwoFieldQueryPanel(String firstFieldName,
+ String firstFieldDefaultValue, String secondFieldName,
+ String secondFieldDefaultValue) {
+ this(null, firstFieldName, firstFieldDefaultValue, secondFieldName,
+ secondFieldDefaultValue);
+ }
+
+ public TwoFieldQueryPanel(String message, String firstFieldName,
+ String firstFieldDefaultValue, String secondFieldName,
+ String secondFieldDefaultValue) {
+ super();
+ this.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.WEST;
+ c.insets = new Insets(3, 5, 3, 5);
+
+ if (message != null && message.length() > 0) {
+ c.gridwidth = 2;
+ c.insets = new Insets(5, 5, 15, 5);
+ this.add(new JLabel(message), c);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 5, 3, 5);
+ }
+
+ this.add(new JLabel(firstFieldName), c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ tfFirstValue = new JTextField(20);
+ if (firstFieldDefaultValue != null) {
+ tfFirstValue.setText(firstFieldDefaultValue);
+ }
+ tfFirstValue.selectAll();
+ tfFirstValue.requestFocusInWindow();
+ this.add(tfFirstValue, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ this.add(new JLabel(secondFieldName), c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ tfSecondValue = new JTextField(20);
+ if (secondFieldDefaultValue != null) {
+ tfSecondValue.setText(secondFieldDefaultValue);
+ }
+ tfSecondValue.selectAll();
+ this.add(tfSecondValue, c);
+ }
+
+ /**
+ * @return Trimmed value from the first text field. Guaranteed to be
+ * non-null.
+ */
+ public String getFirstValue() {
+ return (tfFirstValue.getText().trim());
+ }
+
+ /**
+ * @return Trimmed value from the second text field. Guaranteed to be
+ * non-null.
+ */
+ public String getSecondValue() {
+ return (tfSecondValue.getText().trim());
+ }
+
+}
[06/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context.xml b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context.xml
new file mode 100644
index 0000000..7fdba26
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="SpreadsheetImportActivityIcon" class="net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportActivityIcon">
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+ <bean id="SpreadsheetImportTemplateService" class="net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService" />
+
+ <bean id="SpreadsheetImportAddTemplateAction" class="net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportAddTemplateAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="SpreadsheetImportAddTemplateMenuAction" class="net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportAddTemplateMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="SpreadsheetImportConfigureMenuAction" class="net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportConfigureMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+ <bean id="SpreadsheetImportContextualViewFactory" class="net.sf.taverna.t2.activities.spreadsheet.views.SpreadsheetImportContextualViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/net/sf/taverna/t2/activities/spreadsheet/iln8/ui-text.properties
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/net/sf/taverna/t2/activities/spreadsheet/iln8/ui-text.properties b/taverna-spreadsheet-import-activity-ui/src/main/resources/net/sf/taverna/t2/activities/spreadsheet/iln8/ui-text.properties
new file mode 100644
index 0000000..2a4480f
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/net/sf/taverna/t2/activities/spreadsheet/iln8/ui-text.properties
@@ -0,0 +1,43 @@
+SpreadsheetImportActivityConfigurationAction.canceButton=Cancel
+SpreadsheetImportActivityConfigurationAction.dialogTitle=Spreadsheet Import Configuration
+SpreadsheetImportActivityConfigurationAction.okButton=Finish
+SpreadsheetImportAddTemplateAction.addMenu=Spreadsheet import
+SpreadsheetImportConfigureMenuAction.configureMenu=Configure Spreadsheet Import
+SpreadsheetImportConfigTableModel.column=Column
+SpreadsheetImportConfigTableModel.portName=Port Name
+SpreadsheetImportConfigView.nextButton=Next
+SpreadsheetImportConfigView.backButton=Back
+SpreadsheetImportConfigView.columnMappingSectionLabel=Column to Port Name Mapping
+SpreadsheetImportConfigView.outputFormatSectionLabel=Output Format
+SpreadsheetImportConfigView.columnSectionLabel=Columns
+SpreadsheetImportConfigView.DEFAULT_MESSAGE=Select the data range
+SpreadsheetImportConfigView.DUPLICATE_PORT_NAME_ERROR_MESSAGE=Duplicate activity port name
+SpreadsheetImportConfigView.EMPTY_FROM_COLUMN_ERROR_MESSAGE='From' column must be specified
+SpreadsheetImportConfigView.EMPTY_FROM_ROW_ERROR_MESSAGE='From' row must be specified
+SpreadsheetImportConfigView.EMPTY_TO_COLUMN_ERROR_MESSAGE='To' column must be specified
+SpreadsheetImportConfigView.emptyCellSectionLabel=Empty cells
+SpreadsheetImportConfigView.emptyStringOption=Use an empty string
+SpreadsheetImportConfigView.excludeHeaderRowOption=Exclude header row
+SpreadsheetImportConfigView.from=From
+SpreadsheetImportConfigView.FROM_COLUMN_ERROR_MESSAGE='From' column can only contain characters A-Z
+SpreadsheetImportConfigView.FROM_ROW_ERROR_MESSAGE='From' row must be a number greater than 0
+SpreadsheetImportConfigView.generateErrorOption=Generate an error value
+SpreadsheetImportConfigView.ignoreBlankRowsOption=Ignore blank rows
+SpreadsheetImportConfigView.multiplePortOption=Multiple outputs (one per spreadsheet column)
+SpreadsheetImportConfigView.singlePortOption=A single CSV formatted output
+SpreadsheetImportConfigView.userDefinedCsvDelimiter=Use this value delimiter character:
+SpreadsheetImportConfigView.INCONSISTENT_COLUMN_MESSAGE='To' column must not be less than 'from' column
+SpreadsheetImportConfigView.INCONSISTENT_ROW_MESSAGE='To'row must not be less than 'from' row
+SpreadsheetImportConfigView.panelTitle=Configure spreadsheet file import
+SpreadsheetImportConfigView.rowSectionLabel=Rows
+SpreadsheetImportConfigView.selectAllRowsOption=All rows
+SpreadsheetImportConfigView.to=to
+SpreadsheetImportConfigView.TO_COLUMN_ERROR_MESSAGE='To' column can only contain characters A-Z
+SpreadsheetImportConfigView.TO_ROW_ERROR_MESSAGE='To' row must be a number greater than 0
+SpreadsheetImportConfigView.userDefinedOption=Use this value:
+SpreadsheetImportContextualView.activityName=Spreadsheet Import Activity
+SpreadsheetImportContextualView.depth=Depth
+SpreadsheetImportContextualView.inputPortName=Input Port Name
+SpreadsheetImportContextualView.outputPortName=Output Port Name
+SpreadsheetImportTemplateService.serviceDescription=A service that imports data from spreadsheets
+SpreadsheetImportTemplateService.serviceName=SpreadsheetImport
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/spreadsheet-import.png
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/spreadsheet-import.png b/taverna-spreadsheet-import-activity-ui/src/main/resources/spreadsheet-import.png
new file mode 100644
index 0000000..886fac3
Binary files /dev/null and b/taverna-spreadsheet-import-activity-ui/src/main/resources/spreadsheet-import.png differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/pom.xml b/taverna-wsdl-activity-ui/pom.xml
new file mode 100644
index 0000000..be2d224
--- /dev/null
+++ b/taverna-wsdl-activity-ui/pom.xml
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>wsdl-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 WSDL Activity UI</name>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+ <!-- Use the java version instead of xmlcommons for javax.* packages -->
+ <Import-Package>javax.xml.namespace;version="0.0.0",javax.xml.parsers;version="0.0.0",org.w3c.dom;version="0.0.0",org.xml.sax;version="0.0.0",*</Import-Package>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>credential-manager-ui</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
new file mode 100644
index 0000000..d92dab9
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
@@ -0,0 +1,156 @@
+package net.sf.taverna.t2.activities.wsdl.actions;
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+import org.apache.log4j.Logger;
+import org.jdom.JDOMException;
+import org.xml.sax.SAXException;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+/**
+ * Abstract superclass of {@link AddXMLOutputSplitterAction} and
+ * {@link AddXMLInputSplitterAction}.
+ * <p>
+ * Pops up a {@link JOptionPane} with the names of all the wsdl ports. The one
+ * that is selected is added as an input/output splitter to the currently open
+ * dataflow using the {@link AddXMLSplitterEdit}
+ *
+ * @author Ian Dunlop
+ * @author Stian Soiland-Reyes
+ * @author Stuart Owen
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class AbstractAddXMLSplitterAction extends AbstractAction {
+
+ private static Logger logger = Logger.getLogger(AddXMLOutputSplitterAction.class);
+
+ protected Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ protected JComponent owner;
+ protected final Activity activity;
+ protected final EditManager editManager;
+ protected final SelectionManager selectionManager;
+
+ public AbstractAddXMLSplitterAction(Activity activity,
+ JComponent owner, EditManager editManager, SelectionManager selectionManager) {
+ this.activity = activity;
+ this.owner = owner;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ }
+
+ public void actionPerformed(ActionEvent ev) {
+ List<String> possibilities;
+ Map<String, TypeDescriptor> typeDescriptors;
+ try {
+ typeDescriptors = getTypeDescriptors();
+ } catch (UnknownOperationException ex) {
+ logger.error("Can't find operation for activity "
+ + activity, ex);
+ return;
+ } catch (IOException | ParserConfigurationException | WSDLException | SAXException | JDOMException ex) {
+ logger.error("Can't read definition for activity "
+ + activity, ex);
+ return;
+ }
+
+ typeDescriptors = filterDescriptors(typeDescriptors);
+
+ possibilities = new ArrayList<String>(typeDescriptors.keySet());
+ if (possibilities.isEmpty()) {
+ logger.warn("No type descriptors found for activity " + activity);
+ return;
+ }
+ Collections.sort(possibilities);
+
+ String portName = (String) JOptionPane.showInputDialog(owner,
+ "Select the port to add the splitter to",
+ "Add output XML splitter", JOptionPane.PLAIN_MESSAGE, null,
+ possibilities.toArray(), possibilities.get(0));
+
+ Workflow workflow = selectionManager.getSelectedWorkflow();
+ Profile profile = selectionManager.getSelectedProfile();
+ TypeDescriptor typeDescriptorForPort = typeDescriptors
+ .get(portName);
+
+ if (typeDescriptorForPort instanceof ArrayTypeDescriptor
+ || typeDescriptorForPort instanceof ComplexTypeDescriptor) {
+ AddXMLSplitterEdit edit = new AddXMLSplitterEdit(workflow, profile,
+ activity, typeDescriptorForPort, portName, isInput());
+ try {
+ editManager.doDataflowEdit(workflow.getParent(), edit);
+ } catch (EditException ex) {
+ logger.error("Could not perform edit to add " + portName, ex);
+ }
+ } else {
+ logger.warn("Unknown typedescriptor for " + portName);
+ }
+ }
+
+ public static Map<String, TypeDescriptor> filterDescriptors(
+ Map<String, TypeDescriptor> descriptors) {
+ Map<String, TypeDescriptor> filtered = new HashMap<String, TypeDescriptor>();
+ for (Entry<String, TypeDescriptor> entry : descriptors.entrySet()) {
+ TypeDescriptor descriptor = entry.getValue();
+ if (descriptor.getMimeType().contains("'text/xml'")) {
+ filtered.put(entry.getKey(), descriptor);
+ }
+ }
+ return filtered;
+ }
+
+ protected abstract boolean isInput();
+
+ public abstract Map<String, TypeDescriptor> getTypeDescriptors()
+ throws UnknownOperationException, IOException, ParserConfigurationException, WSDLException, SAXException, JDOMException;
+
+ public void setOwner(JComponent owner) {
+ this.owner = owner;
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLInputSplitterAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLInputSplitterAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLInputSplitterAction.java
new file mode 100644
index 0000000..6faee9d
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLInputSplitterAction.java
@@ -0,0 +1,104 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.actions;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.AddXMLSplitterEdit;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+import net.sf.taverna.wsdl.xmlsplitter.XMLSplitterSerialisationHelper;
+
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+import org.xml.sax.SAXException;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+/**
+ * Pops up a {@link JOptionPane} with the names of all the wsdl ports. The one
+ * that is selected is added as an input splitter to the currently open dataflow
+ * using the {@link AddXMLSplitterEdit}
+ *
+ * @author Ian Dunlop
+ * @author Stian Soiland-Reyes
+ */
+@SuppressWarnings("serial")
+public class AddXMLInputSplitterAction extends AbstractAddXMLSplitterAction {
+
+ public AddXMLInputSplitterAction(Activity activity, JComponent owner, EditManager editManager,
+ SelectionManager selectionManager) {
+ super(activity, owner, editManager, selectionManager);
+ putValue(NAME, "Add input XML splitter");
+ }
+
+ @Override
+ public Map<String, TypeDescriptor> getTypeDescriptors() throws UnknownOperationException, IOException, ParserConfigurationException, WSDLException, SAXException, JDOMException {
+ Map<String, TypeDescriptor> descriptors = new HashMap<String, TypeDescriptor>();
+ Configuration configuration = scufl2Tools.configurationFor(activity, selectionManager.getSelectedProfile());
+ if (activity.getType().equals(WSDLServiceDescription.ACTIVITY_TYPE)) {
+ String wsdlLocation = configuration.getJson().get("operation").get("wsdl").textValue();
+ String operationName = configuration.getJson().get("operation").get("name").textValue();
+ List<TypeDescriptor> inputDescriptors = new WSDLParser(wsdlLocation)
+ .getOperationInputParameters(operationName);
+ for (TypeDescriptor descriptor : inputDescriptors) {
+ descriptors.put(descriptor.getName(), descriptor);
+ }
+ } else if (activity.getType().equals(WSDLServiceDescription.INPUT_SPLITTER_TYPE)) {
+ String wrappedType = configuration.getJson().get("wrappedType").textValue();
+ Element element = new SAXBuilder().build(new StringReader(wrappedType)).getRootElement();
+ TypeDescriptor typeDescriptor = XMLSplitterSerialisationHelper.extensionXMLToTypeDescriptor(element);
+ if (typeDescriptor instanceof ComplexTypeDescriptor) {
+ for (TypeDescriptor desc : ((ComplexTypeDescriptor)typeDescriptor).getElements()) {
+ descriptors.put(desc.getName(), desc);
+ }
+ }
+ else if (typeDescriptor instanceof ArrayTypeDescriptor) {
+ TypeDescriptor desc = ((ArrayTypeDescriptor)typeDescriptor).getElementType();
+ descriptors.put(typeDescriptor.getName(), desc);
+ }
+ }
+ return descriptors;
+ }
+
+ @Override
+ protected boolean isInput() {
+ return true;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLOutputSplitterAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLOutputSplitterAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLOutputSplitterAction.java
new file mode 100644
index 0000000..60cba69
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLOutputSplitterAction.java
@@ -0,0 +1,105 @@
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.actions;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+import org.xml.sax.SAXException;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.AddXMLSplitterEdit;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+import net.sf.taverna.wsdl.xmlsplitter.XMLSplitterSerialisationHelper;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+/**
+ * Pops up a {@link JOptionPane} with the names of all the wsdl ports. The one
+ * that is selected is added as an output splitter to the currently open
+ * dataflow using the {@link AddXMLSplitterEdit}
+ *
+ * @author Ian Dunlop
+ * @author Stian Soiland-Reyes
+ */
+@SuppressWarnings("serial")
+public class AddXMLOutputSplitterAction extends AbstractAddXMLSplitterAction {
+
+ public AddXMLOutputSplitterAction(Activity activity, JComponent owner, EditManager editManager,
+ SelectionManager selectionManager) {
+ super(activity, owner, editManager, selectionManager);
+ putValue(NAME, "Add output XML splitter");
+
+ }
+
+ @Override
+ public Map<String, TypeDescriptor> getTypeDescriptors() throws UnknownOperationException, IOException, ParserConfigurationException, WSDLException, SAXException, JDOMException {
+ Map<String, TypeDescriptor> descriptors = new HashMap<String, TypeDescriptor>();
+ Configuration configuration = scufl2Tools.configurationFor(activity, selectionManager.getSelectedProfile());
+ if (activity.getType().equals(WSDLServiceDescription.ACTIVITY_TYPE)) {
+ String wsdlLocation = configuration.getJson().get("operation").get("wsdl").textValue();
+ String operationName = configuration.getJson().get("operation").get("name").textValue();
+ List<TypeDescriptor> inputDescriptors = new WSDLParser(wsdlLocation)
+ .getOperationOutputParameters(operationName);
+ for (TypeDescriptor descriptor : inputDescriptors) {
+ descriptors.put(descriptor.getName(), descriptor);
+ }
+ } else if (activity.getType().equals(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE)) {
+ String wrappedType = configuration.getJson().get("wrappedType").textValue();
+ Element element = new SAXBuilder().build(new StringReader(wrappedType)).getRootElement();
+ TypeDescriptor typeDescriptor = XMLSplitterSerialisationHelper.extensionXMLToTypeDescriptor(element);
+ if (typeDescriptor instanceof ComplexTypeDescriptor) {
+ for (TypeDescriptor desc : ((ComplexTypeDescriptor) typeDescriptor)
+ .getElements()) {
+ descriptors.put(desc.getName(), desc);
+ }
+ }
+ else if (typeDescriptor instanceof ArrayTypeDescriptor) {
+ TypeDescriptor desc = ((ArrayTypeDescriptor)typeDescriptor).getElementType();
+ descriptors.put(typeDescriptor.getName(), desc);
+ }
+ }
+ return descriptors;
+ }
+
+ @Override
+ protected boolean isInput() {
+ return false;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLSplitterEdit.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLSplitterEdit.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLSplitterEdit.java
new file mode 100644
index 0000000..484feac
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AddXMLSplitterEdit.java
@@ -0,0 +1,315 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.actions;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBeanBuilder;
+import net.sf.taverna.t2.workbench.edits.CompoundEdit;
+import net.sf.taverna.t2.workbench.edits.Edit;
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workflow.edits.AddChildEdit;
+import net.sf.taverna.t2.workflow.edits.AddDataLinkEdit;
+import net.sf.taverna.t2.workflow.edits.AddProcessorEdit;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.xmlsplitter.XMLSplitterSerialisationHelper;
+
+import org.jdom.Element;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.core.DataLink;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.iterationstrategy.CrossProduct;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+import uk.org.taverna.scufl2.api.profiles.ProcessorBinding;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class AddXMLSplitterEdit implements Edit<Workflow> {
+
+ public static final URI INPUT_SPLITTER_TYPE = URI
+ .create("http://ns.taverna.org.uk/2010/activity/xml-splitter/in");
+ public static final URI OUTPUT_SPLITTER_TYPE = URI
+ .create("http://ns.taverna.org.uk/2010/activity/xml-splitter/out");
+ public static final URI SPLITTER_CONFIG_TYPE = URI
+ .create("http://ns.taverna.org.uk/2010/activity/xml-splitter#Config");
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private final Workflow workflow;
+ private final Profile profile;
+ private final Activity activity;
+ private TypeDescriptor typeDescriptor;
+ private final String portName;
+ private final boolean isInput;
+
+ private CompoundEdit compoundEdit1 = null;
+ private Edit<?> linkUpEdit;
+ private boolean applied = false;
+
+ public AddXMLSplitterEdit(Workflow workflow, Profile profile, Activity activity,
+ TypeDescriptor typeDescriptor, String portName, boolean isInput) {
+ this.workflow = workflow;
+ this.profile = profile;
+ this.activity = activity;
+ this.typeDescriptor = typeDescriptor;
+ this.portName = portName;
+ this.isInput = isInput;
+ }
+
+ @Override
+ public Workflow doEdit() throws EditException {
+ if (applied) {
+ throw new EditException("Edit has already been applied!");
+ }
+
+ Activity splitter = null;
+ Configuration splitterConfiguration = null;
+ String sourcePortName = "";
+ Processor sourceProcessor = null;
+
+ String sinkPortName = "";
+ Processor sinkProcessor = null;
+
+ Processor activityProcessor = null;
+ List<ProcessorBinding> processorBindingsToActivity = scufl2Tools
+ .processorBindingsToActivity(activity);
+ for (ProcessorBinding processorBinding : processorBindingsToActivity) {
+ activityProcessor = processorBinding.getBoundProcessor();
+ break;
+ }
+ if (activityProcessor == null) {
+ throw new EditException("Cannot find the processor that the activity belongs to");
+ }
+
+ String displayName = portName;
+ if (portName.equals("parameters")) {
+ displayName = isInput ? "input" : "output";
+ }
+ String processorName = activityProcessor.getName();
+ String candidateName;
+ if (displayName.startsWith(processorName)) {
+ // No need to make GetRequest_GetRequestResponse
+ candidateName = displayName;
+ } else {
+ // Combine with processor name
+ String displayProcessorName;
+ if (activity.getType().equals(INPUT_SPLITTER_TYPE)
+ || activity.getType().equals(OUTPUT_SPLITTER_TYPE)) {
+ // For splitters on splitters - avoid adding up blah_bluh_blih_more_stuff
+ String[] processorNameSplit = processorName.replace("_input", "")
+ .replace("_output", "").split("_");
+ displayProcessorName = processorNameSplit[processorNameSplit.length - 1];
+ } else {
+ displayProcessorName = activityProcessor.getName();
+ }
+ candidateName = displayProcessorName + "_" + displayName;
+ }
+
+ Processor splitterProcessor = new Processor();
+ splitterProcessor.setName(candidateName);
+
+ CrossProduct crossProduct = new CrossProduct();
+ crossProduct.setParent(splitterProcessor.getIterationStrategyStack());
+
+ ProcessorBinding processorBinding = new ProcessorBinding();
+ processorBinding.setBoundProcessor(splitterProcessor);
+
+ try {
+ if (activity.getType().equals(INPUT_SPLITTER_TYPE)) {
+ if (!isInput) {
+ throw new EditException(
+ "Can only add an input splitter to another input splitter");
+ }
+ if (typeDescriptor instanceof ArrayTypeDescriptor
+ && !((ArrayTypeDescriptor) typeDescriptor).isWrapped()) {
+ typeDescriptor = ((ArrayTypeDescriptor) typeDescriptor).getElementType();
+ }
+
+ Element element = XMLSplitterSerialisationHelper
+ .typeDescriptorToExtensionXML(typeDescriptor);
+// String wrappedType = new XMLOutputter().outputString(element);
+
+ splitter = new Activity();
+ splitter.setType(INPUT_SPLITTER_TYPE);
+ splitterConfiguration = new Configuration();
+ splitterConfiguration.setType(SPLITTER_CONFIG_TYPE);
+ splitterConfiguration.setConfigures(splitter);
+// ((ObjectNode) splitterConfiguration.getJson()).put("wrappedType", wrappedType);
+
+ JsonNode bean = XMLSplitterConfigurationBeanBuilder.buildBeanForInput(element);
+ splitterConfiguration.setJson(bean);
+
+ XMLSplitterPortBuilder.addPortsForInput(element, splitter, splitterProcessor,
+ processorBinding);
+
+ } else if (activity.getType().equals(OUTPUT_SPLITTER_TYPE)) {
+ if (isInput) {
+ throw new EditException(
+ "Can only add an output splitter to another output splitter");
+ }
+ if (typeDescriptor instanceof ArrayTypeDescriptor
+ && !((ArrayTypeDescriptor) typeDescriptor).isWrapped()) {
+ typeDescriptor = ((ArrayTypeDescriptor) typeDescriptor).getElementType();
+ }
+
+ Element element = XMLSplitterSerialisationHelper
+ .typeDescriptorToExtensionXML(typeDescriptor);
+// String wrappedType = new XMLOutputter().outputString(element);
+
+ splitter = new Activity();
+ splitter.setType(OUTPUT_SPLITTER_TYPE);
+ splitterConfiguration = new Configuration();
+ splitterConfiguration.setType(SPLITTER_CONFIG_TYPE);
+ splitterConfiguration.setConfigures(splitter);
+// ((ObjectNode) splitterConfiguration.getJson()).put("wrappedType", wrappedType);
+
+ JsonNode bean = XMLSplitterConfigurationBeanBuilder.buildBeanForOutput(element);
+ splitterConfiguration.setJson(bean);
+
+ XMLSplitterPortBuilder.addPortsForOutput(element, splitter, splitterProcessor,
+ processorBinding);
+
+ } else if (activity.getType().equals(WSDLServiceDescription.ACTIVITY_TYPE)) {
+ if (isInput) {
+ Element element = XMLSplitterSerialisationHelper
+ .typeDescriptorToExtensionXML(typeDescriptor);
+// String wrappedType = new XMLOutputter().outputString(element);
+
+ splitter = new Activity();
+ splitter.setType(WSDLServiceDescription.INPUT_SPLITTER_TYPE);
+ splitterConfiguration = new Configuration();
+ splitterConfiguration.setType(SPLITTER_CONFIG_TYPE);
+ splitterConfiguration.setConfigures(splitter);
+// ((ObjectNode) splitterConfiguration.getJson()).put("wrappedType", wrappedType);
+
+ JsonNode bean = XMLSplitterConfigurationBeanBuilder.buildBeanForInput(element);
+ splitterConfiguration.setJson(bean);
+
+ XMLSplitterPortBuilder.addPortsForInput(element, splitter, splitterProcessor,
+ processorBinding);
+
+ } else {
+ Element element = XMLSplitterSerialisationHelper
+ .typeDescriptorToExtensionXML(typeDescriptor);
+// String wrappedType = new XMLOutputter().outputString(element);
+
+ splitter = new Activity();
+ splitter.setType(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE);
+ splitterConfiguration = new Configuration();
+ splitterConfiguration.setType(SPLITTER_CONFIG_TYPE);
+ splitterConfiguration.setConfigures(splitter);
+// ((ObjectNode) splitterConfiguration.getJson()).put("wrappedType", wrappedType);
+
+ JsonNode bean = XMLSplitterConfigurationBeanBuilder.buildBeanForOutput(element);
+ splitterConfiguration.setJson(bean);
+
+ XMLSplitterPortBuilder.addPortsForOutput(element, splitter, splitterProcessor,
+ processorBinding);
+ }
+ } else {
+ throw new EditException(
+ "The activity type is not suitable for adding xml processing processors");
+ }
+ } catch (Exception e) {
+ throw new EditException(
+ "An error occured whilst tyring to add an XMLSplitter to the activity:"
+ + activity, e);
+ }
+
+ if (isInput) {
+ sourcePortName = "output";
+ sinkPortName = portName;
+ sinkProcessor = activityProcessor;
+ sourceProcessor = splitterProcessor;
+ } else {
+ sourcePortName = portName;
+ sinkPortName = "input";
+ sinkProcessor = splitterProcessor;
+ sourceProcessor = activityProcessor;
+ }
+
+ processorBinding.setBoundActivity(splitter);
+
+ List<Edit<?>> editList = new ArrayList<Edit<?>>();
+ editList.add(new AddChildEdit<Profile>(profile, splitter));
+ editList.add(new AddChildEdit<Profile>(profile, splitterConfiguration));
+ editList.add(new AddChildEdit<Profile>(profile, processorBinding));
+ editList.add(new AddProcessorEdit(workflow, splitterProcessor));
+
+ compoundEdit1 = new CompoundEdit(editList);
+ compoundEdit1.doEdit();
+
+ List<Edit<?>> linkUpEditList = new ArrayList<Edit<?>>();
+
+ OutputProcessorPort source = sourceProcessor.getOutputPorts().getByName(sourcePortName);
+ InputProcessorPort sink = sinkProcessor.getInputPorts().getByName(sinkPortName);
+
+ if (source == null)
+ throw new EditException("Unable to find the source port when linking up "
+ + sourcePortName + " to " + sinkPortName);
+ if (sink == null)
+ throw new EditException("Unable to find the sink port when linking up "
+ + sourcePortName + " to " + sinkPortName);
+
+ DataLink dataLink = new DataLink();
+ dataLink.setReceivesFrom(source);
+ dataLink.setSendsTo(sink);
+ linkUpEditList.add(new AddDataLinkEdit(workflow, dataLink));
+
+ linkUpEdit = new CompoundEdit(linkUpEditList);
+ linkUpEdit.doEdit();
+ applied = true;
+ return workflow;
+ }
+
+ @Override
+ public void undo() {
+ if (!applied) {
+ throw new RuntimeException("Attempt to undo edit that was never applied");
+ }
+ if (linkUpEdit.isApplied())
+ linkUpEdit.undo();
+ if (compoundEdit1.isApplied())
+ compoundEdit1.undo();
+ applied = false;
+ }
+
+ @Override
+ public boolean isApplied() {
+ return applied;
+ }
+
+ @Override
+ public Object getSubject() {
+ return workflow;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/WSDLActivityConfigureAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/WSDLActivityConfigureAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/WSDLActivityConfigureAction.java
new file mode 100644
index 0000000..92a8fb6
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/WSDLActivityConfigureAction.java
@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+import javax.swing.JDialog;
+
+import net.sf.taverna.t2.activities.wsdl.views.WSDLActivityConfigurationView;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class WSDLActivityConfigureAction extends ActivityConfigurationAction {
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final CredentialManager credentialManager;
+
+ public WSDLActivityConfigureAction(Activity activity, Frame owner, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, CredentialManager credentialManager) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.credentialManager = credentialManager;
+ putValue(Action.NAME, "Configure security");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ JDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+ final ActivityConfigurationPanel rshellConfigView = new WSDLActivityConfigurationView(
+ getActivity(), credentialManager);
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
+ rshellConfigView, editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/XMLSplitterPortBuilder.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/XMLSplitterPortBuilder.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/XMLSplitterPortBuilder.java
new file mode 100644
index 0000000..f41f298
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/XMLSplitterPortBuilder.java
@@ -0,0 +1,127 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.actions;
+
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.BaseTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.xmlsplitter.XMLSplitterSerialisationHelper;
+
+import org.jdom.Element;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.NamedSet;
+import uk.org.taverna.scufl2.api.core.Processor;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.InputProcessorPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputProcessorPort;
+import uk.org.taverna.scufl2.api.profiles.ProcessorBinding;
+import uk.org.taverna.scufl2.api.profiles.ProcessorInputPortBinding;
+import uk.org.taverna.scufl2.api.profiles.ProcessorOutputPortBinding;
+
+/**
+ * A helper class to facilitate in building XMLSplitter ports
+ * from the type descriptor XML.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class XMLSplitterPortBuilder {
+
+ public static void addPortsForInput(Element element, Activity activity, Processor processor,
+ ProcessorBinding binding) {
+ TypeDescriptor descriptor = XMLSplitterSerialisationHelper.extensionXMLToTypeDescriptor(element);
+ addOutputPort("output", 0, activity, processor, binding);
+
+ if (descriptor instanceof ComplexTypeDescriptor) {
+ for (TypeDescriptor typeDescriptor : ((ComplexTypeDescriptor) descriptor).getElements()) {
+ addInputPort(typeDescriptor.getName(), depthForDescriptor(typeDescriptor), activity, processor,
+ binding);
+ }
+ NamedSet<InputActivityPort> inputPorts = activity.getInputPorts();
+ for (TypeDescriptor typeDescriptor : ((ComplexTypeDescriptor) descriptor).getAttributes()) {
+ String name = typeDescriptor.getName();
+ if (inputPorts.containsName(name)) {
+ name = "1" + name;
+ }
+ addInputPort(name, depthForDescriptor(typeDescriptor), activity, processor, binding);
+ }
+ } else if (descriptor instanceof ArrayTypeDescriptor) {
+ addInputPort(descriptor.getName(), 1, activity, processor, binding);
+ }
+ }
+
+ public static void addPortsForOutput(Element element, Activity activity, Processor processor,
+ ProcessorBinding binding) {
+ TypeDescriptor descriptor = XMLSplitterSerialisationHelper.extensionXMLToTypeDescriptor(element);
+ addInputPort("input", 0, activity, processor, binding);
+
+ if (descriptor instanceof ComplexTypeDescriptor) {
+ for (TypeDescriptor typeDescriptor : ((ComplexTypeDescriptor) descriptor).getElements()) {
+ addOutputPort(typeDescriptor.getName(), depthForDescriptor(typeDescriptor), activity, processor,
+ binding);
+ }
+ NamedSet<OutputActivityPort> outputPorts = activity.getOutputPorts();
+ for (TypeDescriptor typeDescriptor : ((ComplexTypeDescriptor) descriptor).getAttributes()) {
+ String name = typeDescriptor.getName();
+ if (outputPorts.containsName(name)) {
+ name = "1" + name;
+ }
+ addOutputPort(name, depthForDescriptor(typeDescriptor), activity, processor, binding);
+ }
+ } else if (descriptor instanceof ArrayTypeDescriptor) {
+ addOutputPort(descriptor.getName(), 1, activity, processor, binding);
+ }
+ }
+
+ private static int depthForDescriptor(TypeDescriptor desc) {
+ if (desc instanceof ArrayTypeDescriptor
+ && (!((ArrayTypeDescriptor) desc).isWrapped() || ((ArrayTypeDescriptor) desc)
+ .getElementType() instanceof BaseTypeDescriptor)) {
+ return 1;
+ } else {
+ return 0;
+ }
+ }
+
+ private static void addOutputPort(String name, int depth, Activity activity,
+ Processor processor, ProcessorBinding binding) {
+ OutputActivityPort activityPort = new OutputActivityPort(activity, name);
+ activityPort.setDepth(depth);
+ activityPort.setGranularDepth(depth);
+ OutputProcessorPort processorPort = new OutputProcessorPort(processor, name);
+ processorPort.setDepth(depth);
+ processorPort.setGranularDepth(depth);
+ new ProcessorOutputPortBinding(binding, activityPort, processorPort);
+ }
+
+ private static void addInputPort(String name, int depth, Activity activity,
+ Processor processor, ProcessorBinding binding) {
+ InputActivityPort activityPort = new InputActivityPort(activity, name);
+ activityPort.setDepth(depth);
+ InputProcessorPort processorPort = new InputProcessorPort(processor, name);
+ processorPort.setDepth(depth);
+ new ProcessorInputPortBinding(binding, processorPort, activityPort);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForWSDLActivityMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForWSDLActivityMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForWSDLActivityMenuAction.java
new file mode 100644
index 0000000..a2935e6
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForWSDLActivityMenuAction.java
@@ -0,0 +1,11 @@
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+
+public class AddXMLInputSplitterForWSDLActivityMenuAction extends AddXMLInputSplitterMenuAction {
+
+ public AddXMLInputSplitterForWSDLActivityMenuAction() {
+ super(WSDLServiceDescription.ACTIVITY_TYPE);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForXMLInputSplitterMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForXMLInputSplitterMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForXMLInputSplitterMenuAction.java
new file mode 100644
index 0000000..070c006
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterForXMLInputSplitterMenuAction.java
@@ -0,0 +1,11 @@
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+
+public class AddXMLInputSplitterForXMLInputSplitterMenuAction extends AddXMLInputSplitterMenuAction {
+
+ public AddXMLInputSplitterForXMLInputSplitterMenuAction() {
+ super(WSDLServiceDescription.INPUT_SPLITTER_TYPE);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterMenuAction.java
new file mode 100644
index 0000000..60ef904
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLInputSplitterMenuAction.java
@@ -0,0 +1,70 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.Map;
+
+import javax.swing.Action;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.jdom.JDOMException;
+import org.xml.sax.SAXException;
+
+import net.sf.taverna.t2.activities.wsdl.InputPortTypeDescriptorActivity;
+import net.sf.taverna.t2.activities.wsdl.actions.AbstractAddXMLSplitterAction;
+import net.sf.taverna.t2.activities.wsdl.actions.AddXMLInputSplitterAction;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.MenuComponent;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+/**
+ * @author alanrw
+ */
+public abstract class AddXMLInputSplitterMenuAction extends AbstractConfigureActivityMenuAction
+ implements MenuComponent, ContextualMenuComponent {
+
+ private static final String ADD_XML_INPUT_SPLITTER = "Add XML Input Splitter";
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public AddXMLInputSplitterMenuAction(URI activityType) {
+ super(activityType);
+ }
+
+ @Override
+ protected Action createAction() {
+ AddXMLInputSplitterAction configAction = new AddXMLInputSplitterAction(findActivity(),
+ null, editManager, selectionManager);
+ Map<String, TypeDescriptor> descriptors;
+ try {
+ descriptors = configAction.getTypeDescriptors();
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ return null;
+ }
+ if (!AbstractAddXMLSplitterAction.filterDescriptors(descriptors).isEmpty()) {
+ configAction.putValue(Action.NAME, ADD_XML_INPUT_SPLITTER);
+ addMenuDots(configAction);
+ return configAction;
+ } else {
+ return null;
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForWSDLActivityMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForWSDLActivityMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForWSDLActivityMenuAction.java
new file mode 100644
index 0000000..58b3724
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForWSDLActivityMenuAction.java
@@ -0,0 +1,11 @@
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+
+public class AddXMLOutputSplitterForWSDLActivityMenuAction extends AddXMLOutputSplitterMenuAction {
+
+ public AddXMLOutputSplitterForWSDLActivityMenuAction() {
+ super(WSDLServiceDescription.ACTIVITY_TYPE);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForXMLOutputSplitterMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForXMLOutputSplitterMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForXMLOutputSplitterMenuAction.java
new file mode 100644
index 0000000..129c996
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterForXMLOutputSplitterMenuAction.java
@@ -0,0 +1,11 @@
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+
+public class AddXMLOutputSplitterForXMLOutputSplitterMenuAction extends AddXMLOutputSplitterMenuAction {
+
+ public AddXMLOutputSplitterForXMLOutputSplitterMenuAction() {
+ super(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterMenuAction.java
new file mode 100644
index 0000000..33541e6
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/AddXMLOutputSplitterMenuAction.java
@@ -0,0 +1,66 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.Map;
+
+import javax.swing.Action;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.activities.wsdl.actions.AbstractAddXMLSplitterAction;
+import net.sf.taverna.t2.activities.wsdl.actions.AddXMLOutputSplitterAction;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+import org.jdom.JDOMException;
+import org.xml.sax.SAXException;
+
+/**
+ * @author alanrw
+ */
+public abstract class AddXMLOutputSplitterMenuAction extends AbstractConfigureActivityMenuAction {
+
+ private static final String ADD_XML_OUTPUT_SPLITTER = "Add XML Output Splitter";
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+
+ public AddXMLOutputSplitterMenuAction(URI activityType) {
+ super(activityType);
+ }
+
+ @Override
+ protected Action createAction() {
+ AddXMLOutputSplitterAction configAction = new AddXMLOutputSplitterAction(
+ findActivity(), null, editManager, selectionManager);
+ Map<String, TypeDescriptor> descriptors;
+ try {
+ descriptors = configAction.getTypeDescriptors();
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ return null;
+ }
+ if (!AbstractAddXMLSplitterAction.filterDescriptors(descriptors).isEmpty()) {
+ configAction.putValue(Action.NAME, ADD_XML_OUTPUT_SPLITTER);
+ addMenuDots(configAction);
+ return configAction;
+ } else {
+ return null;
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/ConfigureWSDLMenuAction.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/ConfigureWSDLMenuAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/ConfigureWSDLMenuAction.java
new file mode 100644
index 0000000..87e7d0f
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/menu/ConfigureWSDLMenuAction.java
@@ -0,0 +1,78 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.menu;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.wsdl.actions.WSDLActivityConfigureAction;
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.MenuComponent;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+public class ConfigureWSDLMenuAction extends AbstractConfigureActivityMenuAction implements
+ MenuComponent, ContextualMenuComponent {
+
+ private EditManager editManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private CredentialManager credentialManager;
+ private FileManager fileManager;
+
+ public ConfigureWSDLMenuAction() {
+ super(WSDLServiceDescription.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ WSDLActivityConfigureAction configAction = new WSDLActivityConfigureAction(findActivity(),
+ getParentFrame(), editManager, fileManager, activityIconManager,
+ serviceDescriptionRegistry, credentialManager);
+ addMenuDots(configAction);
+ return configAction;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/AddWSDLServiceDialog.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/AddWSDLServiceDialog.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/AddWSDLServiceDialog.java
new file mode 100644
index 0000000..b2b31ae
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/AddWSDLServiceDialog.java
@@ -0,0 +1,303 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLConnection;
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.workbench.MainWindow;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Dialog that lets user specify a URL of a WSDL service they want
+ * to add to the Service Panel. In the case the WSDL URL is behind
+ * HTTPS or service's endpoints require HTTPS it will ask user to confirm
+ * if they want to trust it.
+ *
+ * @author Alex Nenadic
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class AddWSDLServiceDialog extends HelpEnabledDialog {
+
+ private JTextField wsdlLocationField;
+ private Logger logger = Logger.getLogger(AddWSDLServiceDialog.class);
+
+ public AddWSDLServiceDialog() {
+ super(MainWindow.getMainWindow(), "Add WSDL service", true, null); // create a non-modal dialog
+ initComponents();
+ setLocationRelativeTo(getParent());
+ }
+
+ private void initComponents() {
+ JPanel mainPanel = new JPanel(new GridBagLayout());
+ mainPanel.setBorder(new EmptyBorder(10,10,10,10));
+
+ JLabel wsdlLocatitionLabel = new JLabel("WSDL location",WSDLActivityIcon.getWSDLIcon(), JLabel.LEFT);
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weighty = 0.0;
+
+ gbc.weightx = 0.0;
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 0);
+ mainPanel.add(wsdlLocatitionLabel, gbc);
+
+ wsdlLocationField = new JTextField("http://somehost/service?wsdl");
+ gbc.weightx = 1.0;
+ gbc.gridx = 1;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 5);
+ mainPanel.add(wsdlLocationField, gbc);
+
+ final JButton addServiceButton = new JButton("Add");
+ addServiceButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ addPressed();
+ }
+ });
+
+ // When user presses "Return" key fire the action on the "Add" button
+ addServiceButton.addKeyListener(new java.awt.event.KeyAdapter() {
+ public void keyPressed(java.awt.event.KeyEvent evt) {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER) {
+ addPressed();
+ }
+ }
+ });
+ getRootPane().setDefaultButton(addServiceButton);
+
+ JPanel buttonsPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ buttonsPanel.add(addServiceButton);
+
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(mainPanel, BorderLayout.CENTER);
+ getContentPane().add(buttonsPanel, BorderLayout.SOUTH);
+
+ setSize(getPreferredSize());
+ pack();
+ }
+
+ /**
+ * 'Add service' button pressed or otherwise activated.
+ */
+ private void addPressed()
+ {
+ final String wsdlURLString = wsdlLocationField.getText().trim();
+ new Thread("Adding WSDL " + wsdlURLString) {
+ public void run() {
+ // Only add the service provider for this service if service URL
+ // starts with 'http'
+ // or if it starts with 'https' and user explicitly said they
+ // wanted to trust this service.
+ /*
+ * if (shouldTrust(wsdlURLString)){ addRegistry(wsdlURLString);
+ * }
+ */
+ try {
+ URL url = new URL(wsdlURLString);
+ URLConnection connection = url.openConnection();
+ try {
+ // If the url starts with 'https' - security hook for
+ // https connection's trust manager
+ // will be engaged and user will be asked automatically
+ // if they want
+ // to trust the connection (if it is not already
+ // trusted). If the urls starts with 'http' -
+ // this will not have any effect apart from checking if
+ // we can open a connection.
+ connection.connect(); // if this does not fail - add the
+ // WSDL
+ // service provider for this service to
+ // the registry
+ } finally {
+ try {
+ connection.getInputStream().close();
+ } catch (IOException ex) {
+ }
+ }
+ addRegistry(wsdlURLString);
+ } catch (Exception ex) { // anything failed
+ JOptionPane.showMessageDialog(null,
+ "Could not read the WSDL definition from "
+ + wsdlURLString + ":\n" + ex,
+ "Could not add WSDL service",
+ JOptionPane.ERROR_MESSAGE);
+
+ logger.error(
+ "Failed to add WSDL service provider for service: "
+ + wsdlURLString, ex);
+
+ }
+ };
+ }.start();
+ closeDialog();
+ }
+
+ /**
+ * If WSDL service's URL starts with 'https' - asks user
+ * whether to trust it or not. If it starts with 'http' -
+ * does not ask anything as the service is implicitly trusted (weird but true).
+ */
+ protected abstract void addRegistry(String wsdl);
+
+ /**
+ * Checks if a service is trusted and if not - asks user if they want to trust it.
+ */
+// public boolean shouldTrust(String wsdlURLString){
+// try {
+// URI wsdlURI = new URI(wsdlURLString);
+// URL wsdlURL = wsdlURI.toURL();
+// String protocol = wsdlURL.getProtocol();
+// if (protocol.toLowerCase().startsWith("https")){
+// logger.info("Checking if service " + wsdlURLString + " is already trusted.");
+// // Check if opening an HTTPS connection will cause a SSLHandshakeException.
+// // This is most probably due to the fact that we do not have this service's
+// // certificate in Credential Manager's truststore
+// try {
+// HttpsURLConnection httpsConnection;
+// httpsConnection = (HttpsURLConnection) wsdlURL.openConnection();
+// httpsConnection.connect();
+// logger.info("HTTPS works out of the box for service " + wsdlURLString);
+// return true; // Opening HTTPS connection worked - so we trust this service already
+// }
+// catch (SSLException sslex) { // most probably due to the fact that service is not trusted, i.e. its certificate is not in Credential Manager's Truststore
+// logger.info("Service " + wsdlURLString + " is not trusted out of the box. Trying to fetch its certificate.");
+// logger.info("The SSLException was caused by: " + sslex.getCause());
+// // Handshake most probably failed as we do not already trust this service -
+// // fetch its certificate and ask user if they want to add this service as trusted
+// try {
+//
+// // This controls SSL socket creation for HTTPS connections
+// // per thread so the damage of switching off certificates
+// // verification is limited
+// ThreadLocalSSLSocketFactory.install();
+// // switch certificate checking off for a moment so we can fetch
+// // service's certificate
+// ThreadLocalSSLSocketFactory.startTrustingEverything();
+//
+// HttpsURLConnection httpsConnection;
+// httpsConnection = (HttpsURLConnection) wsdlURL
+// .openConnection();
+// httpsConnection.connect();
+// // Stop being overly trusting
+// ThreadLocalSSLSocketFactory.stopTrustingEverything();
+// Certificate[] certificates = httpsConnection
+// .getServerCertificates();
+// logger.info("Need to ask user if they want to trust service " + wsdlURLString);
+// // Ask user if they want to trust this service
+// ConfirmTrustedCertificateDialog confirmCertTrustDialog = new ConfirmTrustedCertificateDialog(
+// this, "Untrusted HTTPS connection", true,
+// (X509Certificate) certificates[0]);
+// confirmCertTrustDialog.setLocationRelativeTo(null);
+// confirmCertTrustDialog.setVisible(true);
+// boolean shouldTrust = confirmCertTrustDialog
+// .shouldTrust();
+// if (shouldTrust) {
+// try {
+// CredentialManager credManager = CredentialManager
+// .getInstance();
+// credManager
+// .saveTrustedCertificate((X509Certificate) certificates[0]);
+// return true;
+// } catch (CMException cme) {
+// logger
+// .error(
+// "Failed to add WSDL service provider for service: "
+// + wsdlURLString
+// + " . Credential Manager failed to "
+// + "save trusted certificate.",
+// cme);
+// return false;
+// }
+// } else {
+// // Do not even add a WSDL service provider for this
+// // service and tell user the service will not be
+// // added to Service Panel
+// JOptionPane
+// .showMessageDialog(
+// this,
+// "As you refused to trust it, the service will not be added to Service Panel.",
+// "Add WSDL service",
+// JOptionPane.INFORMATION_MESSAGE);
+// return false;
+// }
+// } catch (Exception e1) {
+// logger
+// .error(
+// "Failed to add WSDL service provider for service: "
+// + wsdlURLString
+// + ". 'Trust everyone' HTTPS connection failed.",
+// e1);
+// return false;
+// } finally {// switch it off here as well if some unexpected exception occurred
+// ThreadLocalSSLSocketFactory.stopTrustingEverything();
+// }
+//
+// } catch (Exception e2) {
+// logger.error("Failed to add WSDL service provider for service: "+ wsdlURLString+". Connecting to service failed.", e2);
+// return false;
+// }
+// }
+// else{ // protocol starts with 'http'
+// return true;
+// }
+// } catch (MalformedURLException e3) {
+// logger.error("Failed to add WSDL service provider: URL "+ wsdlURLString+" was malformed.", e3);
+// return false;
+// } catch (URISyntaxException e4) {
+// logger.error("Failed to add WSDL service provider: URI "+ wsdlURLString+" could not be parsed.", e4);
+// return false;
+// }
+// }
+
+ /**
+ * Closes the dialog.
+ */
+ private void closeDialog() {
+ setVisible(false);
+ dispose();
+ }
+}
[13/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/InvocationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/InvocationPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/InvocationPanel.java
new file mode 100644
index 0000000..803328b
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/InvocationPanel.java
@@ -0,0 +1,396 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Comparator;
+
+import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityHealthChecker;
+import net.sf.taverna.t2.activities.externaltool.configuration.ToolInvocationConfiguration;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroup;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupAddedEvent;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupRemovedEvent;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationManagerEvent;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismAddedEvent;
+import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismRemovedEvent;
+import net.sf.taverna.t2.activities.externaltool.manager.ToolInvocationConfigurationPanel;
+import net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl;
+import net.sf.taverna.t2.lang.observer.Observable;
+import net.sf.taverna.t2.lang.observer.Observer;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.workbench.ui.impl.configuration.ui.T2ConfigurationFrame;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author alanrw
+ *
+ */
+public class InvocationPanel extends JPanel implements Observer<InvocationManagerEvent> {
+
+ private static final String LOCATION_DESCRIPTION = ToolInvocationConfigurationPanel.HEADER_TEXT;
+ private final JComboBox mechanismSelection;
+ private final JComboBox groupSelection;
+
+ private DefaultComboBoxModel mechanismSelectionModel = new DefaultComboBoxModel();
+ private DefaultComboBoxModel groupSelectionModel = new DefaultComboBoxModel();
+
+ private static InvocationGroupManagerImpl manager = InvocationGroupManagerImpl.getInstance();
+
+ private static Logger logger = Logger
+ .getLogger(InvocationPanel.class);
+
+ private JRadioButton unmanagedLocation;
+ private JRadioButton groupSelected;
+ private JRadioButton mechanismSelected;
+ private JButton manageInvocation;
+ private ButtonGroup mechanismOrGroup;
+ private ExternalToolActivityConfigurationBean configuration;
+
+ private ActionListener radioChangeListener;
+
+ boolean unmanagedShown = false;
+
+ public InvocationPanel(ExternalToolActivityConfigurationBean configuration) {
+ super();
+ manager.addObserver(this);
+
+ mechanismSelection = new JComboBox();
+ populateMechanismList();
+ mechanismSelection.setModel(mechanismSelectionModel);
+
+ groupSelection = new JComboBox();
+ populateGroupList();
+ groupSelection.setModel(groupSelectionModel);
+ populateInvocationPanel(configuration);
+
+ radioChangeListener = new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (unmanagedShown && unmanagedLocation.isSelected()) {
+ setUnmanagedLocationSelectability(true);
+ setMechanismSelectability(false);
+ setGroupSelectability(false);
+ return;
+ }
+ if (mechanismSelected.isSelected()) {
+ if (unmanagedShown) {
+ setUnmanagedLocationSelectability(false);
+ }
+ setMechanismSelectability(true);
+ setGroupSelectability(false);
+ return;
+ }
+ if (unmanagedShown) {
+ setUnmanagedLocationSelectability(false);
+ }
+ setMechanismSelectability(false);
+ setGroupSelectability(true);
+ return; }
+
+ };
+ if (unmanagedShown) {
+ unmanagedLocation.addActionListener(radioChangeListener);
+ }
+ groupSelected.addActionListener(radioChangeListener);
+ mechanismSelected.addActionListener(radioChangeListener);
+ }
+
+ private void populateMechanismList() {
+ InvocationMechanism currentSelection = (InvocationMechanism) mechanismSelection.getSelectedItem();
+ InvocationMechanism[] mechanisms = InvocationGroupManagerImpl.getInstance()
+ .getMechanisms().toArray(new InvocationMechanism[] {});
+ Arrays.sort(mechanisms, new Comparator<InvocationMechanism>() {
+
+ @Override
+ public int compare(InvocationMechanism arg0, InvocationMechanism arg1) {
+ return arg0.getName().compareTo(
+ arg1.getName());
+ }
+ });
+ mechanismSelectionModel.removeAllElements();
+ for (InvocationMechanism mechanism : mechanisms) {
+ mechanismSelectionModel.addElement(mechanism);
+ logger.info("Added mechanism " + mechanism.hashCode());
+ }
+ if (currentSelection != null) {
+ mechanismSelection.setSelectedItem(currentSelection);
+ }
+
+ }
+
+ private void populateGroupList() {
+ InvocationGroup currentSelection = (InvocationGroup) groupSelection.getSelectedItem();
+ InvocationGroup[] groups = InvocationGroupManagerImpl.getInstance()
+ .getInvocationGroups().toArray(new InvocationGroup[] {});
+ Arrays.sort(groups, new Comparator<InvocationGroup>() {
+
+ @Override
+ public int compare(InvocationGroup arg0, InvocationGroup arg1) {
+ return arg0.getName().compareTo(
+ arg1.getName());
+ }
+ });
+ groupSelectionModel.removeAllElements();
+ for (InvocationGroup group : groups) {
+ groupSelectionModel.addElement(group);
+ logger.info("Added group " + group.hashCode());
+ }
+ if (currentSelection != null) {
+ groupSelection.setSelectedItem(currentSelection);
+ }
+
+ }
+
+
+ private void populateInvocationPanel(ExternalToolActivityConfigurationBean configuration) {
+ this.configuration = configuration;
+ this.removeAll();
+ this.setLayout(new BorderLayout());
+
+ JTextArea descriptionText = new JTextArea(
+ LOCATION_DESCRIPTION);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+ descriptionText.setLineWrap(true);
+ descriptionText.setWrapStyleWord(true);
+ descriptionText.setRows(3);
+ this.add(descriptionText, BorderLayout.NORTH);
+
+ JPanel innerPanel = new JPanel(new BorderLayout());
+
+ mechanismOrGroup = new ButtonGroup();
+
+ JPanel subPanel = new JPanel(new GridLayout(4,1));
+
+ if (isUnmanaged(configuration)) {
+ createUnmanagedLocation(subPanel);
+ unmanagedShown = true;
+ }
+
+ subPanel.add(createMechanismPanel());
+
+ subPanel.add(createGroupPanel());
+
+ subPanel.add(createButtonPanel());
+
+ innerPanel.add(subPanel, BorderLayout.NORTH);
+ innerPanel.add(new JPanel(), BorderLayout.CENTER);
+
+ initializeSelectability();
+ this.add(innerPanel, BorderLayout.CENTER);
+ this.repaint();
+ }
+
+ private boolean isUnmanaged(
+ ExternalToolActivityConfigurationBean configuration2) {
+ return (!ExternalToolActivityHealthChecker.updateLocation(configuration2));
+ }
+
+ private void initializeSelectability() {
+ if (isUnmanaged(configuration)) {
+ unmanagedLocation.setSelected(true);
+ setUnmanagedLocationSelectability(true);
+ setMechanismSelectability(false);
+ setGroupSelectability(false);
+ return;
+ }
+ if (configuration.getInvocationGroup() == null) {
+ mechanismSelected.setSelected(true);
+ if (unmanagedShown) {
+ setUnmanagedLocationSelectability(false);
+ }
+ setMechanismSelectability(true);
+ setGroupSelectability(false);
+ return;
+ }
+ groupSelected.setSelected(true);
+ if (unmanagedShown) {
+ setUnmanagedLocationSelectability(false);
+ }
+ setMechanismSelectability(false);
+ setGroupSelectability(true);
+ return;
+ }
+
+ private void setGroupSelectability(boolean b) {
+ groupSelection.setEnabled(b);
+ }
+
+ private void setMechanismSelectability(boolean b) {
+ mechanismSelection.setEnabled(b);
+ }
+
+ private void setUnmanagedLocationSelectability(boolean b) {
+ // Nothing to do
+ }
+
+ private JPanel createGroupPanel() {
+ JPanel groupPanel = new JPanel(new BorderLayout());
+
+ JPanel groupSelectionPanel = new JPanel(new GridLayout(1, 2));
+ groupSelected = new JRadioButton("Select a symbolic location");
+ mechanismOrGroup.add(groupSelected);
+ groupSelected.setBorder(new EmptyBorder(10, 10, 10, 10));
+ groupSelectionPanel.add(groupSelected);
+
+ groupSelection.setRenderer(new DefaultListCellRenderer() {
+
+ @Override
+ public Component getListCellRendererComponent(JList arg0,
+ Object arg1, int arg2, boolean arg3, boolean arg4) {
+ if (arg1 instanceof InvocationGroup) {
+ return super.getListCellRendererComponent(arg0,
+ ((InvocationGroup) arg1).getName(),
+ arg2, arg3, arg4);
+ }
+ return super.getListCellRendererComponent(arg0, arg1, arg2,
+ arg3, arg4);
+ }
+ });
+
+ groupSelectionPanel.add(groupSelection);
+
+ groupPanel.add(groupSelectionPanel, BorderLayout.CENTER);
+
+ if (configuration.getInvocationGroup() != null) {
+ groupSelection.setSelectedItem(configuration.getInvocationGroup());
+ } else {
+ groupSelection.setSelectedItem(manager.getDefaultGroup());
+ }
+
+ return groupPanel;
+ }
+
+ private JPanel createMechanismPanel() {
+ JPanel mechanismPanel = new JPanel(new BorderLayout());
+ JPanel mechanismSelectionPanel = new JPanel(new GridLayout(1, 3));
+ mechanismSelected = new JRadioButton("Select an explicit location");
+ mechanismOrGroup.add(mechanismSelected);
+ mechanismSelected.setBorder(new EmptyBorder(10, 10, 10, 10));
+ mechanismSelectionPanel.add(mechanismSelected);
+
+ mechanismSelection.setRenderer(new DefaultListCellRenderer() {
+
+ @Override
+ public Component getListCellRendererComponent(JList arg0,
+ Object arg1, int arg2, boolean arg3, boolean arg4) {
+ if (arg1 instanceof InvocationMechanism) {
+ return super.getListCellRendererComponent(arg0,
+ ((InvocationMechanism) arg1).getName(),
+ arg2, arg3, arg4);
+ }
+ return super.getListCellRendererComponent(arg0, arg1, arg2,
+ arg3, arg4);
+ }
+ });
+
+ mechanismSelectionPanel.add(mechanismSelection);
+
+ mechanismPanel.add(mechanismSelectionPanel, BorderLayout.CENTER);
+ if (configuration.getMechanism() != null) {
+ mechanismSelection.setSelectedItem(configuration.getMechanism());
+ } else {
+ mechanismSelection.setSelectedItem(manager.getDefaultMechanism());
+ }
+ return mechanismPanel;
+
+ }
+
+ private JPanel createButtonPanel() {
+ JPanel buttonPanel = new JPanel(new FlowLayout());
+ manageInvocation = new DeselectingButton("Manage locations",
+ new AbstractAction() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ T2ConfigurationFrame.showConfiguration(ToolInvocationConfiguration.getInstance().getDisplayName());
+ }});
+ buttonPanel.add(manageInvocation);
+ return buttonPanel;
+ }
+
+ private void createUnmanagedLocation(JPanel subPanel) {
+ unmanagedLocation = new JRadioButton("Continue using unmanaged location");
+ subPanel.add(unmanagedLocation);
+ mechanismOrGroup.add(unmanagedLocation);
+ }
+
+ private void handleInvocationManagerMessage(InvocationManagerEvent message) {
+ if (message instanceof InvocationMechanismRemovedEvent) {
+ InvocationMechanism removedMechanism = ((InvocationMechanismRemovedEvent) message).getRemovedMechanism();
+ InvocationMechanism replacementMechanism = ((InvocationMechanismRemovedEvent) message).getReplacementMechanism();
+ if (mechanismSelection.getSelectedItem().equals(removedMechanism)) {
+ mechanismSelection.setSelectedItem(replacementMechanism);
+ }
+ mechanismSelectionModel.removeElement(removedMechanism);
+ } else if (message instanceof InvocationMechanismAddedEvent) {
+ populateMechanismList();
+ }
+ else if (message instanceof InvocationGroupRemovedEvent) {
+ InvocationGroup removedGroup = ((InvocationGroupRemovedEvent) message).getRemovedGroup();
+ InvocationGroup replacementGroup = ((InvocationGroupRemovedEvent) message).getReplacementGroup();
+ if (groupSelection.getSelectedItem().equals(removedGroup)) {
+ groupSelection.setSelectedItem(replacementGroup);
+ }
+ groupSelectionModel.removeElement(removedGroup);
+ } else if (message instanceof InvocationGroupAddedEvent) {
+ populateGroupList();
+ }
+ }
+
+ @Override
+ public void notify(Observable<InvocationManagerEvent> sender,
+ final InvocationManagerEvent message) throws Exception {
+ if (SwingUtilities.isEventDispatchThread()) {
+ handleInvocationManagerMessage(message);
+ } else {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ handleInvocationManagerMessage(message);
+ }
+ });
+ } }
+
+ public void fillInConfiguration(
+ ExternalToolActivityConfigurationBean newConfiguration) {
+ if (unmanagedShown && unmanagedLocation.isSelected()) {
+ return;
+ }
+ if (mechanismSelected.isSelected()) {
+ newConfiguration.setMechanism((InvocationMechanism) mechanismSelection.getSelectedItem());
+ return;
+ }
+ newConfiguration.setInvocationGroup((InvocationGroup) groupSelection.getSelectedItem());
+ }
+
+ public void stopObserving() {
+ manager.removeObserver(this);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/LoadDescriptionAction.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/LoadDescriptionAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/LoadDescriptionAction.java
new file mode 100644
index 0000000..7f0d82f
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/LoadDescriptionAction.java
@@ -0,0 +1,89 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.io.StringBufferInputStream;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.lang.ui.FileTools;
+
+import org.jdom.Document;
+import org.jdom.JDOMException;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseEnumeration;
+
+final class LoadDescriptionAction extends AbstractAction {
+ /**
+ *
+ */
+ private final ScriptPanel scriptPanel;
+ private final ExternalToolConfigView view;
+
+ LoadDescriptionAction(ScriptPanel scriptPanel, ExternalToolConfigView view) {
+ this.scriptPanel = scriptPanel;
+ this.view = view;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String descriptionsString = FileTools.readStringFromFile(
+ this.scriptPanel, "Load tool description",
+ ".xml");
+ if (descriptionsString != null) {
+ String errorMessage = null;
+ try {
+ Document doc = ScriptPanel.builder
+ .build(new StringReader(descriptionsString));
+ List<UseCaseDescription> descriptions = UseCaseEnumeration.readDescriptionsFromStream(new StringBufferInputStream(descriptionsString));
+ if (descriptions.isEmpty()) {
+ JOptionPane.showMessageDialog(this.scriptPanel, "No tool descriptions found", "File content", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ if (descriptions.size() == 1) {
+ view.getConfiguration().setUseCaseDescription(descriptions.get(0));
+ view.refreshConfiguration(view.getConfiguration());
+ return;
+ }
+
+ List<String> descriptionNames = new ArrayList();
+ for (UseCaseDescription ud : descriptions) {
+ descriptionNames.add(ud.getUsecaseid());
+ }
+ Collections.sort(descriptionNames);
+ String chosenName = (String) JOptionPane.showInputDialog(this.scriptPanel, "Please select a tool description",
+ "Select tool description", JOptionPane.PLAIN_MESSAGE, null, descriptionNames.toArray(), descriptionNames.get(0));
+ if (chosenName != null) {
+ for (UseCaseDescription ud : descriptions) {
+ if (ud.getUsecaseid().equals(chosenName)) {
+ view.getConfiguration().setUseCaseDescription(ud);
+ view.refreshConfiguration(view.getConfiguration());
+ return;
+
+ }
+ }
+ }
+ } catch (JDOMException e1) {
+ errorMessage = e1.getMessage();
+ } catch (IOException e1) {
+ errorMessage = e1.getMessage();
+ } catch (Exception e1) {
+ errorMessage = e1.getMessage();
+ }
+ if (errorMessage != null) {
+ JOptionPane.showMessageDialog(null, errorMessage,
+ "Tool description load error",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/SaveDescriptionAction.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/SaveDescriptionAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/SaveDescriptionAction.java
new file mode 100644
index 0000000..31266b4
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/SaveDescriptionAction.java
@@ -0,0 +1,124 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.prefs.Preferences;
+
+import javax.swing.AbstractAction;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.lang.ui.ExtensionFileFilter;
+import net.sf.taverna.t2.lang.ui.FileTools;
+
+import org.apache.log4j.Logger;
+import org.jdom.Element;
+import org.jdom.output.Format;
+import org.jdom.output.XMLOutputter;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseEnumeration;
+
+final class SaveDescriptionAction extends AbstractAction {
+ /**
+ *
+ */
+ private final ScriptPanel scriptPanel;
+ private final ExternalToolConfigView view;
+
+ private static Logger logger = Logger.getLogger(SaveDescriptionAction.class);
+
+ private static XMLOutputter outputter = new XMLOutputter(Format
+ .getPrettyFormat());
+
+ SaveDescriptionAction(ScriptPanel scriptPanel, ExternalToolConfigView view) {
+ this.scriptPanel = scriptPanel;
+ this.view = view;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ UseCaseDescription currentDescription = view.makeConfiguration().getUseCaseDescription();
+ String usecaseid = currentDescription.getUsecaseid();
+ String description = currentDescription.getDescription();
+ String group = currentDescription.getGroup();
+ if ((usecaseid == null) || usecaseid.isEmpty() || (description == null) || description.isEmpty() || (group == null) || group.isEmpty()) {
+ JOptionPane.showMessageDialog(view, "Please fill in the tool annotation and\nthen re-export the description", "Missing annotation", JOptionPane.PLAIN_MESSAGE, null);
+ view.showAnnotationPanel();
+ } else {
+ saveStringToFile(this.scriptPanel,
+ "Save tool description", ".xml", currentDescription);
+ }
+ }
+
+ public static boolean saveStringToFile(Component parent, String dialogTitle, String extension, UseCaseDescription description) {
+ JFileChooser fileChooser = new JFileChooser();
+ fileChooser.setDialogTitle(dialogTitle);
+
+ fileChooser.resetChoosableFileFilters();
+ fileChooser.setAcceptAllFileFilterUsed(true);
+
+ fileChooser.setFileFilter(new ExtensionFileFilter(new String[] { extension }));
+
+ Preferences prefs = Preferences.userNodeForPackage(FileTools.class);
+ String curDir = prefs
+ .get("currentDir", System.getProperty("user.home"));
+ fileChooser.setCurrentDirectory(new File(curDir));
+
+ boolean tryAgain = true;
+ while (tryAgain) {
+ tryAgain = false;
+ int returnVal = fileChooser.showSaveDialog(parent);
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ prefs.put("currentDir", fileChooser.getCurrentDirectory()
+ .toString());
+ File file = fileChooser.getSelectedFile();
+ if (!file.getName().contains(".")) {
+ String newName = file.getName() + extension;
+ file = new File(file.getParentFile(), newName);
+ }
+
+ // TODO: Open in separate thread to avoid hanging UI
+ try {
+ List<UseCaseDescription> currentDescriptions;
+ if (file.exists()) {
+ currentDescriptions = UseCaseEnumeration.readDescriptionsFromStream(new FileInputStream(file));
+ } else {
+ currentDescriptions = new ArrayList<UseCaseDescription>();
+ }
+ Element overallElement = new Element("usecases");
+ for (UseCaseDescription ud : currentDescriptions) {
+ if (!ud.getUsecaseid().equals(description.getUsecaseid())) {
+ overallElement.addContent(ud.writeToXMLElement());
+ }
+ }
+
+ overallElement.addContent(description.writeToXMLElement());
+ BufferedWriter out = new BufferedWriter(new FileWriter(file));
+ out.write(outputter.outputString(overallElement));
+ out.close();
+ logger.info("Saved content by overwriting " + file);
+ return true;
+ } catch (IOException ex) {
+ logger.warn("Could not save content to " + file, ex);
+ JOptionPane.showMessageDialog(parent,
+ "Could not save to " + file + ": \n\n"
+ + ex.getMessage(), "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+ }
+ }
+ return false;
+ }
+
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ScriptPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ScriptPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ScriptPanel.java
new file mode 100644
index 0000000..ba15219
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ScriptPanel.java
@@ -0,0 +1,149 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+import javax.swing.text.JTextComponent;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.LineEnabledTextPanel;
+
+import org.jdom.input.SAXBuilder;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseEnumeration;
+
+
+/**
+ * @author alanrw
+ *
+ */
+public class ScriptPanel extends JPanel {
+
+ private static final String SCRIPT_DESCRIPTION = "Specify the commands that you want to run. You can use data arriving at an input port to replace parts of the command or to write to a file. You can also take data written to a file and send it to an output port.";
+ static SAXBuilder builder = new SAXBuilder();
+ private final JTextComponent scriptTextArea;
+
+ public ScriptPanel(final ExternalToolConfigView view, JTextComponent scriptTextArea, JCheckBox stdInCheckBox, JCheckBox stdOutCheckBox, JCheckBox stdErrCheckBox, JTextField returnCodesField) {
+ super();
+ this.setLayout(new BorderLayout());
+
+ JTextArea descriptionText = new JTextArea(
+ SCRIPT_DESCRIPTION);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+ descriptionText.setLineWrap(true);
+ descriptionText.setWrapStyleWord(true);
+ this.add(descriptionText, BorderLayout.NORTH);
+
+ this.scriptTextArea = scriptTextArea;
+
+ this.add(new LineEnabledTextPanel(scriptTextArea),
+ BorderLayout.CENTER);
+
+
+ UseCaseDescription useCaseDescription = view.getConfiguration().getUseCaseDescription();
+ stdInCheckBox.setSelected(useCaseDescription.isIncludeStdIn());
+ stdOutCheckBox.setSelected(useCaseDescription.isIncludeStdOut());
+ stdErrCheckBox.setSelected(useCaseDescription.isIncludeStdErr());
+ returnCodesField.setText(useCaseDescription.getReturnCodesAsText());
+
+ JPanel codesPanel = new JPanel(new FlowLayout());
+ codesPanel.add(new JLabel("Valid return codes:"));
+ codesPanel.add(returnCodesField);
+
+ JPanel streamPanel = new JPanel(new FlowLayout());
+ streamPanel.add(stdInCheckBox);
+ streamPanel.add(stdOutCheckBox);
+ streamPanel.add(stdErrCheckBox);
+
+ JPanel buttonPanel = new JPanel(new FlowLayout());
+ if (view.isOriginallyFromRepository()) {
+ JButton revertButton = new DeselectingButton("Revert to original description",
+ new AbstractAction(){
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ExternalToolActivityConfigurationBean bean = view.makeConfiguration();
+ String repositoryUrl = bean.getRepositoryUrl();
+ String id = bean.getExternaltoolid();
+ UseCaseDescription usecase = null;
+ try {
+ usecase = UseCaseEnumeration.readDescriptionFromUrl(
+ repositoryUrl, id);
+ }
+ catch (IOException ex) {
+ // Already logged
+ }
+ if (usecase != null) {
+ bean.setUseCaseDescription(usecase);
+ view.setEditable(false, bean);
+ } else {
+ JOptionPane.showMessageDialog(view, "Unable to find tool description " + id, "Missing tool description", JOptionPane.ERROR_MESSAGE);
+ }
+ }});
+ revertButton.setToolTipText("Revert to the tool description from the repository");
+ buttonPanel.add(revertButton);
+ }
+ JButton loadScriptButton = new DeselectingButton("Load description",
+ new LoadDescriptionAction(this, view));
+ loadScriptButton.setToolTipText("Load tool description from a file");
+
+ JButton saveScriptButton = new DeselectingButton("Export description",
+ new SaveDescriptionAction(this, view));
+ saveScriptButton.setToolTipText("Export the tool description to a file");
+
+ JButton clearScriptButton = new DeselectingButton("Clear script",
+ new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+ clearScript();
+ }
+
+ });
+ clearScriptButton.setToolTipText("Clear the script from the edit area");
+
+ buttonPanel.add(loadScriptButton);
+ buttonPanel.add(saveScriptButton);
+ buttonPanel.add(clearScriptButton);
+
+ JPanel subPanel = new JPanel(new GridLayout(3,1));
+ subPanel.add(codesPanel);
+ subPanel.add(streamPanel);
+ subPanel.add(buttonPanel);
+
+ this.add(subPanel, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Method for clearing the script
+ *
+ */
+ private void clearScript() {
+ if (JOptionPane.showConfirmDialog(this,
+ "Do you really want to clear the tool description?",
+ "Clearing the tool description", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ scriptTextArea.setText("");
+ }
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticStringPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticStringPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticStringPanel.java
new file mode 100644
index 0000000..885cab5
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticStringPanel.java
@@ -0,0 +1,106 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+
+/**
+ * @author alanrw
+ *
+ */
+public class StaticStringPanel extends JPanel {
+
+ private static final String STATIC_STRING_DESCRIPTION = "A fixed string can be written to the specified file.";
+ private final List<ExternalToolStaticStringViewer> staticStringViewList;
+
+ int staticGridy = 1;
+
+ private static String[] elementLabels = new String[] {"String to copy", "To file"};
+
+ public StaticStringPanel(final List<ExternalToolStaticStringViewer> staticStringViewList) {
+ super(new BorderLayout());
+ this.staticStringViewList = staticStringViewList;
+ final JPanel staticEditPanel = new JPanel(new GridBagLayout());
+
+ final GridBagConstraints staticConstraint = new GridBagConstraints();
+ staticConstraint.insets = new Insets(5, 5, 5, 5);
+ staticConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ staticConstraint.gridx = 0;
+ staticConstraint.gridy = 0;
+ staticConstraint.weightx = 0.1;
+ staticConstraint.fill = GridBagConstraints.BOTH;
+
+ staticConstraint.gridx = 0;
+ synchronized (staticStringViewList) {
+ for (ExternalToolStaticStringViewer staticView : staticStringViewList) {
+ addStaticStringViewer(StaticStringPanel.this, staticEditPanel,
+ staticView);
+ }
+ }
+
+ JTextArea descriptionText = new ReadOnlyTextArea(
+ STATIC_STRING_DESCRIPTION);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+ this.add(descriptionText, BorderLayout.NORTH);
+
+ this.add(new JScrollPane(staticEditPanel),
+ BorderLayout.CENTER);
+ JButton addStaticStringButton = new DeselectingButton("Add string",
+ new AbstractAction() {
+ // FIXME refactor this into a method
+ public void actionPerformed(ActionEvent e) {
+
+ ExternalToolStaticStringViewer newViewer = new ExternalToolStaticStringViewer();
+ synchronized (staticStringViewList) {
+ staticStringViewList.add(newViewer);
+ addStaticStringViewer(StaticStringPanel.this, staticEditPanel,
+ newViewer);
+ staticEditPanel.revalidate();
+ staticEditPanel.repaint();
+ }
+ }
+
+ });
+
+ JPanel buttonPanel = new JPanel(new BorderLayout());
+
+ buttonPanel.add(addStaticStringButton, BorderLayout.EAST);
+
+ this.add(buttonPanel, BorderLayout.SOUTH);
+
+ }
+
+ private void addStaticStringViewer(final JPanel outerPanel,
+ final JPanel panel, ExternalToolStaticStringViewer viewer) {
+ Tools.addViewer(panel,
+ elementLabels,
+ new JComponent[] {new JScrollPane(viewer.getContentField()), viewer.getValueField()},
+ staticStringViewList,
+ viewer,
+ outerPanel);
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticUrlPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticUrlPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticUrlPanel.java
new file mode 100644
index 0000000..ba441f4
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StaticUrlPanel.java
@@ -0,0 +1,108 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea;
+
+/**
+ * @author alanrw
+ *
+ */
+public class StaticUrlPanel extends JPanel {
+
+ private static final String STATIC_URL_DESCRIPTION = "The data at a URL can be downloaded and stored in the specified file.";
+ private final List<ExternalToolStaticUrlViewer> staticUrlViewList;
+ private int staticGridy = 1;
+
+ private static String[] elementLabels = new String[] {"Copy from URL", "To file"};
+
+
+ public StaticUrlPanel(final List<ExternalToolStaticUrlViewer> staticUrlViewList) {
+
+ super(new BorderLayout());
+ this.staticUrlViewList = staticUrlViewList;
+ final JPanel staticEditPanel = new JPanel(new GridBagLayout());
+
+ final GridBagConstraints staticConstraint = new GridBagConstraints();
+ staticConstraint.insets = new Insets(5, 5, 5, 5);
+ staticConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ staticConstraint.gridx = 0;
+ staticConstraint.gridy = 0;
+ staticConstraint.weightx = 0.1;
+ staticConstraint.fill = GridBagConstraints.BOTH;
+
+ staticConstraint.gridx = 0;
+ synchronized (staticUrlViewList) {
+ for (ExternalToolStaticUrlViewer staticView : staticUrlViewList) {
+ addStaticUrlViewer(this, staticEditPanel,
+ staticView);
+ }
+ }
+
+ this.add(new JScrollPane(staticEditPanel),
+ BorderLayout.CENTER);
+
+ JTextArea descriptionText = new ReadOnlyTextArea(
+ STATIC_URL_DESCRIPTION);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+
+ this.add(descriptionText, BorderLayout.NORTH);
+
+ JButton addstaticPortButton = new DeselectingButton("Add URL",
+ new AbstractAction() {
+ // FIXME refactor this into a method
+ public void actionPerformed(ActionEvent e) {
+
+ ExternalToolStaticUrlViewer newViewer = new ExternalToolStaticUrlViewer();
+ synchronized (staticUrlViewList) {
+ staticUrlViewList.add(newViewer);
+ addStaticUrlViewer(StaticUrlPanel.this, staticEditPanel,
+ newViewer);
+ staticEditPanel.revalidate();
+ staticEditPanel.repaint();
+ }
+ }
+
+ });
+ JPanel buttonPanel = new JPanel(new BorderLayout());
+
+ buttonPanel.add(addstaticPortButton, BorderLayout.EAST);
+
+ this.add(buttonPanel, BorderLayout.SOUTH);
+
+ }
+
+ private void addStaticUrlViewer(final JPanel outerPanel,
+ final JPanel panel, ExternalToolStaticUrlViewer viewer) {
+ Tools.addViewer(panel,
+ elementLabels,
+ new JComponent[] {viewer.getContentField(), viewer.getValueField()},
+ staticUrlViewList,
+ viewer,
+ outerPanel);
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StringReplacementPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StringReplacementPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StringReplacementPanel.java
new file mode 100644
index 0000000..1f85d3a
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/StringReplacementPanel.java
@@ -0,0 +1,134 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+
+import net.sf.taverna.t2.activities.externaltool.manager.ssh.ExternalToolSshNodeViewer;
+import net.sf.taverna.t2.activities.externaltool.utils.Tools;
+import net.sf.taverna.t2.lang.ui.DeselectingButton;
+
+/**
+ * @author alanrw
+ *
+ */
+public class StringReplacementPanel extends JPanel {
+
+ private static final String STRING_REPLACEMENT_DESCRIPTION = "You can use a string replacement to " +
+ "feed data into the service via an input port and have that data replace part of the " +
+ "command.";
+ private final List<ExternalToolStringReplacementViewer> stringReplacementViewList;
+ private int stringReplacementGridy = 1;
+ private final ExternalToolConfigView view;
+
+ private static Insets insets = new Insets(1,5,1,5);
+
+ private static String[] elementLabels = new String[] {"Taverna port name", "Replace port name", "String to replace"};
+
+ private static CompoundBorder border = BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(5,5,5,5), BorderFactory.createLineBorder(Color.BLACK, 1));
+
+
+ public StringReplacementPanel(final ExternalToolConfigView view, final List<ExternalToolStringReplacementViewer> stringReplacementViewList) {
+ super(new BorderLayout());
+ this.view = view;
+ this.stringReplacementViewList = stringReplacementViewList;
+
+ final JPanel inputEditPanel = new JPanel(new GridBagLayout());
+
+ final GridBagConstraints inputConstraint = new GridBagConstraints();
+
+ inputConstraint.anchor = GridBagConstraints.FIRST_LINE_START;
+ inputConstraint.gridx = 0;
+ inputConstraint.gridy = 0;
+ inputConstraint.weightx = 0.1;
+ inputConstraint.fill = GridBagConstraints.BOTH;
+
+ inputConstraint.gridx = 0;
+ synchronized (stringReplacementViewList) {
+ for (ExternalToolStringReplacementViewer inputView : stringReplacementViewList) {
+ addStringReplacementViewer(this, inputEditPanel,
+ inputView, elementLabels);
+
+ }
+ }
+
+ JTextArea descriptionText = new JTextArea(
+ STRING_REPLACEMENT_DESCRIPTION);
+ descriptionText.setEditable(false);
+ descriptionText.setFocusable(false);
+ descriptionText.setBorder(new EmptyBorder(5, 5, 10, 5));
+ descriptionText.setLineWrap(true);
+ descriptionText.setWrapStyleWord(true);
+
+ this.add(descriptionText, BorderLayout.NORTH);
+ this.add(new JScrollPane(inputEditPanel),
+ BorderLayout.CENTER);
+ JButton addInputPortButton = new DeselectingButton("Add string replacement",
+ new AbstractAction() {
+
+ public void actionPerformed(ActionEvent e) {
+
+ int portNumber = 1;
+ String name2 = "in" + portNumber++;
+ boolean nameExists = true;
+ while (nameExists == true) {
+ nameExists = view.portNameExists(name2);
+ if (nameExists) {
+ name2 = "in" + portNumber++;
+ }
+ }
+
+ ExternalToolStringReplacementViewer newViewer = new ExternalToolStringReplacementViewer(
+ name2);
+ synchronized (stringReplacementViewList) {
+ stringReplacementViewList.add(newViewer);
+ addStringReplacementViewer(StringReplacementPanel.this, inputEditPanel,
+ newViewer, elementLabels);
+ inputEditPanel.revalidate();
+ inputEditPanel.repaint();
+ }
+
+ }
+
+ });
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new BorderLayout());
+
+ buttonPanel.add(addInputPortButton, BorderLayout.EAST);
+
+ this.add(buttonPanel, BorderLayout.SOUTH);
+ }
+
+ private void addStringReplacementViewer(final JPanel outerPanel,
+ final JPanel innerPanel, final ExternalToolStringReplacementViewer viewer, String[] elementLabels) {
+ Tools.addViewer(innerPanel,
+ elementLabels,
+ new JComponent[] {viewer.getNameField(), viewer.getValueFromField(), viewer.getValueField()},
+ stringReplacementViewList,
+ viewer,
+ outerPanel);
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ToolXMLPanel.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ToolXMLPanel.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ToolXMLPanel.java
new file mode 100644
index 0000000..b49211f
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/views/ToolXMLPanel.java
@@ -0,0 +1,33 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.externaltool.views;
+
+import java.awt.BorderLayout;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+
+import net.sf.taverna.t2.renderers.impl.XMLTree;
+
+import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ToolXMLPanel extends JPanel {
+
+ public ToolXMLPanel(UseCaseDescription useCaseDescription) {
+ super(new BorderLayout());
+ XMLTree xmlTree = new XMLTree(useCaseDescription.writeToXMLElement());
+ this.add(new JScrollPane(xmlTree), BorderLayout.CENTER);
+ }
+
+ public void regenerateTree(UseCaseDescription useCaseDescription) {
+ this.removeAll();
+ XMLTree xmlTree = new XMLTree(useCaseDescription.writeToXMLElement());
+ this.add(new JScrollPane(xmlTree), BorderLayout.CENTER);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor
new file mode 100644
index 0000000..9307977
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor
@@ -0,0 +1,2 @@
+net.sf.taverna.t2.activities.externaltool.manager.local.LocalInvocationMechanismEditor
+net.sf.taverna.t2.activities.externaltool.manager.ssh.SshInvocationMechanismEditor
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..e94cf6e
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1,2 @@
+net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolServiceProvider
+net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolTemplateServiceDescription
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..db316f2
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,4 @@
+net.sf.taverna.t2.activities.externaltool.menu.ConfigureExternalToolMenuAction
+# net.sf.taverna.t2.activities.externaltool.menu.FeedbackMenuAction
+net.sf.taverna.t2.activities.externaltool.menu.AddExternalToolContextualMenuAction
+net.sf.taverna.t2.activities.externaltool.menu.AddExternalToolMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
new file mode 100644
index 0000000..e6686a0
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ShutdownSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManagerShutdownHook
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.StartupSPI
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.StartupSPI b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.StartupSPI
new file mode 100644
index 0000000..0dd97e4
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.StartupSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManagerStartupHook
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..cdafd5d
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolActivityIcon
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
new file mode 100644
index 0000000..b3d1525
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.configuration.ConfigurationUIFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.externaltool.manager.ToolInvocationConfigurationUIFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..ca0d30f
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.externaltool.views.ExternalToolActivityViewFactory
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context-osgi.xml b/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..3d7110c
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context-osgi.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="ToolInvocationConfigurationUIFactory" interface="uk.org.taverna.configuration.ConfigurationUIFactory" />
+
+ <service ref="InvocationGroupManagerStartupHook" interface="net.sf.taverna.t2.workbench.StartupSPI" />
+
+ <service ref="ExternalToolActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="LocalInvocationMechanismEditor" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor" />
+ <service ref="SshInvocationMechanismEditor" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor" />
+
+ <service ref="ExternalToolServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+ <service ref="ExternalToolTemplateServiceDescription" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="ConfigureExternalToolMenuAction" auto-export="interfaces" />
+ <service ref="AddExternalToolContextualMenuAction" auto-export="interfaces" />
+ <service ref="AddExternalToolMenuAction" auto-export="interfaces" />
+
+ <service ref="InvocationGroupManagerShutdownHook" interface="net.sf.taverna.t2.workbench.ShutdownSPI" />
+
+ <service ref="ExternalToolActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <list id="mechanismCreators" interface="net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator" cardinality="0..N" />
+ <list id="invocationMechanismEditors" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanismEditor" cardinality="0..N" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context.xml b/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context.xml
new file mode 100644
index 0000000..7cf7f63
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/resources/META-INF/spring/external-tool-activity-ui-context.xml
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="ToolInvocationConfigurationUIFactory" class="net.sf.taverna.t2.activities.externaltool.manager.ToolInvocationConfigurationUIFactory">
+ <property name="mechanismCreators" ref="mechanismCreators" />
+ <property name="invocationMechanismEditors" ref="invocationMechanismEditors" />
+ </bean>
+
+ <bean id="InvocationGroupManagerStartupHook" class="net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManagerStartupHook" />
+
+ <bean id="ExternalToolActivityIcon" class="net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolActivityIcon">
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+ <bean id="LocalInvocationMechanismEditor" class="net.sf.taverna.t2.activities.externaltool.manager.local.LocalInvocationMechanismEditor" />
+ <bean id="SshInvocationMechanismEditor" class="net.sf.taverna.t2.activities.externaltool.manager.ssh.SshInvocationMechanismEditor" />
+
+ <bean id="ExternalToolServiceProvider" class="net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolServiceProvider" />
+ <bean id="ExternalToolTemplateServiceDescription" class="net.sf.taverna.t2.activities.externaltool.servicedescriptions.ExternalToolTemplateServiceDescription" />
+
+ <bean id="ConfigureExternalToolMenuAction" class="net.sf.taverna.t2.activities.externaltool.menu.ConfigureExternalToolMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ </bean>
+ <bean id="AddExternalToolContextualMenuAction" class="net.sf.taverna.t2.activities.externaltool.menu.AddExternalToolContextualMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ </bean>
+ <bean id="AddExternalToolMenuAction" class="net.sf.taverna.t2.activities.externaltool.menu.AddExternalToolMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ </bean>
+
+ <bean id="InvocationGroupManagerShutdownHook" class="net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManagerShutdownHook" />
+
+ <bean id="ExternalToolActivityViewFactory" class="net.sf.taverna.t2.activities.externaltool.views.ExternalToolActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/resources/externaltool.png
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diff --git a/taverna-external-tool-activity-ui/src/main/resources/externaltool.png b/taverna-external-tool-activity-ui/src/main/resources/externaltool.png
new file mode 100644
index 0000000..a9e84e6
Binary files /dev/null and b/taverna-external-tool-activity-ui/src/main/resources/externaltool.png differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/pom.xml
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diff --git a/taverna-localworker-activity-ui/pom.xml b/taverna-localworker-activity-ui/pom.xml
new file mode 100644
index 0000000..556de86
--- /dev/null
+++ b/taverna-localworker-activity-ui/pom.xml
@@ -0,0 +1,142 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>localworker-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 Localworker Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>beanshell-activity-ui</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.2.2</version>
+ </dependency>
+
+ <!-- category:biojava -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker -->
+ <!-- net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker -->
+ <dependency>
+ <groupId>uk.org.mygrid.resources</groupId>
+ <artifactId>biojava</artifactId>
+ <version>1.4pre1</version>
+ </dependency>
+ <!-- category:xml -->
+ <!-- net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker -->
+ <dependency>
+ <groupId>org.dom4j</groupId>
+ <artifactId>com.springsource.org.dom4j</artifactId>
+ <version>${dom4j.version}</version>
+ </dependency>
+ <!-- <dependency>
+ <groupId>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6</version>
+ </dependency> -->
+ <!-- category:net -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.SendEmail -->
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>com.springsource.javax.mail</artifactId>
+ <version>${mail.version}</version>
+ </dependency>
+ <!-- <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>mail</artifactId>
+ <version>1.4</version>
+ </dependency> -->
+ <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>com.springsource.javax.activation</artifactId>
+ <version>1.1.1</version>
+ </dependency>
+ <!-- <dependency>
+ <groupId>javax.activation</groupId>
+ <artifactId>activation</artifactId>
+ <version>1.1</version>
+ </dependency> -->
+ <!-- category:base64 -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.EncodeBase64 -->
+ <!-- org.embl.ebi.escience.scuflworkers.java.DecodeBase64 -->
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>${commons.codec.version}</version>
+ </dependency>
+ <!-- <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.3</version>
+ </dependency> -->
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
new file mode 100644
index 0000000..2016ad0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.localworker.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityConfigView;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * The {@link LocalworkerActivity}s have pre-defined scripts, ports etc in a serialised form on
+ * disk. So if the user wants to change them they have to do so at own risk.
+ *
+ * @author Ian Dunlop
+ */
+@SuppressWarnings("serial")
+public class LocalworkerActivityConfigurationAction extends ActivityConfigurationAction {
+
+ public static final String EDIT_LOCALWORKER_SCRIPT = "Edit beanshell script";
+
+ private final EditManager editManager;
+
+ private final FileManager fileManager;
+
+ private final ApplicationConfiguration applicationConfiguration;
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ public LocalworkerActivityConfigurationAction(Activity activity, Frame owner,
+ EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.applicationConfiguration = applicationConfiguration;
+ putValue(Action.NAME, EDIT_LOCALWORKER_SCRIPT);
+ }
+
+ /**
+ * If the localworker has not been changed it pops up a {@link JOptionPane} warning the user
+ * that they change things at their own risk. Otherwise just show the config view
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object[] options = { "Continue", "Cancel" };
+ Configuration configuration = scufl2Tools.configurationFor(activity, activity.getParent());
+ JsonNode json = configuration.getJson();
+ if (!json.get("isAltered").booleanValue()) {
+ int n = JOptionPane
+ .showOptionDialog(
+ null,
+ "Changing the properties of a Local Worker may affect its behaviour. Do you want to continue?",
+ "WARNING", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE,
+ null, // do not use a
+ // custom Icon
+ options, options[0]);
+
+ if (n == 0) {
+ // continue was clicked so prepare for config
+ openDialog();
+ } else {
+ // do nothing
+ }
+ } else {
+ openDialog();
+ }
+ }
+
+ private void openDialog() {
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction
+ .getDialog(getActivity());
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+ final LocalworkerActivityConfigView localworkerConfigView = new LocalworkerActivityConfigView(
+ getActivity(), applicationConfiguration);
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
+ localworkerConfigView, editManager);
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
new file mode 100644
index 0000000..3afed8d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
@@ -0,0 +1,62 @@
+package net.sf.taverna.t2.activities.localworker.menu;
+
+import javax.swing.Action;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+
+import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
+import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
+import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
+import net.sf.taverna.t2.ui.menu.MenuComponent;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+public class ConfigureLocalworkerMenuAction extends AbstractConfigureActivityMenuAction implements
+ MenuComponent, ContextualMenuComponent {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ApplicationConfiguration applicationConfiguration;
+
+ public ConfigureLocalworkerMenuAction() {
+ super(LocalworkerServiceDescription.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ Action result = null;
+ result = new LocalworkerActivityConfigurationAction(findActivity(), getParentFrame(),
+ editManager, fileManager, activityIconManager, serviceDescriptionRegistry,
+ applicationConfiguration);
+ result.putValue(Action.NAME, BeanshellActivityConfigurationAction.EDIT_BEANSHELL_SCRIPT);
+ addMenuDots(result);
+ return result;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
new file mode 100644
index 0000000..7d6bb5a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
@@ -0,0 +1,58 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.localworker.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+
+/**
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+public class LocalworkerActivityIcon implements ActivityIconSPI {
+
+ private static Icon icon;
+
+ public int canProvideIconScore(URI activityType) {
+ if (LocalworkerServiceDescription.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getLocalworkerIcon();
+ }
+
+ public static Icon getLocalworkerIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(LocalworkerActivityIcon.class
+ .getResource("/localworker.png"));
+ }
+ return icon;
+ }
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
new file mode 100644
index 0000000..38718b8
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
@@ -0,0 +1,105 @@
+package net.sf.taverna.t2.activities.localworker.servicedescriptions;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class LocalworkerServiceDescription extends ServiceDescription {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/localworker");
+
+ private static final String LOCALWORKER = ServiceDescription.LOCAL_SERVICES;
+
+ private JsonNode json;
+ private String operation;
+ private String category;
+ private String provider;
+ private String localworkerName;
+
+ public JsonNode getJson() {
+ return json;
+ }
+
+ public void setJson(JsonNode json) {
+ this.json = json;
+ }
+
+ public String getOperation() {
+ return operation;
+ }
+
+ public void setOperation(String operation) {
+ this.operation = operation;
+ }
+
+ public String getCategory() {
+ return category;
+ }
+
+ public void setCategory(String category) {
+ this.category = category;
+ }
+
+ public String getProvider() {
+ return provider;
+ }
+
+ public void setProvider(String provider) {
+ this.provider = provider;
+ }
+
+ public String getLocalworkerName() {
+ return localworkerName;
+ }
+
+ public void setLocalworkerName(String localworkerName) {
+ this.localworkerName = localworkerName;
+ }
+
+ public String getType() {
+ return "Localworker";
+ }
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ configuration.setJson(getJson());
+ return configuration;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return LocalworkerActivityIcon.getLocalworkerIcon();
+ }
+
+ @Override
+ public String getName() {
+ return operation;
+ }
+
+ @Override
+ public List<? extends Comparable<?>> getPath() {
+ List<String> result =
+ Arrays.asList (LOCALWORKER, category);
+ return result;
+ }
+
+ @Override
+ protected List<Object> getIdentifyingData() {
+ return Arrays.<Object>asList(getJson());
+ }
+
+}
[02/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanel.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanel.java
new file mode 100644
index 0000000..4342a4a
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanel.java
@@ -0,0 +1,1202 @@
+package net.sf.taverna.t2.activities.xpath.ui.config;
+
+import java.awt.AWTEvent;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Toolkit;
+import java.awt.event.AWTEventListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Area;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.prefs.Preferences;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.JToggleButton;
+import javax.swing.ListSelectionModel;
+import javax.swing.Popup;
+import javax.swing.PopupFactory;
+import javax.swing.SwingUtilities;
+import javax.swing.Timer;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.table.DefaultTableModel;
+
+import net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean;
+import net.sf.taverna.t2.activities.xpath.ui.config.xmltree.TableCellListener;
+import net.sf.taverna.t2.activities.xpath.ui.config.xmltree.XPathActivityXMLTree;
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathActivityIcon;
+import net.sf.taverna.t2.workbench.icons.WorkbenchIcons;
+
+import org.apache.log4j.Logger;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.dom4j.InvalidXPathException;
+import org.dom4j.Node;
+import org.dom4j.XPath;
+import org.dom4j.XPathException;
+
+/**
+ * @author Sergejs Aleksejevs
+ */
+@SuppressWarnings("serial")
+public class XPathActivityConfigurationPanel extends JPanel {
+
+ private Logger logger = Logger.getLogger(XPathActivityConfigurationPanel.class);
+
+ // --- CONSTANTS ---
+ public static final int MAX_NUMBER_OF_MATCHING_NODES_TO_HIGHLIGHT_IN_THE_TREE = 100;
+
+ private static final Color INACTIVE_PANEL_BACKGROUND_COLOR = new Color(215,
+ 215, 215);
+
+ private static final String EXAMPLE_XML_PROMPT = "Paste example XML here...";
+
+ private static final String XPATH_XML_DOCUMENT_DIR_PROPERTY="XPathXMLDocumentDir";
+
+ private XPathActivityConfigurationPanel thisPanel;
+
+ // --- COMPONENTS FOR ACTIVITY CONFIGURATION PANEL ---
+ private JPanel jpActivityConfiguration;
+
+ private JPanel jpLeft;
+ private JPanel jpRight;
+
+ private JToggleButton bShowXMLTreeSettings;
+ private Popup xmlTreeSettingsMenu;
+ private long xmlTreeSettingsMenuLastShownAt;
+ private JButton bGenerateXPathExpression;
+ private JPanel jpXMLTreeSettingsMenuContents;
+ private JCheckBoxMenuItem miIncludeAttributes;
+ private JCheckBoxMenuItem miIncludeValues;
+ private JCheckBoxMenuItem miIncludeNamespaces;
+
+ private JTextArea taSourceXML;
+ private JButton bLoadXMLDocument;
+ private JButton bParseXML;
+ private XPathActivityXMLTree xmlTree;
+ private JScrollPane spXMLTreePlaceholder;
+
+ // --- COMPONENTS FOR XPATH EDITING PANEL ---
+ private JLabel jlXPathExpressionStatus;
+ private JLabel jlXPathExpression;
+ private JTextField tfXPathExpression;
+ private Map<String, String> xpathNamespaceMap;
+ private JButton bRunXPath;
+
+ private JLabel jlShowHideNamespaceMappings;
+ private JTable jtXPathNamespaceMappings;
+ private JButton bAddMapping;
+ private JButton bRemoveMapping;
+ private JPanel jpNamespaceMappingsWithButton;
+
+ // --- COMPONENTS FOR XPATH TESTING PANEL ---
+ private JPanel jpXPathTesting;
+
+ private JTextField tfExecutedXPathExpression;
+ private JTextField tfMatchingElementCount;
+
+ private JTabbedPane tpExecutedXPathExpressionResults;
+ private JTextArea taExecutedXPathExpressionResultsAsText;
+ private JScrollPane spExecutedXPathExpressionResultsAsText;
+ private JTextArea taExecutedXPathExpressionResultsAsXML;
+ private JScrollPane spExecutedXPathExpressionResultsAsXML;
+
+ public XPathActivityConfigurationPanel() {
+ this.thisPanel = this;
+
+ this.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 1.0;
+ c.weighty = 0.50;
+ c.insets = new Insets(0, 10, 10, 10);
+ this.jpActivityConfiguration = createActivityConfigurationPanel();
+ this.add(this.jpActivityConfiguration, c);
+
+ c.gridy++;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weighty = 0;
+ c.insets = new Insets(0, 10, 0, 10);
+ this.add(new JSeparator(), c);
+
+ // XPath expression editing panel
+ c.gridy++;
+ c.fill = GridBagConstraints.BOTH;
+ c.weighty = 0.05;
+ c.insets = new Insets(5, 10, 5, 10);
+ this.add(createXPathExpressionEditingPanel(), c);
+
+ c.gridy++;
+ ;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weighty = 0;
+ c.insets = new Insets(0, 10, 0, 10);
+ this.add(new JSeparator(), c);
+
+ // XPath expression testing panel
+ c.gridy++;
+ c.fill = GridBagConstraints.BOTH;
+ c.weighty = 0.35;
+ c.insets = new Insets(5, 10, 0, 10);
+ this.jpXPathTesting = createXPathExpressionTestingPanel();
+ this.add(this.jpXPathTesting, c);
+ }
+
+ private JPanel createActivityConfigurationPanel() {
+ JPanel jpConfig = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ // text area for example XML document
+ c.gridx = 0;
+ c.gridy = 0;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 0.5;
+ c.weighty = 1.0;
+ c.insets = new Insets(5, 0, 0, 5);
+ taSourceXML = new JTextArea(10, 30);
+ taSourceXML
+ .setToolTipText("<html>Use this text area to paste or load an example XML document.<br>"
+ + "This document can then be parsed by clicking the button<br>"
+ + "with a green arrow in order to see its tree structure.</html>");
+ taSourceXML.setText(EXAMPLE_XML_PROMPT);
+ taSourceXML.addFocusListener(new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ taSourceXML.selectAll();
+ }
+
+ public void focusLost(FocusEvent e) { /* do nothing */
+ }
+ });
+ taSourceXML.addCaretListener(new CaretListener() {
+ public void caretUpdate(CaretEvent e) {
+ // make sure that it is only allowed to "parse example XML"
+ // when something is actually present in the text area
+ bParseXML.setEnabled(taSourceXML.getText().trim().length() > 0
+ && !taSourceXML.getText().trim().equals(
+ EXAMPLE_XML_PROMPT));
+ }
+ });
+ jpLeft = new JPanel(new GridLayout(1, 1));
+ jpLeft.add(new JScrollPane(taSourceXML));
+ jpConfig.add(jpLeft, c);
+
+ // button to parse example XML document
+
+ c.gridx++;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.insets = new Insets(0, 0, 0, 0);
+ bParseXML = new JButton(
+ XPathActivityIcon
+ .getIconById(XPathActivityIcon.XPATH_ACTIVITY_CONFIGURATION_PARSE_XML_ICON));
+ bParseXML
+ .setToolTipText("Parse example XML document and generate its tree structure");
+ bParseXML.setEnabled(false);
+ bParseXML.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ parseXML();
+ }
+ });
+ jpConfig.add(bParseXML, c);
+
+ // placeholder for XML tree (will be replaced by a real tree when the
+ // parsing is done)
+
+ c.gridx++;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 0.5;
+ c.weighty = 1.0;
+ c.insets = new Insets(5, 5, 0, 0);
+ JTextArea taXMLTreePlaceholder = new JTextArea(10, 30);
+ taXMLTreePlaceholder
+ .setToolTipText("<html>This area will show tree structure of the example XML after you<br>"
+ + "paste it into the space on the left-hand side and press 'Parse'<br>"
+ + "button with the green arrow.</html>");
+ taXMLTreePlaceholder.setEditable(false);
+ taXMLTreePlaceholder.setBackground(INACTIVE_PANEL_BACKGROUND_COLOR);
+ spXMLTreePlaceholder = new JScrollPane(taXMLTreePlaceholder);
+ jpRight = new JPanel(new GridLayout(1, 1));
+ jpRight.add(spXMLTreePlaceholder);
+ jpConfig.add(jpRight, c);
+
+ // Button to load XML document from a file
+
+ bLoadXMLDocument = new JButton("Load XML from file", WorkbenchIcons.openIcon);
+ bLoadXMLDocument.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fileChooser = new JFileChooser();
+ Preferences prefs = Preferences.userNodeForPackage(getClass());
+ String curDir = prefs.get(XPATH_XML_DOCUMENT_DIR_PROPERTY, System.getProperty("user.home"));
+ fileChooser.setDialogTitle("Select file to load XML from");
+ fileChooser.setFileFilter(new FileFilter() {
+ public boolean accept(File f) {
+ return f.isDirectory() || f.getName().toLowerCase().endsWith(".xml");
+ }
+
+ public String getDescription() {
+ return ".xml files";
+ }
+ });
+ fileChooser.setCurrentDirectory(new File(curDir));
+ int returnVal = fileChooser.showOpenDialog(((JButton) e
+ .getSource()).getParent());
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ prefs.put(XPATH_XML_DOCUMENT_DIR_PROPERTY, fileChooser
+ .getCurrentDirectory().toString());
+ File file = fileChooser.getSelectedFile();
+ // Read the contents of a file into a string
+ // and set the value of the XML document text area to it
+ FileInputStream fis = null;
+ try{
+ byte[] fileBytes = new byte[(int)file.length()];
+ fis = new FileInputStream(file);
+ fis.read(fileBytes);
+ String xmlDocument = new String(fileBytes, "UTF-8");
+ setSourceXML(xmlDocument);
+ }
+ catch(Exception ex){
+ logger.error("An error occured while trying to read the XML document from file " + file.getAbsolutePath(), ex);
+ JOptionPane.showMessageDialog(
+ ((JButton) e.getSource()).getParent(),
+ "There was an error while trying to read the file",
+ "XPath Activity",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ finally{
+ try {
+ fis.close();
+ } catch (IOException e1) {
+ // Ignore
+ }
+ }
+
+ }
+ }
+ });
+ c.gridx = 0;
+ c.gridy++;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.insets = new Insets(5, 0, 0, 5);
+ c.anchor = GridBagConstraints.EAST;
+ jpConfig.add(bLoadXMLDocument, c);
+
+ // settings for the view of XML tree from example XML document
+
+ miIncludeAttributes = new JCheckBoxMenuItem("Show XML node attributes");
+ miIncludeAttributes.setSelected(true);
+ miIncludeAttributes.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ refreshXMLTreeUI();
+ }
+ });
+
+ miIncludeValues = new JCheckBoxMenuItem(
+ "Show values of XML elements and attributes");
+ miIncludeValues.setSelected(true);
+ miIncludeValues.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ refreshXMLTreeUI();
+ }
+ });
+
+ miIncludeNamespaces = new JCheckBoxMenuItem(
+ "Show namespaces of XML elements");
+ miIncludeNamespaces.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ refreshXMLTreeUI();
+ }
+ });
+
+ jpXMLTreeSettingsMenuContents = new JPanel();
+ jpXMLTreeSettingsMenuContents.setBorder(BorderFactory
+ .createRaisedBevelBorder());
+ jpXMLTreeSettingsMenuContents.setLayout(new BoxLayout(
+ jpXMLTreeSettingsMenuContents, BoxLayout.Y_AXIS));
+ jpXMLTreeSettingsMenuContents.add(miIncludeAttributes);
+ jpXMLTreeSettingsMenuContents.add(miIncludeValues);
+ jpXMLTreeSettingsMenuContents.add(miIncludeNamespaces);
+
+ bShowXMLTreeSettings = new JToggleButton("Show XML tree settings...",
+ XPathActivityIcon.getIconById(XPathActivityIcon.UNFOLD_ICON));
+ bShowXMLTreeSettings.setSelectedIcon(XPathActivityIcon
+ .getIconById(XPathActivityIcon.FOLD_ICON));
+ bShowXMLTreeSettings.setEnabled(false);
+ bShowXMLTreeSettings.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ if (xmlTreeSettingsMenu == null) {
+ xmlTreeSettingsMenuLastShownAt = System.currentTimeMillis();
+
+ Point parentPosition = bShowXMLTreeSettings
+ .getLocationOnScreen();
+ xmlTreeSettingsMenu = PopupFactory.getSharedInstance()
+ .getPopup(
+ bShowXMLTreeSettings,
+ jpXMLTreeSettingsMenuContents,
+ parentPosition.x,
+ parentPosition.y
+ + bShowXMLTreeSettings.getHeight());
+ xmlTreeSettingsMenu.show();
+ } else {
+ bShowXMLTreeSettings.setSelected(false);
+ }
+ }
+ });
+
+ bGenerateXPathExpression = new JButton("Generate XPath expression",
+ XPathActivityIcon
+ .getIconById(XPathActivityIcon.XML_TREE_NODE_ICON));
+ bGenerateXPathExpression.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ updateXPathEditingPanelValues();
+ }
+ });
+
+ JPanel xmlTreeButtonPanel = new JPanel();
+ xmlTreeButtonPanel.add(bGenerateXPathExpression);
+ xmlTreeButtonPanel.add(bShowXMLTreeSettings);
+
+ c.gridx = 2;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.insets = new Insets(5, 0, 0, 0);
+ c.anchor = GridBagConstraints.EAST;
+ jpConfig.add(xmlTreeButtonPanel, c);
+
+ // register a new listener for all AWT mouse events - this will be used
+ // to identify clicks outside of the XML tree popup menu and the toggle
+ // button used to show/hide it
+ Toolkit.getDefaultToolkit().addAWTEventListener(new AWTEventListener() {
+ public void eventDispatched(AWTEvent event) {
+ if (event instanceof MouseEvent && xmlTreeSettingsMenu != null) {
+ MouseEvent e = (MouseEvent) event;
+ if (e.getClickCount() > 0
+ && (e.getWhen() - xmlTreeSettingsMenuLastShownAt) > 100) {
+ // convert a point where mouse click was made from
+ // relative coordinates of the source component
+ // to the coordinates of the panel that represents the
+ // contents of the popup menu
+ Point clickRelativeToOverlay = SwingUtilities
+ .convertPoint((Component) e.getSource(), e
+ .getPoint(),
+ jpXMLTreeSettingsMenuContents);
+
+ Area areaOfPopupPanelAndToggleButton = new Area(
+ jpXMLTreeSettingsMenuContents.getBounds());
+
+ // only hide the popup menu if a click was made outside
+ // of the calculated area --
+ // plus not on one of the associated toggle buttons
+ if (!areaOfPopupPanelAndToggleButton
+ .contains(clickRelativeToOverlay)) {
+ xmlTreeSettingsMenu.hide();
+ bShowXMLTreeSettings.setSelected(false);
+
+ // if the popup menu was dismissed by a click on the
+ // toggle button that
+ // has made it visible, this timer makes sure that
+ // this click doesn't
+ // re-show the popup menu
+ new Timer(100, new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ ((Timer) e.getSource()).stop();
+ xmlTreeSettingsMenu = null;
+ }
+ }).start();
+
+ }
+ }
+ }
+ }
+ }, AWTEvent.MOUSE_EVENT_MASK);
+
+ return (jpConfig);
+ }
+
+ private JPanel createXPathExpressionEditingPanel() {
+ this.jlXPathExpressionStatus = new JLabel();
+
+ this.jlXPathExpression = new JLabel("XPath expression");
+
+ this.bRunXPath = new JButton("Run XPath");
+ this.bRunXPath.setEnabled(false);
+ this.bRunXPath.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ runXPath(true);
+ }
+ });
+
+ this.tfXPathExpression = new JTextField(30);
+ this.tfXPathExpression.setPreferredSize(new Dimension(0, this.bRunXPath
+ .getPreferredSize().height));
+ this.tfXPathExpression.setMinimumSize(new Dimension(0, this.bRunXPath
+ .getPreferredSize().height));
+ this.tfXPathExpression.addCaretListener(new CaretListener() {
+ public void caretUpdate(CaretEvent e) {
+ validateXPathAndUpdateUI();
+ }
+ });
+ this.tfXPathExpression.addKeyListener(new KeyListener() {
+ public void keyPressed(KeyEvent e) {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER) {
+ if (bRunXPath.isEnabled()) {
+ // it is safe to check that ENTER key may execute the
+ // XPath expression if the
+ // "Run XPath" button is enabled, as expression
+ // validation is responsible for
+ // enabling / disabling the button as the expression
+ // changes
+ runXPath(true);
+ }
+ }
+ }
+
+ public void keyReleased(KeyEvent e) { /* not in use */
+ }
+
+ public void keyTyped(KeyEvent e) { /* not in use */
+ }
+ });
+
+ JPanel jpXPath = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weighty = 0;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.weightx = 0;
+ jpXPath.add(jlXPathExpressionStatus);
+
+ c.gridx++;
+ c.weightx = 0.0;
+ c.insets = new Insets(0, 10, 0, 0);
+ jpXPath.add(jlXPathExpression, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(0, 10, 0, 10);
+ jpXPath.add(tfXPathExpression, c);
+
+ c.gridx++;
+ c.weightx = 0;
+ c.insets = new Insets(0, 0, 0, 0);
+ jpXPath.add(bRunXPath, c);
+
+ c.gridx = 2;
+ c.gridy++;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.NONE;
+ c.anchor = GridBagConstraints.WEST;
+ c.insets = new Insets(0, 10, 0, 10);
+ jlShowHideNamespaceMappings = new JLabel("Show namespace mappings...");
+ jlShowHideNamespaceMappings.setForeground(Color.BLUE);
+ jlShowHideNamespaceMappings.setCursor(new Cursor(Cursor.HAND_CURSOR));
+ jlShowHideNamespaceMappings.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ jpNamespaceMappingsWithButton
+ .setVisible(!jpNamespaceMappingsWithButton.isVisible());
+ jlShowHideNamespaceMappings
+ .setText((jpNamespaceMappingsWithButton.isVisible() ? "Hide"
+ : "Show")
+ + " namespace mappings...");
+ thisPanel.validate();
+ }
+ });
+ jpXPath.add(jlShowHideNamespaceMappings, c);
+
+ // namespace mapping table
+ DefaultTableModel tableModel = new DefaultTableModel();
+ tableModel.addColumn("Namespace Prefix");
+ tableModel.addColumn("Namespace URI");
+
+ jtXPathNamespaceMappings = new JTable();
+ jtXPathNamespaceMappings.setModel(tableModel);
+ // ((DefaultCellEditor)jtXPathNamespaceMappings.getDefaultEditor(String.class)).setClickCountToStart(1);
+ // // TODO - enable if one-click-to-start-editing behaviour is required
+ // TODO - next line is to be enabled when Taverna is migrated to Java
+ // 1.6; for now it's fine to run without this
+ // jtXPathNamespaceMappings.setFillsViewportHeight(true); // makes sure
+ // that when the dedicated area is larger than the table, the latter is
+ // stretched vertically to fill the empty space
+ jtXPathNamespaceMappings
+ .setSelectionMode(ListSelectionModel.SINGLE_SELECTION); // only one row can be selected at a time
+ jtXPathNamespaceMappings
+ .setPreferredScrollableViewportSize(new Dimension(200, 50)); // NB! this prevents the table from occupying most of the space in the panel when screen is maximized
+ jtXPathNamespaceMappings.addKeyListener(new KeyAdapter() {
+ public void keyReleased(KeyEvent e) {
+ if (e.getKeyCode() == KeyEvent.VK_DELETE) {
+ removeNamespaceMapping();
+ }
+ }
+ });
+
+ TableCellListener cellListener = new TableCellListener(
+ jtXPathNamespaceMappings, new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+ TableCellListener tcl = (TableCellListener) e
+ .getSource();
+
+ if (tcl.getColumn() == 0) {
+ // prefix was modified
+ String newPrefix = (String) tcl.getNewValue();
+ if (xpathNamespaceMap.containsKey(newPrefix)) {
+ // such prefix already exists - change won't be
+ // saved
+ JOptionPane
+ .showMessageDialog(
+ thisPanel,
+ "Cannot update namespace prefix: "
+ + "updated value already exists",
+ "XPath Activity",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ // update the map with the new prefix for the
+ // same URI value
+ String oldPrefix = (String) tcl.getOldValue();
+ xpathNamespaceMap.put(newPrefix,
+ xpathNamespaceMap.remove(oldPrefix));
+ }
+ } else {
+ // simple case - just the URI value has changed:
+ // just overwrite the value in the namespace map
+ String prefixOfUpdatedURI = (String) jtXPathNamespaceMappings
+ .getModel().getValueAt(tcl.getRow(), 0);
+ xpathNamespaceMap.put(prefixOfUpdatedURI,
+ (String) tcl.getNewValue());
+ }
+
+ // either way - reload from the local map (map could be
+ // not updated if the validation didn't succeed)
+ reloadNamespaceMappingTableFromLocalMap();
+ }
+ });
+
+ jtXPathNamespaceMappings.getColumnModel().getColumn(0)
+ .setPreferredWidth(20); // set relative sizes of columns
+ jtXPathNamespaceMappings.getColumnModel().getColumn(1)
+ .setPreferredWidth(300);
+
+ JScrollPane spXPathNamespaceMappings = new JScrollPane(
+ jtXPathNamespaceMappings);
+ spXPathNamespaceMappings.setAlignmentY(TOP_ALIGNMENT);
+ spXPathNamespaceMappings.setMinimumSize(new Dimension(200, 50)); // makes the table to have at least two rows visible in all cases - no matter how small the parent panel is
+
+ bAddMapping = new JButton("Add Mapping");
+ bAddMapping.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ addNamespaceMapping();
+ }
+ });
+
+ bRemoveMapping = new JButton("Remove Mapping");
+ bRemoveMapping.setEnabled(false);
+ bRemoveMapping.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ removeNamespaceMapping();
+ }
+ });
+
+ bAddMapping.setMinimumSize(bRemoveMapping.getPreferredSize()); // make sure that the 'Add Mapping' button is of the same size as 'Remove Mapping'
+
+ bAddMapping.setPreferredSize(bRemoveMapping.getPreferredSize()); // -- both are required to achieve desired behaviour when window is resized / namespace mapping table is enabled/disabled
+
+ bRunXPath.setMinimumSize(bRemoveMapping.getPreferredSize()); // do the same for 'Run XPath' button
+
+ bRunXPath.setPreferredSize(bRemoveMapping.getPreferredSize());
+
+ JPanel jpAddRemoveButtons = new JPanel();
+ jpAddRemoveButtons.setLayout(new GridBagLayout());
+ GridBagConstraints cAddRemove = new GridBagConstraints();
+ cAddRemove.gridx = 0;
+ cAddRemove.gridy = 0;
+ cAddRemove.weightx = 1.0;
+ cAddRemove.anchor = GridBagConstraints.NORTH;
+ cAddRemove.fill = GridBagConstraints.HORIZONTAL;
+ jpAddRemoveButtons.add(bAddMapping, cAddRemove);
+ cAddRemove.gridy++;
+ cAddRemove.weighty = 1.0;
+ cAddRemove.insets = new Insets(2, 0, 0, 0);
+ jpAddRemoveButtons.add(bRemoveMapping, cAddRemove);
+
+ jpNamespaceMappingsWithButton = new JPanel();
+ jpNamespaceMappingsWithButton.setVisible(false);
+ jpNamespaceMappingsWithButton.setLayout(new BorderLayout(10, 0));
+ jpNamespaceMappingsWithButton.add(spXPathNamespaceMappings,
+ BorderLayout.CENTER);
+ jpNamespaceMappingsWithButton
+ .add(jpAddRemoveButtons, BorderLayout.EAST);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.gridwidth = 4;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 1.0;
+ c.weighty = 1.0;
+ c.insets = new Insets(5, 0, 0, 0);
+ jpXPath.add(jpNamespaceMappingsWithButton, c);
+
+ // initialise some values / tooltips
+ resetXPathEditingPanel();
+
+ return (jpXPath);
+ }
+
+ protected void addNamespaceMapping() {
+ TwoFieldQueryPanel queryPanel = new TwoFieldQueryPanel(
+ "Namespace prefix:", "Namespace URI:");
+ int result = JOptionPane.showConfirmDialog(this, queryPanel,
+ "XPath Activity - Create new namespace mapping",
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (result == JOptionPane.OK_OPTION) {
+ boolean bInvalidMapping = true;
+ do {
+ bInvalidMapping = queryPanel.getFirstValue().length() == 0
+ || queryPanel.getSecondValue().length() == 0
+ || xpathNamespaceMap.containsKey(queryPanel
+ .getFirstValue());
+
+ if (bInvalidMapping) {
+ queryPanel = new TwoFieldQueryPanel(
+ "<html><center><font color=\"red\">ERROR: you must "
+ + "enter values for both namespace prefix and URI. Prefix must be<br>"
+ + "unique in the mapping table - duplicates are not allowed!</font></center></html>",
+ "Namespace prefix:", queryPanel.getFirstValue(),
+ "Namespace URI:", queryPanel.getSecondValue());
+ result = JOptionPane.showConfirmDialog(this, queryPanel,
+ "XPath Activity - Create new namespace mapping",
+ JOptionPane.OK_CANCEL_OPTION);
+ }
+ } while (bInvalidMapping && result == JOptionPane.OK_OPTION);
+
+ if (result == JOptionPane.OK_OPTION && !bInvalidMapping) {
+ // the value appears to be valid and OK was pressed - create new
+ // mapping
+ this.xpathNamespaceMap.put(queryPanel.getFirstValue(),
+ queryPanel.getSecondValue());
+ reloadNamespaceMappingTableFromLocalMap();
+ }
+ }
+ }
+
+ protected void removeNamespaceMapping() {
+ int selectedRow = jtXPathNamespaceMappings.getSelectedRow();
+ if (selectedRow != -1) {
+ // some row is selected - need to delete it and refresh table's UI
+ // (but first stop editing to avoid
+ // problems with cell editor trying to store an edited value after
+ // edited row has been deleted)
+ if (jtXPathNamespaceMappings.getCellEditor() != null) {
+ jtXPathNamespaceMappings.getCellEditor().stopCellEditing();
+ }
+ xpathNamespaceMap.remove(jtXPathNamespaceMappings.getValueAt(
+ selectedRow, 0));
+ reloadNamespaceMappingTableFromLocalMap();
+
+ // select another row in the table
+ int rowCount = jtXPathNamespaceMappings.getRowCount();
+ if (rowCount > 0) {
+ if (selectedRow < jtXPathNamespaceMappings.getRowCount()) {
+ // select the row that followed the one that was deleted
+ jtXPathNamespaceMappings.getSelectionModel()
+ .setSelectionInterval(selectedRow, selectedRow);
+ } else {
+ // last row in the table was deleted - select the one that
+ // is the new last row
+ jtXPathNamespaceMappings.getSelectionModel()
+ .setSelectionInterval(rowCount - 1, rowCount - 1);
+ }
+ }
+ } else {
+ JOptionPane.showMessageDialog(thisPanel,
+ "Please select a mapping to delete in the table first!",
+ "XPath Activity", JOptionPane.WARNING_MESSAGE);
+ }
+ }
+
+ private JPanel createXPathExpressionTestingPanel() {
+ JPanel jpTesting = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.gridwidth = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.insets = new Insets(0, 0, 10, 10);
+ jpTesting.add(new JLabel("Executed XPath expression:"), c);
+
+ c.gridx++;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.insets = new Insets(0, 0, 10, 10);
+ tfExecutedXPathExpression = new JTextField();
+ tfExecutedXPathExpression.setEditable(false);
+ tfExecutedXPathExpression.setBorder(null);
+ jpTesting.add(tfExecutedXPathExpression, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.insets = new Insets(0, 0, 5, 10);
+ jpTesting.add(new JLabel("Number of matching nodes:"), c);
+
+ c.gridx++;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ c.weighty = 0;
+ c.insets = new Insets(0, 0, 5, 10);
+ tfMatchingElementCount = new JTextField();
+ tfMatchingElementCount.setEditable(false);
+ tfMatchingElementCount.setBorder(null);
+ jpTesting.add(tfMatchingElementCount, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.gridwidth = 2;
+ c.fill = GridBagConstraints.BOTH;
+ c.weightx = 1.0;
+ c.weighty = 1.0;
+ tpExecutedXPathExpressionResults = new JTabbedPane();
+ jpTesting.add(tpExecutedXPathExpressionResults, c);
+
+ taExecutedXPathExpressionResultsAsText = new JTextArea();
+ taExecutedXPathExpressionResultsAsText.setEditable(false);
+ spExecutedXPathExpressionResultsAsText = new JScrollPane(
+ taExecutedXPathExpressionResultsAsText);
+ spExecutedXPathExpressionResultsAsText.setPreferredSize(new Dimension(
+ 200, 60));
+ spExecutedXPathExpressionResultsAsText.setBorder(BorderFactory
+ .createLineBorder(INACTIVE_PANEL_BACKGROUND_COLOR, 3));
+ tpExecutedXPathExpressionResults.add("Results as text",
+ spExecutedXPathExpressionResultsAsText);
+
+ taExecutedXPathExpressionResultsAsXML = new JTextArea();
+ taExecutedXPathExpressionResultsAsXML.setEditable(false);
+ spExecutedXPathExpressionResultsAsXML = new JScrollPane(
+ taExecutedXPathExpressionResultsAsXML);
+ spExecutedXPathExpressionResultsAsXML.setPreferredSize(new Dimension(
+ 200, 60));
+ spExecutedXPathExpressionResultsAsXML.setBorder(BorderFactory
+ .createLineBorder(INACTIVE_PANEL_BACKGROUND_COLOR, 3));
+ tpExecutedXPathExpressionResults.add("Results as XML",
+ spExecutedXPathExpressionResultsAsXML);
+
+ // initialise some values / tooltips
+ resetXPathTestingPanel();
+
+ return (jpTesting);
+ }
+
+ protected void parseXML() {
+ String xmlData = taSourceXML.getText();
+
+ try {
+ xmlTree = XPathActivityXMLTree.createFromXMLData(xmlData,
+ miIncludeAttributes.isSelected(), miIncludeValues
+ .isSelected(), miIncludeNamespaces.isSelected(),
+ this);
+ xmlTree
+ .setToolTipText("<html>This is a tree structure of the XML document that you have pasted.<br><br>"
+ + "Clicking on the nodes in this tree will automatically generate a<br>"
+ + "corresponding XPath expression. Multiple <b>identical</b> nodes can<br>"
+ + "be selected at once - in this case <b>wildcards</b> will be used in the<br>"
+ + "generated XPath expression to if selected nodes have different<br>"
+ + "ancestors. Other nodes that match the generated XPath expression<br>"
+ + "will also be selected in the tree.<br><br>"
+ + "Contextual menu provides convenience methods for expanding or<br>"
+ + "collapsing the tree." + "</html>");
+ xmlTree.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+ JScrollPane spXMLTree = new JScrollPane(xmlTree);
+ spXMLTree.setPreferredSize(spXMLTreePlaceholder.getPreferredSize());
+ jpRight.removeAll();
+ jpRight.add(spXMLTree);
+
+ // all successful - enable options to modify the tree
+ this.bShowXMLTreeSettings.setEnabled(true);
+
+ // data structures inside the XML tree were reset (as the tree was
+ // re-created) -
+ // now reset the UI to the initial state as well
+ resetXPathEditingPanel();
+ resetXPathTestingPanel();
+
+ // XML tree has pre-populated the namespace map with the namespaces
+ // specified in the
+ // root element of the tree - load these values
+ updateXPathEditingPanelValues();
+
+ this.validate();
+ this.repaint();
+ } catch (DocumentException e) {
+ JOptionPane.showMessageDialog(this, e.getMessage(),
+ "XPath Activity", JOptionPane.ERROR_MESSAGE);
+ this.taSourceXML.requestFocusInWindow();
+ return;
+ }
+ }
+
+ /**
+ * Makes the {@link XPathActivityXMLTree} to refresh its UI from the
+ * original XML document that was used to create it in first place.
+ *
+ * The reason for using this method is to apply new options to the way the
+ * tree is rendered - e.g. attributes shown/hidden in the tree, values and
+ * namespaces shown/hidden, etc.
+ */
+ protected void refreshXMLTreeUI() {
+ this.xmlTree.refreshFromExistingDocument(this.miIncludeAttributes
+ .isSelected(), this.miIncludeValues.isSelected(),
+ this.miIncludeNamespaces.isSelected());
+ }
+
+ /**
+ * Initialises XPath Editing panel: -- resets XPath expression that is being
+ * shown; -- resets local copy of namespace map; -- resets UI of namespace
+ * mapping table;
+ */
+ private void resetXPathEditingPanel() {
+ tfXPathExpression.setText("");
+ validateXPathAndUpdateUI();
+
+ // clear the local copy of namespace map
+ xpathNamespaceMap = new HashMap<String, String>();
+
+ // clear the namespace mapping table and reload the data from the map
+ DefaultTableModel tableModel = (DefaultTableModel) jtXPathNamespaceMappings
+ .getModel();
+ tableModel.getDataVector().removeAllElements();
+ }
+
+ /**
+ * Initialises XPath testing panel which shows results of executing current
+ * XPath expression against the example XML - the panel is returned to the
+ * way it looks when it is first loaded.
+ */
+ private void resetXPathTestingPanel() {
+ this.tfExecutedXPathExpression.setText("--");
+ this.tfMatchingElementCount.setText("--");
+
+ this.taExecutedXPathExpressionResultsAsText.setText("");
+ this.taExecutedXPathExpressionResultsAsText
+ .setBackground(INACTIVE_PANEL_BACKGROUND_COLOR);
+
+ this.taExecutedXPathExpressionResultsAsXML.setText("");
+ this.taExecutedXPathExpressionResultsAsXML
+ .setBackground(INACTIVE_PANEL_BACKGROUND_COLOR);
+ }
+
+ public void updateXPathEditingPanelValues() {
+ if (xmlTree.getCurrentXPathExpression() != null) {
+ tfXPathExpression.setText(xmlTree.getCurrentXPathExpression()
+ .getText());
+ }
+
+ // clear the local copy of namespace map and update it with all values
+ // from
+ // the map in XML tree instance (which was apparently just re-generated
+ // on user request)
+ xpathNamespaceMap.clear();
+ xpathNamespaceMap.putAll(xmlTree.getCurrentXPathNamespaces());
+
+ // clear the namespace mapping table and reload the data from the map
+ reloadNamespaceMappingTableFromLocalMap();
+ }
+
+ protected void reloadNamespaceMappingTableFromLocalMap() {
+ // clear the namespace mapping table and reload the data from the map
+ DefaultTableModel tableModel = (DefaultTableModel) jtXPathNamespaceMappings
+ .getModel();
+ tableModel.getDataVector().removeAllElements();
+ for (Map.Entry<String, String> mapping : this.xpathNamespaceMap
+ .entrySet()) {
+ tableModel.addRow(new Object[] { mapping.getKey(),
+ mapping.getValue() });
+ }
+
+ bRemoveMapping.setEnabled(this.xpathNamespaceMap.entrySet().size() > 0);
+
+ repaint();
+ }
+
+ private String getXPathValidationErrorMessage() {
+ try {
+ // try to parse the XPath expression...
+ DocumentHelper.createXPath(tfXPathExpression.getText().trim());
+ // ...success
+ return ("");
+ } catch (InvalidXPathException e) {
+ // ...failed to parse the XPath expression: notify of the error
+ return (e.getMessage());
+ }
+ }
+
+ /**
+ * Validates the current XPath expression and updates UI accordingly: --
+ * XPath status icon is updated; -- tooltip for the icon explains the
+ * status; -- 'Run XPath' button is enabled/disabled depending on validity
+ * of XPath expression and existence of example data in the XML tree
+ */
+ protected void validateXPathAndUpdateUI() {
+ String candidatePath = tfXPathExpression.getText();
+ int xpathStatus = XPathActivityConfigurationBean
+ .validateXPath(candidatePath);
+
+ switch (xpathStatus) {
+ case XPathActivityConfigurationBean.XPATH_VALID:
+ // success: expression is correct
+ jlXPathExpressionStatus.setIcon(XPathActivityIcon
+ .getIconById(XPathActivityIcon.XPATH_STATUS_OK_ICON));
+ jlXPathExpressionStatus
+ .setToolTipText("Current XPath expression is well-formed and valid");
+
+ // could allow to execute against example XML, with only condition:
+ // XML tree must be populated
+ // (that is, there should be something to run the expression
+ // against)
+ if (xmlTree != null) {
+ this.bRunXPath.setEnabled(true);
+ this.bRunXPath
+ .setToolTipText("<html>Evaluate current XPath expression against the XML document<br>"
+ + "whose structure is shown in the tree view above.</html>");
+ } else {
+ this.bRunXPath.setEnabled(false);
+ this.bRunXPath
+ .setToolTipText("<html>No XML document to evaluate the current XPath expression against.<br><br>"
+ + "Paste some example XML into the area in the top-left section of the<br>"
+ + "window, then parse it by clicking on the button with the green arrow<br>"
+ + "in order to test your XPath expression.</html>");
+ }
+ break;
+
+ case XPathActivityConfigurationBean.XPATH_EMPTY:
+ // no XPath expression - can't tell if it is correct + nothing to
+ // execute
+ jlXPathExpressionStatus.setIcon(XPathActivityIcon
+ .getIconById(XPathActivityIcon.XPATH_STATUS_UNKNOWN_ICON));
+ jlXPathExpressionStatus
+ .setToolTipText("<html>There is no XPath expression to validate.<br><br>"
+ + "<b>Hint:</b> select something in the tree view showing the structure<br>"
+ + "of the XML document that you have pasted (or type the XPath<br>"
+ + "expression manually).</html>");
+ this.bRunXPath.setEnabled(false);
+ this.bRunXPath.setToolTipText("No XPath expression to execute");
+ break;
+
+ case XPathActivityConfigurationBean.XPATH_INVALID:
+ // failed to parse the XPath expression: notify of the error
+ jlXPathExpressionStatus.setIcon(XPathActivityIcon
+ .getIconById(XPathActivityIcon.XPATH_STATUS_ERROR_ICON));
+ jlXPathExpressionStatus
+ .setToolTipText(getXPathValidationErrorMessage());
+
+ this.bRunXPath.setEnabled(false);
+ this.bRunXPath
+ .setToolTipText("Cannot execute invalid XPath expression");
+ break;
+ }
+
+ }
+
+ /**
+ * Executes the current XPath expression against the current XML tree.
+ *
+ * @param displayResults
+ * <code>true</code> to execute and display results in the XPath
+ * activity configuration panel (this happens when the 'Run
+ * XPath' button is clicked);<br/>
+ * <false> to run the expression quietly and simply return the
+ * number of matching nodes.
+ * @return Number of nodes in the XML tree that match the current XPath
+ * expression. (Or <code>-1</code> if an error has occurred during
+ * the execution -- error messages will only be shown if
+ * <code>displayResults == true</code>).
+ */
+ public int runXPath(boolean displayResults) {
+ // ----- RUNNING THE XPath EXPRESSION -----
+ XPath expr = null;
+ try {
+ expr = DocumentHelper.createXPath(this.tfXPathExpression.getText());
+ expr.setNamespaceURIs(this.xpathNamespaceMap);
+ } catch (InvalidXPathException e) {
+ if (displayResults) {
+ JOptionPane
+ .showMessageDialog(
+ thisPanel,
+ "Incorrect XPath Expression\n\n"
+ + "Please check the expression if you have manually modified it;\n"
+ + "Alternatively, try to select another node from the XML tree.\n\n"
+ + "------------------------------------------------------------------------------------\n\n"
+ + "XPath processing library reported the following error:\n"
+ + e.getMessage(), "XPath Activity",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ return (-1);
+ }
+
+ Document doc = xmlTree.getDocumentUsedToPopulateTree();
+ List<Node> matchingNodes = null;
+ int matchingNodeCount = -1;
+ try {
+ matchingNodes = expr.selectNodes(doc);
+ matchingNodeCount = matchingNodes.size();
+ } catch (XPathException e) {
+ if (displayResults) {
+ JOptionPane
+ .showMessageDialog(
+ thisPanel,
+ "Unexpected error has occurred while executing the XPath expression.\n\n"
+ + "If you have manually modified the XPath expression and/or namespace mappings,\n"
+ + "please check you changes. Alternatively, make your selection in the XML tree and\n"
+ + "a correct XPath expression with corresponding namespace mapping will be generated.\n\n"
+ + "-------------------------------------------------------------------------------------------------------------\n\n"
+ + "XPath processing library reported the following error:\n"
+ + e.getMessage(), "XPath Activity",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ return (-1);
+ }
+
+ // ----- DISPLAYING THE RESULTS -----
+ if (displayResults) {
+ tfExecutedXPathExpression.setText(expr.getText());
+ tfMatchingElementCount.setText("" + matchingNodeCount);
+
+ StringBuffer outNodesText = new StringBuffer();
+ StringBuffer outNodesXML = new StringBuffer();
+ for (Node n : matchingNodes) {
+ if (n.getStringValue() != null
+ && n.getStringValue().length() > 0) {
+ outNodesText.append(n.getStringValue() + "\n");
+ }
+ outNodesXML.append(n.asXML() + "\n");
+ }
+
+ // tpExecutedXPathExpressionResults.setSelectedIndex(0); // open the
+ // first tab (should be the one with textual results) // TODO -
+ // enable if needed
+
+ taExecutedXPathExpressionResultsAsText.setText(outNodesText
+ .toString());
+ taExecutedXPathExpressionResultsAsText.setBackground(Color.WHITE);
+ taExecutedXPathExpressionResultsAsText.setCaretPosition(0);
+ spExecutedXPathExpressionResultsAsText.setBorder(BorderFactory
+ .createLineBorder(Color.WHITE, 3));
+
+ taExecutedXPathExpressionResultsAsXML.setText(outNodesXML
+ .toString());
+ taExecutedXPathExpressionResultsAsXML.setBackground(Color.WHITE);
+ taExecutedXPathExpressionResultsAsXML.setCaretPosition(0);
+ spExecutedXPathExpressionResultsAsXML.setBorder(BorderFactory
+ .createLineBorder(Color.WHITE, 3));
+ }
+
+ return (matchingNodeCount);
+ }
+
+ protected void setSourceXML(String xmlData) {
+ this.taSourceXML.setText(xmlData);
+ }
+
+ protected String getCurrentXPathExpression() {
+ return (this.tfXPathExpression.getText().trim());
+ }
+
+ protected void setCurrentXPathExpression(String xpathExpression) {
+ this.tfXPathExpression.setText(xpathExpression);
+ }
+
+ protected Map<String, String> getCurrentXPathNamespaceMap() {
+ return (this.xpathNamespaceMap);
+ }
+
+ /**
+ * This method doesn't simply set a reference to the passed map, but rather
+ * performs a shallow copy of values.
+ *
+ * This is because the method is used during configuration panel's
+ * initialisation from the values that are held in the configuration bean.
+ * In case of simple reference assignment, any changes made to map in the
+ * configuration panel are also taking effect on the same map - referenced
+ * from the configuration bean, which leads to undesired behaviour.
+ */
+ protected void setCurrentXPathNamespaceMapValues(
+ Map<String, String> xpathNamespaceMap) {
+ this.xpathNamespaceMap.clear();
+ this.xpathNamespaceMap.putAll(xpathNamespaceMap);
+ }
+
+ protected XPathActivityXMLTree getCurrentXMLTree() {
+ return (this.xmlTree);
+ }
+
+ /**
+ * For testing
+ */
+ public static void main(String[] args) {
+ JFrame frame = new JFrame();
+ frame.getContentPane().add(new XPathActivityConfigurationPanel());
+ frame.pack();
+ frame.setSize(new Dimension(900, 600));
+ frame.setLocationRelativeTo(null);
+ frame.setVisible(true);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanelProvider.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanelProvider.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanelProvider.java
new file mode 100644
index 0000000..5954986
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigurationPanelProvider.java
@@ -0,0 +1,158 @@
+package net.sf.taverna.t2.activities.xpath.ui.config;
+
+import java.awt.BorderLayout;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.swing.BorderFactory;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class XPathActivityConfigurationPanelProvider extends ActivityConfigurationPanel {
+
+ private XPathActivityConfigurationPanel configPanel;
+ private final ServiceRegistry serviceRegistry;
+
+ public XPathActivityConfigurationPanelProvider(Activity activity, ServiceRegistry serviceRegistry) {
+ super(activity);
+ this.serviceRegistry = serviceRegistry;
+ initialise();
+ }
+
+ @Override
+ protected void initialise() {
+ super.initialise();
+ removeAll();
+ setLayout(new BorderLayout());
+
+ // create actual contents of the config panel
+ this.configPanel = new XPathActivityConfigurationPanel();
+ add(configPanel, BorderLayout.CENTER);
+
+ // place the whole configuration panel into a raised area, so that
+ // automatically added 'Apply' / 'Close' buttons visually apply to
+ // the whole of the panel, not just part of it
+ this.setBorder(BorderFactory.createCompoundBorder(
+ BorderFactory.createEmptyBorder(12, 12, 2, 12),
+ BorderFactory.createRaisedBevelBorder()));
+
+ // Populate fields from activity configuration bean
+ refreshConfiguration();
+ }
+
+ /**
+ * Prepare a new configuration bean from the UI, to be returned with
+ * getConfiguration()
+ */
+ @Override
+ public void noteConfiguration() {
+ if (configPanel.getCurrentXMLTree() != null) {
+ setProperty("exampleXmlDocument", configPanel.getCurrentXMLTree()
+ .getDocumentUsedToPopulateTree().asXML());
+ }
+ setProperty("xpathExpression", configPanel.getCurrentXPathExpression());
+
+ Map<String, String> xPathNamespaceMap = configPanel.getCurrentXPathNamespaceMap();
+ if (xPathNamespaceMap.isEmpty()) {
+ json.remove("xpathNamespaceMap");
+ } else {
+ ArrayNode namespaceMapNode = json.arrayNode();
+ for (Entry<String, String> namespaceMapping : xPathNamespaceMap.entrySet()) {
+ namespaceMapNode.addObject().put("prefix", namespaceMapping.getKey()).put("uri", namespaceMapping.getValue());
+ }
+ json.set("xpathNamespaceMap", namespaceMapNode);
+ }
+
+ configureInputPorts(serviceRegistry);
+ configureOutputPorts(serviceRegistry);
+}
+
+ /**
+ * Check that user values in the UI are valid.
+ */
+ @Override
+ public boolean checkValues() {
+ // the only validity condition is the correctness of the XPath
+ // expression -- so checking that
+ int xpathExpressionStatus = XPathActivityConfigurationBean.validateXPath(this.configPanel
+ .getCurrentXPathExpression());
+
+ // show an explicit warning message to explain the problem
+ if (xpathExpressionStatus == XPathActivityConfigurationBean.XPATH_EMPTY) {
+ JOptionPane.showMessageDialog(this, "XPath expression should not be empty",
+ "XPath Activity", JOptionPane.WARNING_MESSAGE);
+ } else if (xpathExpressionStatus == XPathActivityConfigurationBean.XPATH_INVALID) {
+ JOptionPane.showMessageDialog(this,
+ "<html><center>XPath expression is invalid - hover the mouse over the XPath status<br>"
+ + "icon to get more information</center></html>", "XPath Activity",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ return (xpathExpressionStatus == XPathActivityConfigurationBean.XPATH_VALID);
+ }
+
+ /**
+ * Update GUI from a changed configuration bean (perhaps by undo / redo).
+ */
+ @Override
+ public void refreshConfiguration() {
+ if (json.has("exampleXmlDocument")) {
+ configPanel.setSourceXML(getProperty("exampleXmlDocument"));
+ configPanel.parseXML();
+ }
+
+ configPanel.setCurrentXPathExpression(getProperty("xpathExpression"));
+
+ Map<String, String> xpathNamespaceMap = new HashMap<>();
+ if (json.has("xpathNamespaceMap")) {
+ for (JsonNode namespaceMapping : json.get("xpathNamespaceMap")) {
+ xpathNamespaceMap.put(namespaceMapping.get("prefix").asText(), namespaceMapping.get("uri").asText());
+ }
+ }
+ configPanel.setCurrentXPathNamespaceMapValues(xpathNamespaceMap);
+ configPanel.reloadNamespaceMappingTableFromLocalMap();
+
+ // if the XML tree was populated, (re-)run the XPath expression
+ // and restore selection of nodes in the tree, if possible
+ if (configPanel.getCurrentXMLTree() != null) {
+ configPanel.runXPath(true);
+
+ // convert the XPath expression into the required list form;
+ // discard the first 'leg', as it's a side effect of
+ // "String.split()" -
+ // non-existent string to the left of the first "/"
+ String[] xpathLegs = getProperty("xpathExpression").split("/");
+ List<String> xpathLegList = new ArrayList<String>();
+ for (int i = 1; i < xpathLegs.length; i++) {
+ xpathLegList.add("/" + xpathLegs[i]);
+ }
+
+ // if nothing was obtained, we should be looking at the root node -
+ // but add the actual expression as it was, just in case
+ if (xpathLegList.size() == 0) {
+ xpathLegList.add(configPanel.getCurrentXPathExpression());
+ }
+
+ // invoke selection handler of the XML tree to do the job
+ configPanel.getCurrentXMLTree().getXMLTreeSelectionHandler()
+ .selectAllNodesThatMatchTheCurrentXPath(xpathLegList, null);
+ }
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigureAction.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigureAction.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigureAction.java
new file mode 100644
index 0000000..4e68948
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/XPathActivityConfigureAction.java
@@ -0,0 +1,52 @@
+package net.sf.taverna.t2.activities.xpath.ui.config;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+/**
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class XPathActivityConfigureAction extends ActivityConfigurationAction {
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ServiceRegistry serviceRegistry;
+
+ public XPathActivityConfigureAction(Activity activity, Frame owner,
+ EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.serviceRegistry = serviceRegistry;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
+
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+
+ XPathActivityConfigurationPanelProvider panel = new XPathActivityConfigurationPanelProvider(
+ getActivity(), serviceRegistry);
+ ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
+ getActivity(), panel, editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/TableCellListener.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/TableCellListener.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/TableCellListener.java
new file mode 100644
index 0000000..872fd70
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/TableCellListener.java
@@ -0,0 +1,186 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import java.awt.event.*;
+import javax.swing.*;
+import java.beans.*;
+
+/**
+ * This class listens for changes made to the data in the table via the
+ * TableCellEditor. When editing is started, the value of the cell is saved
+ * When editing is stopped the new value is saved. When the oold and new
+ * values are different, then the provided Action is invoked.
+ *
+ * The source of the Action is a TableCellListener instance.
+ *
+ * TODO: update to work with Java 1.6, when Taverna is migrated to that version
+ * (see the next TODO tag - this is where the change needs to be made)
+ *
+ * @author Robert Camick
+ *
+ * @see <a href="http://tips4java.wordpress.com/2009/06/07/table-cell-listener/">http://tips4java.wordpress.com/2009/06/07/table-cell-listener/</a>
+ * @see <a href="http://www.camick.com/java/source/TableCellListener.java">http://www.camick.com/java/source/TableCellListener.java</a>
+ */
+public class TableCellListener implements PropertyChangeListener, Runnable
+{
+ private JTable table;
+ private Action action;
+
+ private int row;
+ private int column;
+ private Object oldValue;
+ private Object newValue;
+
+ /**
+ * Create a TableCellListener.
+ *
+ * @param table the table to be monitored for data changes
+ * @param action the Action to invoke when cell data is changed
+ */
+ public TableCellListener(JTable table, Action action)
+ {
+ this.table = table;
+ this.action = action;
+ this.table.addPropertyChangeListener( this );
+ }
+
+ /**
+ * Create a TableCellListener with a copy of all the data relevant to
+ * the change of data for a given cell.
+ *
+ * @param row the row of the changed cell
+ * @param column the column of the changed cell
+ * @param oldValue the old data of the changed cell
+ * @param newValue the new data of the changed cell
+ */
+ private TableCellListener(JTable table, int row, int column, Object oldValue, Object newValue)
+ {
+ this.table = table;
+ this.row = row;
+ this.column = column;
+ this.oldValue = oldValue;
+ this.newValue = newValue;
+ }
+
+ /**
+ * Get the column that was last edited - value as in table model, not in the UI
+ *
+ * @return the column that was edited
+ */
+ public int getColumn()
+ {
+ return column;
+ }
+
+ /**
+ * Get the new value in the cell
+ *
+ * @return the new value in the cell
+ */
+ public Object getNewValue()
+ {
+ return newValue;
+ }
+
+ /**
+ * Get the old value of the cell
+ *
+ * @return the old value of the cell
+ */
+ public Object getOldValue()
+ {
+ return oldValue;
+ }
+
+ /**
+ * Get the row that was last edited - value as in table model, not in the UI
+ *
+ * @return the row that was edited
+ */
+ public int getRow()
+ {
+ return row;
+ }
+
+ /**
+ * Get the table of the cell that was changed
+ *
+ * @return the table of the cell that was changed
+ */
+ public JTable getTable()
+ {
+ return table;
+ }
+
+ //
+ // Implement the PropertyChangeListener interface
+ //
+ public void propertyChange(PropertyChangeEvent e)
+ {
+ // A cell has started/stopped editing
+
+ if ("tableCellEditor".equals(e.getPropertyName()))
+ {
+ if (table.isEditing())
+ processEditingStarted();
+ else
+ processEditingStopped();
+ }
+ }
+
+ /*
+ * Save information of the cell about to be edited
+ */
+ private void processEditingStarted()
+ {
+ // The invokeLater is necessary because the editing row and editing
+ // column of the table have not been set when the "tableCellEditor"
+ // PropertyChangeEvent is fired.
+ // This results in the "run" method being invoked
+
+ SwingUtilities.invokeLater( this );
+ }
+
+ /*
+ * See above.
+ */
+ public void run()
+ {
+// TODO - the next line is a correct implementation for Java 1.6
+// row = table.convertRowIndexToModel( table.getEditingRow() );
+
+// in Java 1.5 which is currently used, tables are not easily sortable
+// (and that is the case for the XPath Activity, where this class is used) --
+// hence, row numbers in the view and in the model will always be identical
+// --> HACK: just use the row number from the view...
+ row = table.getEditingRow();
+
+ column = table.convertColumnIndexToModel( table.getEditingColumn() );
+ oldValue = table.getModel().getValueAt(row, column);
+ newValue = null;
+ }
+
+ /*
+ * Update the Cell history when necessary
+ */
+ private void processEditingStopped()
+ {
+ newValue = table.getModel().getValueAt(row, column);
+
+ // The data has changed, invoke the supplied Action
+
+ if (! newValue.equals(oldValue))
+ {
+ // Make a copy of the data in case another cell starts editing
+ // while processing this change
+
+ TableCellListener tcl = new TableCellListener(
+ getTable(), getRow(), getColumn(), getOldValue(), getNewValue());
+
+ ActionEvent event = new ActionEvent(
+ tcl,
+ ActionEvent.ACTION_PERFORMED,
+ "");
+ action.actionPerformed(event);
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTree.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTree.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTree.java
new file mode 100644
index 0000000..4f98851
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTree.java
@@ -0,0 +1,572 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JTree;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.text.Position;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeCellRenderer;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreePath;
+
+import net.sf.taverna.t2.activities.xpath.ui.config.XPathActivityConfigurationPanel;
+import net.sf.taverna.t2.activities.xpath.ui.servicedescription.XPathActivityIcon;
+
+import org.dom4j.Attribute;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Element;
+import org.dom4j.Namespace;
+import org.dom4j.QName;
+import org.dom4j.XPath;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityXMLTree extends JTree
+{
+ private XPathActivityXMLTree instanceOfSelf;
+ private XPathActivityXMLTreeRenderer treeRenderer;
+
+ private JPopupMenu contextualMenu;
+
+ private TreeSelectionListener[] allSelectionListeners;
+ private XPathActivityXMLTreeSelectionHandler xmlTreeSelectionHandler;
+
+ /**
+ *
+ */
+ private XPathActivityConfigurationPanel parentConfigPanel;
+
+ private Document documentUsedToPopulateTree;
+
+ /**
+ * holds value of the current XPath expression obtained from
+ * the combination of nodes selected in the XML tree
+ */
+ private XPath currentXPathExpression;
+
+ private Map<String,String> currentXPathNamespaces;
+
+
+
+ private XPathActivityXMLTree(XPathActivityXMLTreeNode root, Document documentUsedToPopulateTree,
+ boolean bIncludeElementValues, boolean bIncludeElementNamespaces, XPathActivityConfigurationPanel parentConfigPanel)
+ {
+ super(root);
+
+ this.instanceOfSelf = this;
+ this.allSelectionListeners = new TreeSelectionListener[0];
+
+ this.parentConfigPanel = parentConfigPanel;
+
+ this.documentUsedToPopulateTree = documentUsedToPopulateTree;
+ this.currentXPathExpression = null;
+ this.currentXPathNamespaces = new HashMap<String,String>();
+ this.prepopulateNamespaceMap();
+
+
+ // custom renderer of the nodes in the XML tree
+ this.treeRenderer = new XPathActivityXMLTreeRenderer(bIncludeElementValues, bIncludeElementNamespaces);
+ this.setCellRenderer(treeRenderer);
+
+
+ // add listener to handle various selections of nodes in the tree
+ this.xmlTreeSelectionHandler = new XPathActivityXMLTreeSelectionHandler(parentConfigPanel, this);
+ this.addTreeSelectionListener(xmlTreeSelectionHandler);
+
+
+ // --- CONTEXTUAL MENU FOR EXPANDING / COLLAPSING THE TREE ---
+
+ // create popup menu for expanding / collapsing all nodes in the tree
+ JMenuItem miExpandAll = new JMenuItem("Expand all", XPathActivityIcon.getIconById(XPathActivityIcon.XML_TREE_EXPAND_ALL_ICON));
+ miExpandAll.setToolTipText("Expand all nodes in the filtering tree");
+ miExpandAll.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ for (int i = 0; i < getRowCount(); i++) {
+ instanceOfSelf.expandRow(i);
+ }
+ }
+ });
+ JMenuItem miCollapseAll = new JMenuItem("Collapse all", XPathActivityIcon.getIconById(XPathActivityIcon.XML_TREE_COLLAPSE_ALL_ICON));
+ miCollapseAll.setToolTipText("Collapse all expanded nodes in the filtering tree");
+ miCollapseAll.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ for (int i = getRowCount() - 1; i >= 0; i--) {
+ instanceOfSelf.collapseRow(i);
+ }
+ }
+ });
+
+ // populate the popup menu with created menu items
+ contextualMenu = new JPopupMenu();
+ contextualMenu.add(miExpandAll);
+ contextualMenu.add(miCollapseAll);
+
+ // mouse events may cause the contextual menu to be shown - adding a listener
+ this.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e) {
+ if (e.isPopupTrigger()) {
+ contextualMenu.show(instanceOfSelf, e.getX(), e.getY());
+ }
+ }
+ public void mouseReleased(MouseEvent e) {
+ if (e.isPopupTrigger()) {
+ // another way a popup menu may be called on different systems
+ contextualMenu.show(instanceOfSelf, e.getX(), e.getY());
+ }
+ }
+ });
+
+ }
+
+
+ /**
+ * Pre-populates namespace map with the namespaced declared in the root
+ * node of the XML document, which was used to populate the tree.
+ */
+ private void prepopulateNamespaceMap()
+ {
+ Document doc = this.getDocumentUsedToPopulateTree();
+ Element root = doc.getRootElement();
+
+ // get opening tag of the root node
+ String rootAsXML = root.asXML().substring(0, root.asXML().indexOf(">"));
+
+ // split the opening tag into tokens (all attributes are separated by a space)
+ String[] rootTokens = rootAsXML.split(" ");
+
+ // for each attribute check if that's a namespace declaration
+ for (String token : rootTokens) {
+ if (token.startsWith("xmlns"))
+ {
+ String[] namespacePrefixAndURI = token.split("=");
+
+ // a prefix is either given explicitly, or an empty one will be used
+ String prefix = namespacePrefixAndURI[0].indexOf(":") == -1 ?
+ "" :
+ namespacePrefixAndURI[0].split(":")[1];
+
+ // URI is the value of the XML attribute, so need to strip out surrounding quotes
+ String URI = namespacePrefixAndURI[1].replaceAll("\"", "");
+
+ // now add the details of the current namespace to the map
+ this.addNamespaceToXPathMap(new Namespace(prefix, URI));
+ }
+ }
+ }
+
+
+ protected XPathActivityConfigurationPanel getParentConfigPanel() {
+ return parentConfigPanel;
+ }
+
+ public XPathActivityXMLTreeSelectionHandler getXMLTreeSelectionHandler() {
+ return xmlTreeSelectionHandler;
+ }
+
+ public Document getDocumentUsedToPopulateTree() {
+ return documentUsedToPopulateTree;
+ }
+
+ public XPath getCurrentXPathExpression() {
+ return currentXPathExpression;
+ }
+ protected void setCurrentXPathExpression(XPath xpathExpression) {
+ this.currentXPathExpression = xpathExpression;
+ }
+
+
+ public Map<String,String> getCurrentXPathNamespaces() {
+ return currentXPathNamespaces;
+ }
+
+
+
+ protected void removeAllSelectionListeners()
+ {
+ this.allSelectionListeners = this.getTreeSelectionListeners();
+ for (TreeSelectionListener listener : this.allSelectionListeners) {
+ this.removeTreeSelectionListener(listener);
+ }
+ }
+
+ protected void restoreAllSelectionListeners()
+ {
+ for (TreeSelectionListener listener : this.allSelectionListeners) {
+ this.addTreeSelectionListener(listener);
+ }
+ }
+
+
+
+ /**
+ * Creates an instance of the XML tree from provided XML data.
+ *
+ * @param xmlData XML document in the form of a <code>String</code> to
+ * derive the tree from.
+ * @param bIncludeAttributesIntoTree
+ * @param bIncludeValuesIntoTree
+ * @param bIncludeElementNamespacesIntoTree
+ * @param parentConfigPanel
+ * @return
+ * @throws DocumentException if <code>xmlData</code> does not
+ * contain a valid XML document.
+ *
+ */
+ public static XPathActivityXMLTree createFromXMLData(String xmlData, boolean bIncludeAttributesIntoTree,
+ boolean bIncludeValuesIntoTree, boolean bIncludeElementNamespacesIntoTree,
+ XPathActivityConfigurationPanel parentConfigPanel) throws DocumentException
+ {
+ // ----- XML DOCUMENT PARSING -----
+ // try to parse the XML document - the next line will throw an exception if
+ // the document is not well-formed; proceed otherwise
+ Document doc = DocumentHelper.parseText(xmlData);
+ Element rootElement = doc.getRootElement();
+
+
+ // ----- POPULATE XML TREE -----
+ XPathActivityXMLTreeElementNode rootNode = new XPathActivityXMLTreeElementNode(rootElement);
+ populate(rootNode, rootElement, bIncludeAttributesIntoTree);
+
+ return (new XPathActivityXMLTree(rootNode, doc, bIncludeValuesIntoTree, bIncludeElementNamespacesIntoTree, parentConfigPanel));
+ }
+
+
+ /**
+ * Worker method for populating the tree recursively from a list of Elements.
+ *
+ * @param node
+ * @param element
+ */
+ private static void populate(DefaultMutableTreeNode node, Element element,
+ boolean bIncludeAttributesIntoTree)
+ {
+ Iterator<Element> elementIterator = element.elements().iterator();
+ while (elementIterator.hasNext()) {
+ Element childElement = elementIterator.next();
+ XPathActivityXMLTreeElementNode childNode = new XPathActivityXMLTreeElementNode(childElement);
+ node.add(childNode);
+
+ // recursively repeat for all children of the current child element
+ populate(childNode, childElement, bIncludeAttributesIntoTree);
+ }
+
+
+ // add attributes of the element as its children, if necessary
+ if (bIncludeAttributesIntoTree) {
+ List<Attribute> attributes = element.attributes();
+ for (Attribute attribute : attributes) {
+ node.add(new XPathActivityXMLTreeAttributeNode(attribute));
+ }
+ }
+ }
+
+
+ // ---------------- RESPONDING TO REQUESTS TO CHANGE APPEARANCE OF EXISTING TREE -----------------
+
+ /**
+ * NB! May be inefficient, as this solution re-generates the whole tree from
+ * stored XML document and replaces the root node of itself with a newly
+ * generated root node (that will be populated with updated children,
+ * according to the new values of options).
+ *
+ * However, this is a simple solution that will work for now.
+ *
+ * @param bIncludeAttributes
+ * @param bIncludeValues
+ * @param bIncludeNamespaces
+ */
+ public void refreshFromExistingDocument(boolean bIncludeAttributes, boolean bIncludeValues, boolean bIncludeNamespaces)
+ {
+ this.setEnabled(false);
+ removeAllSelectionListeners();
+
+ // store expansion and selection state of the XML tree
+ // see documentation for restoreExpandedPaths() for more details
+ //
+ // stored paths to expanded nodes are quite reliable, as paths are recorded;
+ // stored selected rows are less reliable, as only indices are kept -- however,
+ // the tree is re-created from the same document, so ordering/number of nodes
+ // cannot change (apart from attributes that may be added / removed - the attributes
+ // appear after other child nodes of some node in the tree, therefore only their
+ // selection could be affected)
+ HashMap<String,ArrayList<String>> toExpand = new HashMap<String,ArrayList<String>>();
+ ArrayList<Integer> toSelect = new ArrayList<Integer>();
+ for( int i = 1; i < this.getRowCount(); i++) {
+ if( this.isExpanded(i) ) {
+ TreePath path = this.getPathForRow(i);
+ String parentPath = path.getParentPath().toString();
+ ArrayList<String> values = toExpand.get(parentPath);
+ if(values == null) {
+ values = new ArrayList<String>();
+ }
+ values.add(path.getLastPathComponent().toString());
+ toExpand.put(parentPath, values);
+ }
+ if (this.isRowSelected(i)) {
+ toSelect.add(i);
+ }
+ }
+
+
+ // update presentation options
+ this.treeRenderer.setIncludeElementValues(bIncludeValues);
+ this.treeRenderer.setIncludeElementNamespaces(bIncludeNamespaces);
+
+ // re-create the root node of the tree and replace the old one with it
+ Element rootElement = this.documentUsedToPopulateTree.getRootElement();
+ XPathActivityXMLTreeNode newRootNode = new XPathActivityXMLTreeElementNode(rootElement);
+ populate(newRootNode, rootElement, bIncludeAttributes);
+ ((DefaultTreeModel)this.getModel()).setRoot(newRootNode);
+
+
+ // restore previous state of the tree from saved values
+ restoreExpandedPaths(toExpand, this.getPathForRow(0));
+ restoreSelectedPaths(toSelect);
+
+ this.restoreAllSelectionListeners();
+ this.setEnabled(true);
+ }
+
+
+ /**
+ * This method can only reliably work when the tree is re-generated from the same
+ * XML document, so that number / order of nodes would not change.
+ *
+ * @param toSelect List of indices of rows to re-select after tree was re-generated.
+ */
+ private void restoreSelectedPaths(ArrayList<Integer> toSelect)
+ {
+ if (toSelect == null || toSelect.isEmpty()) return;
+
+ // something definitely needs to be selected, so include root element into selection
+ this.addSelectionRow(0);
+
+ // select all stored rows
+ for (Integer value : toSelect) {
+ this.addSelectionRow(value);
+ }
+ }
+
+
+
+ /**
+ * Taken from: <a href="http://java.itags.org/java-core-gui-apis/58504/">http://java.itags.org/java-core-gui-apis/58504/</a>
+ *
+ * This method recursively expands all previously stored paths.
+ * Works under assumption that the name of the root node did not change.
+ * Otherwise, it can handle changed structure of the tree.
+ *
+ * To achieve its goal, it cannot simply use stored TreePath from your the original tree,
+ * since the paths are invalid after the tree is refreshed. Instead, a HashMap which links
+ * a String representation of the parent tree path to all expanded child node names is used.
+ *
+ * @param toExpand Map which links a String representation of the parent tree path to all
+ * expanded child node names is used.
+ * @param rootPath Path to root node.
+ */
+ void restoreExpandedPaths(HashMap<String,ArrayList<String>> toExpand, TreePath rootPath)
+ {
+ ArrayList<String> values = toExpand.remove(rootPath.toString());
+ if (values == null) return;
+
+ int row = this.getRowForPath(rootPath);
+ for (String value : values)
+ {
+ TreePath nextMatch = this.getNextMatch(value, row, Position.Bias.Forward);
+ this.expandPath(nextMatch);
+ if (toExpand.containsKey(nextMatch.toString())) {
+ restoreExpandedPaths(toExpand, nextMatch);
+ }
+ }
+ }
+
+
+
+ // ---------------- TREE SELECTION MODEL + XPath GENERATION -----------------
+
+
+ protected String generateXPathFromTreePath(TreePath path)
+ {
+ StringBuilder xpath = new StringBuilder();
+
+ for (String leg : generateXPathFromTreePathAsLegList(path)) {
+ xpath.append(leg);
+ }
+
+ return (xpath.toString());
+ }
+
+
+ protected List<String> generateXPathFromTreePathAsLegList(TreePath path)
+ {
+ List<String> pathLegs = new LinkedList<String>();
+
+ TreePath parentPath = path;
+ for (int i = 0; i < path.getPathCount(); i++)
+ {
+ XPathActivityXMLTreeNode lastXMLTreeNodeInThisPath = (XPathActivityXMLTreeNode)parentPath.getLastPathComponent();
+ pathLegs.add(0, this.getXMLTreeNodeEffectiveQualifiedNameAsXPathLeg(lastXMLTreeNodeInThisPath));
+
+ parentPath = parentPath.getParentPath();
+ }
+
+ return (pathLegs);
+ }
+
+
+ protected String getXMLTreeNodeEffectiveQualifiedNameAsXPathLeg(XPathActivityXMLTreeNode node)
+ {
+ QName qname = node.getNodeQName();
+ String effectiveNamespacePrefix = addNamespaceToXPathMap(qname.getNamespace());
+
+ return("/" +
+ (node.isAttribute() ? "@" : "") +
+ (effectiveNamespacePrefix.length() > 0 ? (effectiveNamespacePrefix + ":") : "") +
+ qname.getName());
+ }
+
+
+
+ private String addNamespaceToXPathMap(Namespace namespace)
+ {
+ // EMTPY PREFIX
+ if (namespace.getPrefix().length() == 0) {
+ if (namespace.getURI().length() == 0) {
+ // DEFAULT NAMESPACE with no URI - nothing to worry about
+ return "";
+ }
+ else {
+ // DEFAULT NAMESPACE WITH NO PREFIX, BUT URI IS KNOWN
+ return (addNamespaceToXPathMap(new Namespace("default", namespace.getURI())));
+ }
+ }
+
+ // NEW NON-EMPTY PREFIX
+ if (!this.currentXPathNamespaces.containsKey(namespace.getPrefix())) {
+ this.currentXPathNamespaces.put(namespace.getPrefix(), namespace.getURI());
+ return (namespace.getPrefix());
+ }
+
+ // EXISTING NON-EMPTY PREFIX AND THE SAME URI - NO NEED TO ADD AGAIN
+ else if (this.currentXPathNamespaces.get(namespace.getPrefix()).equals(namespace.getURI())) {
+ return (namespace.getPrefix());
+ }
+
+ // EXISTING NON-EMPTY PREFIX, BUT DIFFERENT URI
+ else {
+ String repeatedPrefix = namespace.getPrefix();
+
+ int i = 0;
+ while (this.currentXPathNamespaces.containsKey(repeatedPrefix + i)) {
+ // check if current alternative prefix wasn't yet applied to current URI
+ if (this.currentXPathNamespaces.get(repeatedPrefix + i).equals(namespace.getURI())) {
+ return (repeatedPrefix + i);
+ }
+ else {
+ // still another URI for the same prefix, keep trying to increase the ID in the prefix
+ i++;
+ }
+ }
+
+ String modifiedPrefix = repeatedPrefix + i;
+ this.currentXPathNamespaces.put(modifiedPrefix, namespace.getURI());
+ return (modifiedPrefix);
+ }
+ }
+
+
+ // ----------------------- Tree Cell Renderer --------------------------
+
+ /**
+ *
+ * @author Sergejs Aleksejevs
+ */
+ private class XPathActivityXMLTreeRenderer extends DefaultTreeCellRenderer
+ {
+ private boolean bIncludeElementValues;
+ private boolean bIncludeElementNamespaces;
+
+ public XPathActivityXMLTreeRenderer(boolean bIncludeElementValues, boolean bIncludeElementNamespaces) {
+ super();
+ this.bIncludeElementValues = bIncludeElementValues;
+ this.bIncludeElementNamespaces = bIncludeElementNamespaces;
+ }
+
+
+ public boolean getIncludeElementValues() {
+ return bIncludeElementValues;
+ }
+ public void setIncludeElementValues(boolean bIncludeElementValues) {
+ this.bIncludeElementValues = bIncludeElementValues;
+ }
+
+ public boolean getIncludeElementNamespaces() {
+ return bIncludeElementNamespaces;
+ }
+ public void setIncludeElementNamespaces(boolean bIncludeElementNamespaces) {
+ this.bIncludeElementNamespaces = bIncludeElementNamespaces;
+ }
+
+
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean selected, boolean expanded, boolean leaf, int row,
+ boolean hasFocus)
+ {
+ // obtain the default rendering, we'll then customize it
+ Component defaultRendering = super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, hasFocus);
+
+ // it is most likely that the default rendering will be a JLabel, check just to be safe
+ if (defaultRendering instanceof JLabel)
+ {
+ JLabel defaultRenderedLabel = ((JLabel)defaultRendering);
+
+ // ---------- CHOOSE APPROPRIATE ICON FOR THE NODE ------------
+ if (row == 0) {
+ // set the icon for the XML tree root node
+ defaultRenderedLabel.setIcon(XPathActivityIcon.getIconById(XPathActivityIcon.XML_TREE_ROOT_ICON));
+ }
+ else {
+ // set the icon for the XML tree node
+ if (value instanceof XPathActivityXMLTreeNode &&
+ ((XPathActivityXMLTreeNode)value).isAttribute())
+ {
+ defaultRenderedLabel.setIcon(XPathActivityIcon.getIconById(XPathActivityIcon.XML_TREE_ATTRIBUTE_ICON));
+ }
+ else {
+ defaultRenderedLabel.setIcon(XPathActivityIcon.getIconById(XPathActivityIcon.XML_TREE_NODE_ICON));
+ }
+ }
+
+
+ // ----------- CHOOSE THE DISPLAY TITLE FOR THE NODE ------------
+ if (value instanceof XPathActivityXMLTreeNode) {
+ defaultRenderedLabel.setText(((XPathActivityXMLTreeNode)value).getTreeNodeDisplayLabel(
+ this.bIncludeElementValues, this.bIncludeElementNamespaces, true));
+ }
+ }
+
+ return (defaultRendering);
+ }
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeAttributeNode.java
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diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeAttributeNode.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeAttributeNode.java
new file mode 100644
index 0000000..d22623f
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeAttributeNode.java
@@ -0,0 +1,50 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import org.dom4j.Attribute;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityXMLTreeAttributeNode extends XPathActivityXMLTreeNode
+{
+ private Attribute associatedAttribute;
+
+ public XPathActivityXMLTreeAttributeNode(Attribute associatedAttribute) {
+ super(associatedAttribute, true);
+ this.associatedAttribute = associatedAttribute;
+ }
+
+ public Attribute getAssociatedAttribute() {
+ return associatedAttribute;
+ }
+
+ public String getTreeNodeDisplayLabel(boolean bIncludeValue, boolean bUseStyling)
+ {
+ StringBuilder label = new StringBuilder();
+
+ // add qualified attribute name (possibly) with styling
+ label.append((bUseStyling ? "<font color=\"purple\">" : "") +
+ this.associatedAttribute.getQualifiedName() +
+ (bUseStyling ? "</font>" : ""));
+
+ // add attribute value
+ if (bIncludeValue)
+ {
+ String attributeTextValue = this.associatedAttribute.getText();
+
+ if (attributeTextValue != null && attributeTextValue.length() > 0) {
+ label.append((bUseStyling ? "<font color=\"gray\"> - </font><font color=\"green\">" : "") +
+ truncateElementTextValue(stripAllHTML(attributeTextValue)) +
+ (bUseStyling ? "</font>" : ""));
+ }
+ }
+
+ if (bUseStyling) {
+ label.insert(0, "<html>");
+ label.append("</html>");
+ }
+
+ return (label.toString());
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeElementNode.java
----------------------------------------------------------------------
diff --git a/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeElementNode.java b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeElementNode.java
new file mode 100644
index 0000000..a151753
--- /dev/null
+++ b/taverna-xpath-activity-ui/src/main/java/net/sf/taverna/t2/activities/xpath/ui/config/xmltree/XPathActivityXMLTreeElementNode.java
@@ -0,0 +1,62 @@
+package net.sf.taverna.t2.activities.xpath.ui.config.xmltree;
+
+import org.dom4j.Element;
+import org.dom4j.Namespace;
+
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class XPathActivityXMLTreeElementNode extends XPathActivityXMLTreeNode
+{
+ private Element associatedElement;
+
+ public XPathActivityXMLTreeElementNode(Element associatedElement) {
+ super(associatedElement, false);
+ this.associatedElement = associatedElement;
+ }
+
+ public Element getAssociatedElement() {
+ return associatedElement;
+ }
+
+ public String getTreeNodeDisplayLabel(boolean bIncludeValue, boolean bIncludeNamespace, boolean bUseStyling)
+ {
+ StringBuilder label = new StringBuilder();
+
+ // add qualified element name
+ label.append(this.associatedElement.getQualifiedName());
+
+ // add element namespace
+ if (bIncludeNamespace)
+ {
+ Namespace ns = this.associatedElement.getNamespace();
+
+ label.append((bUseStyling ? "<font color=\"gray\">" : "") +
+ " - xmlns" + (ns.getPrefix().length() > 0 ? (":" + ns.getPrefix()) : "") + "=\"" +
+ this.associatedElement.getNamespaceURI() +
+ (bUseStyling ? "\"</font>" : ""));
+ }
+
+ // add element value
+ if (bIncludeValue)
+ {
+ String elementTextValue = this.associatedElement.getTextTrim();
+
+ if (elementTextValue != null && elementTextValue.length() > 0) {
+ label.append((bUseStyling ? "<font color=\"gray\"> - </font><font color=\"blue\">" : "") +
+ truncateElementTextValue(stripAllHTML(elementTextValue)) +
+ (bUseStyling ? "</font>" : ""));
+ }
+ }
+
+ if (bUseStyling) {
+ label.insert(0, "<html>");
+ label.append("</html>");
+ }
+
+ return (label.toString());
+ }
+
+}
\ No newline at end of file
[11/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
new file mode 100644
index 0000000..6e9adb4
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
@@ -0,0 +1,76 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>BufferedReader getReader (String fileUrl, String encoding) throws IOException {
+ InputStreamReader reader;
+ try {
+ if (encoding == null) {
+ reader = new FileReader(fileUrl);
+ } else {
+ reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
+ }
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ if (encoding == null) {
+ reader = new InputStreamReader (url.openStream());
+ } else {
+ reader = new InputStreamReader (url.openStream(), encoding);
+ }
+ }
+ return new BufferedReader(reader);
+ }
+
+
+
+StringBuffer sb = new StringBuffer(4000);
+
+if (encoding == void) {
+ encoding = null;
+}
+
+BufferedReader in = getReader(fileurl, encoding);
+String str;
+String lineEnding = System.getProperty("line.separator");
+
+while ((str = in.readLine()) != null) {
+ sb.append(str);
+ sb.append(lineEnding);
+}
+in.close();
+filecontents = sb.toString();
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>fileurl</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>filecontents</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
new file mode 100644
index 0000000..1424433
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "BufferedReader getReader (String fileUrl, String encoding) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\tif (encoding == null) {\n\t\t\t\treader = new FileReader(fileUrl);\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader(new FileInputStream(fileUrl),encoding); \n\t\t\t}\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\tif (encoding == null) {\n\t\t\t\treader = new InputStreamReader (url.openStream());\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader (url.openStream(), encoding);\n\t\t\t}\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\n\n\nStringBuffer sb = new StringBuffer(4000);\n\nif (encoding == void) {\n\tencoding = null;\n}\n\nBufferedReader in = getReader(fileurl, encoding);\nString str;\nString lineEnding = System.getProperty(\"line.separator\");\n\nwhile ((str = in.readLine()) != null) {\n\tsb.append(str);\n\tsb.append(lineEnding);\n}\nin.close();
\nfilecontents = sb.toString();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileReader",
+ "inputPorts" : [ {
+ "name" : "fileurl",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filecontents",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
new file mode 100644
index 0000000..88ac962
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
@@ -0,0 +1,57 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>
+ BufferedWriter out;
+ if (encoding == void) {
+ out = new BufferedWriter(new FileWriter(outputFile));
+ }
+ else {
+ out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding));
+ }
+out.write(filecontents);
+out.flush();
+out.close();
+outputFile = filecontents;
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>outputFile</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>filecontents</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>encoding</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputFile</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
new file mode 100644
index 0000000..5a9f368
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n BufferedWriter out;\n if (encoding == void) {\n \tout = new BufferedWriter(new FileWriter(outputFile));\n }\n else {\n \tout = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding)); \n }\nout.write(filecontents);\nout.flush();\nout.close();\noutputFile = filecontents;\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
+ "inputPorts" : [ {
+ "name" : "outputFile",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "filecontents",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputFile",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
new file mode 100644
index 0000000..b6263cf
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
@@ -0,0 +1,309 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="password" to="password" /><map from="userid" to="userid" /><map from="params" to="params" /><map from="url" to="url" /><map from="provideXml" to="provideXml" /><map from="driver" to="driver" /><map from="sql" to="sql" /></inputMap><outputMap><map from="resultList" to="resultList" /><map from="xmlresults" to="xmlresults" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+
+ <script>
+ import java.sql.Driver;
+import java.sql.DriverManager;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.ResultSetMetaData;
+import java.sql.SQLException;
+
+import javax.sql.rowset.WebRowSet;
+
+import com.sun.rowset.WebRowSetImpl;
+
+
+
+if ((driver == void) || (driver == null) || driver.equals("")) {
+ throw new RuntimeException("The driver must be specified");
+}
+
+if ((url == void) || (url == null) || url.equals("")) {
+ throw new RuntimeException("The url must be specified");
+}
+
+boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
+
+if ((params == void) || (params == null)) {
+ params = new ArrayList();
+}
+
+if ((sql == void) || (sql == null) || sql.equals("")) {
+ throw new RuntimeException("The sql must be specified");
+}
+
+Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
+
+if (c == null) {
+ throw new RuntimeException("Class " + driver + " not found");
+}
+
+Driver d = c.newInstance();
+if (d == null) {
+ throw new RuntimeException("Could not create instance of driver");
+}
+
+Properties p = new Properties();
+
+if ((userid == void) || (userid == null)) {
+ userid = "";
+}
+
+p.setProperty("user", userid);
+
+if ((password == void) || (password == null)) {
+ password = "";
+}
+
+p.setProperty("password", password);
+
+Connection con = null;
+PreparedStatement ps = null;
+ResultSet rs = null;
+try {
+
+ con = d.connect(url, p);
+ ps = con.prepareStatement(sql);
+
+ int paramSize = params.size();
+ for (int i = 0; i < paramSize; i++) {
+ ps.setObject(i + 1, params.get(i));
+ }
+
+ rs = ps.executeQuery();
+
+ if (provideXmlBoolean) {
+ WebRowSet webrs = new WebRowSetImpl();
+ StringWriter sw = new StringWriter();
+ webrs.writeXml(rs, sw);
+ xmlresults = sw.toString();
+ } else {
+ xmlresults = "";
+ }
+
+ try {
+ rs.beforeFirst();
+ } catch (SQLException e) {
+ // redo the query
+ rs = ps.executeQuery();
+ }
+
+ ResultSetMetaData rsmd = rs.getMetaData();
+ int numCols = rsmd.getColumnCount();
+ resultList = new ArrayList();
+
+ // put the results into the results list.
+ while (rs.next()) {
+ List row = new ArrayList(numCols);
+ for (int i = 0; i < numCols; i++) {
+ String str = rs.getString(i + 1);
+ row.add(str == null ? "null" : str);
+ }
+ resultList.add(row);
+ }
+}
+finally {
+ if (rs != null) {
+ rs.close();
+ }
+ if (ps != null) {
+ ps.close();
+ }
+ if (con != null) {
+ con.close();
+ }
+}
+
+
+ </script>
+
+ <dependencies />
+
+ <classLoaderSharing>system</classLoaderSharing>
+
+ <localDependencies />
+
+ <artifactDependencies />
+
+ <inputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>driver</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>password</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>userid</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>url</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>provideXml</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>sql</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>params</name>
+
+ <depth>1</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ </inputs>
+
+ <outputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <granularDepth>2</granularDepth>
+
+ <name>resultList</name>
+
+ <depth>2</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <granularDepth>0</granularDepth>
+
+ <name>xmlresults</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ </outputs>
+
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
new file mode 100644
index 0000000..da1f005
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
@@ -0,0 +1,44 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\nimport java.sql.ResultSet;\nimport java.sql.ResultSetMetaData;\nimport java.sql.SQLException;\n\nimport javax.sql.rowset.WebRowSet;\n\nimport com.sun.rowset.WebRowSetImpl;\n\n\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nboolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\t
throw new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\nResultSet rs = null;\ntry {\n\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramSize = params.size();\n\tfor (int i = 0; i < paramSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\trs = ps.executeQuery();\n\n\tif (provideXmlBoolean) {\n\t\tWebRowSet webrs = new WebRowSetImpl();\n\t\tStringWriter sw = new StringWriter();\n\t\twebrs.writeXml(rs, sw);\n\t\txmlresults = sw.toString();\n\t} else {\n\t\txmlresults = \"\";\n\t}\n\n\ttry {\n\t\trs.beforeF
irst();\n\t} catch (SQLException e) {\n\t\t// redo the query\n\t\trs = ps.executeQuery();\n\t}\n\n\tResultSetMetaData rsmd = rs.getMetaData();\n\tint numCols = rsmd.getColumnCount();\n\tresultList = new ArrayList();\n\t\n\t// put the results into the results list.\n\twhile (rs.next()) {\n\t\tList row = new ArrayList(numCols);\n\t\tfor (int i = 0; i < numCols; i++) {\n\t\t\tString str = rs.getString(i + 1); \n\t\t\trow.add(str == null ? \"null\" : str); \n\t\t}\n\t\tresultList.add(row);\n\t}\n}\nfinally {\n\tif (rs != null) {\n\t\trs.close();\n\t}\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n \n\n ",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "provideXml",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "depth" : 2,
+ "granularDepth" : 2
+ }, {
+ "name" : "xmlresults",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
new file mode 100644
index 0000000..fa0748c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
@@ -0,0 +1,229 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="password" to="password" /><map from="userid" to="userid" /><map from="params" to="params" /><map from="url" to="url" /><map from="provideXml" to="provideXml" /><map from="driver" to="driver" /><map from="sql" to="sql" /></inputMap><outputMap><map from="resultList" to="resultList" /><map from="xmlresults" to="xmlresults" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+
+ <script>import java.sql.Driver;
+import java.sql.DriverManager;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+
+if ((driver == void) || (driver == null) || driver.equals("")) {
+ throw new RuntimeException("The driver must be specified");
+}
+
+if ((url == void) || (url == null) || url.equals("")) {
+ throw new RuntimeException("The url must be specified");
+}
+
+if ((params == void) || (params == null)) {
+ params = new ArrayList();
+}
+
+if ((sql == void) || (sql == null) || sql.equals("")) {
+ throw new RuntimeException("The sql must be specified");
+}
+
+Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
+
+if (c == null) {
+ throw new RuntimeException("Class " + driver + " not found");
+}
+
+Driver d = c.newInstance();
+if (d == null) {
+ throw new RuntimeException("Could not create instance of driver");
+}
+
+Properties p = new Properties();
+
+if ((userid == void) || (userid == null)) {
+ userid = "";
+}
+
+p.setProperty("user", userid);
+
+if ((password == void) || (password == null)) {
+ password = "";
+}
+
+p.setProperty("password", password);
+
+Connection con = null;
+PreparedStatement ps = null;
+
+try {
+ con = d.connect(url, p);
+ ps = con.prepareStatement(sql);
+
+ int paramsSize = params.size();
+ for (int i = 0; i < paramsSize; i++) {
+ ps.setObject(i + 1, params.get(i));
+ }
+
+ ps.executeUpdate();
+
+ resultList = "update successful";
+}
+finally {
+ if (ps != null) {
+ ps.close();
+ }
+ if (con != null) {
+ con.close();
+ }
+}
+
+</script>
+
+ <dependencies />
+
+ <classLoaderSharing>system</classLoaderSharing>
+ <localDependencies />
+
+ <artifactDependencies />
+
+ <inputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>driver</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>password</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>userid</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>url</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>sql</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>params</name>
+
+ <depth>1</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ </inputs>
+
+ <outputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <granularDepth>0</granularDepth>
+
+ <name>resultList</name>
+
+ <depth>0</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ </outputs>
+
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
new file mode 100644
index 0000000..3144afd
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
@@ -0,0 +1,36 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\tthrow new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"
\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\n\ntry {\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramsSize = params.size();\n\tfor (int i = 0; i < paramsSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\tps.executeUpdate();\n\n\tresultList = \"update successful\";\n}\nfinally {\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
new file mode 100644
index 0000000..8b7a680
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
new file mode 100644
index 0000000..feb26cc
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
new file mode 100644
index 0000000..80f791a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=nucleotide&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
new file mode 100644
index 0000000..e616f51
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
new file mode 100644
index 0000000..2ce601b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
new file mode 100644
index 0000000..8dfbdbe
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
new file mode 100644
index 0000000..aad694a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
new file mode 100644
index 0000000..3867455
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
new file mode 100644
index 0000000..c07b04e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
new file mode 100644
index 0000000..fc5b181
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
new file mode 100644
index 0000000..bf85c2b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=protein&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
new file mode 100644
index 0000000..160ce92
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
new file mode 100644
index 0000000..c82209f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
new file mode 100644
index 0000000..6e36120
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
new file mode 100644
index 0000000..b6f9337
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
@@ -0,0 +1,45 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
new file mode 100644
index 0000000..471e000
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
new file mode 100644
index 0000000..71fef3c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
@@ -0,0 +1,68 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((id == void) || (id == null) || id.equals("")) {
+ throw new RunTimeException("port id must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed" +
+"&rettype=" + (((rettype == void ) || (rettype == null)) ? "full" : rettype) +
+"&retmode=" + (((retmode == void) || (retmode == null)) ? "xml" : retmode) +
+"&id=" + id);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>id</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>rettype</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>retmode</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
new file mode 100644
index 0000000..5e2a7df
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed\" +\n\"&rettype=\" + (((rettype == void ) || (rettype == null)) ? \"full\" : rettype) +\n\"&retmode=\" + (((retmode == void) || (retmode == null)) ? \"xml\" : retmode) +\n\"&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
+ "inputPorts" : [ {
+ "name" : "id",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "rettype",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retmode",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
new file mode 100644
index 0000000..37c440c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
@@ -0,0 +1,124 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((term == void) || (term == null) || term.equals("")) {
+ throw new RunTimeException("port term must have a non-empty value");
+}
+
+URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed" +
+(field == void ? "" : ("&field=" + field)) +
+(retstart == void ? "" : ("&retstart=" + retstart)) +
+(retmax == void ? "" : ("&retmax=" + retmax)) +
+(mindate == void ? "" : ("&mindate=" + mindate)) +
+(maxdate == void ? "" : ("&maxdate=" + maxdate)) +
+"&rettype=" + (rettype == void ? "full" : rettype) +
+"&retmode=" + (retmode == void ? "xml" : retmode) +
+"&tool=taverna" +
+"&term=" + term);
+
+BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
+StringWriter writer = new StringWriter();
+
+char[] buffer = new char[1024];
+ while (true) {
+ int r = reader.read(buffer);
+ if (r <= 0) {
+ break;
+ }
+ writer.write(buffer, 0, r);
+ }
+reader.close();
+outputText = writer.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>term</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>db</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>field</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>retstart</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>retmax</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>mindate</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>maxdate</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>rettype</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>outputText</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
new file mode 100644
index 0000000..bd29f82
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
@@ -0,0 +1,44 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((term == void) || (term == null) || term.equals(\"\")) {\n\tthrow new RunTimeException(\"port term must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed\" +\n(field == void ? \"\" : (\"&field=\" + field)) +\n(retstart == void ? \"\" : (\"&retstart=\" + retstart)) +\n(retmax == void ? \"\" : (\"&retmax=\" + retmax)) +\n(mindate == void ? \"\" : (\"&mindate=\" + mindate)) +\n(maxdate == void ? \"\" : (\"&maxdate=\" + maxdate)) +\n\"&rettype=\" + (rettype == void ? \"full\" : rettype) +\n\"&retmode=\" + (retmode == void ? \"xml\" : retmode) +\n\"&tool=taverna\" +\n\"&term=\" + term);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n
}\nreader.close();\noutputText = writer.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
+ "inputPorts" : [ {
+ "name" : "term",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "db",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "field",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retstart",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "retmax",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "mindate",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "maxdate",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "rettype",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputText",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
new file mode 100644
index 0000000..a2317c5
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
@@ -0,0 +1,31 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <name>url</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>text/plain</string>
+ </mimeTypes>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs />
+ <classLoaderSharing>workflow</classLoaderSharing>
+ <localDependencies />
+ <artifactDependencies />
+ <script>import java.awt.Desktop;
+import java.net.URI;
+
+if ((url == void) || (url == null)) {
+ throw new RuntimeException("Url must be specified");
+}
+
+URI uri = null;
+
+uri = new URI(url);
+
+Desktop.getDesktop().browse(uri);</script>
+ <dependencies />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
new file mode 100644
index 0000000..1a2155e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.awt.Desktop;\nimport java.net.URI;\n\nif ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"Url must be specified\");\n}\n\nURI uri = null;\n\nuri = new URI(url);\n\nDesktop.getDesktop().browse(uri);",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
[09/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json
new file mode 100644
index 0000000..4992e0b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.FlattenList.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "flatten(inputs, outputs, depth) {\n\tfor (i = inputs.iterator(); i.hasNext();) {\n\t element = i.next();\n\t\tif (element instanceof Collection && depth > 0) {\n\t\t\tflatten(element, outputs, depth - 1);\n\t\t} else {\n\t\t\toutputs.add(element);\n\t\t}\n\t}\n}\n\noutputlist = new ArrayList();\n\nflatten(inputlist, outputlist, 1);",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.FlattenList",
+ "inputPorts" : [ {
+ "name" : "inputlist",
+ "depth" : 2,
+ "type" : "byte[]"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber
new file mode 100644
index 0000000..3edd0cf
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber
@@ -0,0 +1,44 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>int targetLengthInt = 7;
+if (targetlength != void) {
+ targetLengthInt = Integer.parseInt(targetlength);
+}
+int currentLength = input.length();
+while (input.length() < targetLengthInt) {
+ input = "0" + input;
+}
+padded = input;</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>input</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>targetlength</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>padded</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json
new file mode 100644
index 0000000..37828ea
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.PadNumber.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "int targetLengthInt = 7;\nif (targetlength != void) {\n\ttargetLengthInt = Integer.parseInt(targetlength);\n}\nint currentLength = input.length();\nwhile (input.length() < targetLengthInt) {\n\tinput = \"0\" + input;\n}\npadded = input;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.PadNumber",
+ "inputPorts" : [ {
+ "name" : "input",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "targetlength",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "padded",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
new file mode 100644
index 0000000..7a4165a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
@@ -0,0 +1,60 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import java.util.regex.*;
+
+filteredlist = new ArrayList();
+Pattern thePat = Pattern.compile(regex);
+int theGroup = Integer.parseInt(group);
+
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ Matcher matcher = thePat.matcher(item);
+
+ if (matcher.find()) {
+ filteredlist.add(matcher.group(theGroup));
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>regex</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>group</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>filteredlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json
new file mode 100644
index 0000000..86378fb
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.util.regex.*;\n\nfilteredlist = new ArrayList();\nPattern thePat = Pattern.compile(regex);\nint theGroup = Integer.parseInt(group);\n\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tMatcher matcher = thePat.matcher(item);\n\n\tif (matcher.find()) {\n\t\tfilteredlist.add(matcher.group(theGroup));\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "group",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filteredlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail
new file mode 100644
index 0000000..f847773
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail
@@ -0,0 +1,85 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import javax.mail.Message;
+import javax.mail.Session;
+import javax.mail.Transport;
+import javax.mail.internet.MimeMessage;
+import javax.mail.internet.InternetAddress;
+
+if (subject == void) {
+ subject = "No subject";
+}
+if (body == void) {
+ throw new Exception("No body specified for message");
+}
+
+Properties mailProps = System.getProperties();
+if (smtpserver != void) {
+ mailProps.put("mail.smtp.host", smtpserver);
+}
+
+Session session = Session.getDefaultInstance(mailProps, null);
+MimeMessage message = new MimeMessage(session);
+message.setFrom(new InternetAddress(from));
+message.addRecipient(Message.RecipientType.TO, new InternetAddress(to));
+message.setSubject(subject);
+message.setText(body);
+Transport.send(message);
+</script>
+ <dependencies>
+ <string>javax.mail:mail:1.4</string>
+ <string>javax.activation:activation:1.1</string>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>to</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>from</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>subject</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>body</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>smtpserver</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs />
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json
new file mode 100644
index 0000000..9a7365d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SendEmail.json
@@ -0,0 +1,27 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import javax.mail.Message;\nimport javax.mail.Session;\nimport javax.mail.Transport;\nimport javax.mail.internet.MimeMessage;\nimport javax.mail.internet.InternetAddress;\n\nif (subject == void) {\n\tsubject = \"No subject\";\n}\nif (body == void) {\n\tthrow new Exception(\"No body specified for message\");\n}\n\nProperties mailProps = System.getProperties();\nif (smtpserver != void) {\n\tmailProps.put(\"mail.smtp.host\", smtpserver);\n}\n\nSession session = Session.getDefaultInstance(mailProps, null);\nMimeMessage message = new MimeMessage(session);\nmessage.setFrom(new InternetAddress(from));\nmessage.addRecipient(Message.RecipientType.TO, new InternetAddress(to));\nmessage.setSubject(subject);\nmessage.setText(body);\nTransport.send(message);\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.SendEmail",
+ "inputPorts" : [ {
+ "name" : "to",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "from",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "subject",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "body",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "smtpserver",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex
new file mode 100644
index 0000000..7c296f3
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex
@@ -0,0 +1,47 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>List split = new ArrayList();
+if (!string.equals("")) {
+ String regexString = ",";
+ if (regex != void) {
+ regexString = regex;
+ }
+ String[] result = string.split(regexString);
+ for (int i = 0; i < result.length; i++) {
+ split.add(result[i]);
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>regex</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>split</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json
new file mode 100644
index 0000000..afbdc78
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.SplitByRegex.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List split = new ArrayList();\nif (!string.equals(\"\")) {\n\tString regexString = \",\";\n\tif (regex != void) {\n\t\tregexString = regex;\n\t}\n\tString[] result = string.split(regexString);\n\tfor (int i = 0; i < result.length; i++) {\n\t\tsplit.add(result[i]);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
+ "inputPorts" : [ {
+ "name" : "string",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "split",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat
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diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat
new file mode 100644
index 0000000..7993975
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat
@@ -0,0 +1,36 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>output = string1 + string2;</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string1</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>string2</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>output</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json
new file mode 100644
index 0000000..24a3fa9
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringConcat.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "output = string1 + string2;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringConcat",
+ "inputPorts" : [ {
+ "name" : "string1",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "string2",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "output",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge
new file mode 100644
index 0000000..cdd408d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge
@@ -0,0 +1,49 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>String seperatorString = "\n";
+if (seperator != void) {
+ seperatorString = seperator;
+}
+StringBuffer sb = new StringBuffer();
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ sb.append(item);
+ if (i.hasNext()) {
+ sb.append(seperatorString);
+ }
+}
+concatenated = sb.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>seperator</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>concatenated</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json
new file mode 100644
index 0000000..a0b860f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringListMerge.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "String seperatorString = \"\\n\";\nif (seperator != void) {\n\tseperatorString = seperator;\n}\nStringBuffer sb = new StringBuffer();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tsb.append(item);\n\tif (i.hasNext()) {\n\t\tsb.append(seperatorString);\n\t}\n}\nconcatenated = sb.toString();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringListMerge",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "seperator",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "concatenated",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference
new file mode 100644
index 0000000..c7bb289
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference
@@ -0,0 +1,49 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>List difference = new ArrayList();
+for (Iterator i = list1.iterator(); i.hasNext();) {
+ Object o = i.next();
+ if (!list2.contains(o)) {
+ difference.add(o);
+ }
+}
+for (Iterator i = list2.iterator(); i.hasNext();) {
+ Object o = i.next();
+ if (!list1.contains(o)) {
+ difference.add(o);
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list1</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list2</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>difference</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json
new file mode 100644
index 0000000..c844322
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetDifference.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List difference = new ArrayList();\nfor (Iterator i = list1.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (!list2.contains(o)) {\n\t\tdifference.add(o);\n\t}\n}\nfor (Iterator i = list2.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (!list1.contains(o)) {\n\t\tdifference.add(o);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "difference",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
new file mode 100644
index 0000000..a4c2f5a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
@@ -0,0 +1,43 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>List intersection = new ArrayList();
+for (Iterator i = list1.iterator(); i.hasNext();) {
+ Object o = i.next();
+ if (list2.contains(o)) {
+ intersection.add(o);
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list1</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list2</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>intersection</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json
new file mode 100644
index 0000000..0404922
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetIntersection.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List intersection = new ArrayList();\nfor (Iterator i = list1.iterator(); i.hasNext();) {\n\tObject o = i.next();\n\tif (list2.contains(o)) {\n\t\tintersection.add(o);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "intersection",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion
new file mode 100644
index 0000000..1ef0958
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion
@@ -0,0 +1,43 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
+
+<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>Set results = new HashSet();
+results.addAll(list1);
+results.addAll(list2);
+List union = new ArrayList();
+union.addAll(results);
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list1</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>list2</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>union</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json
new file mode 100644
index 0000000..25960be
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringSetUnion.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "Set results = new HashSet();\nresults.addAll(list1);\nresults.addAll(list2);\nList union = new ArrayList();\nunion.addAll(results);\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
+ "inputPorts" : [ {
+ "name" : "list1",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "list2",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "union",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
new file mode 100644
index 0000000..310dccc
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
@@ -0,0 +1,33 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>List strippedlist = new ArrayList();
+for (Iterator i = stringlist.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+ if (strippedlist.contains(item) == false) {
+ strippedlist.add(item);
+ }
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>stringlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>strippedlist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json
new file mode 100644
index 0000000..c5fecee
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "List strippedlist = new ArrayList();\nfor (Iterator i = stringlist.iterator(); i.hasNext();) {\n\tString item = (String) i.next();\n\tif (strippedlist.contains(item) == false) {\n\t\tstrippedlist.add(item);\n\t}\n}\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
+ "inputPorts" : [ {
+ "name" : "stringlist",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "strippedlist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
new file mode 100644
index 0000000..790073a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
@@ -0,0 +1,36 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>throw new Exception("This script fails");</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>foo</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>bar</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>urgle</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json
new file mode 100644
index 0000000..4a5b7d8
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "throw new Exception(\"This script fails\");",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
+ "inputPorts" : [ {
+ "name" : "foo",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "bar",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "urgle",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
new file mode 100644
index 0000000..90e8ba8
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
@@ -0,0 +1,34 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import java.util.Random;
+
+Random r = new Random();
+
+if ((r.nextInt() % 4) == 0) {
+ throw new RuntimeException("Fails every four runs!");
+}
+
+out = in;</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>in</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>out</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json
new file mode 100644
index 0000000..9ecf11d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.TestSometimesFails.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.util.Random;\n\nRandom r = new Random();\n\nif ((r.nextInt() % 4) == 0) {\n\tthrow new RuntimeException(\"Fails every four runs!\");\n}\n\nout = in;",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
+ "inputPorts" : [ {
+ "name" : "in",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "out",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
new file mode 100644
index 0000000..db3a73a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
@@ -0,0 +1,64 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((url == void) || (url == null)) {
+ throw new RuntimeException("The url must be specified");
+}
+
+URL inputURL = null;
+if (base != void) {
+ inputURL = new URL(new URL(base), url);
+} else {
+ inputURL = new URL(url);
+}
+
+int bytesRead = 0;
+int totalBytesRead = 0;
+InputStream is = inputURL.openStream();
+ByteArrayOutputStream os = new ByteArrayOutputStream();
+byte[] buffer = new byte[2048];
+while (true) {
+ bytesRead = is.read(buffer);
+ if (bytesRead == -1) {
+ break;
+ }
+
+ os.write(buffer, 0, bytesRead);
+}
+
+image = os.toByteArray();
+is.close();
+os.close();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>url</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/x-taverna-web-url'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>base</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/x-taverna-web-url'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>image</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'image/*'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json
new file mode 100644
index 0000000..a65b448
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebImageFetcher.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nURL inputURL = null;\nif (base != void) {\n\tinputURL = new URL(new URL(base), url);\n} else {\n\tinputURL = new URL(url);\n}\n\nint bytesRead = 0;\nint totalBytesRead = 0;\nInputStream is = inputURL.openStream();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nbyte[] buffer = new byte[2048];\nwhile (true) {\n\tbytesRead = is.read(buffer);\n\tif (bytesRead == -1) {\n\t\tbreak;\t\n\t}\n\n\tos.write(buffer, 0, bytesRead);\n}\n\nimage = os.toByteArray();\nis.close();\nos.close();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "base",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "image",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
new file mode 100644
index 0000000..dcd76a6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
@@ -0,0 +1,68 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if ((url == void) || (url == null)) {
+ throw new RuntimeException("The url must be specified");
+}
+
+URL inputURL = null;
+if (base != void) {
+ inputURL = new URL(new URL(base), url);
+}
+else {
+ inputURL = new URL(url);
+}
+URLConnection con = inputURL.openConnection();
+InputStream in = con.getInputStream();
+
+StringBuffer result = new StringBuffer();
+BufferedReader reader;
+
+String encoding = con.getContentEncoding();
+if (encoding == null) {
+ reader = new BufferedReader(new InputStreamReader(in));
+} else {
+ reader = new BufferedReader(new InputStreamReader(in, encoding));
+}
+String line = null;
+String NEWLINE = System.getProperty("line.separator");
+while ((line = reader.readLine()) != null) {
+ result.append(line);
+ result.append(NEWLINE);
+}
+
+reader.close();
+contents = result.toString();
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>url</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/x-taverna-web-url'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>base</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/x-taverna-web-url'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>contents</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain,text/html'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json
new file mode 100644
index 0000000..ad7a5b6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/org.embl.ebi.escience.scuflworkers.java.WebPageFetcher.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nURL inputURL = null;\nif (base != void) {\n inputURL = new URL(new URL(base), url);\n}\nelse {\n inputURL = new URL(url);\n}\nURLConnection con = inputURL.openConnection();\nInputStream in = con.getInputStream();\n\nStringBuffer result = new StringBuffer();\nBufferedReader reader;\n\nString encoding = con.getContentEncoding();\nif (encoding == null) {\n reader = new BufferedReader(new InputStreamReader(in));\n} else {\n reader = new BufferedReader(new InputStreamReader(in, encoding));\n}\nString line = null;\nString NEWLINE = System.getProperty(\"line.separator\");\nwhile ((line = reader.readLine()) != null) {\n\tresult.append(line);\n\tresult.append(NEWLINE);\n}\n\nreader.close();\ncontents = result.toString();\n",
+ "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
+ "inputPorts" : [ {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "base",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "contents",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/pom.xml b/taverna-rest-activity-ui/pom.xml
new file mode 100644
index 0000000..99ac649
--- /dev/null
+++ b/taverna-rest-activity-ui/pom.xml
@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>rest-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>REST Activity - UI bindings</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>rest-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>workbench-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>report-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/HTTPHeadersTableModel.java
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/HTTPHeadersTableModel.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/HTTPHeadersTableModel.java
new file mode 100644
index 0000000..30507c9
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/HTTPHeadersTableModel.java
@@ -0,0 +1,119 @@
+package net.sf.taverna.t2.activities.rest.ui.config;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+
+import javax.swing.table.AbstractTableModel;
+
+@SuppressWarnings("serial")
+public class HTTPHeadersTableModel extends AbstractTableModel {
+
+ protected String[] columnNames;
+ protected ArrayList<ArrayList<String>> data;
+
+ public HTTPHeadersTableModel() {
+ columnNames = new String[] {"HTTP Header Name", "HTTP Header Value"};
+ data = new ArrayList<ArrayList<String>>();
+ }
+
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+
+ public boolean isCellEditable(int row, int column) {
+ return true;
+ }
+
+ public int getColumnCount()
+ {
+ return columnNames.length;
+ }
+
+ public int getRowCount()
+ {
+ return data.size();
+ }
+
+ public Object getValueAt(int row, int column)
+ {
+ return data.get(row).get(column);
+ }
+
+ public void setValueAt(Object value, int row, int column) {
+ if ((row < 0) || (column < 0)) {
+ throw new IllegalArgumentException("Invalid row/column setting");
+ }
+ data.get(row).set(column, (String)value);
+ }
+
+ /**
+ * Get the class at of the cells at the given column position.
+ */
+ public Class<? extends Object> getColumnClass(int iCol)
+ {
+ return getValueAt(0, iCol).getClass();
+ }
+
+
+ public void addEmptyRow() {
+ data.add(new ArrayList<String>(Arrays.asList("", ""))); // add empty row
+ fireTableRowsInserted(
+ data.size() - 1,
+ data.size() - 1);
+ }
+
+ public void addRow(ArrayList<String> headerValuePair) {
+ data.add(headerValuePair);
+ fireTableRowsInserted(
+ data.size() - 1,
+ data.size() - 1);
+ }
+
+ public void removeRow(int row)
+ {
+ if (row >=0 && row < data.size()){
+ data.remove(row);
+ fireTableRowsDeleted(row, row);
+ }
+ }
+
+ public ArrayList<ArrayList<String>> getHTTPHeaderData(){
+ // Return a deep copy of the 2-dimensional array
+ return deepCopy(data);
+ }
+
+ public void setHTTPHeaderData(ArrayList<ArrayList<String>> data){
+ this.data = deepCopy(data);
+ fireTableChanged(null);
+ }
+
+ public ArrayList<String> getHTTPHeaderNames(){
+ ArrayList<String> headerNames = new ArrayList<String>();
+ for (ArrayList<String> headerNameValuePair : data){
+ headerNames.add(headerNameValuePair.get(0));
+ }
+ return headerNames;
+ }
+
+ public ArrayList<String> getHTTPHeaderValues(){
+ ArrayList<String> headerValues = new ArrayList<String>();
+ for (ArrayList<String> headerNameValuePair : data){
+ headerValues.add(headerNameValuePair.get(1));
+ }
+ return headerValues;
+ }
+
+ public static ArrayList<ArrayList<String>> deepCopy(ArrayList<ArrayList<String>> src)
+ {
+ ArrayList<ArrayList<String>> dest = new ArrayList<ArrayList<String>>();
+
+ for (int i = 0; i< src.size(); i++){
+ dest.add(new ArrayList<String>(Arrays.asList(new String[src.get(i).size()])));
+ Collections.copy(dest.get(i), src.get(i));
+ }
+ return dest;
+ }
+
+}
+
[08/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigurationPanel.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigurationPanel.java
new file mode 100644
index 0000000..d6b46e1
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigurationPanel.java
@@ -0,0 +1,670 @@
+package net.sf.taverna.t2.activities.rest.ui.config;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.activities.rest.RESTActivity.DATA_FORMAT;
+import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD;
+import net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean;
+import net.sf.taverna.t2.activities.rest.URISignatureHandler;
+import net.sf.taverna.t2.activities.rest.URISignatureHandler.URISignatureParsingException;
+import net.sf.taverna.t2.workbench.MainWindow;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.MultiPageActivityConfigurationPanel;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+@SuppressWarnings("serial")
+public class RESTActivityConfigurationPanel extends MultiPageActivityConfigurationPanel {
+ private static final Icon infoIcon = new ImageIcon(
+ RESTActivityConfigurationPanel.class.getResource("information.png"));
+
+ // GENERAL tab
+ private JComboBox<HTTP_METHOD> cbHTTPMethod; // HTTP method of this REST activity
+ private JTextField tfURLSignature; // URL signature that determines its
+ // input ports
+ private JComboBox<String> cbAccepts; // for Accepts header
+ private JLabel jlContentTypeExplanation;
+ private JLabel jlContentTypeExplanationPlaceholder;
+ private JLabel jlContentType;
+ private JLabel jlContentTypeLabelPlaceholder; // this placeholder label will
+ // take up space of the
+ // ContentType combo-box
+ // when the latter is not
+ // shown
+ private JLabel jlContentTypeFieldPlaceholder;
+ private JComboBox<String> cbContentType; // for MIME type of data sent to the server
+ // by POST / PUT methods
+ private JLabel jlSendDataAs;
+ private JComboBox<DATA_FORMAT> cbSendDataAs;
+ private JLabel jlSendDataAsLabelPlaceholder;
+ private JLabel jlSendDataAsFieldPlaceholder;
+
+ // ADVANCED tab
+ private JCheckBox cbSendHTTPExpectHeader;
+ private JCheckBox cbShowRedirectionOutputPort;
+ private JCheckBox cbShowActualUrlPort;
+ private JCheckBox cbShowResponseHeadersPort;
+ private JCheckBox cbEscapeParameters;
+ private JButton addHeaderButton;
+ private JButton removeHeaderButton;
+ private JTable httpHeadersTable;
+ private HTTPHeadersTableModel httpHeadersTableModel;
+
+ private String[] mediaTypes;
+
+ private final ServiceRegistry serviceRegistry;
+
+ public RESTActivityConfigurationPanel(Activity activity, ServiceRegistry serviceRegistry) {
+ super(activity);
+ this.serviceRegistry = serviceRegistry;
+ initialise();
+ }
+
+ @Override
+ protected void initialise() {
+ super.initialise();
+ removeAllPages();
+ addPage("General", createGeneralTab());
+ addPage("Advanced", createAdvancedTab());
+ refreshConfiguration();
+ }
+
+ @Override
+ public void noteConfiguration() {
+ ObjectNode requestNode = json.objectNode();
+
+ String methodName = ((HTTP_METHOD) cbHTTPMethod.getSelectedItem()).name();
+ requestNode.put("httpMethod", methodName);
+ requestNode.put("absoluteURITemplate", tfURLSignature.getText().trim());
+
+ ArrayNode headersNode = requestNode.arrayNode();
+ headersNode.addObject().put("header", "Accept").put("value", (String) cbAccepts.getSelectedItem());
+ headersNode.addObject().put("header", "Content-Type").put("value", (String) cbContentType.getSelectedItem());
+ if (cbSendHTTPExpectHeader.isSelected()) {
+ headersNode.addObject().put("header", "Expect").put("value", "100-continue");
+ }
+ ArrayList<String> headerNames = httpHeadersTableModel.getHTTPHeaderNames();
+ ArrayList<String> headerValues = httpHeadersTableModel.getHTTPHeaderValues();
+ for (int i = 0; i < headerNames.size(); i++) {
+ headersNode.addObject().put("header", headerNames.get(i)).put("value", headerValues.get(i));
+ }
+
+ requestNode.set("headers", headersNode);
+ json.set("request", requestNode);
+
+ json.put("outgoingDataFormat", ((DATA_FORMAT) cbSendDataAs.getSelectedItem()).name());
+ json.put("showRedirectionOutputPort", cbShowRedirectionOutputPort
+ .isSelected());
+ json.put("showActualURLPort", cbShowActualUrlPort.isSelected());
+ json.put("showResponseHeadersPort", cbShowResponseHeadersPort.isSelected());
+ json.put("escapeParameters", cbEscapeParameters.isSelected());
+
+ configureInputPorts(serviceRegistry);
+ configureOutputPorts(serviceRegistry);
+ }
+
+ /**
+ * Check that user values in the UI are valid.
+ */
+ @Override
+ public boolean checkValues() {
+ // HTTP method is a fixed selection combo-box - no validation required
+
+ // URL signature must be present and be valid
+ String candidateURLSignature = tfURLSignature.getText().trim();
+ if (candidateURLSignature == null
+ || candidateURLSignature.length() == 0) {
+ JOptionPane.showMessageDialog(MainWindow.getMainWindow(),
+ "URL signature must not be empty",
+ "REST Activity Configuration - Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return (false);
+ } else {
+ try {
+ // Test if any exceptions will be thrown - if not, proceed to
+ // other validations
+ URISignatureHandler.validate(candidateURLSignature);
+ } catch (URISignatureParsingException e) {
+ JOptionPane.showMessageDialog(MainWindow.getMainWindow(), e
+ .getMessage(), "REST Activity Configuration - Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return (false);
+ }
+
+ // Test if the URL string contains "unsafe" characters, i.e. characters
+ // that need URL-encoding.
+ // From RFC 1738: "...Only alphanumerics [0-9a-zA-Z], the special
+ // characters "$-_.+!*'()," (not including the quotes) and reserved
+ // characters used for their reserved purposes may be
+ // used unencoded within a URL."
+ // Reserved characters are: ";/?:@&=" ..." (excluding quotes) and "%" used
+ // for escaping.
+ // We do not warn the user if they have not properly enclosed parameter
+ // names in curly braces as this check is already being done elsewhere in the code.
+ // We do not check the characters in parameter names either.
+ try {
+ // Test if any exceptions will be thrown - if not, proceed to
+ // other validations
+ URISignatureHandler.checkForUnsafeCharacters(candidateURLSignature);
+ } catch (URISignatureParsingException e) {
+ JOptionPane.showMessageDialog(MainWindow.getMainWindow(), e
+ .getMessage(), "REST Activity Configuration - Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return (false);
+ }
+
+ // Other HTTP headers configured must not have empty names
+ ArrayList<String> otherHTTPHeaderNames = httpHeadersTableModel.getHTTPHeaderNames();
+ for (String headerName : otherHTTPHeaderNames){
+ if (headerName.equals("")){
+ JOptionPane.showMessageDialog(MainWindow.getMainWindow(), "One of the HTTP header names is empty", "REST Activity Configuration - Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+ }
+ }
+
+ // All valid, return true
+ return true;
+ }
+
+ /**
+ * Update GUI from a changed configuration bean (perhaps by undo / redo).
+ */
+ @Override
+ public void refreshConfiguration() {
+ RESTActivityConfigurationBean configBean = new RESTActivityConfigurationBean(json);
+
+ cbHTTPMethod.setSelectedItem(configBean.getHttpMethod());
+ tfURLSignature.setText(configBean.getUrlSignature());
+ tfURLSignature.setCaretPosition(0);
+ cbAccepts.setSelectedItem(configBean.getAcceptsHeaderValue());
+ cbContentType.setSelectedItem(configBean.getContentTypeForUpdates());
+ cbSendDataAs.setSelectedItem(configBean.getOutgoingDataFormat());
+ cbSendHTTPExpectHeader.setSelected(configBean
+ .getSendHTTPExpectRequestHeader());
+ cbShowRedirectionOutputPort.setSelected(configBean
+ .getShowRedirectionOutputPort());
+ cbShowActualUrlPort.setSelected(configBean.getShowActualUrlPort());
+ cbShowResponseHeadersPort.setSelected(configBean.getShowResponseHeadersPort());
+ cbEscapeParameters.setSelected(configBean.getEscapeParameters());
+ httpHeadersTableModel.setHTTPHeaderData(configBean.getOtherHTTPHeaders());
+ }
+
+ private JPanel createGeneralTab() {
+ JPanel jpGeneral = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ // All components to be anchored WEST
+ c.anchor = GridBagConstraints.WEST;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.gridwidth = 1;
+ c.insets = new Insets(7, 7, 3, 3);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ JLabel labelMethod = new JLabel("HTTP Method:", infoIcon, JLabel.LEFT);
+ labelMethod
+ .setToolTipText("<html>HTTP method determines how a request to the remote server will be made.<br><br>"
+ + "Supported HTTP methods are normally used for different purposes:<br>"
+ + "<b>GET</b> - to fetch data;<br>"
+ + "<b>POST</b> - to create new resources;<br>"
+ + "<b>PUT</b> - to update existing resources;<br>"
+ + "<b>DELETE</b> - to remove existing resources.<br><br>"
+ + "Documentation of the server that is about to be used may suggest the<br>"
+ + "HTTP method that should be used.</html>");
+ jpGeneral.add(labelMethod, c);
+
+ // the HTTP method combo-box will always contain the same values - it is
+ // the selected
+ // method which is important; therefore, can prepopulate as the set of
+ // values is known
+ c.gridx++;
+ c.insets = new Insets(7, 3, 3, 7);
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ cbHTTPMethod = new JComboBox<>(HTTP_METHOD.values());
+ cbHTTPMethod.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ boolean contentTypeSelEnabled = RESTActivity
+ .hasMessageBodyInputPort((HTTP_METHOD) cbHTTPMethod
+ .getSelectedItem());
+
+ jlContentTypeExplanation.setVisible(contentTypeSelEnabled);
+ jlContentType.setVisible(contentTypeSelEnabled);
+ cbContentType.setVisible(contentTypeSelEnabled);
+ jlSendDataAs.setVisible(contentTypeSelEnabled);
+ cbSendDataAs.setVisible(contentTypeSelEnabled);
+
+ jlContentTypeExplanationPlaceholder
+ .setVisible(!contentTypeSelEnabled);
+ jlContentTypeLabelPlaceholder
+ .setVisible(!contentTypeSelEnabled);
+ jlContentTypeFieldPlaceholder
+ .setVisible(!contentTypeSelEnabled);
+ jlSendDataAsLabelPlaceholder.setVisible(!contentTypeSelEnabled);
+ jlSendDataAsFieldPlaceholder.setVisible(!contentTypeSelEnabled);
+ }
+ });
+ jpGeneral.add(cbHTTPMethod, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 7, 3, 3);
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0.0;
+ JLabel labelString = new JLabel("URL Template:", infoIcon, JLabel.LEFT);
+ labelString
+ .setToolTipText("<html>URL template enables to define a URL with <b>configurable<br>"
+ + "parameters</b> that will be used to access a remote server.<br><br>"
+ + "The template may contain zero or more <b>parameters</b> - each<br>"
+ + "enclosed within curly braces <b>\"{\"</b> and <b>\"}\"</b>.<br>"
+ + "Taverna will automatically create an individual input port for<br>"
+ + "this activity for each parameter.<br><br>"
+ + "Values extracted from these input ports during the workflow<br>"
+ + "execution these will be used to replace the parameters to<br>"
+ + "produce complete URLs.<br><br>"
+ + "For example, if the URL template is configured as<br>"
+ + "\"<i>http://www.myexperiment.org/user.xml?id={userID}</i>\", a<br>"
+ + "single input port with the name \"<i>userID</i>\" will be created.</html>");
+ labelString.setLabelFor(tfURLSignature);
+ jpGeneral.add(labelString, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 3, 7);
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ tfURLSignature = new JTextField(40);
+ tfURLSignature.addFocusListener(new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ tfURLSignature.selectAll();
+ }
+
+ public void focusLost(FocusEvent e) { /* do nothing */
+ }
+ });
+ jpGeneral.add(tfURLSignature, c);
+
+ c.gridx = 0;
+ c.gridwidth = 2;
+ c.gridy++;
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(18, 7, 3, 7);
+ JLabel jlAcceptsExplanation = new JLabel(
+ "Preferred MIME type for data to be fetched from the remote server --");
+ jpGeneral.add(jlAcceptsExplanation, c);
+ c.gridwidth = 1;
+
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 7, 3, 3);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ JLabel jlAccepts = new JLabel("'Accept' header:", infoIcon, JLabel.LEFT);
+ jlAccepts
+ .setToolTipText("<html>Select a MIME type from the drop-down menu or type your own.<br>Select blank if you do not want this header to be set.</br>");
+ jlAccepts.setLabelFor(cbAccepts);
+ jpGeneral.add(jlAccepts, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 3, 7);
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ cbAccepts = new JComboBox<>(getMediaTypes());
+ cbAccepts.setEditable(true);
+ cbAccepts.getEditor().getEditorComponent().addFocusListener(
+ new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ cbAccepts.getEditor().selectAll();
+ }
+
+ public void focusLost(FocusEvent e) { /* do nothing */
+ }
+ });
+ jpGeneral.add(cbAccepts, c);
+
+ c.gridx = 0;
+ c.gridwidth = 2;
+ c.gridy++;
+ c.insets = new Insets(18, 7, 3, 7);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ jlContentTypeExplanation = new JLabel(
+ "MIME type of data that will be sent to the remote server --");
+ jpGeneral.add(jlContentTypeExplanation, c);
+ c.gridwidth = 1;
+
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 7, 3, 3);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ jlContentType = new JLabel("'Content-Type' header:", infoIcon,
+ JLabel.LEFT);
+ jlContentType
+ .setToolTipText("<html>Select a MIME type from the drop-down menu or type your own.<br>Select blank if you do not want this header to be set.</html>");
+ jlContentType.setLabelFor(cbContentType);
+ jpGeneral.add(jlContentType, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 3, 7);
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ cbContentType = new JComboBox<>(getMediaTypes());
+ cbContentType.setEditable(true);
+ cbContentType.getEditor().getEditorComponent().addFocusListener(
+ new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ cbContentType.getEditor().selectAll();
+ }
+
+ public void focusLost(FocusEvent e) { /* do nothing */
+ }
+ });
+ cbContentType.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ // change selection in the "Send data as" combo-box, based on
+ // the selection of Content-Type
+ String selectedContentType = (String) cbContentType
+ .getSelectedItem();
+ if (selectedContentType.startsWith("text")) {
+ cbSendDataAs.setSelectedItem(DATA_FORMAT.String);
+ } else {
+ cbSendDataAs.setSelectedItem(DATA_FORMAT.Binary);
+ }
+ }
+ });
+ jpGeneral.add(cbContentType, c);
+
+ c.gridx = 0;
+ c.gridwidth = 2;
+ c.gridy++;
+ c.insets = new Insets(18, 7, 3, 7);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ jlContentTypeExplanationPlaceholder = new JLabel();
+ jlContentTypeExplanationPlaceholder
+ .setPreferredSize(jlContentTypeExplanation.getPreferredSize());
+ jpGeneral.add(jlContentTypeExplanationPlaceholder, c);
+ c.gridwidth = 1;
+
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 7, 3, 3);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ jlContentTypeLabelPlaceholder = new JLabel();
+ jlContentTypeLabelPlaceholder.setPreferredSize(jlContentType
+ .getPreferredSize());
+ jpGeneral.add(jlContentTypeLabelPlaceholder, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 3, 7);
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ jlContentTypeFieldPlaceholder = new JLabel();
+ jlContentTypeFieldPlaceholder.setPreferredSize(cbContentType
+ .getPreferredSize());
+ jpGeneral.add(jlContentTypeFieldPlaceholder, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(3, 7, 8, 3);
+ jlSendDataAs = new JLabel("Send data as:", infoIcon, JLabel.LEFT);
+ jlSendDataAs
+ .setToolTipText("Select the format for the data to be sent to the remote server");
+ jlSendDataAs.setLabelFor(cbSendDataAs);
+ jpGeneral.add(jlSendDataAs, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 8, 7);
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ cbSendDataAs = new JComboBox<>(DATA_FORMAT.values());
+ cbSendDataAs.setEditable(false);
+ jpGeneral.add(cbSendDataAs, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.insets = new Insets(3, 7, 8, 3);
+ c.weightx = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ jlSendDataAsLabelPlaceholder = new JLabel();
+ jlSendDataAsLabelPlaceholder.setPreferredSize(jlSendDataAs
+ .getPreferredSize());
+ jpGeneral.add(jlSendDataAsLabelPlaceholder, c);
+
+ c.gridx++;
+ c.insets = new Insets(3, 3, 8, 7);
+ c.weightx = 1.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ jlSendDataAsFieldPlaceholder = new JLabel();
+ jlSendDataAsFieldPlaceholder.setPreferredSize(cbSendDataAs
+ .getPreferredSize());
+ jpGeneral.add(jlSendDataAsFieldPlaceholder, c);
+
+ JPanel finalPanel = new JPanel(new BorderLayout());
+ finalPanel.add(jpGeneral, BorderLayout.NORTH);
+ return (finalPanel);
+ }
+
+ private String[] getMediaTypes() {
+ if (mediaTypes != null) {
+ return mediaTypes;
+ }
+ List<String> types = new ArrayList<String>();
+ InputStream typesStream = getClass().getResourceAsStream(
+ "mediatypes.txt");
+ try {
+ // media types must be ASCII and can't have whitespace
+ Scanner scanner = new Scanner(typesStream, "ascii");
+ while (scanner.hasNext()) {
+ types.add(scanner.next());
+ }
+ scanner.close();
+ } finally {
+ try {
+ typesStream.close();
+ } catch (IOException ex) {
+ }
+ }
+ mediaTypes = types.toArray(new String[0]);
+
+ return mediaTypes;
+ }
+
+ private JPanel createAdvancedTab() {
+ JPanel jpAdvanced = new JPanel(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.BOTH;
+ c.insets = new Insets(8, 10, 2, 4);
+ JLabel jlExpectHeaderInfoIcon = new JLabel(infoIcon);
+ jlExpectHeaderInfoIcon
+ .setToolTipText("<html>Ticking this checkbox may significantly improve performance when<br>"
+ + "large volumes of data are sent to the remote server and a redirect<br>"
+ + "from the original URL to the one specified by the server is likely.<br>"
+ + "<br>"
+ + "However, this checkbox <b>must not</b> be ticked to allow this activity<br>"
+ + "to post updates to Twitter.</html>");
+ jpAdvanced.add(jlExpectHeaderInfoIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(8, 0, 2, 8);
+ cbSendHTTPExpectHeader = new JCheckBox(
+ "Send HTTP Expect request-header field");
+ jpAdvanced.add(cbSendHTTPExpectHeader, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ c.insets = new Insets(2, 10, 5, 4);
+ JLabel jlShowRedirectionOutputPortInfoIcon = new JLabel(infoIcon);
+ jlShowRedirectionOutputPortInfoIcon
+ .setToolTipText("<html>\"Redirection\" output port displays the URL of the final redirect<br>"
+ + "that has yielded the output data on the \"Response Body\" port.</html>");
+ jpAdvanced.add(jlShowRedirectionOutputPortInfoIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(2, 0, 5, 8);
+ cbShowRedirectionOutputPort = new JCheckBox(
+ "Show \"Redirection\" output port");
+ jpAdvanced.add(cbShowRedirectionOutputPort, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ c.insets = new Insets(2, 10, 5, 4);
+ JLabel jlShowActualUrlPortInfoIcon = new JLabel(infoIcon);
+ jlShowActualUrlPortInfoIcon
+ .setToolTipText("<html>\"Actual URL\" output port displays the URL used by the REST service<br>"
+ + "with the actual parameter values.</html>");
+ jpAdvanced.add(jlShowActualUrlPortInfoIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(2, 0, 5, 8);
+ cbShowActualUrlPort = new JCheckBox(
+ "Show \"Actual URL\" output port");
+ jpAdvanced.add(cbShowActualUrlPort, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ c.insets = new Insets(2, 10, 5, 4);
+ JLabel jlShowResponseHeadersPortInfoIcon = new JLabel(infoIcon);
+ jlShowResponseHeadersPortInfoIcon
+ .setToolTipText("<html>\"Response headers\" output port displays the HTTP headers<br>"
+ + "received from the final (after redirection) HTTP call.</html>");
+ jpAdvanced.add(jlShowResponseHeadersPortInfoIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(2, 0, 5, 8);
+ cbShowResponseHeadersPort = new JCheckBox(
+ "Show \"Response headers\" output port");
+ jpAdvanced.add(cbShowResponseHeadersPort, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ c.insets = new Insets(2, 10, 5, 4);
+ JLabel jlEscapeParametersInfoIcon = new JLabel(infoIcon);
+ jlEscapeParametersInfoIcon
+ .setToolTipText("<html>Determines if parameters you pass to form the full URL<br>" +
+ " of the REST service will be URL-escaped.</html>");
+ jpAdvanced.add(jlEscapeParametersInfoIcon, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.insets = new Insets(2, 0, 5, 8);
+ cbEscapeParameters = new JCheckBox("Escape URL parameter values");
+ jpAdvanced.add(cbEscapeParameters, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ c.weightx = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(2, 10, 5, 4);
+ JLabel jlHTTPHeadersInfoIcon = new JLabel(infoIcon);
+ jlHTTPHeadersInfoIcon
+ .setToolTipText("<html>Set additional HTTP headers</html>");
+ jpAdvanced.add(jlHTTPHeadersInfoIcon, c);
+
+ c.gridx = 1;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.NONE;
+ c.insets = new Insets(2, 10, 5, 4);
+ addHeaderButton = new JButton("Add HTTP header");
+ addHeaderButton.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ httpHeadersTableModel.addEmptyRow();
+ httpHeadersTable.getSelectionModel().setSelectionInterval(httpHeadersTableModel.getRowCount() - 1, httpHeadersTableModel.getRowCount() - 1); }
+ });
+ removeHeaderButton = new JButton("Remove HTTP header");
+ removeHeaderButton.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ int row = httpHeadersTable.getSelectedRow();
+ httpHeadersTableModel.removeRow(row);
+ }
+ });
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.add(addHeaderButton, FlowLayout.LEFT);
+ buttonPanel.add(removeHeaderButton);
+ jpAdvanced.add(buttonPanel, c);
+
+ c.gridx = 1;
+ c.gridy++;
+ c.weightx = 0;
+ c.weighty = 1.0;
+ c.fill = GridBagConstraints.BOTH;
+ c.insets = new Insets(2, 10, 5, 4);
+ httpHeadersTableModel = new HTTPHeadersTableModel();
+ httpHeadersTable = new JTable(httpHeadersTableModel);
+ httpHeadersTable.setGridColor(Color.GRAY);
+ httpHeadersTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ setVisibleRowCount(httpHeadersTable, 3);
+ JScrollPane headersTableScrollPane = new JScrollPane(httpHeadersTable);
+ jpAdvanced.add(headersTableScrollPane, c);
+
+ return (jpAdvanced);
+ }
+
+ /*
+ * Based on http://www.javalobby.org/java/forums/t19559.html
+ */
+ public static void setVisibleRowCount(JTable table, int visibleRows){
+ int height = 0;
+ for(int row = 0; row < visibleRows; row++)
+ height += table.getRowHeight(row);
+
+ table.setPreferredScrollableViewportSize(new Dimension(
+ table.getPreferredScrollableViewportSize().width,
+ height));
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigureAction.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigureAction.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigureAction.java
new file mode 100644
index 0000000..bfb50d0
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+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/config/RESTActivityConfigureAction.java
@@ -0,0 +1,51 @@
+package net.sf.taverna.t2.activities.rest.ui.config;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+/**
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class RESTActivityConfigureAction extends ActivityConfigurationAction {
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ServiceRegistry serviceRegistry;
+
+ public RESTActivityConfigureAction(Activity activity, Frame owner, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.serviceRegistry = serviceRegistry;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction
+ .getDialog(getActivity());
+
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+
+ RESTActivityConfigurationPanel panel = new RESTActivityConfigurationPanel(getActivity(), serviceRegistry);
+ ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(), panel,
+ editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateAction.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateAction.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateAction.java
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index 0000000..96326f6
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateAction.java
@@ -0,0 +1,107 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.rest.ui.menu;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+/**
+ * An action to add a REST activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class AddRESTTemplateAction extends AbstractContextualMenuAction {
+
+ private static final String ADD_REST = "REST";
+
+ private static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceRegistry serviceRegistry;
+
+ public AddRESTTemplateAction() {
+ super(insertSection, 500);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+
+ return new AddRestAction();
+ }
+
+ protected class AddRestAction extends AbstractAction {
+ AddRestAction() {
+ super(ADD_REST, activityIconManager
+ .iconForActivity(GenericRESTTemplateService.ACTIVITY_TYPE));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(
+ GenericRESTTemplateService.getServiceDescription(), false, editManager,
+ menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateMenuAction.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateMenuAction.java
new file mode 100644
index 0000000..ec738e2
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/menu/AddRESTTemplateMenuAction.java
@@ -0,0 +1,114 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.rest.ui.menu;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService;
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+/**
+ * An action to add a REST activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author alanrw
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class AddRESTTemplateMenuAction extends AbstractMenuAction {
+
+ private static final String ADD_REST = "REST";
+
+ private static final URI INSERT = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#insert");
+
+ private static final URI ADD_REST_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuAddREST");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceRegistry serviceRegistry;
+
+ public AddRESTTemplateMenuAction() {
+ super(INSERT, 500, ADD_REST_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddRESTMenuAction();
+ }
+
+ protected class AddRESTMenuAction extends AbstractAction implements DesignOnlyAction {
+ AddRESTMenuAction() {
+ super();
+ putValue(SMALL_ICON, activityIconManager.iconForActivity(GenericRESTTemplateService.ACTIVITY_TYPE));
+ putValue(NAME, ADD_REST);
+ putValue(SHORT_DESCRIPTION, "REST service");
+ putValue(
+ Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_H, InputEvent.SHIFT_DOWN_MASK
+ | InputEvent.ALT_DOWN_MASK));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(
+ GenericRESTTemplateService.getServiceDescription(), false, editManager,
+ menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/GenericRESTTemplateService.java
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/GenericRESTTemplateService.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/GenericRESTTemplateService.java
new file mode 100644
index 0000000..69a3b96
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/GenericRESTTemplateService.java
@@ -0,0 +1,76 @@
+package net.sf.taverna.t2.activities.rest.ui.servicedescription;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.servicedescriptions.AbstractTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class GenericRESTTemplateService extends AbstractTemplateService {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/rest");
+
+ private static final String REST = "REST";
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ ObjectNode json = (ObjectNode) configuration.getJson();
+ ObjectNode requestNode = json.objectNode();
+
+ requestNode.put("httpMethod", RESTActivity.HTTP_METHOD.GET.name());
+ requestNode.put("absoluteURITemplate", "http://www.uniprot.org/uniprot/{id}.xml");
+
+ ArrayNode headersNode = requestNode.arrayNode();
+ headersNode.addObject().put("header", "Accept").put("value", "application/xml");
+ headersNode.addObject().put("header", "Content-Type").put("value", "application/xml");
+
+ requestNode.set("headers", headersNode);
+ json.set("request", requestNode);
+ json.put("outgoingDataFormat", RESTActivity.DATA_FORMAT.String.name());
+ json.put("showRedirectionOutputPort", false);
+ json.put("showActualURLPort", false);
+ json.put("showResponseHeadersPort", false);
+ json.put("escapeParameters", true);
+ return configuration;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return RESTActivityIcon.getRESTActivityIcon();
+ }
+
+ public String getName() {
+ return REST;
+ }
+
+ public String getDescription() {
+ return "A generic REST service that can handle all HTTP methods";
+ }
+
+ public static ServiceDescription getServiceDescription() {
+ GenericRESTTemplateService gts = new GenericRESTTemplateService();
+ return gts.templateService;
+ }
+
+ public String getId() {
+ return "http://www.taverna.org.uk/2010/services/rest";
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/RESTActivityIcon.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/RESTActivityIcon.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/RESTActivityIcon.java
new file mode 100644
index 0000000..c2309a9
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/servicedescription/RESTActivityIcon.java
@@ -0,0 +1,54 @@
+package net.sf.taverna.t2.activities.rest.ui.servicedescription;
+
+import java.awt.Color;
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+
+/**
+ *
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class RESTActivityIcon implements ActivityIconSPI {
+ private static final Color PROCESSOR_COLOUR = Color.decode("#7AAFFF");
+
+ private static ImageIcon icon;
+
+ public int canProvideIconScore(URI activityType) {
+ if (GenericRESTTemplateService.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getRESTActivityIcon();
+ }
+
+ public static Icon getRESTActivityIcon() {
+ if (icon == null) {
+ synchronized (RESTActivityIcon.class) {
+ if (icon == null) {
+ try {
+ icon = new ImageIcon(
+ RESTActivityIcon.class.getResource("service_type_rest.png"));
+ } catch (NullPointerException e) {
+ /* icon wasn't found - do nothing, but no icon will be available */
+ }
+ }
+ }
+ }
+ return (icon);
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ // set colour for REST processors in the workflow diagram
+ colourManager.setPreferredColour(GenericRESTTemplateService.ACTIVITY_TYPE.toString(), PROCESSOR_COLOUR);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceDesc.java.bak
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceDesc.java.bak b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceDesc.java.bak
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@@ -0,0 +1,99 @@
+package net.sf.taverna.t2.activities.rest.ui.serviceprovider;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean;
+
+public class ExampleServiceDesc extends ServiceDescription<RESTActivityConfigurationBean>
+{
+ /**
+ * The subclass of Activity which should be instantiated when adding a service
+ * for this description
+ */
+ @Override
+ public Class<? extends Activity<RESTActivityConfigurationBean>> getActivityClass() {
+ return RESTActivity.class;
+ }
+
+ /**
+ * The configuration bean which is to be used for configuring the instantiated activity.
+ * Making this bean will typically require some of the fields set on this service
+ * description, like an endpoint URL or method name.
+ *
+ */
+ @Override
+ public RESTActivityConfigurationBean getActivityConfiguration() {
+ RESTActivityConfigurationBean bean = new RESTActivityConfigurationBean();
+ bean.setExampleString(exampleString);
+ bean.setExampleUri(exampleUri);
+ return bean;
+ }
+
+ /**
+ * An icon to represent this service description in the service palette.
+ */
+ @Override
+ public Icon getIcon() {
+ return null;
+ }
+
+ /**
+ * The display name that will be shown in service palette and will
+ * be used as a template for processor name when added to workflow.
+ */
+ @Override
+ public String getName() {
+ return exampleString;
+ }
+
+ /**
+ * The path to this service description in the service palette. Folders
+ * will be created for each element of the returned path.
+ */
+ @Override
+ public List<String> getPath() {
+ // For deeper paths you may return several strings
+ return Arrays.asList("Service templates", "Examples " + exampleUri);
+ }
+
+ /**
+ * Return a list of data values uniquely identifying this service
+ * description (to avoid duplicates). Include only primary key like fields,
+ * ie. ignore descriptions, icons, etc.
+ */
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ // FIXME: Use your fields instead of example fields
+ return Arrays.<Object>asList(exampleString, exampleUri);
+ }
+
+
+ // FIXME: Replace example fields and getters/setters with any required
+ // and optional fields. (All fields are searchable in the Service palette,
+ // for instance try a search for exampleString:3)
+ private String exampleString;
+ private URI exampleUri;
+ public String getExampleString() {
+ return exampleString;
+ }
+ public URI getExampleUri() {
+ return exampleUri;
+ }
+ public void setExampleString(String exampleString) {
+ this.exampleString = exampleString;
+ }
+ public void setExampleUri(URI exampleUri) {
+ this.exampleUri = exampleUri;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProvider.java.bak
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProvider.java.bak b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProvider.java.bak
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+package net.sf.taverna.t2.activities.rest.ui.serviceprovider;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
+import net.sf.taverna.t2.workflowmodel.ConfigurationException;
+
+public class ExampleServiceProvider extends AbstractConfigurableServiceProvider<ExampleServiceProviderConfig>
+ implements ConfigurableServiceProvider<ExampleServiceProviderConfig>
+{
+ public ExampleServiceProvider()
+ {
+ super(new ExampleServiceProviderConfig());
+ }
+
+ /**
+ * Do the actual search for services. Return using the callBack parameter.
+ */
+ @SuppressWarnings("unchecked")
+ public void findServiceDescriptionsAsync(
+ FindServiceDescriptionsCallBack callBack) {
+ // Use callback.status() for long-running searches
+ // callBack.status("Resolving example services");
+
+ List<ServiceDescription> results = new ArrayList<ServiceDescription>();
+
+ // FIXME: Implement the actual service search/lookup instead
+ // of dummy for-loop
+ for (int i = 1; i <= getConfiguration().getNumberOfServices(); i++) {
+ ExampleServiceDesc service = new ExampleServiceDesc();
+ // Populate the service description bean
+ service.setExampleString("Example " + i);
+ service.setExampleUri(getConfiguration().getUri());
+
+ // Optional: set description
+ service.setDescription("Service example number " + i);
+ results.add(service);
+ }
+
+ // partialResults() can also be called several times from inside
+ // for-loop if the full search takes a long time
+ callBack.partialResults(results);
+
+ // No more results will be coming
+ callBack.finished();
+ }
+
+
+// @Override
+// /**
+// * This allows to have a few configured service providers in the Service Panel at startup;
+// * useful if there are some prototypical ones that are useful + need to allow users to add their own
+// * through manual config.
+// */
+// public List<ExampleServiceProviderConfig> getDefaultConfigurations() {
+// ExampleServiceProviderConfig a = new ExampleServiceProviderConfig();
+// a.setUri(URI.create("http://localhost:8181/serviceA"));
+// ExampleServiceProviderConfig b = new ExampleServiceProviderConfig();
+// b.setUri(URI.create("http://fish.com/serviceB"));
+// b.setNumberOfServices(2);
+// return Arrays.asList(a, b);
+// }
+
+
+
+ /**
+ * Icon for service provider
+ */
+ public Icon getIcon() {
+ return null;
+ }
+
+
+ /**
+ * Appears in "Import new services..." in Service Panel
+ */
+ public String getName() {
+ return "My example service";
+ }
+
+ @Override
+ /**
+ * Name of service provider, appears in right click for 'Remove service
+ * provider'
+ */
+ public String toString() {
+ return getName() + " " + getConfiguration().getUri();
+ }
+
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ return Arrays.asList(getConfiguration().getUri());
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProviderConfig.java.bak
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProviderConfig.java.bak b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/serviceprovider/ExampleServiceProviderConfig.java.bak
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+package net.sf.taverna.t2.activities.rest.ui.serviceprovider;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+
+public class ExampleServiceProviderConfig extends PropertyAnnotated
+{
+ private URI uri = URI.create("http://www.example.com");
+ private int numberOfServices = 5;
+
+ @PropertyAnnotation(displayName="Provider URI", preferred=true)
+ public URI getUri() {
+ return uri;
+ }
+
+ public void setUri(URI uri) {
+ this.uri = uri;
+ }
+
+ @PropertyAnnotation(displayName="Number of services")
+ public int getNumberOfServices() {
+ return numberOfServices;
+ }
+
+ public void setNumberOfServices(int numberOfServices) {
+ this.numberOfServices = numberOfServices;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/ConfigureRESTActivityMenuAction.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/ConfigureRESTActivityMenuAction.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/ConfigureRESTActivityMenuAction.java
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+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/ConfigureRESTActivityMenuAction.java
@@ -0,0 +1,66 @@
+package net.sf.taverna.t2.activities.rest.ui.view;
+
+import javax.swing.Action;
+
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+import net.sf.taverna.t2.activities.rest.ui.config.RESTActivityConfigureAction;
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+/**
+ * This action is responsible for enabling the contextual menu entry on processors that perform
+ * RESTActivity'ies.
+ * NB! As a side-effect this also enables the pop-up with for configuration of the processor when it
+ * is added to the workflow from the Service Panel.
+ *
+ * @author Sergejs Aleksejevs
+ * @author David Withers
+ */
+public class ConfigureRESTActivityMenuAction extends AbstractConfigureActivityMenuAction {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public ConfigureRESTActivityMenuAction() {
+ super(GenericRESTTemplateService.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ RESTActivityConfigureAction configAction = new RESTActivityConfigureAction(findActivity(),
+ getParentFrame(), editManager, fileManager, activityIconManager,
+ serviceDescriptionRegistry, serviceRegistry);
+ configAction.putValue(Action.NAME, "Configure REST service");
+ addMenuDots(configAction);
+ return configAction;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextViewFactory.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextViewFactory.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextViewFactory.java
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+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextViewFactory.java
@@ -0,0 +1,62 @@
+package net.sf.taverna.t2.activities.rest.ui.view;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class RESTActivityMainContextViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public boolean canHandle(Object selection) {
+ return selection instanceof Activity
+ && ((Activity) selection).getType()
+ .equals(GenericRESTTemplateService.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity selection) {
+ return Arrays.<ContextualView> asList(new RESTActivityMainContextualView(selection,
+ editManager, fileManager, activityIconManager, colourManager,
+ serviceDescriptionRegistry, serviceRegistry));
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextualView.java
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diff --git a/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextualView.java b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextualView.java
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+++ b/taverna-rest-activity-ui/src/main/java/net/sf/taverna/t2/activities/rest/ui/view/RESTActivityMainContextualView.java
@@ -0,0 +1,220 @@
+package net.sf.taverna.t2.activities.rest.ui.view;
+
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.Action;
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import net.sf.taverna.t2.activities.rest.RESTActivity;
+import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD;
+import net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean;
+import net.sf.taverna.t2.activities.rest.ui.config.RESTActivityConfigureAction;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+@SuppressWarnings("serial")
+public class RESTActivityMainContextualView extends ContextualView {
+
+ private final Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private final Activity activity;
+
+ private JPanel jpMainPanel;
+ private JTextField tfHTTPMethod;
+ private JTextArea taURLSignature;
+ private JTextField tfAcceptHeader;
+ private JLabel jlContentType;
+ private JTextField tfContentTypeHeader;
+ private JLabel jlSendDataAs;
+ private JTextField tfSendDataAs;
+ private JLabel jlSendHTTPExpectRequestHeader;
+ private JTextField tfSendHTTPExpectRequestHeader;
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ColourManager colourManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final ServiceRegistry serviceRegistry;
+
+ public RESTActivityMainContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ColourManager colourManager, ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ServiceRegistry serviceRegistry) {
+ this.activity = activity;
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.colourManager = colourManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.serviceRegistry = serviceRegistry;
+ initView();
+ }
+
+ @Override
+ public JComponent getMainFrame() {
+ jpMainPanel = new JPanel(new GridBagLayout());
+ jpMainPanel
+ .setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(4, 2,
+ 4, 2), BorderFactory.createLineBorder(
+ colourManager.getPreferredColour(RESTActivity.class.getCanonicalName()), 2)));
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.WEST;
+ c.weighty = 0;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ c.insets = new Insets(5, 5, 5, 5);
+ JLabel jlHTTPMethod = new JLabel("HTTP Method:");
+ jlHTTPMethod.setFont(jlHTTPMethod.getFont().deriveFont(Font.BOLD));
+ jpMainPanel.add(jlHTTPMethod, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ tfHTTPMethod = new JTextField();
+ tfHTTPMethod.setEditable(false);
+ jpMainPanel.add(tfHTTPMethod, c);
+ c.weightx = 0;
+
+ c.gridx = 0;
+ c.gridy++;
+ JLabel jlURLSignature = new JLabel("URL Template:");
+ jlURLSignature.setFont(jlURLSignature.getFont().deriveFont(Font.BOLD));
+ jpMainPanel.add(jlURLSignature, c);
+
+ c.gridx++;
+ taURLSignature = new JTextArea(3, 30);
+ taURLSignature.setEditable(false);
+ taURLSignature.setLineWrap(true);
+ JScrollPane spURLSignature = new JScrollPane(taURLSignature);
+ jpMainPanel.add(spURLSignature, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ JLabel jlAcceptHeader = new JLabel("'Accept' header:");
+ jlAcceptHeader.setFont(jlAcceptHeader.getFont().deriveFont(Font.BOLD));
+ jpMainPanel.add(jlAcceptHeader, c);
+
+ c.gridx++;
+ tfAcceptHeader = new JTextField();
+ tfAcceptHeader.setEditable(false);
+ jpMainPanel.add(tfAcceptHeader, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ jlContentType = new JLabel("'Content-Type' header:");
+ jlContentType.setFont(jlContentType.getFont().deriveFont(Font.BOLD));
+ jlContentType.setVisible(false);
+ jpMainPanel.add(jlContentType, c);
+
+ c.gridx++;
+ tfContentTypeHeader = new JTextField();
+ tfContentTypeHeader.setEditable(false);
+ tfContentTypeHeader.setVisible(false);
+ jpMainPanel.add(tfContentTypeHeader, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ jlSendDataAs = new JLabel("Send data as:");
+ jlSendDataAs.setFont(jlSendDataAs.getFont().deriveFont(Font.BOLD));
+ jlSendDataAs.setVisible(false);
+ jpMainPanel.add(jlSendDataAs, c);
+
+ c.gridx++;
+ tfSendDataAs = new JTextField();
+ tfSendDataAs.setEditable(false);
+ tfSendDataAs.setVisible(false);
+ jpMainPanel.add(tfSendDataAs, c);
+
+ c.gridx = 0;
+ c.gridy++;
+ jlSendHTTPExpectRequestHeader = new JLabel("Send HTTP 'Expect' header:");
+ jlSendHTTPExpectRequestHeader.setFont(jlSendHTTPExpectRequestHeader.getFont().deriveFont(
+ Font.BOLD));
+ jlSendHTTPExpectRequestHeader.setVisible(false);
+ jpMainPanel.add(jlSendHTTPExpectRequestHeader, c);
+
+ c.gridx++;
+ tfSendHTTPExpectRequestHeader = new JTextField();
+ tfSendHTTPExpectRequestHeader.setEditable(false);
+ tfSendHTTPExpectRequestHeader.setVisible(false);
+ jpMainPanel.add(tfSendHTTPExpectRequestHeader, c);
+
+ // populate the view with values
+ refreshView();
+
+ return jpMainPanel;
+ }
+
+ @Override
+ /**
+ * This is the title of the contextual view - shown in the list of other available
+ * views (even when this contextual view is collapsed).
+ */
+ public String getViewTitle() {
+ return "REST Service Details";
+ }
+
+ /**
+ * Typically called when the activity configuration has changed.
+ */
+ @Override
+ public void refreshView() {
+ Configuration configuration = scufl2Tools.configurationFor(activity, activity.getParent());
+ RESTActivityConfigurationBean configurationBean = new RESTActivityConfigurationBean(configuration.getJson());
+
+ // toggle visibility of the elements that do not always appear
+ HTTP_METHOD httpMethod = configurationBean.getHttpMethod();
+ jlContentType.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ tfContentTypeHeader.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ jlSendDataAs.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ tfSendDataAs.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ jlSendHTTPExpectRequestHeader.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ tfSendHTTPExpectRequestHeader.setVisible(httpMethod == HTTP_METHOD.POST || httpMethod == HTTP_METHOD.PUT);
+ jpMainPanel.revalidate();
+
+ tfHTTPMethod.setText("" + configurationBean.getHttpMethod());
+ taURLSignature.setText(configurationBean.getUrlSignature());
+ tfAcceptHeader.setText(configurationBean.getAcceptsHeaderValue());
+ tfContentTypeHeader.setText(configurationBean.getContentTypeForUpdates());
+ tfSendDataAs.setText("" + configurationBean.getOutgoingDataFormat());
+ tfSendHTTPExpectRequestHeader.setText("" + configurationBean.getSendHTTPExpectRequestHeader());
+ }
+
+ /**
+ * View position hint
+ */
+ @Override
+ public int getPreferredPosition() {
+ // want to be on top, as it's the main contextual view for this activity
+ return 100;
+ }
+
+ @Override
+ public Action getConfigureAction(final Frame owner) {
+ // "Configure" button appears because of this action being returned
+ return new RESTActivityConfigureAction(activity, owner, editManager, fileManager,
+ activityIconManager, serviceDescriptionRegistry, serviceRegistry);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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+net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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@@ -0,0 +1,3 @@
+net.sf.taverna.t2.activities.rest.ui.view.ConfigureRESTActivityMenuAction
+net.sf.taverna.t2.activities.rest.ui.menu.AddRESTTemplateAction
+net.sf.taverna.t2.activities.rest.ui.menu.AddRESTTemplateMenuAction
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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+net.sf.taverna.t2.activities.rest.ui.servicedescription.RESTActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..5325bf1
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+ net.sf.taverna.t2.activities.rest.ui.view.RESTActivityMainContextViewFactory
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context-osgi.xml b/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..643d5be
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context-osgi.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="RESTActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="GenericRESTTemplateService" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="ConfigureRESTActivityMenuAction" auto-export="interfaces" />
+ <service ref="AddRESTTemplateAction" auto-export="interfaces" />
+ <service ref="AddRESTTemplateMenuAction" auto-export="interfaces" />
+
+ <service ref="RESTActivityMainContextViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context.xml
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diff --git a/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context.xml b/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context.xml
new file mode 100644
index 0000000..2b699e7
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/resources/META-INF/spring/rest-activity-ui-context.xml
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="RESTActivityIcon"
+ class="net.sf.taverna.t2.activities.rest.ui.servicedescription.RESTActivityIcon">
+ <property name="colourManager" ref="colourManager" />
+ </bean>
+
+ <bean id="GenericRESTTemplateService"
+ class="net.sf.taverna.t2.activities.rest.ui.servicedescription.GenericRESTTemplateService" />
+
+ <bean id="ConfigureRESTActivityMenuAction"
+ class="net.sf.taverna.t2.activities.rest.ui.view.ConfigureRESTActivityMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="AddRESTTemplateAction"
+ class="net.sf.taverna.t2.activities.rest.ui.menu.AddRESTTemplateAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="AddRESTTemplateMenuAction"
+ class="net.sf.taverna.t2.activities.rest.ui.menu.AddRESTTemplateMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+ <bean id="RESTActivityMainContextViewFactory"
+ class="net.sf.taverna.t2.activities.rest.ui.view.RESTActivityMainContextViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/information.png
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/information.png b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/information.png
new file mode 100644
index 0000000..12cd1ae
Binary files /dev/null and b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/information.png differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/mediatypes.txt
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/mediatypes.txt b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/mediatypes.txt
new file mode 100644
index 0000000..4f0f0f4
--- /dev/null
+++ b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/config/mediatypes.txt
@@ -0,0 +1,65 @@
+application/atom+xml
+application/http
+application/javascript
+application/json
+application/octet-stream
+application/ogg
+application/pdf
+application/postscript
+application/rdf+xml
+application/sparql-query
+application/sparql-results+xml
+application/vnd.taverna.scufl+xml
+application/vnd.taverna.t2flow+xml
+application/x-gzip
+application/x-rar-compressed
+application/x-shockwave-flash
+application/x-tar
+application/x-www-form-urlencoded
+application/xhtml+xml
+application/xml
+application/zip
+audio/mp4
+audio/mpeg
+audio/mpeg4-generic
+audio/ogg
+audio/vnd.wave
+audio/vorbis
+audio/webm
+audio/x-ms-wma
+image/gif
+image/jpeg
+image/png
+image/svg+xml
+image/tiff
+image/vnd.microsoft.icon
+message/http
+message/rfc822
+multipart/alternative
+multipart/byteranges
+multipart/digest
+multipart/encrypted
+multipart/form-data
+multipart/mixed
+multipart/related
+multipart/signed
+text/css
+text/csv
+text/html
+text/javascript
+text/n3
+text/plain
+text/tab-separated-values
+text/turtle
+text/uri-list
+text/vcard
+text/xml
+video/H264
+video/MPV
+video/mp4
+video/mpeg
+video/mpeg4-generic
+video/ogg
+video/quicktime
+video/webm
+video/x-ms-wmv
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/servicedescription/service_type_rest.png
----------------------------------------------------------------------
diff --git a/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/servicedescription/service_type_rest.png b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/servicedescription/service_type_rest.png
new file mode 100644
index 0000000..a4276c2
Binary files /dev/null and b/taverna-rest-activity-ui/src/main/resources/net/sf/taverna/t2/activities/rest/ui/servicedescription/service_type_rest.png differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/pom.xml b/taverna-spreadsheet-import-activity-ui/pom.xml
new file mode 100644
index 0000000..1672ebf
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/pom.xml
@@ -0,0 +1,107 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>spreadsheet-import-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 Spreadsheet Import Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>spreadsheet-import-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <!-- taverna lang -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+ <!-- taverna ui-api -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <!-- taverna ui-components -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}
+ </version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson-databind.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.lang</artifactId>
+ <version>${commons.lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.log4j</groupId>
+ <artifactId>com.springsource.org.apache.log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/actions/SpreadsheetImportActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/actions/SpreadsheetImportActivityConfigurationAction.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/actions/SpreadsheetImportActivityConfigurationAction.java
new file mode 100644
index 0000000..0a70680
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/actions/SpreadsheetImportActivityConfigurationAction.java
@@ -0,0 +1,72 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import net.sf.taverna.t2.activities.spreadsheet.views.SpreadsheetImportConfigView;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+/**
+ * The configuration action for a SpreadsheetImport activity.
+ *
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class SpreadsheetImportActivityConfigurationAction extends ActivityConfigurationAction {
+
+ private static final String CONFIGURE = "Configure";
+
+ private final EditManager editManager;
+
+ private final FileManager fileManager;
+
+ private final ServiceRegistry serviceRegistry;
+
+ public SpreadsheetImportActivityConfigurationAction(Activity activity,
+ Frame owner, EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.serviceRegistry = serviceRegistry;
+ putValue(NAME, CONFIGURE);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final SpreadsheetImportConfigView spreadsheetConfigView = new SpreadsheetImportConfigView(
+ getActivity(), serviceRegistry);
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
+ spreadsheetConfigView, editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+
+ }
+}
[16/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
Revert "Temporarily empty repository"
This reverts commit b4725724cecebe7fff940832c4cbaa4ed62dd621.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/commit/54050685
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/tree/54050685
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/diff/54050685
Branch: refs/heads/master
Commit: 54050685ced90e271dd5974b5b285ce5ca2691ce
Parents: b472572
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Feb 23 10:23:03 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Feb 23 10:23:03 2015 +0000
----------------------------------------------------------------------
pom.xml | 42 +
taverna-beanshell-activity-ui/pom.xml | 100 +
.../BeanshellActivityConfigurationAction.java | 71 +
.../menu/AddBeanshellTemplateAction.java | 113 ++
.../menu/AddBeanshellTemplateMenuAction.java | 121 ++
.../menu/ConfigureBeanshellMenuAction.java | 67 +
.../BeanshellActivityIcon.java | 58 +
.../BeanshellTemplateService.java | 57 +
.../views/BeanshellActivityViewFactory.java | 84 +
.../views/BeanshellConfigurationPanel.java | 231 +++
.../views/BeanshellContextualView.java | 104 +
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 3 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../beanshell-activity-ui-context-osgi.xml | 29 +
.../spring/beanshell-activity-ui-context.xml | 43 +
.../src/main/resources/beanshell.png | Bin 0 -> 1015 bytes
.../t2/activities/beanshell/views/keys.txt | 90 +
taverna-external-tool-activity-ui/pom.xml | 108 +
.../ExternalToolActivityConfigureAction.java | 83 +
.../ToolInvocationConfiguration.java | 57 +
.../externaltool/manager/GroupPanel.java | 113 ++
.../InvocationGroupManagerShutdownHook.java | 34 +
.../InvocationGroupManagerStartupHook.java | 47 +
.../manager/InvocationMechanismEditor.java | 28 +
.../externaltool/manager/MechanismPanel.java | 121 ++
.../ToolInvocationConfigurationPanel.java | 379 ++++
.../ToolInvocationConfigurationUIFactory.java | 54 +
.../local/LocalInvocationMechanismEditor.java | 122 ++
.../manager/ssh/ExternalToolSshNodeViewer.java | 110 +
.../ssh/SshInvocationMechanismEditor.java | 234 +++
.../AddExternalToolContextualMenuAction.java | 111 +
.../menu/AddExternalToolMenuAction.java | 111 +
.../menu/ConfigureExternalToolMenuAction.java | 69 +
.../externaltool/menu/FeedbackMenuAction.java | 82 +
.../AddExternalToolServiceDialog.java | 189 ++
.../ExternalToolActivityIcon.java | 73 +
.../ExternalToolServiceDescription.java | 149 ++
.../ExternalToolServiceProvider.java | 132 ++
.../ExternalToolServiceProviderConfig.java | 56 +
.../ExternalToolTemplateServiceDescription.java | 77 +
.../t2/activities/externaltool/utils/Tools.java | 129 ++
.../externaltool/views/AnnotationPanel.java | 41 +
.../externaltool/views/EditablePanel.java | 76 +
.../ExternalToolActivityContextualView.java | 181 ++
.../views/ExternalToolActivityViewFactory.java | 76 +
.../views/ExternalToolConfigView.java | 868 ++++++++
.../views/ExternalToolFileViewer.java | 103 +
.../ExternalToolRuntimeEnvironmentViewer.java | 56 +
.../views/ExternalToolStaticStringViewer.java | 53 +
.../views/ExternalToolStaticUrlViewer.java | 56 +
.../ExternalToolStringReplacementViewer.java | 97 +
.../externaltool/views/FilePanel.java | 119 ++
.../externaltool/views/InvocationPanel.java | 396 ++++
.../views/LoadDescriptionAction.java | 89 +
.../views/SaveDescriptionAction.java | 124 ++
.../externaltool/views/ScriptPanel.java | 149 ++
.../externaltool/views/StaticStringPanel.java | 106 +
.../externaltool/views/StaticUrlPanel.java | 108 +
.../views/StringReplacementPanel.java | 134 ++
.../externaltool/views/ToolXMLPanel.java | 33 +
...ternaltool.manager.InvocationMechanismEditor | 2 +
...rvicedescriptions.ServiceDescriptionProvider | 2 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 4 +
.../net.sf.taverna.t2.workbench.ShutdownSPI | 1 +
.../net.sf.taverna.t2.workbench.StartupSPI | 1 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...rkbench.configuration.ConfigurationUIFactory | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../external-tool-activity-ui-context-osgi.xml | 39 +
.../external-tool-activity-ui-context.xml | 50 +
.../src/main/resources/externaltool.png | Bin 0 -> 743 bytes
taverna-localworker-activity-ui/pom.xml | 142 ++
.../LocalworkerActivityConfigurationAction.java | 117 ++
.../menu/ConfigureLocalworkerMenuAction.java | 62 +
.../LocalworkerActivityIcon.java | 58 +
.../LocalworkerServiceDescription.java | 105 +
.../LocalworkerServiceProvider.java | 297 +++
.../views/LocalworkerActivityConfigView.java | 42 +
.../LocalworkerActivityContextualView.java | 115 ++
.../views/LocalworkerActivityViewFactory.java | 82 +
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../localworker-activity-ui-context-osgi.xml | 24 +
.../spring/localworker-activity-ui-context.xml | 27 +
.../src/main/resources/localworker.png | Bin 0 -> 706 bytes
.../src/main/resources/localworker_names | 67 +
...rna.scuflworkers.biojava.GenBankParserWorker | 74 +
...cuflworkers.biojava.GenBankParserWorker.json | 16 +
...verna.scuflworkers.biojava.ReverseCompWorker | 43 +
....scuflworkers.biojava.ReverseCompWorker.json | 16 +
...a.scuflworkers.biojava.SwissProtParserWorker | 72 +
...flworkers.biojava.SwissProtParserWorker.json | 16 +
...averna.scuflworkers.biojava.TranscribeWorker | 48 +
...a.scuflworkers.biojava.TranscribeWorker.json | 16 +
...na.scuflworkers.io.ConcatenateFileListWorker | 101 +
...uflworkers.io.ConcatenateFileListWorker.json | 24 +
...ge.taverna.scuflworkers.io.EnvVariableWorker | 33 +
...verna.scuflworkers.io.EnvVariableWorker.json | 11 +
...ge.taverna.scuflworkers.io.FileListByExtTask | 73 +
...verna.scuflworkers.io.FileListByExtTask.json | 20 +
....taverna.scuflworkers.io.FileListByRegexTask | 71 +
...rna.scuflworkers.io.FileListByRegexTask.json | 20 +
...ceforge.taverna.scuflworkers.io.LocalCommand | 80 +
...ge.taverna.scuflworkers.io.LocalCommand.json | 20 +
...forge.taverna.scuflworkers.io.TextFileReader | 76 +
....taverna.scuflworkers.io.TextFileReader.json | 20 +
...forge.taverna.scuflworkers.io.TextFileWriter | 57 +
....taverna.scuflworkers.io.TextFileWriter.json | 24 +
...rge.taverna.scuflworkers.jdbc.SQLQueryWorker | 309 +++
...averna.scuflworkers.jdbc.SQLQueryWorker.json | 44 +
...ge.taverna.scuflworkers.jdbc.SQLUpdateWorker | 229 +++
...verna.scuflworkers.jdbc.SQLUpdateWorker.json | 36 +
...erna.scuflworkers.ncbi.NucleotideFastaWorker | 45 +
...scuflworkers.ncbi.NucleotideFastaWorker.json | 16 +
...erna.scuflworkers.ncbi.NucleotideGBSeqWorker | 45 +
...scuflworkers.ncbi.NucleotideGBSeqWorker.json | 16 +
...scuflworkers.ncbi.NucleotideINSDSeqXMLWorker | 45 +
...workers.ncbi.NucleotideINSDSeqXMLWorker.json | 16 +
...scuflworkers.ncbi.NucleotideTinySeqXMLWorker | 45 +
...workers.ncbi.NucleotideTinySeqXMLWorker.json | 16 +
...taverna.scuflworkers.ncbi.ProteinFastaWorker | 45 +
...na.scuflworkers.ncbi.ProteinFastaWorker.json | 16 +
...taverna.scuflworkers.ncbi.ProteinGBSeqWorker | 45 +
...na.scuflworkers.ncbi.ProteinGBSeqWorker.json | 16 +
...na.scuflworkers.ncbi.ProteinINSDSeqXMLWorker | 45 +
...uflworkers.ncbi.ProteinINSDSeqXMLWorker.json | 16 +
...na.scuflworkers.ncbi.ProteinTinySeqXMLWorker | 45 +
...uflworkers.ncbi.ProteinTinySeqXMLWorker.json | 16 +
...taverna.scuflworkers.ncbi.PubMedEFetchWorker | 68 +
...na.scuflworkers.ncbi.PubMedEFetchWorker.json | 24 +
...averna.scuflworkers.ncbi.PubMedESearchWorker | 124 ++
...a.scuflworkers.ncbi.PubMedESearchWorker.json | 44 +
...urceforge.taverna.scuflworkers.net.BrowseUrl | 31 +
...orge.taverna.scuflworkers.net.BrowseUrl.json | 11 +
...forge.taverna.scuflworkers.net.ExtractHeader | 55 +
....taverna.scuflworkers.net.ExtractHeader.json | 20 +
...ourceforge.taverna.scuflworkers.ui.AskWorker | 41 +
...forge.taverna.scuflworkers.ui.AskWorker.json | 20 +
...ceforge.taverna.scuflworkers.ui.ChooseWorker | 80 +
...ge.taverna.scuflworkers.ui.ChooseWorker.json | 24 +
...rge.taverna.scuflworkers.ui.SelectFileWorker | 116 ++
...averna.scuflworkers.ui.SelectFileWorker.json | 24 +
...ceforge.taverna.scuflworkers.ui.SelectWorker | 53 +
...ge.taverna.scuflworkers.ui.SelectWorker.json | 24 +
...urceforge.taverna.scuflworkers.ui.TellWorker | 42 +
...orge.taverna.scuflworkers.ui.TellWorker.json | 20 +
...urceforge.taverna.scuflworkers.ui.WarnWorker | 42 +
...orge.taverna.scuflworkers.ui.WarnWorker.json | 20 +
...rge.taverna.scuflworkers.xml.XPathTextWorker | 75 +
...averna.scuflworkers.xml.XPathTextWorker.json | 24 +
...rceforge.taverna.scuflworkers.xml.XSLTWorker | 152 ++
...rge.taverna.scuflworkers.xml.XSLTWorker.json | 28 +
...na.scuflworkers.xml.XSLTWorkerWithParameters | 100 +
...uflworkers.xml.XSLTWorkerWithParameters.json | 24 +
...escience.scuflworkers.java.ByteArrayToString | 44 +
...nce.scuflworkers.java.ByteArrayToString.json | 20 +
....ebi.escience.scuflworkers.java.DecodeBase64 | 31 +
...escience.scuflworkers.java.DecodeBase64.json | 16 +
...embl.ebi.escience.scuflworkers.java.EchoList | 26 +
...ebi.escience.scuflworkers.java.EchoList.json | 16 +
...escience.scuflworkers.java.EmitLotsOfStrings | 19 +
...nce.scuflworkers.java.EmitLotsOfStrings.json | 11 +
....ebi.escience.scuflworkers.java.EncodeBase64 | 30 +
...escience.scuflworkers.java.EncodeBase64.json | 16 +
...escience.scuflworkers.java.ExtractImageLinks | 41 +
...nce.scuflworkers.java.ExtractImageLinks.json | 16 +
....escience.scuflworkers.java.FilterStringList | 43 +
...ence.scuflworkers.java.FilterStringList.json | 20 +
...l.ebi.escience.scuflworkers.java.FlattenList | 39 +
....escience.scuflworkers.java.FlattenList.json | 16 +
...mbl.ebi.escience.scuflworkers.java.PadNumber | 44 +
...bi.escience.scuflworkers.java.PadNumber.json | 20 +
...cuflworkers.java.RegularExpressionStringList | 60 +
...orkers.java.RegularExpressionStringList.json | 24 +
...mbl.ebi.escience.scuflworkers.java.SendEmail | 85 +
...bi.escience.scuflworkers.java.SendEmail.json | 27 +
....ebi.escience.scuflworkers.java.SplitByRegex | 47 +
...escience.scuflworkers.java.SplitByRegex.json | 20 +
....ebi.escience.scuflworkers.java.StringConcat | 36 +
...escience.scuflworkers.java.StringConcat.json | 20 +
...i.escience.scuflworkers.java.StringListMerge | 49 +
...ience.scuflworkers.java.StringListMerge.json | 20 +
...cience.scuflworkers.java.StringSetDifference | 49 +
...e.scuflworkers.java.StringSetDifference.json | 20 +
...ence.scuflworkers.java.StringSetIntersection | 43 +
...scuflworkers.java.StringSetIntersection.json | 20 +
...bi.escience.scuflworkers.java.StringSetUnion | 43 +
...cience.scuflworkers.java.StringSetUnion.json | 20 +
...ence.scuflworkers.java.StringStripDuplicates | 33 +
...scuflworkers.java.StringStripDuplicates.json | 16 +
...scuflworkers.java.TestAlwaysFailingProcessor | 36 +
...workers.java.TestAlwaysFailingProcessor.json | 20 +
...science.scuflworkers.java.TestSometimesFails | 34 +
...ce.scuflworkers.java.TestSometimesFails.json | 16 +
...i.escience.scuflworkers.java.WebImageFetcher | 64 +
...ience.scuflworkers.java.WebImageFetcher.json | 20 +
...bi.escience.scuflworkers.java.WebPageFetcher | 68 +
...cience.scuflworkers.java.WebPageFetcher.json | 20 +
taverna-rest-activity-ui/pom.xml | 74 +
.../rest/ui/config/HTTPHeadersTableModel.java | 119 ++
.../config/RESTActivityConfigurationPanel.java | 670 +++++++
.../ui/config/RESTActivityConfigureAction.java | 51 +
.../rest/ui/menu/AddRESTTemplateAction.java | 107 +
.../rest/ui/menu/AddRESTTemplateMenuAction.java | 114 ++
.../GenericRESTTemplateService.java | 76 +
.../ui/servicedescription/RESTActivityIcon.java | 54 +
.../serviceprovider/ExampleServiceDesc.java.bak | 99 +
.../ExampleServiceProvider.java.bak | 106 +
.../ExampleServiceProviderConfig.java.bak | 31 +
.../view/ConfigureRESTActivityMenuAction.java | 66 +
.../RESTActivityMainContextViewFactory.java | 62 +
.../ui/view/RESTActivityMainContextualView.java | 220 ++
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 3 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../spring/rest-activity-ui-context-osgi.xml | 28 +
.../spring/rest-activity-ui-context.xml | 50 +
.../activities/rest/ui/config/information.png | Bin 0 -> 778 bytes
.../t2/activities/rest/ui/config/mediatypes.txt | 65 +
.../ui/servicedescription/service_type_rest.png | Bin 0 -> 1137 bytes
taverna-spreadsheet-import-activity-ui/pom.xml | 107 +
...dsheetImportActivityConfigurationAction.java | 72 +
.../il8n/SpreadsheetImportUIText.java | 46 +
.../SpreadsheetImportAddTemplateAction.java | 110 +
.../SpreadsheetImportAddTemplateMenuAction.java | 124 ++
.../SpreadsheetImportConfigureMenuAction.java | 84 +
.../SpreadsheetImportActivityIcon.java | 71 +
.../SpreadsheetImportTemplateService.java | 95 +
.../SpreadsheetImportConfigTableModel.java | 190 ++
.../views/SpreadsheetImportConfigView.java | 1082 ++++++++++
.../views/SpreadsheetImportContextualView.java | 121 ++
.../SpreadsheetImportContextualViewFactory.java | 87 +
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 3 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
...eadsheet-import-activity-ui-context-osgi.xml | 28 +
.../spreadsheet-import-activity-ui-context.xml | 45 +
.../spreadsheet/iln8/ui-text.properties | 43 +
.../src/main/resources/spreadsheet-import.png | Bin 0 -> 4610 bytes
taverna-wsdl-activity-ui/pom.xml | 95 +
.../actions/AbstractAddXMLSplitterAction.java | 156 ++
.../wsdl/actions/AddXMLInputSplitterAction.java | 104 +
.../actions/AddXMLOutputSplitterAction.java | 105 +
.../wsdl/actions/AddXMLSplitterEdit.java | 315 +++
.../actions/WSDLActivityConfigureAction.java | 71 +
.../wsdl/actions/XMLSplitterPortBuilder.java | 127 ++
...LInputSplitterForWSDLActivityMenuAction.java | 11 +
...utSplitterForXMLInputSplitterMenuAction.java | 11 +
.../menu/AddXMLInputSplitterMenuAction.java | 70 +
...OutputSplitterForWSDLActivityMenuAction.java | 11 +
...tSplitterForXMLOutputSplitterMenuAction.java | 11 +
.../menu/AddXMLOutputSplitterMenuAction.java | 66 +
.../wsdl/menu/ConfigureWSDLMenuAction.java | 78 +
.../AddWSDLServiceDialog.java | 303 +++
.../ConfirmTrustedCertificateDialog.java | 586 ++++++
.../servicedescriptions/WSDLActivityIcon.java | 60 +
.../WSDLServiceDescription.java | 154 ++
.../WSDLServiceProvider.java | 206 ++
.../WSDLServiceProviderConfig.java | 32 +
.../XMLInputSplitterActivityIcon.java | 63 +
.../XMLOutputSplitterActivityIcon.java | 64 +
.../views/AbstractXMLSplitterActionView.java | 159 ++
.../views/WSDLActivityConfigurationView.java | 446 +++++
.../wsdl/views/WSDLActivityContextualView.java | 108 +
.../wsdl/views/WSDLActivityViewFactory.java | 88 +
.../wsdl/views/XMLSplitterContextualView.java | 78 +
.../wsdl/views/XMLSplitterViewFactory.java | 66 +
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 5 +
...a.t2.workbench.activityicons.ActivityIconSPI | 3 +
...ntextualviews.activity.ContextualViewFactory | 2 +
.../spring/wsdl-activity-ui-context-osgi.xml | 37 +
.../spring/wsdl-activity-ui-context.xml | 53 +
.../src/main/resources/wsdl.png | Bin 0 -> 748 bytes
.../src/main/resources/xml-input-splitter.png | Bin 0 -> 309 bytes
.../src/main/resources/xml-output-splitter.png | Bin 0 -> 298 bytes
.../src/main/resources/xml-splitter.png | Bin 0 -> 327 bytes
.../views/TestWSDLActivityContextualView.java | 53 +
.../src/test/resources/GMService.wsdl | 68 +
.../src/test/resources/kegg.wsdl | 1889 ++++++++++++++++++
taverna-xpath-activity-ui/pom.xml | 68 +
.../xpath/ui/config/TwoFieldQueryPanel.java | 110 +
.../config/XPathActivityConfigurationPanel.java | 1202 +++++++++++
...XPathActivityConfigurationPanelProvider.java | 158 ++
.../ui/config/XPathActivityConfigureAction.java | 52 +
.../ui/config/xmltree/TableCellListener.java | 186 ++
.../ui/config/xmltree/XPathActivityXMLTree.java | 572 ++++++
.../XPathActivityXMLTreeAttributeNode.java | 50 +
.../XPathActivityXMLTreeElementNode.java | 62 +
.../xmltree/XPathActivityXMLTreeNode.java | 81 +
.../XPathActivityXMLTreeSelectionHandler.java | 251 +++
.../ConfigureXPathActivityMenuAction.java | 65 +
.../XPathActivityMainContextViewFactory.java | 59 +
.../XPathActivityMainContextualView.java | 209 ++
.../xpath/ui/menu/AddXPathTemplateAction.java | 110 +
.../ui/menu/AddXPathTemplateMenuAction.java | 117 ++
.../servicedescription/XPathActivityIcon.java | 86 +
.../XPathTemplateService.java | 57 +
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 3 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../spring/xpath-activity-ui-context-osgi.xml | 28 +
.../spring/xpath-activity-ui-context.xml | 49 +
.../xpath/ui/servicedescription/arrow_right.png | Bin 0 -> 596 bytes
.../famfamfam_silk/accept.png | Bin 0 -> 781 bytes
.../famfamfam_silk/exclamation.png | Bin 0 -> 701 bytes
.../servicedescription/famfamfam_silk/help.png | Bin 0 -> 786 bytes
.../famfamfam_silk/page_white_code.png | Bin 0 -> 603 bytes
.../servicedescription/famfamfam_silk/tag.png | Bin 0 -> 389 bytes
.../text_linespacing (collapse).png | Bin 0 -> 371 bytes
.../famfamfam_silk/text_linespacing.png | Bin 0 -> 363 bytes
.../xpath/ui/servicedescription/folds/fold.png | Bin 0 -> 331 bytes
.../ui/servicedescription/folds/unfold.png | Bin 0 -> 334 bytes
.../ui/servicedescription/xpath_attribute.png | Bin 0 -> 1426 bytes
.../src/test/java/Dom4JTest.java | 71 +
322 files changed, 26407 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..0c60cf1
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,42 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>1-incubating-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.workbench.commonactivities</groupId>
+ <artifactId>taverna-workbench-commonactivities</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache Taverna Workbench Common Activities</name>
+ <description>User interface and Workbench integration for common activities</description>
+ <properties>
+ <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
+ <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
+ <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
+ <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
+ <taverna.workbench.version>3.1.0-incubating-SNAPSHOT</taverna.workbench.version>
+ </properties>
+ <modules>
+ <module>taverna-beanshell-activity-ui</module>
+ <module>taverna-external-tool-activity-ui</module>
+ <module>taverna-localworker-activity-ui</module>
+ <module>taverna-rest-activity-ui</module>
+ <module>taverna-spreadsheet-import-activity-ui</module>
+ <module>taverna-wsdl-activity-ui</module>
+ <module>taverna-xpath-activity-ui</module>
+ </modules>
+ <repositories>
+ <repository>
+ <id>taverna-incubating</id>
+ <name>Apache Taverna incubating Repository</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ </repositories>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/pom.xml b/taverna-beanshell-activity-ui/pom.xml
new file mode 100644
index 0000000..0afe9ef
--- /dev/null
+++ b/taverna-beanshell-activity-ui/pom.xml
@@ -0,0 +1,100 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>beanshell-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 Beanshell Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.commons</groupId>
+ <artifactId>taverna-services-api</artifactId>
+ <version>0.1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/actions/BeanshellActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/actions/BeanshellActivityConfigurationAction.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/actions/BeanshellActivityConfigurationAction.java
new file mode 100644
index 0000000..fe6159c
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/actions/BeanshellActivityConfigurationAction.java
@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigurationPanel;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class BeanshellActivityConfigurationAction extends ActivityConfigurationAction {
+
+ public static final String EDIT_BEANSHELL_SCRIPT = "Edit beanshell script";
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ApplicationConfiguration applicationConfiguration;
+
+ public BeanshellActivityConfigurationAction(Activity activity, Frame owner,
+ EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.applicationConfiguration = applicationConfiguration;
+ putValue(NAME, EDIT_BEANSHELL_SCRIPT);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+ final BeanshellConfigurationPanel beanshellConfigView = new BeanshellConfigurationPanel(
+ getActivity(), applicationConfiguration);
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
+ beanshellConfigView, editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateAction.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateAction.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateAction.java
new file mode 100644
index 0000000..97eab18
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateAction.java
@@ -0,0 +1,113 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.menu;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+/**
+ * An action to add a beanshell activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class AddBeanshellTemplateAction extends AbstractContextualMenuAction {
+
+ private static final String ADD_BEANSHELL = "Beanshell";
+
+ private static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public AddBeanshellTemplateAction() {
+ super(insertSection, 300);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+
+ return new AddBeanshellAction();
+ }
+
+ protected class AddBeanshellAction extends AbstractAction {
+ AddBeanshellAction() {
+ super(ADD_BEANSHELL, activityIconManager
+ .iconForActivity(BeanshellTemplateService.ACTIVITY_TYPE));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(serviceDescriptionRegistry
+ .getServiceDescription(BeanshellTemplateService.ACTIVITY_TYPE), false,
+ editManager, menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateMenuAction.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateMenuAction.java
new file mode 100644
index 0000000..7933000
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/AddBeanshellTemplateMenuAction.java
@@ -0,0 +1,121 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.menu;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+/**
+ * An action to add a beanshell activity + a wrapping processor to the workflow.
+ *
+ * @author Alex Nenadic
+ * @author alanrw
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class AddBeanshellTemplateMenuAction extends AbstractMenuAction {
+
+ private static final String ADD_BEANSHELL = "Beanshell";
+
+ private static final URI INSERT = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#insert");
+
+ private static final URI ADD_BEANSHELL_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuAddBeanshell");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public AddBeanshellTemplateMenuAction() {
+ super(INSERT, 300, ADD_BEANSHELL_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddBeanshellMenuAction();
+ }
+
+ protected class AddBeanshellMenuAction extends AbstractAction implements DesignOnlyAction {
+ AddBeanshellMenuAction() {
+ super();
+ putValue(SMALL_ICON,
+ activityIconManager.iconForActivity(BeanshellTemplateService.ACTIVITY_TYPE));
+ putValue(NAME, ADD_BEANSHELL);
+ putValue(SHORT_DESCRIPTION, "Beanshell service");
+ putValue(
+ Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_B, InputEvent.SHIFT_DOWN_MASK
+ | InputEvent.ALT_DOWN_MASK));
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(serviceDescriptionRegistry
+ .getServiceDescription(BeanshellTemplateService.ACTIVITY_TYPE), false,
+ editManager, menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/ConfigureBeanshellMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/ConfigureBeanshellMenuAction.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/ConfigureBeanshellMenuAction.java
new file mode 100644
index 0000000..64ef0c8
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/menu/ConfigureBeanshellMenuAction.java
@@ -0,0 +1,67 @@
+package net.sf.taverna.t2.activities.beanshell.menu;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
+import net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+import javax.swing.Action;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class ConfigureBeanshellMenuAction extends AbstractConfigureActivityMenuAction {
+
+ public static final URI LOCALWORKER_ACTIVITY = URI
+ .create("http://ns.taverna.org.uk/2010/activity/localworker");
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ApplicationConfiguration applicationConfiguration;
+
+ public ConfigureBeanshellMenuAction() {
+ super(BeanshellTemplateService.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ Activity a = findActivity();
+ Action result = null;
+ if (!(a.getType().equals(LOCALWORKER_ACTIVITY))) {
+ result = new BeanshellActivityConfigurationAction(findActivity(), getParentFrame(),
+ editManager, fileManager, activityIconManager, serviceDescriptionRegistry,
+ applicationConfiguration);
+ result.putValue(Action.NAME, BeanshellActivityConfigurationAction.EDIT_BEANSHELL_SCRIPT);
+ addMenuDots(result);
+ }
+ return result;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellActivityIcon.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellActivityIcon.java
new file mode 100644
index 0000000..055aa81
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellActivityIcon.java
@@ -0,0 +1,58 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+
+/**
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+public class BeanshellActivityIcon implements ActivityIconSPI {
+
+ private static Icon icon = null;
+
+ @Override
+ public int canProvideIconScore(URI activityType) {
+ if (BeanshellTemplateService.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ @Override
+ public Icon getIcon(URI activityType) {
+ return getBeanshellIcon();
+ }
+
+ public static Icon getBeanshellIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(BeanshellActivityIcon.class.getResource("/beanshell.png"));
+ }
+ return icon;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellTemplateService.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellTemplateService.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellTemplateService.java
new file mode 100644
index 0000000..c2cb38f
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/servicedescriptions/BeanshellTemplateService.java
@@ -0,0 +1,57 @@
+package net.sf.taverna.t2.activities.beanshell.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.servicedescriptions.AbstractTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+public class BeanshellTemplateService extends AbstractTemplateService {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/beanshell");
+
+ private static final String BEANSHELL = "Beanshell";
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/beanshell");
+
+ public String getName() {
+ return BEANSHELL;
+ }
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ configuration.getJsonAsObjectNode().put("script", "");
+ configuration.getJsonAsObjectNode().put("classLoaderSharing", "workflow");
+ return configuration;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return BeanshellActivityIcon.getBeanshellIcon();
+ }
+
+ @Override
+ public String getDescription() {
+ return "A service that allows Beanshell scripts, with dependencies on libraries";
+ }
+
+ public static ServiceDescription getServiceDescription() {
+ BeanshellTemplateService bts = new BeanshellTemplateService();
+ return bts.templateService;
+ }
+
+ public String getId() {
+ return providerId.toString();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellActivityViewFactory.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellActivityViewFactory.java
new file mode 100644
index 0000000..5c83730
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellActivityViewFactory.java
@@ -0,0 +1,84 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.views;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class BeanshellActivityViewFactory implements ContextualViewFactory<Activity> {
+
+ private static final URI ACTIVITY_TYPE = URI
+ .create("http://ns.taverna.org.uk/2010/activity/beanshell");
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+
+ private ApplicationConfiguration applicationConfiguration;
+
+ public boolean canHandle(Object object) {
+ return object instanceof Activity && ((Activity) object).getType().equals(ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new BeanshellContextualView(activity,
+ editManager, fileManager, activityIconManager, colourManager,
+ serviceDescriptionRegistry, applicationConfiguration) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellConfigurationPanel.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellConfigurationPanel.java
new file mode 100644
index 0000000..8489d7a
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellConfigurationPanel.java
@@ -0,0 +1,231 @@
+/*******************************************************************************
+ * Copyright (C) 2012 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.views;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+import net.sf.taverna.t2.lang.ui.EditorKeySetUtil;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityPortConfiguration;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.DependencyConfigurationPanel;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ListConfigurationComponent;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.MultiPageActivityConfigurationPanel;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ScriptConfigurationComponent;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ValidatingTextField;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ValidatingTextGroup;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+/**
+ * Component for configuring a Beanshell activity.
+ *
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class BeanshellConfigurationPanel extends MultiPageActivityConfigurationPanel {
+
+ private ScriptConfigurationComponent scriptConfigurationComponent;
+ private ValidatingTextGroup inputTextGroup, outputTextGroup;
+ private DependencyConfigurationPanel dependencyConfigurationPanel;
+ private File libDir;
+
+ public BeanshellConfigurationPanel(Activity activity,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity);
+ libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
+ if (!libDir.exists()) {
+ libDir.mkdir();
+ }
+ initialise();
+ }
+
+ @Override
+ protected void initialise() {
+ super.initialise();
+ removeAllPages();
+ addPage("Script", createScriptEditPanel());
+ addPage("Input ports", createInputPanel());
+ addPage("Output ports", createOutputPanel());
+ addPage("Dependencies", createDependenciesPanel());
+ setPreferredSize(new Dimension(600, 500));
+ }
+
+ @Override
+ public void noteConfiguration() {
+ setProperty("script", scriptConfigurationComponent.getScript());
+ setProperty("classLoaderSharing", dependencyConfigurationPanel.getClassLoaderSharing());
+ List<String> localDependencies = dependencyConfigurationPanel.getLocalDependencies();
+ if (localDependencies == null || localDependencies.isEmpty()) {
+ getJson().remove("localDependency");
+ } else {
+ ArrayNode localDependenciesArray = getJson().arrayNode();
+ for (String localDependency : localDependencies) {
+ localDependenciesArray.add(localDependency);
+ }
+ getJson().put("localDependency", localDependenciesArray);
+ }
+ }
+
+ @Override
+ public boolean checkValues() {
+ return true;
+ }
+
+ private Component createScriptEditPanel() {
+ Set<String> keywords = EditorKeySetUtil.loadKeySet(getClass().getResourceAsStream(
+ "keys.txt"));
+ Set<String> ports = new HashSet<>();
+ for (InputActivityPort ip : getActivity().getInputPorts()) {
+ ports.add(ip.getName());
+ }
+ for (OutputActivityPort op : getActivity().getOutputPorts()) {
+ ports.add(op.getName());
+ }
+ scriptConfigurationComponent = new ScriptConfigurationComponent(getProperty("script"),
+ keywords, ports, "Beanshell", ".bsh");
+ return scriptConfigurationComponent;
+ }
+
+ private Component createInputPanel() {
+ inputTextGroup = new ValidatingTextGroup();
+ ListConfigurationComponent<ActivityPortConfiguration> inputPanel = new ListConfigurationComponent<ActivityPortConfiguration>(
+ "Input Port", getInputPorts()) {
+ @Override
+ protected Component createItemComponent(ActivityPortConfiguration port) {
+ return new PortComponent(port, inputTextGroup);
+ }
+
+ @Override
+ protected ActivityPortConfiguration createDefaultItem() {
+ return new ActivityPortConfiguration("in", 0);
+ }
+ };
+ return inputPanel;
+ }
+
+ private Component createOutputPanel() {
+ outputTextGroup = new ValidatingTextGroup();
+ ListConfigurationComponent<ActivityPortConfiguration> inputPanel = new ListConfigurationComponent<ActivityPortConfiguration>(
+ "Output Port", getOutputPorts()) {
+ @Override
+ protected Component createItemComponent(ActivityPortConfiguration port) {
+ return new PortComponent(port, outputTextGroup);
+ }
+
+ @Override
+ protected ActivityPortConfiguration createDefaultItem() {
+ return new ActivityPortConfiguration("out", 0);
+ }
+ };
+ return inputPanel;
+ }
+
+ private Component createDependenciesPanel() {
+ String classLoaderSharing = getProperty("classLoaderSharing");
+ List<String> localDependencies = new ArrayList<>();
+ if (getJson().has("localDependency")) {
+ for (JsonNode localDependency : getJson().get("localDependency")) {
+ localDependencies.add(localDependency.textValue());
+ }
+ }
+ dependencyConfigurationPanel = new DependencyConfigurationPanel(classLoaderSharing,
+ localDependencies, libDir);
+ return dependencyConfigurationPanel;
+ }
+
+ class PortComponent extends JPanel {
+
+ private ValidatingTextField nameField;
+ private SpinnerNumberModel depthModel;
+ private final ValidatingTextGroup validatingTextGroup;
+
+ public PortComponent(final ActivityPortConfiguration portConfiguration,
+ ValidatingTextGroup validatingTextGroup) {
+ this.validatingTextGroup = validatingTextGroup;
+
+ nameField = new ValidatingTextField(portConfiguration.getName());
+ nameField.getDocument().addDocumentListener(new DocumentListener() {
+ @Override
+ public void removeUpdate(DocumentEvent e) {
+ portConfiguration.setName(nameField.getText());
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e) {
+ portConfiguration.setName(nameField.getText());
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e) {
+ portConfiguration.setName(nameField.getText());
+ }
+ });
+ validatingTextGroup.addValidTextComponent(nameField);
+ depthModel = new SpinnerNumberModel(portConfiguration.getDepth(), 0, 100, 1);
+ depthModel.addChangeListener(new ChangeListener() {
+ @Override
+ public void stateChanged(ChangeEvent e) {
+ portConfiguration.setDepth(depthModel.getNumber().intValue());
+ }
+ });
+
+ setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.WEST;
+ add(new JLabel("Name"), c);
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1;
+ add(nameField, c);
+ c.fill = GridBagConstraints.NONE;
+ c.weightx = 0;
+ add(new JLabel("Depth"), c);
+ add(new JSpinner(depthModel), c);
+
+ }
+
+ public void removeNotify() {
+ validatingTextGroup.removeTextComponent(nameField);
+ }
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellContextualView.java b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellContextualView.java
new file mode 100644
index 0000000..e738e38
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/java/net/sf/taverna/t2/activities/beanshell/views/BeanshellContextualView.java
@@ -0,0 +1,104 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.beanshell.views;
+
+import java.awt.Frame;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+/**
+ * A simple non editable HTML table view over a {@link BeanshellActivity}.
+ * Clicking on the configure button shows the editable {@link BeanshellConfigView}
+ *
+ * @author Ian Dunlop
+ * @author Stuart Owen
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class BeanshellContextualView extends HTMLBasedActivityContextualView {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final ApplicationConfiguration applicationConfiguration;
+
+ public BeanshellContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ColourManager colourManager, ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.applicationConfiguration = applicationConfiguration;
+ init();
+ }
+
+ private void init() {
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ StringBuilder html = new StringBuilder();
+ html.append("<tr><th>Input Port Name</th><th>Depth</th></tr>");
+ for (InputActivityPort inputActivityPort : getActivity().getInputPorts()) {
+ html.append("<tr><td>" + inputActivityPort.getName() + "</td><td>");
+ html.append(inputActivityPort.getDepth() + "</td></tr>");
+ }
+ html.append("<tr><th>Output Port Name</th><th>Depth</th></tr>");
+ for (OutputActivityPort outputActivityPort : getActivity().getOutputPorts()) {
+ html.append("<tr><td>" + outputActivityPort.getName() + "</td><td>");
+ html.append(outputActivityPort.getDepth() + "</td></tr>");
+ }
+ return html.toString();
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Beanshell service";
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new BeanshellActivityConfigurationAction(getActivity(), owner, editManager,
+ fileManager, activityIconManager, serviceDescriptionRegistry, applicationConfiguration);
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..a77db8d
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellTemplateService
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..a3c71cd
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.activities.beanshell.menu.AddBeanshellTemplateAction
+net.sf.taverna.t2.activities.beanshell.menu.AddBeanshellTemplateMenuAction
+net.sf.taverna.t2.activities.beanshell.menu.ConfigureBeanshellMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..a268bf1
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
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--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.beanshell.views.BeanshellActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context-osgi.xml
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context-osgi.xml b/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..58a3e18
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context-osgi.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="BeanshellActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="BeanshellTemplateService" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="AddBeanshellTemplateAction" auto-export="interfaces" />
+ <service ref="AddBeanshellTemplateMenuAction" auto-export="interfaces" />
+ <service ref="ConfigureBeanshellMenuAction" auto-export="interfaces" />
+
+ <service ref="BeanshellActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+ <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context.xml
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context.xml b/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context.xml
new file mode 100644
index 0000000..fc6d5d4
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/META-INF/spring/beanshell-activity-ui-context.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="BeanshellActivityIcon" class="net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellActivityIcon" />
+
+ <bean id="BeanshellTemplateService" class="net.sf.taverna.t2.activities.beanshell.servicedescriptions.BeanshellTemplateService" />
+
+ <bean id="AddBeanshellTemplateAction" class="net.sf.taverna.t2.activities.beanshell.menu.AddBeanshellTemplateAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="AddBeanshellTemplateMenuAction" class="net.sf.taverna.t2.activities.beanshell.menu.AddBeanshellTemplateMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="menuManager" ref="menuManager" />
+ <property name="selectionManager" ref="selectionManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+ <bean id="ConfigureBeanshellMenuAction" class="net.sf.taverna.t2.activities.beanshell.menu.ConfigureBeanshellMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+ <bean id="BeanshellActivityViewFactory" class="net.sf.taverna.t2.activities.beanshell.views.BeanshellActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/beanshell.png
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/beanshell.png b/taverna-beanshell-activity-ui/src/main/resources/beanshell.png
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index 0000000..8f6edfb
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-beanshell-activity-ui/src/main/resources/net/sf/taverna/t2/activities/beanshell/views/keys.txt
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diff --git a/taverna-beanshell-activity-ui/src/main/resources/net/sf/taverna/t2/activities/beanshell/views/keys.txt b/taverna-beanshell-activity-ui/src/main/resources/net/sf/taverna/t2/activities/beanshell/views/keys.txt
new file mode 100644
index 0000000..15cb51b
--- /dev/null
+++ b/taverna-beanshell-activity-ui/src/main/resources/net/sf/taverna/t2/activities/beanshell/views/keys.txt
@@ -0,0 +1,90 @@
+++
+--
++
+-
+~
+!
+*
+/
+%
+<<
+>>
+>>>
+<
+>
+<=
+>=
+==
+!=
+&
+^
+|
+&&
+||
+:
+=
++=
+-=
+*=
+/=
+%=
+&=
+^=
+|=
+<<=
+>>=
+>>>=
+=
+abstract
+assert
+boolean
+break
+byte
+case
+catch
+char
+class
+const
+continue
+default
+do
+double
+else
+enum
+extends
+false
+final
+finally
+float
+for
+goto
+if
+implements
+import
+instanceof
+int
+interface
+long
+native
+new
+null
+package
+private
+protected
+public
+return
+short
+static
+strictfp
+super
+switch
+synchronized
+this
+throw
+throws
+transient
+true
+try
+void
+volatile
+while
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/pom.xml
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diff --git a/taverna-external-tool-activity-ui/pom.xml b/taverna-external-tool-activity-ui/pom.xml
new file mode 100644
index 0000000..376cd5c
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+++ b/taverna-external-tool-activity-ui/pom.xml
@@ -0,0 +1,108 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>external-tool-activity-ui</artifactId>
+ <name>Taverna 2 ExternalTool Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>graph-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>contextual-views-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>workflow-view</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>renderers-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+
+ <!-- testing dependencies -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>activity-palette-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <!-- function dependencies for invocation -->
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>external-tool-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/actions/ExternalToolActivityConfigureAction.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/actions/ExternalToolActivityConfigureAction.java b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/actions/ExternalToolActivityConfigureAction.java
new file mode 100644
index 0000000..398ee7c
--- /dev/null
+++ b/taverna-external-tool-activity-ui/src/main/java/net/sf/taverna/t2/activities/externaltool/actions/ExternalToolActivityConfigureAction.java
@@ -0,0 +1,83 @@
+/*******************************************************************************
+ * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
+ * modified 2010 Hajo Nils Krabbenhoeft, spratpix GmbH & Co. KG
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.externaltool.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
+import net.sf.taverna.t2.activities.externaltool.views.ExternalToolConfigView;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+
+/**
+ * This class implements an ActivityConfigurationAction to configure the ExternalToolActivity
+ * plugin. The configuration action is called "Configure UseCase invocation" and is implemented in
+ * the KnowARCConfigurationDialog inside the knowarc-usecases maven artifact.
+ *
+ * @author Hajo Nils Krabbenhoeft
+ */
+@SuppressWarnings("serial")
+public class ExternalToolActivityConfigureAction extends
+ ActivityConfigurationAction<ExternalToolActivity, ExternalToolActivityConfigurationBean> {
+
+ private final Frame owner;
+ private final EditManager editManager;
+ private final FileManager fileManager;
+
+ public ExternalToolActivityConfigureAction(ExternalToolActivity activity, Frame owner,
+ EditManager editManager, FileManager fileManager, ActivityIconManager activityIconManager) {
+ super(activity, activityIconManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ putValue(Action.NAME, "Configure tool invocation");
+ this.owner = owner;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ /*
+ * if (getActivity().getConfiguration() instanceof
+ * RegisteredExternalToolActivityConfigurationBean) { new KnowARCConfigurationDialog(owner,
+ * false, KnowARCConfigurationFactory.getConfiguration()).setVisible(true); } else
+ */{
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction
+ .getDialog(getActivity());
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+ final ExternalToolConfigView externalToolConfigView = new ExternalToolConfigView(
+ (ExternalToolActivity) getActivity());
+ final ActivityConfigurationDialog<ExternalToolActivity, ExternalToolActivityConfigurationBean> dialog = new ActivityConfigurationDialog<ExternalToolActivity, ExternalToolActivityConfigurationBean>(
+ getActivity(), externalToolConfigView, editManager, fileManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+ }
+ }
+}
[07/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/il8n/SpreadsheetImportUIText.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/il8n/SpreadsheetImportUIText.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/il8n/SpreadsheetImportUIText.java
new file mode 100644
index 0000000..82f8436
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/il8n/SpreadsheetImportUIText.java
@@ -0,0 +1,46 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.il8n;
+
+import java.util.MissingResourceException;
+import java.util.ResourceBundle;
+
+/**
+ * Access to a resource bundle containing UI text.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportUIText {
+ private static final String BUNDLE_NAME = "net.sf.taverna.t2.activities.spreadsheet.iln8.ui-text";
+
+ private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle(BUNDLE_NAME);
+
+ private SpreadsheetImportUIText() {
+ }
+
+ public static String getString(String key) {
+ try {
+ return RESOURCE_BUNDLE.getString(key);
+ } catch (MissingResourceException e) {
+ return '!' + key + '!';
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateAction.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateAction.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateAction.java
new file mode 100644
index 0000000..3073acb
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateAction.java
@@ -0,0 +1,110 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.menu;
+
+import java.awt.event.ActionEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.core.Workflow;
+
+/**
+ * An action to add a spreadsheet import activity + a wrapping processor to the workflow.
+ *
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class SpreadsheetImportAddTemplateAction extends AbstractContextualMenuAction {
+
+ private static final URI insertSection = URI
+ .create("http://taverna.sf.net/2009/contextMenu/insert");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public SpreadsheetImportAddTemplateAction() {
+ super(insertSection, 700);
+ }
+
+ @Override
+ public boolean isEnabled() {
+ return super.isEnabled() && getContextualSelection().getSelection() instanceof Workflow;
+ }
+
+ @Override
+ protected Action createAction() {
+
+ AbstractAction action = new AbstractAction(
+ SpreadsheetImportUIText.getString("SpreadsheetImportAddTemplateAction.addMenu"),
+ activityIconManager.iconForActivity(SpreadsheetImportTemplateService.ACTIVITY_TYPE)) {
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(serviceDescriptionRegistry
+ .getServiceDescription(SpreadsheetImportTemplateService.ACTIVITY_TYPE), false,
+ editManager, menuManager, selectionManager, serviceRegistry);
+ }
+
+ };
+
+ return action;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateMenuAction.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateMenuAction.java
new file mode 100644
index 0000000..048073a
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportAddTemplateMenuAction.java
@@ -0,0 +1,124 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.menu;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.net.URI;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.KeyStroke;
+
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.ui.menu.AbstractMenuAction;
+import net.sf.taverna.t2.ui.menu.DesignOnlyAction;
+import net.sf.taverna.t2.ui.menu.MenuManager;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+/**
+ * An action to add a spreadsheet import activity + a wrapping processor to the workflow.
+ *
+ * @author Alan R Williams
+ */
+@SuppressWarnings("serial")
+public class SpreadsheetImportAddTemplateMenuAction extends AbstractMenuAction {
+
+ private static final URI ADD_SPREADSHEET_IMPORT_URI = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#graphMenuAddSpreadsheetImport");
+
+ private static final URI INSERT = URI
+ .create("http://taverna.sf.net/2008/t2workbench/menu#insert");
+
+ private static String ADD_SPREADSHEET_IMPORT = SpreadsheetImportUIText
+ .getString("SpreadsheetImportAddTemplateAction.addMenu");
+
+ private EditManager editManager;
+ private MenuManager menuManager;
+ private SelectionManager selectionManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public SpreadsheetImportAddTemplateMenuAction() {
+ super(INSERT, 700, ADD_SPREADSHEET_IMPORT_URI);
+ }
+
+ @Override
+ protected Action createAction() {
+ return new AddSpreadsheetImportMenuAction();
+ }
+
+ protected class AddSpreadsheetImportMenuAction extends AbstractAction implements
+ DesignOnlyAction {
+ AddSpreadsheetImportMenuAction() {
+ super();
+ putValue(SMALL_ICON,
+ activityIconManager
+ .iconForActivity(SpreadsheetImportTemplateService.ACTIVITY_TYPE));
+ putValue(NAME, ADD_SPREADSHEET_IMPORT);
+ putValue(SHORT_DESCRIPTION, ADD_SPREADSHEET_IMPORT);
+ putValue(
+ Action.ACCELERATOR_KEY,
+ KeyStroke.getKeyStroke(KeyEvent.VK_X, InputEvent.SHIFT_DOWN_MASK
+ | InputEvent.ALT_DOWN_MASK));
+
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ WorkflowView.importServiceDescription(serviceDescriptionRegistry
+ .getServiceDescription(SpreadsheetImportTemplateService.ACTIVITY_TYPE), false,
+ editManager, menuManager, selectionManager, serviceRegistry);
+ }
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setMenuManager(MenuManager menuManager) {
+ this.menuManager = menuManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportConfigureMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportConfigureMenuAction.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportConfigureMenuAction.java
new file mode 100644
index 0000000..7d1fa0a
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/menu/SpreadsheetImportConfigureMenuAction.java
@@ -0,0 +1,84 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.menu;
+
+import javax.swing.Action;
+
+import uk.org.taverna.commons.services.ServiceRegistry;
+
+import net.sf.taverna.t2.activities.spreadsheet.actions.SpreadsheetImportActivityConfigurationAction;
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+
+/**
+ * Menu action for SpreadsheetImport activity configuration.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportConfigureMenuAction extends AbstractConfigureActivityMenuAction {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public SpreadsheetImportConfigureMenuAction() {
+ super(SpreadsheetImportTemplateService.ACTIVITY_TYPE);
+ }
+
+ @Override
+ protected Action createAction() {
+ Action result = new SpreadsheetImportActivityConfigurationAction(findActivity(),
+ getParentFrame(), editManager, fileManager, activityIconManager,
+ serviceDescriptionRegistry, serviceRegistry);
+ result.putValue(Action.NAME, SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigureMenuAction.configureMenu"));
+ addMenuDots(result);
+ return result;
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportActivityIcon.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportActivityIcon.java
new file mode 100644
index 0000000..1987364
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportActivityIcon.java
@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.servicedescriptions;
+
+import java.awt.Color;
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+
+/**
+ * UI icon for the SpreadsheetImport Activity.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportActivityIcon implements ActivityIconSPI {
+
+ public static final String SPREADSHEET_COLOUR_HTML = "#40e0d0";
+ public static final Color SPREADSHEET_COLOUR = Color.decode(SPREADSHEET_COLOUR_HTML);
+
+ private static Icon icon = null;
+
+ @Override
+ public int canProvideIconScore(URI activityType) {
+ if (SpreadsheetImportTemplateService.ACTIVITY_TYPE.equals(activityType))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ @Override
+ public Icon getIcon(URI activityType) {
+ return getSpreadsheetImportIcon();
+ }
+
+ public static Icon getSpreadsheetImportIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(
+ SpreadsheetImportActivityIcon.class.getResource("/spreadsheet-import.png"));
+ }
+ return icon;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ colourManager.setPreferredColour(
+ "http://ns.taverna.org.uk/2010/activity/spreadsheet-import",
+ SPREADSHEET_COLOUR);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportTemplateService.java
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportTemplateService.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportTemplateService.java
new file mode 100644
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--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/servicedescriptions/SpreadsheetImportTemplateService.java
@@ -0,0 +1,95 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.servicedescriptions.AbstractTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+/**
+ * Definition of the SpreadsheetImport spreadsheet import template service.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportTemplateService extends AbstractTemplateService {
+
+ public static final URI ACTIVITY_TYPE = URI
+ .create("http://ns.taverna.org.uk/2010/activity/spreadsheet-import");
+
+ private static final String SERVICE_NAME = SpreadsheetImportUIText
+ .getString("SpreadsheetImportTemplateService.serviceName");
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/spreadsheet");
+
+ public String getName() {
+ return SERVICE_NAME;
+ }
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ ObjectNode json = (ObjectNode) configuration.getJson();
+ json.put("columnRange", json.objectNode().put("start", 0).put("end", 1));
+ json.put("rowRange", json.objectNode().put("start", 0).put("end", -1));
+ json.put("emptyCellValue", "");
+ json.put("allRows", true);
+ json.put("excludeFirstRow", false);
+ json.put("ignoreBlankRows", false);
+ json.put("emptyCellPolicy", "EMPTY_STRING");
+ json.put("outputFormat", "PORT_PER_COLUMN");
+ json.put("csvDelimiter", ",");
+ return configuration;
+ }
+
+ @Override
+ public Icon getIcon() {
+ return SpreadsheetImportActivityIcon.getSpreadsheetImportIcon();
+ }
+
+ @Override
+ public String getDescription() {
+ return SpreadsheetImportUIText
+ .getString("SpreadsheetImportTemplateService.serviceDescription");
+ }
+
+ public static ServiceDescription getServiceDescription() {
+ SpreadsheetImportTemplateService bts = new SpreadsheetImportTemplateService();
+ return bts.templateService;
+ }
+
+ public String getId() {
+ return providerId.toString();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigTableModel.java
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigTableModel.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigTableModel.java
new file mode 100644
index 0000000..0409b8e
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigTableModel.java
@@ -0,0 +1,190 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+package net.sf.taverna.t2.activities.spreadsheet.views;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.table.AbstractTableModel;
+
+import net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils;
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+
+/**
+ * TableModel for mapping column labels to port names.
+ * <p>
+ * The default mapping is for the port name to be the same as the column label. The
+ * columnToPortMapping only contains entries for port names that are not the same as the column
+ * label.
+ *
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class SpreadsheetImportConfigTableModel extends AbstractTableModel {
+
+ private Map<String, String> columnToPortMapping;
+
+ private int fromColumn, toColumn;
+
+ /**
+ * Constructs a TableModel that maps column labels to port names for the specified range of
+ * columns.
+ *
+ * @param fromColumn
+ * the start of the column range
+ * @param toColumn
+ * the end of the column range
+ * @param columnToPortMapping
+ * existing column to port mappings (can be null)
+ */
+ public SpreadsheetImportConfigTableModel(String fromColumn, String toColumn,
+ Map<String, String> columnToPortMapping) {
+ if (columnToPortMapping == null) {
+ this.columnToPortMapping = new HashMap<String, String>();
+ } else {
+ this.columnToPortMapping = new HashMap<String, String>(columnToPortMapping);
+ }
+ this.fromColumn = SpreadsheetUtils.getColumnIndex(fromColumn);
+ this.toColumn = SpreadsheetUtils.getColumnIndex(toColumn);
+ }
+
+ /**
+ * Sets the start of the column range.
+ *
+ * @param fromColumn
+ * the start of the column range
+ */
+ public void setFromColumn(int fromColumn) {
+ if (this.fromColumn != fromColumn) {
+ this.fromColumn = fromColumn;
+ fireTableStructureChanged();
+ }
+ }
+
+ /**
+ * Sets the end of the column range.
+ *
+ * @param toColumn
+ * the end of the column range
+ */
+ public void setToColumn(int toColumn) {
+ if (this.toColumn != toColumn) {
+ this.toColumn = toColumn;
+ fireTableStructureChanged();
+ }
+ }
+
+ /**
+ * Returns the port name for the given column label.
+ * <p>
+ * If the columnLabel is the columnToPortMapping the value is returned; otherwise the
+ * columnLabel is returned.
+ *
+ * @param columnLabel
+ * the column to find the port name for
+ * @return the port name for the given column label
+ */
+ public String getPortName(String columnLabel) {
+ String portName;
+ if (columnToPortMapping.containsKey(columnLabel)) {
+ portName = columnToPortMapping.get(columnLabel);
+ } else {
+ portName = columnLabel;
+ }
+ return portName;
+ }
+
+ /**
+ * Sets the port name for the column label.
+ * <p>
+ * If the port name is not the same as the column label the port name is added the
+ * columnToPortMapping.
+ *
+ * @param columnLabel
+ * @param portName
+ */
+ public void setPortName(String columnLabel, String portName) {
+ if (columnLabel.equals(portName)) {
+ columnToPortMapping.remove(columnLabel);
+ } else {
+ columnToPortMapping.put(columnLabel, portName);
+ }
+ }
+
+ /**
+ * Returns the map of column labels to port names.
+ * <p>
+ * The map only contains entries for port names that are not the same as their corresponding
+ * column label.
+ *
+ * @return the map of column labels to port names
+ */
+ public Map<String, String> getColumnToPortMapping() {
+ return columnToPortMapping;
+ }
+
+ // TableModel methods
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex) {
+ return String.class;
+ }
+
+ public int getColumnCount() {
+ return 2;
+ }
+
+ @Override
+ public String getColumnName(int columnIndex) {
+ if (columnIndex == 0) {
+ return SpreadsheetImportUIText.getString("SpreadsheetImportConfigTableModel.column");
+ } else {
+ return SpreadsheetImportUIText.getString("SpreadsheetImportConfigTableModel.portName");
+ }
+ }
+
+ public int getRowCount() {
+ return toColumn - fromColumn + 1;
+ }
+
+ public Object getValueAt(int rowIndex, int columnIndex) {
+ String columnLabel = SpreadsheetUtils.getColumnLabel(rowIndex + fromColumn);
+ if (columnIndex == 0) {
+ return columnLabel;
+ } else {
+ return getPortName(columnLabel);
+ }
+ }
+
+ @Override
+ public boolean isCellEditable(int rowIndex, int columnIndex) {
+ return columnIndex == 1;
+ }
+
+ @Override
+ public void setValueAt(Object value, int rowIndex, int columnIndex) {
+ if (columnIndex == 1) {
+ setPortName(SpreadsheetUtils.getColumnLabel(rowIndex + fromColumn), value.toString());
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigView.java
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigView.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigView.java
new file mode 100644
index 0000000..af57c44
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportConfigView.java
@@ -0,0 +1,1082 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.views;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Stack;
+
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultCellEditor;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.table.DefaultTableColumnModel;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableColumn;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.JTextComponent;
+import javax.swing.text.PlainDocument;
+
+import net.sf.taverna.t2.activities.spreadsheet.Range;
+import net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils;
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.lang.ui.DialogTextArea;
+import net.sf.taverna.t2.lang.ui.icons.Icons;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * Configuration panel for the spreadsheet import activity.
+ *
+ * @author David Withers
+ */
+@SuppressWarnings("serial")
+public class SpreadsheetImportConfigView extends ActivityConfigurationPanel {
+
+ private static final String INCONSISTENT_ROW_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.INCONSISTENT_ROW_MESSAGE");
+
+ private static final String INCONSISTENT_COLUMN_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.INCONSISTENT_COLUMN_MESSAGE");
+
+ private static final String FROM_COLUMN_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.FROM_COLUMN_ERROR_MESSAGE");
+
+ private static final String TO_COLUMN_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.TO_COLUMN_ERROR_MESSAGE");
+
+ private static final String FROM_ROW_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.FROM_ROW_ERROR_MESSAGE");
+
+ private static final String TO_ROW_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.TO_ROW_ERROR_MESSAGE");
+
+ private static final String DEFAULT_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.DEFAULT_MESSAGE");
+
+ private static final String EMPTY_FROM_ROW_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.EMPTY_FROM_ROW_ERROR_MESSAGE");
+
+ private static final String EMPTY_FROM_COLUMN_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.EMPTY_FROM_COLUMN_ERROR_MESSAGE");
+
+ private static final String EMPTY_TO_COLUMN_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.EMPTY_TO_COLUMN_ERROR_MESSAGE");
+
+ private static final String DUPLICATE_PORT_NAME_ERROR_MESSAGE = SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.DUPLICATE_PORT_NAME_ERROR_MESSAGE");
+
+ private static Logger logger = Logger.getLogger(SpreadsheetImportConfigView.class);
+
+ private JPanel titlePanel, contentPanel, buttonPanel, page1, page2;
+
+ private JLabel titleLabel, titleIcon, rowLabel, columnLabel;
+
+ private JLabel emptyCellLabel, outputFormatLabel, outputFormatDelimiterLabel, columnMappingLabel;
+
+ private DialogTextArea titleMessage;
+
+ private JTextField columnFromValue, columnToValue, rowFromValue, rowToValue;
+
+ private JTextField emptyCellUserDefinedValue, outputFormatDelimiter;
+
+ private JCheckBox rowSelectAllOption, rowExcludeFirstOption, rowIgnoreBlankRows;
+
+ private ButtonGroup emptyCellButtonGroup, outputFormatButtonGroup;
+
+ private JRadioButton emptyCellEmptyStringOption, emptyCellUserDefinedOption,
+ emptyCellErrorValueOption;
+
+ private JRadioButton outputFormatMultiplePort, outputFormatSinglePort;
+
+ private JTable columnMappingTable;
+
+ private SpreadsheetImportConfigTableModel columnMappingTableModel;
+
+ private JButton nextButton, backButton;
+
+ private CardLayout cardLayout = new CardLayout();
+
+ private Stack<String> warningMessages = new Stack<String>();
+
+ private Stack<String> errorMessages = new Stack<String>();
+
+ private ObjectNode newConfiguration;
+
+ private final ServiceRegistry serviceRegistry;
+
+ /**
+ * Constructs a configuration view for an SpreadsheetImport Activity.
+ *
+ * @param activity
+ */
+ public SpreadsheetImportConfigView(Activity activity, ServiceRegistry serviceRegistry) {
+ super(activity);
+ this.serviceRegistry = serviceRegistry;
+ initialise();
+ }
+
+ @Override
+ protected void initialise() {
+ super.initialise();
+ newConfiguration = getJson().deepCopy();
+
+ // title
+ titlePanel = new JPanel(new BorderLayout());
+ titlePanel.setBackground(Color.WHITE);
+ addDivider(titlePanel, SwingConstants.BOTTOM, true);
+
+ titleLabel = new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.panelTitle"));
+ titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD, 13.5f));
+ titleIcon = new JLabel("");
+ titleMessage = new DialogTextArea(DEFAULT_MESSAGE);
+ titleMessage.setMargin(new Insets(5, 10, 10, 10));
+ // titleMessage.setMinimumSize(new Dimension(0, 30));
+ titleMessage.setFont(titleMessage.getFont().deriveFont(11f));
+ titleMessage.setEditable(false);
+ titleMessage.setFocusable(false);
+ // titleMessage.setFont(titleLabel.getFont().deriveFont(Font.PLAIN,
+ // 12f));
+
+ // column range
+ columnLabel = new JLabel(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.columnSectionLabel"));
+
+ JsonNode columnRange = newConfiguration.get("columnRange");
+ columnFromValue = new JTextField(new UpperCaseDocument(), SpreadsheetUtils.getColumnLabel(columnRange.get("start").intValue()), 4);
+ columnFromValue.setMinimumSize(columnFromValue.getPreferredSize());
+ columnToValue = new JTextField(new UpperCaseDocument(), SpreadsheetUtils.getColumnLabel(columnRange.get("end").intValue()), 4);
+ columnToValue.setMinimumSize(columnToValue.getPreferredSize());
+
+ columnFromValue.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ checkValue(columnFromValue.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ checkValue(columnFromValue.getText());
+ }
+
+ private void checkValue(String text) {
+ if (text.trim().equals("")) {
+ addErrorMessage(EMPTY_FROM_COLUMN_ERROR_MESSAGE);
+ } else if (text.trim().matches("[A-Za-z]+")) {
+ String fromColumn = columnFromValue.getText().toUpperCase();
+ String toColumn = columnToValue.getText().toUpperCase();
+ int fromColumnIndex = SpreadsheetUtils.getColumnIndex(fromColumn);
+ int toColumnIndex = SpreadsheetUtils.getColumnIndex(toColumn);
+ if (checkColumnRange(fromColumnIndex, toColumnIndex)) {
+ columnMappingTableModel.setFromColumn(fromColumnIndex);
+ columnMappingTableModel.setToColumn(toColumnIndex);
+ newConfiguration.set("columnRange", newConfiguration.objectNode().put("start", fromColumnIndex).put("end", toColumnIndex));
+ validatePortNames();
+ }
+ removeErrorMessage(FROM_COLUMN_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_FROM_COLUMN_ERROR_MESSAGE);
+ } else {
+ addErrorMessage(FROM_COLUMN_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_FROM_COLUMN_ERROR_MESSAGE);
+ }
+ }
+
+ });
+
+ columnToValue.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ checkValue(columnToValue.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ checkValue(columnToValue.getText());
+ }
+
+ private void checkValue(String text) {
+ if (text.trim().equals("")) {
+ addErrorMessage(EMPTY_TO_COLUMN_ERROR_MESSAGE);
+ } else if (text.trim().matches("[A-Za-z]+")) {
+ String fromColumn = columnFromValue.getText().toUpperCase();
+ String toColumn = columnToValue.getText().toUpperCase();
+ int fromColumnIndex = SpreadsheetUtils.getColumnIndex(fromColumn);
+ int toColumnIndex = SpreadsheetUtils.getColumnIndex(toColumn);
+ if (checkColumnRange(fromColumnIndex, toColumnIndex)) {
+ columnMappingTableModel.setFromColumn(fromColumnIndex);
+ columnMappingTableModel.setToColumn(toColumnIndex);
+ newConfiguration.set("columnRange", newConfiguration.objectNode().put("start", fromColumnIndex).put("end", toColumnIndex));
+ validatePortNames();
+ }
+ removeErrorMessage(TO_COLUMN_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_TO_COLUMN_ERROR_MESSAGE);
+
+ } else {
+ addErrorMessage(TO_COLUMN_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_TO_COLUMN_ERROR_MESSAGE);
+ }
+ }
+ });
+
+ // row range
+ rowLabel = new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.rowSectionLabel"));
+ addDivider(rowLabel, SwingConstants.TOP, false);
+
+ rowSelectAllOption = new JCheckBox(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.selectAllRowsOption"));
+ rowExcludeFirstOption = new JCheckBox(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.excludeHeaderRowOption"));
+ rowIgnoreBlankRows = new JCheckBox(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.ignoreBlankRowsOption"));
+ rowSelectAllOption.setFocusable(false);
+ rowExcludeFirstOption.setFocusable(false);
+
+ JsonNode rowRange = newConfiguration.get("rowRange");
+ rowFromValue = new JTextField(new NumericDocument(), String.valueOf(rowRange.get("start").intValue() + 1), 4);
+ if (rowRange.get("end").intValue() == -1) {
+ rowToValue = new JTextField(new NumericDocument(), "", 4);
+ } else {
+ rowToValue = new JTextField(new NumericDocument(), String.valueOf(rowRange.get("end").intValue() + 1), 4);
+ }
+ rowFromValue.setMinimumSize(rowFromValue.getPreferredSize());
+ rowToValue.setMinimumSize(rowToValue.getPreferredSize());
+
+ if (newConfiguration.get("allRows").booleanValue()) {
+ rowSelectAllOption.setSelected(true);
+ rowFromValue.setEditable(false);
+ rowFromValue.setEnabled(false);
+ rowToValue.setEditable(false);
+ rowToValue.setEnabled(false);
+ } else {
+ rowExcludeFirstOption.setEnabled(false);
+ }
+ rowExcludeFirstOption.setSelected(newConfiguration.get("excludeFirstRow").booleanValue());
+ rowIgnoreBlankRows.setSelected(newConfiguration.get("ignoreBlankRows").booleanValue());
+
+ rowFromValue.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ checkValue(rowFromValue.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ checkValue(rowFromValue.getText());
+ }
+
+ private void checkValue(String text) {
+ if (text.trim().equals("")) {
+ addErrorMessage(EMPTY_FROM_ROW_ERROR_MESSAGE);
+ } else if (text.trim().matches("[1-9][0-9]*")) {
+ checkRowRange(rowFromValue.getText(), rowToValue.getText());
+ int fromRow = Integer.parseInt(rowFromValue.getText());
+ ((ObjectNode) newConfiguration.get("rowRange")).put("start", fromRow - 1);
+ removeErrorMessage(FROM_ROW_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_FROM_ROW_ERROR_MESSAGE);
+ } else {
+ addErrorMessage(FROM_ROW_ERROR_MESSAGE);
+ removeErrorMessage(EMPTY_FROM_ROW_ERROR_MESSAGE);
+ }
+ }
+ });
+
+ rowToValue.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ checkValue(rowToValue.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ checkValue(rowToValue.getText());
+ }
+
+ private void checkValue(String text) {
+ if (text.trim().equals("")) {
+ ((ObjectNode) newConfiguration.get("rowRange")).put("end", -1);
+ removeErrorMessage(TO_ROW_ERROR_MESSAGE);
+ removeErrorMessage(INCONSISTENT_ROW_MESSAGE);
+ } else if (text.trim().matches("[0-9]+")) {
+ checkRowRange(rowFromValue.getText(), rowToValue.getText());
+ int toRow = Integer.parseInt(rowToValue.getText());
+ ((ObjectNode) newConfiguration.get("rowRange")).put("end", toRow - 1);
+ removeErrorMessage(TO_ROW_ERROR_MESSAGE);
+ } else {
+ addErrorMessage(TO_ROW_ERROR_MESSAGE);
+ }
+ }
+ });
+
+ rowSelectAllOption.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ newConfiguration.put("allRows", true);
+ rowExcludeFirstOption.setEnabled(true);
+ if (rowExcludeFirstOption.isSelected()) {
+ rowFromValue.setText("2");
+ } else {
+ rowFromValue.setText("1");
+ }
+ rowToValue.setText("");
+ rowFromValue.setEditable(false);
+ rowFromValue.setEnabled(false);
+ rowToValue.setEditable(false);
+ rowToValue.setEnabled(false);
+ } else {
+ newConfiguration.put("allRows", false);
+ rowExcludeFirstOption.setEnabled(false);
+ rowFromValue.setEditable(true);
+ rowFromValue.setEnabled(true);
+ rowToValue.setEditable(true);
+ rowToValue.setEnabled(true);
+ }
+ }
+ });
+
+ rowExcludeFirstOption.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ newConfiguration.put("excludeFirstRow", true);
+ rowFromValue.setText("2");
+ ((ObjectNode) newConfiguration.get("rowRange")).put("start", 1);
+ } else {
+ newConfiguration.put("excludeFirstRow", false);
+ rowFromValue.setText("1");
+ ((ObjectNode) newConfiguration.get("rowRange")).put("start", 0);
+ }
+ }
+ });
+
+ rowIgnoreBlankRows.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent e) {
+ newConfiguration.put("ignoreBlankRows", e.getStateChange() == ItemEvent.SELECTED);
+ }
+ });
+
+ // empty cells
+ emptyCellLabel = new JLabel(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.emptyCellSectionLabel"));
+ addDivider(emptyCellLabel, SwingConstants.TOP, false);
+
+ emptyCellButtonGroup = new ButtonGroup();
+ emptyCellEmptyStringOption = new JRadioButton(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.emptyStringOption"));
+ emptyCellUserDefinedOption = new JRadioButton(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.userDefinedOption"));
+ emptyCellErrorValueOption = new JRadioButton(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.generateErrorOption"));
+ emptyCellEmptyStringOption.setFocusable(false);
+ emptyCellUserDefinedOption.setFocusable(false);
+ emptyCellErrorValueOption.setFocusable(false);
+
+ emptyCellUserDefinedValue = new JTextField(newConfiguration.get("emptyCellValue").textValue());
+
+ emptyCellButtonGroup.add(emptyCellEmptyStringOption);
+ emptyCellButtonGroup.add(emptyCellUserDefinedOption);
+ emptyCellButtonGroup.add(emptyCellErrorValueOption);
+
+ if (newConfiguration.get("emptyCellPolicy").textValue().equals("GENERATE_ERROR")) {
+ emptyCellErrorValueOption.setSelected(true);
+ emptyCellUserDefinedValue.setEnabled(false);
+ emptyCellUserDefinedValue.setEditable(false);
+ } else if (newConfiguration.get("emptyCellPolicy").textValue().equals("EMPTY_STRING")) {
+ emptyCellEmptyStringOption.setSelected(true);
+ emptyCellUserDefinedValue.setEnabled(false);
+ emptyCellUserDefinedValue.setEditable(false);
+ } else {
+ emptyCellUserDefinedOption.setSelected(true);
+ emptyCellUserDefinedValue.setText(newConfiguration.get("emptyCellValue").textValue());
+ emptyCellUserDefinedValue.setEnabled(true);
+ emptyCellUserDefinedValue.setEditable(true);
+ }
+
+ emptyCellEmptyStringOption.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ newConfiguration.put("emptyCellPolicy", "EMPTY_STRING");
+ emptyCellUserDefinedValue.setEnabled(false);
+ emptyCellUserDefinedValue.setEditable(false);
+ }
+ });
+ emptyCellUserDefinedOption.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ newConfiguration.put("emptyCellPolicy", "USER_DEFINED");
+ emptyCellUserDefinedValue.setEnabled(true);
+ emptyCellUserDefinedValue.setEditable(true);
+ emptyCellUserDefinedValue.requestFocusInWindow();
+ }
+ });
+ emptyCellErrorValueOption.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ newConfiguration.put("emptyCellPolicy", "GENERATE_ERROR");
+ emptyCellUserDefinedValue.setEnabled(false);
+ emptyCellUserDefinedValue.setEditable(false);
+ }
+ });
+
+ emptyCellUserDefinedValue.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ newConfiguration.put("emptyCellValue", emptyCellUserDefinedValue.getText());
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ newConfiguration.put("emptyCellValue", emptyCellUserDefinedValue.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ newConfiguration.put("emptyCellValue", emptyCellUserDefinedValue.getText());
+ }
+ });
+
+ // column mappings
+ columnMappingLabel = new JLabel(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.columnMappingSectionLabel"));
+ addDivider(columnMappingLabel, SwingConstants.TOP, false);
+
+ Map<String, String> columnToPortMapping = new HashMap<>();
+ if (newConfiguration.has("columnNames")) {
+ for (JsonNode columnName : newConfiguration.get("columnNames")) {
+ columnToPortMapping.put(columnName.get("column").textValue(), columnName.get("port").textValue());
+ }
+ }
+ columnMappingTableModel = new SpreadsheetImportConfigTableModel(columnFromValue.getText(),
+ columnToValue.getText(), columnToPortMapping);
+
+ columnMappingTable = new JTable();
+ columnMappingTable.setRowSelectionAllowed(false);
+ columnMappingTable.getTableHeader().setReorderingAllowed(false);
+ columnMappingTable.setGridColor(Color.LIGHT_GRAY);
+ // columnMappingTable.setFocusable(false);
+
+ columnMappingTable.setColumnModel(new DefaultTableColumnModel() {
+ public TableColumn getColumn(int columnIndex) {
+ TableColumn column = super.getColumn(columnIndex);
+ if (columnIndex == 0) {
+ column.setMaxWidth(100);
+ }
+ return column;
+ }
+ });
+
+ TableCellEditor defaultEditor = columnMappingTable.getDefaultEditor(String.class);
+ if (defaultEditor instanceof DefaultCellEditor) {
+ DefaultCellEditor defaultCellEditor = (DefaultCellEditor) defaultEditor;
+ defaultCellEditor.setClickCountToStart(1);
+ Component editorComponent = defaultCellEditor.getComponent();
+ if (editorComponent instanceof JTextComponent) {
+ final JTextComponent textField = (JTextComponent) editorComponent;
+ textField.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ updateModel(textField.getText());
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ updateModel(textField.getText());
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ updateModel(textField.getText());
+ }
+
+ private void updateModel(String text) {
+ int row = columnMappingTable.getEditingRow();
+ int column = columnMappingTable.getEditingColumn();
+ columnMappingTableModel.setValueAt(text, row, column);
+
+ ArrayNode columnNames = newConfiguration.arrayNode();
+ Map<String, String> columnToPortMapping = columnMappingTableModel.getColumnToPortMapping();
+ for (Entry<String,String> entry : columnToPortMapping.entrySet()) {
+ columnNames.add(newConfiguration.objectNode().put("column", entry.getKey()).put("port", entry.getValue()));
+ }
+ newConfiguration.put("columnNames", columnNames);
+ validatePortNames();
+ }
+
+ });
+ }
+ }
+
+ columnMappingTable.setModel(columnMappingTableModel);
+
+ // output format
+ outputFormatLabel = new JLabel(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.outputFormatSectionLabel"));
+
+ outputFormatMultiplePort = new JRadioButton(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.multiplePortOption"));
+ outputFormatSinglePort = new JRadioButton(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.singlePortOption"));
+ outputFormatMultiplePort.setFocusable(false);
+ outputFormatSinglePort.setFocusable(false);
+
+ outputFormatDelimiterLabel = new JLabel(SpreadsheetImportUIText
+ .getString("SpreadsheetImportConfigView.userDefinedCsvDelimiter"));
+ outputFormatDelimiter = new JTextField(newConfiguration.get("csvDelimiter").textValue(), 5);
+
+ outputFormatButtonGroup = new ButtonGroup();
+ outputFormatButtonGroup.add(outputFormatMultiplePort);
+ outputFormatButtonGroup.add(outputFormatSinglePort);
+
+ if (newConfiguration.get("outputFormat").textValue().equals("PORT_PER_COLUMN")) {
+ outputFormatMultiplePort.setSelected(true);
+ outputFormatDelimiterLabel.setEnabled(false);
+ outputFormatDelimiter.setEnabled(false);
+ } else {
+ outputFormatSinglePort.setSelected(true);
+ columnMappingLabel.setEnabled(false);
+ enableTable(columnMappingTable, false);
+ }
+
+ outputFormatMultiplePort.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ outputFormatDelimiterLabel.setEnabled(false);
+ outputFormatDelimiter.setEnabled(false);
+ columnMappingLabel.setEnabled(true);
+ enableTable(columnMappingTable, true);
+ newConfiguration.put("outputFormat", "PORT_PER_COLUMN");
+ }
+ });
+ outputFormatSinglePort.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ outputFormatDelimiterLabel.setEnabled(true);
+ outputFormatDelimiter.setEnabled(true);
+ columnMappingLabel.setEnabled(false);
+ enableTable(columnMappingTable, false);
+ newConfiguration.put("outputFormat", "SINGLE_PORT");
+ }
+
+ });
+ outputFormatDelimiter.getDocument().addDocumentListener(new DocumentListener() {
+ public void changedUpdate(DocumentEvent e) {
+ handleUpdate();
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ handleUpdate();
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ handleUpdate();
+ }
+
+ private void handleUpdate() {
+ String text = null;
+ try {
+ text = StringEscapeUtils.unescapeJava(outputFormatDelimiter.getText());
+ } catch (RuntimeException re) {}
+ if (text == null || text.length() == 0) {
+ newConfiguration.put("csvDelimiter", ",");
+ } else {
+ newConfiguration.put("csvDelimiter", text.substring(0, 1));
+ }
+ }
+
+ });
+
+ // buttons
+ nextButton = new JButton(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.nextButton"));
+ nextButton.setFocusable(false);
+ nextButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ backButton.setVisible(true);
+ nextButton.setVisible(false);
+ cardLayout.last(contentPanel);
+ }
+ });
+
+ backButton = new JButton(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.backButton"));
+ backButton.setFocusable(false);
+ backButton.setVisible(false);
+ backButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ nextButton.setVisible(true);
+ backButton.setVisible(false);
+ cardLayout.first(contentPanel);
+ }
+ });
+
+ buttonPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ addDivider(buttonPanel, SwingConstants.TOP, true);
+
+ removeAll();
+ layoutPanel();
+ }
+
+ @Override
+ public void noteConfiguration() {
+ setJson(newConfiguration);
+ configureInputPorts(serviceRegistry);
+ configureOutputPorts(serviceRegistry);
+ }
+
+ @Override
+ public boolean checkValues() {
+ return errorMessages.isEmpty();
+ }
+
+ private void layoutPanel() {
+ setPreferredSize(new Dimension(450, 400));
+ setLayout(new BorderLayout());
+
+ page1 = new JPanel(new GridBagLayout());
+ page2 = new JPanel(new GridBagLayout());
+
+ contentPanel = new JPanel(cardLayout);
+ contentPanel.add(page1, "page1");
+ contentPanel.add(page2, "page2");
+ add(contentPanel, BorderLayout.CENTER);
+
+ // title
+ titlePanel.setBorder(new CompoundBorder(titlePanel.getBorder(), new EmptyBorder(10, 10, 0, 10)));
+ add(titlePanel, BorderLayout.NORTH);
+ titlePanel.add(titleLabel, BorderLayout.NORTH);
+ titlePanel.add(titleIcon, BorderLayout.WEST);
+ titlePanel.add(titleMessage, BorderLayout.CENTER);
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1;
+ c.gridx = 0;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+
+ // column range
+ c.insets = new Insets(10, 10, 0, 10);
+ page1.add(columnLabel, c);
+
+ c.insets = new Insets(10, 25, 0, 0);
+ c.gridwidth = 1;
+ c.weightx = 0;
+ page1.add(new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.from")), c);
+ c.insets = new Insets(10, 0, 0, 0);
+ c.gridx = 1;
+ page1.add(columnFromValue, c);
+ c.gridx = 2;
+ page1.add(new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.to")), c);
+ c.gridx = 3;
+ page1.add(columnToValue, c);
+
+ c.gridx = 0;
+ c.weightx = 1;
+ c.insets = new Insets(10, 10, 0, 10);
+ c.gridwidth = GridBagConstraints.REMAINDER;
+
+ // row range
+ page1.add(rowLabel, c);
+
+ c.insets = new Insets(10, 25, 0, 0);
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.weightx = 0;
+ page1.add(new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.from")), c);
+ c.insets = new Insets(10, 0, 0, 0);
+ c.gridx = 1;
+ page1.add(rowFromValue, c);
+ c.gridx = 2;
+ page1.add(new JLabel(SpreadsheetImportUIText.getString("SpreadsheetImportConfigView.to")), c);
+ c.gridx = 3;
+ page1.add(rowToValue, c);
+ c.gridx = 4;
+ page1.add(rowSelectAllOption, c);
+ c.gridx = 5;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ c.insets = new Insets(10, 0, 0, 10);
+ page1.add(rowExcludeFirstOption, c);
+ c.insets = new Insets(10, 25, 0, 0);
+ c.gridx = 0;
+ page1.add(rowIgnoreBlankRows, c);
+
+ c.gridx = 0;
+
+ // empty cells
+ c.insets = new Insets(10, 10, 10, 10);
+ page1.add(emptyCellLabel, c);
+
+ c.insets = new Insets(0, 25, 0, 10);
+ page1.add(emptyCellEmptyStringOption, c);
+ JPanel userDefinedPanel = new JPanel(new BorderLayout());
+ userDefinedPanel.add(emptyCellUserDefinedOption, BorderLayout.WEST);
+ userDefinedPanel.add(emptyCellUserDefinedValue, BorderLayout.CENTER);
+ page1.add(userDefinedPanel, c);
+ c.weighty = 1;
+ c.anchor = GridBagConstraints.NORTHWEST;
+ page1.add(emptyCellErrorValueOption, c);
+
+ // output format
+ c.insets = new Insets(10, 10, 10, 10);
+ c.weighty = 0;
+ c.weightx = 1;
+ page2.add(outputFormatLabel, c);
+
+ c.insets = new Insets(0, 25, 0, 10);
+ page2.add(outputFormatMultiplePort, c);
+ page2.add(outputFormatSinglePort, c);
+
+ c.insets = new Insets(0, 50, 0, 10);
+ JPanel outputFormatDelimiterPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ outputFormatDelimiterPanel.add(outputFormatDelimiterLabel);
+ outputFormatDelimiterPanel.add(outputFormatDelimiter);
+ page2.add(outputFormatDelimiterPanel, c);
+
+ // column mapping
+ c.insets = new Insets(10, 10, 0, 10);
+ page2.add(columnMappingLabel, c);
+
+ c.insets = new Insets(10, 10, 10, 10);
+ c.fill = GridBagConstraints.BOTH;
+ c.weighty = 1;
+ page2.add(new JScrollPane(columnMappingTable), c);
+
+ buttonPanel.add(backButton);
+ buttonPanel.add(nextButton);
+ add(buttonPanel, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Displays the message with no icon.
+ *
+ * @param message
+ * the message to display
+ */
+ public void setMessage(String message) {
+ titleIcon.setIcon(null);
+ titleMessage.setText(message);
+ }
+
+ /**
+ * Adds the message to the top of the warning message stack. If the message is already in the
+ * stack it is moved to the top. If there are no error messages the message is displayed.
+ *
+ * @param message
+ * the warning message to add
+ */
+ public void addWarningMessage(String message) {
+ if (warningMessages.contains(message)) {
+ warningMessages.remove(message);
+ }
+ warningMessages.push(message);
+ if (errorMessages.isEmpty()) {
+ setWarningMessage(message);
+ }
+ }
+
+ /**
+ * Removes the message from the warning message stack. If there are no error messages the next
+ * warning message is displayed. If there are no warning messages the default message is
+ * displayed.
+ *
+ * @param message
+ * the warning message to remove
+ */
+ public void removeWarningMessage(String message) {
+ warningMessages.remove(message);
+ if (errorMessages.isEmpty()) {
+ if (warningMessages.isEmpty()) {
+ setMessage(DEFAULT_MESSAGE);
+ } else {
+ setWarningMessage(warningMessages.peek());
+ }
+ }
+ }
+
+ /**
+ * Displays the message and a warning icon.
+ *
+ * @param message
+ * the warning message to display
+ */
+ public void setWarningMessage(String message) {
+ titleIcon.setIcon(Icons.warningIcon);
+ titleMessage.setText(message);
+ }
+
+ /**
+ * Adds the message to the top of the error message stack. If the message is already in the
+ * stack it is moved to the top. The message is then displayed.
+ *
+ * @param message
+ * the error message to add
+ */
+ public void addErrorMessage(String message) {
+ if (errorMessages.contains(message)) {
+ errorMessages.remove(message);
+ }
+ errorMessages.push(message);
+ setErrorMessage(message);
+ }
+
+ /**
+ * Removes the message from the error message stack and displays the next error message. If
+ * there are no error messages the next warning message is displayed. If there are no warning
+ * messages the default message is displayed.
+ *
+ * @param message
+ * the error message to remove
+ */
+ public void removeErrorMessage(String message) {
+ errorMessages.remove(message);
+ if (errorMessages.isEmpty()) {
+ if (warningMessages.isEmpty()) {
+ setMessage(DEFAULT_MESSAGE);
+ } else {
+ setWarningMessage(warningMessages.peek());
+ }
+ } else {
+ setErrorMessage(errorMessages.peek());
+ }
+ }
+
+ /**
+ * Displays the message and an error icon.
+ *
+ * @param message
+ * the error message to display
+ */
+ public void setErrorMessage(String message) {
+ titleIcon.setIcon(Icons.severeIcon);
+ titleMessage.setText(message);
+ }
+
+ protected boolean validatePortNames() {
+ boolean isValid = true;
+ Range columnRange = SpreadsheetUtils.getRange(newConfiguration.get("columnRange"));
+ Map<String, String> mapping = new HashMap<>();
+ if (newConfiguration.has("columnNames")) {
+ for (JsonNode columnName : newConfiguration.get("columnNames")) {
+ mapping.put(columnName.get("column").textValue(), columnName.get("port").textValue());
+ }
+ }
+ Set<String> usedNames = new HashSet<String>();
+ for (Entry<String, String> entry : mapping.entrySet()) {
+ if (columnRange.contains(SpreadsheetUtils.getColumnIndex(entry.getKey()))) {
+ String portName = entry.getValue();
+ if (!usedNames.add(portName)) {
+ isValid = false;
+ break;
+ }
+ if (portName.matches("[A-Z]+")) {
+ if (!mapping.containsKey(portName)) {
+ int columnIndex = SpreadsheetUtils.getColumnIndex(portName);
+ if (columnRange.contains(columnIndex)) {
+ isValid = false;
+ break;
+ }
+ }
+ }
+ }
+ }
+ if (isValid) {
+ removeErrorMessage(DUPLICATE_PORT_NAME_ERROR_MESSAGE);
+ } else {
+ addErrorMessage(DUPLICATE_PORT_NAME_ERROR_MESSAGE);
+ }
+ return isValid;
+ }
+
+ protected boolean checkRowRange(String from, String to) {
+ boolean result = false;
+ try {
+ int fromRow = Integer.parseInt(from);
+ int toRow = Integer.parseInt(to);
+ if (toRow < fromRow) {
+ addErrorMessage(INCONSISTENT_ROW_MESSAGE);
+ } else {
+ removeErrorMessage(INCONSISTENT_ROW_MESSAGE);
+ result = true;
+ }
+ } catch (NumberFormatException e) {
+ logger.warn("Problem checking row range", e);
+ }
+ return result;
+ }
+
+ protected boolean checkColumnRange(int fromColumn, int toColumn) {
+ boolean result = false;
+ if (toColumn < fromColumn) {
+ addErrorMessage(INCONSISTENT_COLUMN_MESSAGE);
+ } else {
+ removeErrorMessage(INCONSISTENT_COLUMN_MESSAGE);
+ result = true;
+ }
+ return result;
+ }
+
+ /**
+ * Adds a light gray or etched border to the top or bottom of a JComponent.
+ *
+ * @param component
+ */
+ protected void addDivider(JComponent component, final int position, final boolean etched) {
+ component.setBorder(new Border() {
+ private final Color borderColor = new Color(.6f, .6f, .6f);
+
+ public Insets getBorderInsets(Component c) {
+ if (position == SwingConstants.TOP) {
+ return new Insets(5, 0, 0, 0);
+ } else {
+ return new Insets(0, 0, 5, 0);
+ }
+ }
+
+ public boolean isBorderOpaque() {
+ return false;
+ }
+
+ public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
+ if (position == SwingConstants.TOP) {
+ if (etched) {
+ g.setColor(borderColor);
+ g.drawLine(x, y, x + width, y);
+ g.setColor(Color.WHITE);
+ g.drawLine(x, y + 1, x + width, y + 1);
+ } else {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(x, y, x + width, y);
+ }
+ } else {
+ if (etched) {
+ g.setColor(borderColor);
+ g.drawLine(x, y + height - 2, x + width, y + height - 2);
+ g.setColor(Color.WHITE);
+ g.drawLine(x, y + height - 1, x + width, y + height - 1);
+ } else {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(x, y + height - 1, x + width, y + height - 1);
+ }
+ }
+ }
+
+ });
+ }
+
+ private void enableTable(JTable table, boolean enabled) {
+ table.setEnabled(enabled);
+ Component editor = table.getEditorComponent();
+ if (editor != null) {
+ editor.setEnabled(enabled);
+ }
+ if (enabled) {
+ table.setForeground(Color.BLACK);
+ table.getTableHeader().setForeground(Color.BLACK);
+ } else {
+ table.setForeground(Color.LIGHT_GRAY);
+ table.getTableHeader().setForeground(Color.LIGHT_GRAY);
+ }
+ }
+
+ static class UpperCaseDocument extends PlainDocument {
+ @Override
+ public void replace(int offset, int length, String text, AttributeSet attrs) throws BadLocationException {
+ if (text.matches("[A-Za-z]+")) {
+ text = text.toUpperCase();
+ super.replace(offset, length, text, attrs);
+ }
+ }
+ }
+
+ static class NumericDocument extends PlainDocument {
+ @Override
+ public void replace(int offset, int length, String text, AttributeSet attrs) throws BadLocationException {
+ if (text.length() == 0 || text.matches("[0-9]+")) {
+ text = text.toUpperCase();
+ super.replace(offset, length, text, attrs);
+ }
+ }
+ }
+
+ /**
+ * Main method for testing the panel.
+ *
+ * @param args
+ * @throws ActivityConfigurationException
+ */
+// public static void main(String[] args) throws ActivityConfigurationException {
+// final JFrame frame = new JFrame();
+// SpreadsheetImportActivity activity = new SpreadsheetImportActivity();
+// activity.configure(new SpreadsheetImportConfiguration());
+// final SpreadsheetImportConfigView config = new SpreadsheetImportConfigView(activity);
+// config.setOkAction(new AbstractAction("Finish") {
+// public void actionPerformed(ActionEvent arg0) {
+// Range columnRange = config.getConfiguration().getColumnRange();
+// String fromColumn = SpreadsheetUtils.getColumnLabel(columnRange.getStart());
+// String toColumn = SpreadsheetUtils.getColumnLabel(columnRange.getEnd());
+// System.out.printf("%s (%s) - %s (%s)", fromColumn, columnRange.getStart(),
+// toColumn, columnRange.getEnd());
+// frame.setVisible(false);
+// frame.dispose();
+// }
+// });
+// config.setCancelAction(new AbstractAction("Cancel") {
+// public void actionPerformed(ActionEvent arg0) {
+// frame.setVisible(false);
+// frame.dispose();
+// }
+// });
+// frame.add(config);
+// frame.pack();
+// frame.setVisible(true);
+// }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualView.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualView.java
new file mode 100644
index 0000000..2078faa
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualView.java
@@ -0,0 +1,121 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.views;
+
+import java.awt.Frame;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.spreadsheet.actions.SpreadsheetImportActivityConfigurationAction;
+import net.sf.taverna.t2.activities.spreadsheet.il8n.SpreadsheetImportUIText;
+import net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportActivityIcon;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+/**
+ * A simple non editable HTML table view over a {@link SpreadsheetImportActivity}. Clicking on the
+ * configure button shows the editable {@link SpreadsheetImportConfigView}
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportContextualView extends HTMLBasedActivityContextualView {
+
+ private static final long serialVersionUID = 1L;
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final ServiceRegistry serviceRegistry;
+
+ public SpreadsheetImportContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ColourManager colourManager, ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.serviceRegistry = serviceRegistry;
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ StringBuilder html = new StringBuilder();
+ html.append("<tr><th>");
+ html.append(SpreadsheetImportUIText
+ .getString("SpreadsheetImportContextualView.inputPortName"));
+ html.append("</th><th>");
+ html.append(SpreadsheetImportUIText.getString("SpreadsheetImportContextualView.depth"));
+ html.append("</th></tr>");
+ for (InputActivityPort port : getActivity().getInputPorts()) {
+ html.append("<tr><td>");
+ html.append(port.getName());
+ html.append("</td><td>");
+ html.append(port.getDepth());
+ html.append("</td></tr>");
+ }
+ html.append("<tr><th>");
+ html.append(SpreadsheetImportUIText
+ .getString("SpreadsheetImportContextualView.outputPortName"));
+ html.append("</th><th>");
+ html.append(SpreadsheetImportUIText.getString("SpreadsheetImportContextualView.depth"));
+ html.append("</th></tr>");
+ for (OutputActivityPort port : getActivity().getOutputPorts()) {
+ html.append("<tr><td>");
+ html.append(port.getName());
+ html.append("</td><td>");
+ html.append(port.getDepth());
+ html.append("</td></tr>");
+ }
+ return html.toString();
+ }
+
+ @Override
+ public String getViewTitle() {
+ return SpreadsheetImportUIText.getString("SpreadsheetImportContextualView.activityName");
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new SpreadsheetImportActivityConfigurationAction(
+ getActivity(), owner, editManager, fileManager,
+ activityIconManager, serviceDescriptionRegistry, serviceRegistry);
+ }
+
+ @Override
+ public String getBackgroundColour() {
+ return SpreadsheetImportActivityIcon.SPREADSHEET_COLOUR_HTML;
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualViewFactory.java
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualViewFactory.java b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualViewFactory.java
new file mode 100644
index 0000000..7e49168
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/java/net/sf/taverna/t2/activities/spreadsheet/views/SpreadsheetImportContextualViewFactory.java
@@ -0,0 +1,87 @@
+/*******************************************************************************
+ * Copyright (C) 2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.spreadsheet.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+/**
+ * Factory for creating contextual a view of the SpreadsheetImport Activity
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportContextualViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public boolean canHandle(Object object) {
+ return object instanceof Activity
+ && ((Activity) object).getType().equals(
+ SpreadsheetImportTemplateService.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new SpreadsheetImportContextualView(activity,
+ editManager, fileManager, activityIconManager, colourManager,
+ serviceDescriptionRegistry, serviceRegistry) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..b1628b6
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportTemplateService
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..6720b04
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,3 @@
+net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportAddTemplateAction
+net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportConfigureMenuAction
+net.sf.taverna.t2.activities.spreadsheet.menu.SpreadsheetImportAddTemplateMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..2dd012f
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.spreadsheet.servicedescriptions.SpreadsheetImportActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..4b9dd11
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.spreadsheet.views.SpreadsheetImportContextualViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context-osgi.xml b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..72ffb77
--- /dev/null
+++ b/taverna-spreadsheet-import-activity-ui/src/main/resources/META-INF/spring/spreadsheet-import-activity-ui-context-osgi.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="SpreadsheetImportActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="SpreadsheetImportTemplateService" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="SpreadsheetImportAddTemplateAction" auto-export="interfaces" />
+ <service ref="SpreadsheetImportConfigureMenuAction" auto-export="interfaces" />
+ <service ref="SpreadsheetImportAddTemplateMenuAction" auto-export="interfaces" />
+
+ <service ref="SpreadsheetImportContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+
+</beans:beans>
[05/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/ConfirmTrustedCertificateDialog.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/ConfirmTrustedCertificateDialog.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/ConfirmTrustedCertificateDialog.java
new file mode 100644
index 0000000..bc58aad
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/ConfirmTrustedCertificateDialog.java
@@ -0,0 +1,586 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.math.BigInteger;
+import java.util.HashMap;
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
+import javax.swing.JSeparator;
+
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.security.cert.CertificateEncodingException;
+import java.security.cert.X509Certificate;
+import javax.security.auth.x500.X500Principal;
+
+import net.sf.taverna.t2.lang.ui.DialogTextArea;
+import net.sf.taverna.t2.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CMUtils;
+import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
+
+import org.apache.log4j.Logger;
+import org.bouncycastle.asn1.ASN1OctetString;
+import org.bouncycastle.asn1.DERBitString;
+import org.bouncycastle.asn1.DEROctetString;
+import org.bouncycastle.asn1.misc.NetscapeCertType;
+
+/**
+ * Displays the details of a X.509 certificate and asks user if they want to
+ * trust it.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class ConfirmTrustedCertificateDialog extends HelpEnabledDialog {
+
+ private static Logger logger = Logger.getLogger(ConfirmTrustedCertificateDialog.class);
+
+ // Stores certificate to display
+ private X509Certificate cert;
+
+ // Stores user's decision as whether to trust this service's certificaet or not.
+ private boolean shouldTrust;
+
+ /**
+ * Creates new ConfirmTrustedCertificateDialog where parent is a Frame.
+ */
+ public ConfirmTrustedCertificateDialog(Frame parent, String title,
+ boolean modal, X509Certificate crt)
+ throws CMException {
+ super(parent, title, modal, null);
+ this.cert = crt;
+ initComponents();
+ }
+
+ /**
+ * Creates new ConfirmTrustedCertificateDialog where parent is a Dialog.
+ */
+ public ConfirmTrustedCertificateDialog(Dialog parent, String title,
+ boolean modal, X509Certificate crt)
+ throws CMException {
+ super(parent, title, modal, null);
+ this.cert = crt;
+ initComponents();
+ }
+
+ /**
+ * Initialise the dialog's GUI components.
+ */
+ private void initComponents(){
+
+ // title panel
+ JPanel titlePanel = new JPanel(new BorderLayout());
+ titlePanel.setBackground(Color.WHITE);
+ JLabel titleLabel = new JLabel("View service's certificate");
+ titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD, 13.5f));
+ titleLabel.setBorder(new EmptyBorder(10, 10, 0, 10));
+ DialogTextArea titleMessage = new DialogTextArea("This service requires HTTPS connection and has identified itself with the certificate below.\n" +
+ "Do you want to trust this service? (Refusing to trust means you will not be able to invoke it from a workflow.)");
+ titleMessage.setMargin(new Insets(5, 20, 10, 10));
+ titleMessage.setFont(titleMessage.getFont().deriveFont(11f));
+ titleMessage.setEditable(false);
+ titleMessage.setFocusable(false);
+ titlePanel.setBorder( new EmptyBorder(10, 10, 0, 10));
+ titlePanel.add(titleLabel, BorderLayout.NORTH);
+ titlePanel.add(titleMessage, BorderLayout.CENTER);
+
+ // Certificate details:
+
+ // Grid Bag Constraints templates for labels (column 1) and
+ // values (column 2) of certificate details
+ GridBagConstraints gbcLabel = new GridBagConstraints();
+ gbcLabel.gridx = 0;
+ gbcLabel.ipadx = 20;
+ gbcLabel.gridwidth = 1;
+ gbcLabel.gridheight = 1;
+ gbcLabel.insets = new Insets(2, 15, 2, 2);
+ gbcLabel.anchor = GridBagConstraints.LINE_START;
+
+ GridBagConstraints gbcValue = new GridBagConstraints();
+ gbcValue.gridx = 1;
+ gbcValue.gridwidth = 1;
+ gbcValue.gridheight = 1;
+ gbcValue.insets = new Insets(2, 5, 2, 2);
+ gbcValue.anchor = GridBagConstraints.LINE_START;
+
+ // Netscape Certificate Type non-critical extension (if any)
+ // defines the intended uses of the certificate - to make it look like
+ // firefox's view certificate dialog
+ byte[] intendedUses = cert.getExtensionValue("2.16.840.1.113730.1.1"); // Netscape Certificate Type OID
+ JLabel jlIntendedUses = null;
+ JTextField jtfIntendedUsesValue = null;
+ JPanel jpUses = null;
+ GridBagConstraints gbc_jpUses = null;
+ if (intendedUses != null) {
+ jlIntendedUses = new JLabel(
+ "This certificate has been approved for the following uses:");
+ jlIntendedUses.setFont(new Font(null, Font.BOLD, 11));
+ jlIntendedUses.setBorder(new EmptyBorder(5, 5, 5, 5));
+
+ jtfIntendedUsesValue = new JTextField(45);
+ jtfIntendedUsesValue.setText(getIntendedUses(intendedUses));
+ jtfIntendedUsesValue.setEditable(false);
+ jtfIntendedUsesValue.setFont(new Font(null, Font.PLAIN, 11));
+
+ jpUses = new JPanel(new BorderLayout());
+ jpUses.add(jlIntendedUses, BorderLayout.NORTH);
+ jpUses.add(jtfIntendedUsesValue, BorderLayout.CENTER);
+ JSeparator jsp = new JSeparator(JSeparator.HORIZONTAL);
+ jpUses.add(jsp, BorderLayout.SOUTH);
+
+ gbc_jpUses = (GridBagConstraints) gbcLabel.clone();
+ gbc_jpUses.gridy = 0;
+ gbc_jpUses.gridwidth = 2; // takes two columns
+ gbc_jpUses.insets = new Insets(5, 5, 5, 5);// has slightly bigger insets
+ }
+
+ // Issued To
+ JLabel jlIssuedTo = new JLabel("Issued To");
+ jlIssuedTo.setFont(new Font(null, Font.BOLD, 11));
+ GridBagConstraints gbc_jlIssuedTo = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlIssuedTo.gridy = 1;
+ gbc_jlIssuedTo.gridwidth = 2; // takes two columns
+ gbc_jlIssuedTo.insets = new Insets(5, 5, 5, 5);// has slightly bigger insets
+ // Distinguished Name (DN)
+ String sDN = cert.getSubjectX500Principal().getName(
+ X500Principal.RFC2253);
+ CMUtils util = new CMUtils();
+ util.parseDN(sDN);
+ // Extract the CN, O, OU and EMAILADDRESS fields
+ String sCN = util.getCN();
+ String sOrg = util.getO();
+ String sOU = util.getOU();
+ // String sEMAILADDRESS = CMX509Util.getEmilAddress();
+ // Common Name (CN)
+ JLabel jlCN = new JLabel("Common Name (CN)");
+ jlCN.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlCN = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlCN.gridy = 2;
+ JLabel jlCNValue = new JLabel(sCN);
+ jlCNValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlCNValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlCNValue.gridy = 2;
+ // Organisation (O)
+ JLabel jlOrg = new JLabel("Organisation (O)");
+ jlOrg.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlOrg = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlOrg.gridy = 3;
+ JLabel jlOrgValue = new JLabel(sOrg);
+ jlOrgValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlOrgValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlOrgValue.gridy = 3;
+ // Organisation Unit (OU)
+ JLabel jlOU = new JLabel("Organisation Unit (OU)");
+ jlOU.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlOU = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlOU.gridy = 4;
+ JLabel jlOUValue = new JLabel(sOU);
+ jlOUValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlOUValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlOUValue.gridy = 4;
+ // E-mail Address
+ // JLabel jlEmail = new JLabel("E-mail Address");
+ // jlEmail.setFont(new Font(null, Font.PLAIN, 11));
+ // GridBagConstraints gbc_jlEmail = (GridBagConstraints)
+ // gbcLabel.clone();
+ // gbc_jlEmail.gridy = 5;
+ // JLabel jlEmailValue = new JLabel(sEMAILADDRESS);
+ // jlEmailValue.setFont(new Font(null, Font.PLAIN, 11));
+ // GridBagConstraints gbc_jlEmailValue = (GridBagConstraints)
+ // gbcValue.clone();
+ // gbc_jlEmailValue.gridy = 5;
+ // Serial Number
+ JLabel jlSN = new JLabel("Serial Number");
+ jlSN.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlSN = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlSN.gridy = 6;
+ JLabel jlSNValue = new JLabel();
+ // Get the hexadecimal serial number
+ StringBuffer strBuff = new StringBuffer(new BigInteger(1, cert
+ .getSerialNumber().toByteArray()).toString(16).toUpperCase());
+ // Place colons at every two hexadecimal characters
+ if (strBuff.length() > 2) {
+ for (int iCnt = 2; iCnt < strBuff.length(); iCnt += 3) {
+ strBuff.insert(iCnt, ':');
+ }
+ }
+ jlSNValue.setText(strBuff.toString());
+ jlSNValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlSNValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlSNValue.gridy = 6;
+ // Version
+ JLabel jlVersion = new JLabel("Version");
+ jlVersion.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlVersion = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlVersion.gridy = 7;
+ JLabel jlVersionValue = new JLabel(Integer.toString(cert.getVersion()));
+ jlVersionValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlVersionValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlVersionValue.gridy = 7;
+
+ // Issued By
+ JLabel jlIssuedBy = new JLabel("Issued By");
+ jlIssuedBy.setFont(new Font(null, Font.BOLD, 11));
+ GridBagConstraints gbc_jlIssuedBy = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlIssuedBy.gridy = 8;
+ gbc_jlIssuedBy.gridwidth = 2; // takes two columns
+ gbc_jlIssuedBy.insets = new Insets(5, 5, 5, 5);// has slightly bigger
+ // insets
+ // Distinguished Name (DN)
+ String iDN = cert.getIssuerX500Principal().getName(
+ X500Principal.RFC2253);
+ util.parseDN(iDN);
+ // Extract the CN, O and OU fields
+ String iCN = util.getCN();
+ String iOrg = util.getO();
+ String iOU = util.getOU();
+ // Common Name (CN)
+ JLabel jlICN = new JLabel("Common Name (CN)");
+ jlICN.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlICN = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlICN.gridy = 9;
+ JLabel jlICNValue = new JLabel(iCN);
+ jlICNValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlICNValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlICNValue.gridy = 9;
+ // Organisation (O)
+ JLabel jlIOrg = new JLabel("Organisation (O)");
+ jlIOrg.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIOrg = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlIOrg.gridy = 10;
+ JLabel jlIOrgValue = new JLabel(iOrg);
+ jlIOrgValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIOrgValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlIOrgValue.gridy = 10;
+ // Organisation Unit (OU)
+ JLabel jlIOU = new JLabel("Organisation Unit (OU)");
+ jlIOU.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIOU = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlIOU.gridy = 11;
+ JLabel jlIOUValue = new JLabel(iOU);
+ jlIOUValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIOUValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlIOUValue.gridy = 11;
+ // Validity
+ JLabel jlValidity = new JLabel("Validity");
+ jlValidity.setFont(new Font(null, Font.BOLD, 11));
+ GridBagConstraints gbc_jlValidity = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlValidity.gridy = 12;
+ gbc_jlValidity.gridwidth = 2; // takes two columns
+ gbc_jlValidity.insets = new Insets(5, 5, 5, 5);// has slightly bigger
+ // insets
+ // Issued On
+ JLabel jlIssuedOn = new JLabel("Issued On");
+ jlIssuedOn.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIssuedOn = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlIssuedOn.gridy = 13;
+ JLabel jlIssuedOnValue = new JLabel(cert.getNotBefore().toString());
+ jlIssuedOnValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlIssuedOnValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlIssuedOnValue.gridy = 13;
+ // Expires On
+ JLabel jlExpiresOn = new JLabel("Expires On");
+ jlExpiresOn.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlExpiresOn = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlExpiresOn.gridy = 14;
+ JLabel jlExpiresOnValue = new JLabel(cert.getNotAfter().toString());
+ jlExpiresOnValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlExpiresOnValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlExpiresOnValue.gridy = 14;
+
+ // Fingerprints
+ byte[] bCert = new byte[0];
+ try {
+ bCert = cert.getEncoded();
+ } catch (CertificateEncodingException ex) {
+ logger.error("Could not get the encoded form of the certificate.", ex);
+ }
+ JLabel jlFingerprints = new JLabel("Fingerprints");
+ jlFingerprints.setFont(new Font(null, Font.BOLD, 11));
+ GridBagConstraints gbc_jlFingerprints = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlFingerprints.gridy = 15;
+ gbc_jlFingerprints.gridwidth = 2; // takes two columns
+ gbc_jlFingerprints.insets = new Insets(5, 5, 5, 5);// has slightly
+ // bigger insets
+ // SHA-1 Fingerprint
+ JLabel jlSHA1Fingerprint = new JLabel("SHA1 Fingerprint");
+ jlSHA1Fingerprint.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlSHA1Fingerprint = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlSHA1Fingerprint.gridy = 16;
+ JLabel jlSHA1FingerprintValue = new JLabel(getMessageDigest(bCert,
+ "SHA1"));
+ jlSHA1FingerprintValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlSHA1FingerprintValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlSHA1FingerprintValue.gridy = 16;
+ // MD5 Fingerprint
+ JLabel jlMD5Fingerprint = new JLabel("MD5 Fingerprint");
+ jlMD5Fingerprint.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlMD5Fingerprint = (GridBagConstraints) gbcLabel
+ .clone();
+ gbc_jlMD5Fingerprint.gridy = 17;
+ JLabel jlMD5FingerprintValue = new JLabel(
+ getMessageDigest(bCert, "MD5"));
+ jlMD5FingerprintValue.setFont(new Font(null, Font.PLAIN, 11));
+ GridBagConstraints gbc_jlMD5FingerprintValue = (GridBagConstraints) gbcValue
+ .clone();
+ gbc_jlMD5FingerprintValue.gridy = 17;
+
+ // Empty label to add a bit space at the bottom of the panel
+ // to make it look like firefox's view certificate dialog
+ JLabel jlEmpty = new JLabel("");
+ GridBagConstraints gbc_jlEmpty = (GridBagConstraints) gbcLabel.clone();
+ gbc_jlEmpty.gridy = 18;
+ gbc_jlEmpty.gridwidth = 2; // takes two columns
+ gbc_jlEmpty.ipady = 40;
+
+ JPanel jpCertificate = new JPanel(new GridBagLayout());
+ jpCertificate.setBorder(new CompoundBorder(new EmptyBorder(15, 15, 15,
+ 15), new EtchedBorder()));
+
+ if (intendedUses != null) {
+ jpCertificate.add(jpUses, gbc_jpUses);
+ }
+ jpCertificate.add(jlIssuedTo, gbc_jlIssuedTo); // Issued To
+ jpCertificate.add(jlCN, gbc_jlCN);
+ jpCertificate.add(jlCNValue, gbc_jlCNValue);
+ jpCertificate.add(jlOrg, gbc_jlOrg);
+ jpCertificate.add(jlOrgValue, gbc_jlOrgValue);
+ jpCertificate.add(jlOU, gbc_jlOU);
+ jpCertificate.add(jlOUValue, gbc_jlOUValue);
+ // jpCertificate.add(jlEmail, gbc_jlEmail);
+ // jpCertificate.add(jlEmailValue, gbc_jlEmailValue);
+ jpCertificate.add(jlSN, gbc_jlSN);
+ jpCertificate.add(jlSNValue, gbc_jlSNValue);
+ jpCertificate.add(jlVersion, gbc_jlVersion);
+ jpCertificate.add(jlVersionValue, gbc_jlVersionValue);
+ jpCertificate.add(jlIssuedBy, gbc_jlIssuedBy); // Issued By
+ jpCertificate.add(jlICN, gbc_jlICN);
+ jpCertificate.add(jlICNValue, gbc_jlICNValue);
+ jpCertificate.add(jlIOrg, gbc_jlIOrg);
+ jpCertificate.add(jlIOrgValue, gbc_jlIOrgValue);
+ jpCertificate.add(jlIOU, gbc_jlIOU);
+ jpCertificate.add(jlIOUValue, gbc_jlIOUValue);
+ jpCertificate.add(jlValidity, gbc_jlValidity); // Validity
+ jpCertificate.add(jlIssuedOn, gbc_jlIssuedOn);
+ jpCertificate.add(jlIssuedOnValue, gbc_jlIssuedOnValue);
+ jpCertificate.add(jlExpiresOn, gbc_jlExpiresOn);
+ jpCertificate.add(jlExpiresOnValue, gbc_jlExpiresOnValue);
+ jpCertificate.add(jlFingerprints, gbc_jlFingerprints); // Fingerprints
+ jpCertificate.add(jlSHA1Fingerprint, gbc_jlSHA1Fingerprint);
+ jpCertificate.add(jlSHA1FingerprintValue, gbc_jlSHA1FingerprintValue);
+ jpCertificate.add(jlMD5Fingerprint, gbc_jlMD5Fingerprint);
+ jpCertificate.add(jlMD5FingerprintValue, gbc_jlMD5FingerprintValue);
+ jpCertificate.add(jlEmpty, gbc_jlEmpty); // Empty label to get some vertical space on the frame
+
+ // OK button
+ JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
+
+ final JButton jbTrust = new JButton("Trust");
+ jbTrust.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent evt) {
+ trustPressed();
+ }
+ });
+ final JButton jbDontTrust = new JButton("Do not trust");
+ jbDontTrust.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent evt) {
+ dontTrustPressed();
+ }
+ });
+
+ jpButtons.add(jbTrust);
+ jpButtons.add(jbDontTrust);
+
+ // Put it all together
+ getContentPane().add(titlePanel, BorderLayout.NORTH);
+ getContentPane().add(jpCertificate, BorderLayout.CENTER);
+ getContentPane().add(jpButtons, BorderLayout.SOUTH);
+
+ // Resizing wreaks havoc
+ setResizable(false);
+
+ addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent evt) {
+ closeDialog();
+ }
+ });
+
+ getRootPane().setDefaultButton(jbTrust);
+
+ pack();
+ }
+
+ /**
+ * Get the digest of a message as a formatted String.
+ *
+ * @param bMessage
+ * The message to digest
+ * @param digestType
+ * The message digest algorithm
+ * @return The message digest
+ */
+ public static String getMessageDigest(byte[] bMessage, String digestType) {
+ // Create message digest object using the supplied algorithm
+ MessageDigest messageDigest;
+ try {
+ messageDigest = MessageDigest.getInstance(digestType);
+ } catch (NoSuchAlgorithmException ex) {
+ logger.error("Failed to create message digest.", ex);
+ return "";
+ }
+
+ // Create raw message digest
+ byte[] bFingerPrint = messageDigest.digest(bMessage);
+
+ // Place the raw message digest into a StringBuffer as a Hex number
+ StringBuffer strBuff = new StringBuffer(new BigInteger(1, bFingerPrint)
+ .toString(16).toUpperCase());
+
+ // Odd number of characters so add in a padding "0"
+ if ((strBuff.length() % 2) != 0) {
+ strBuff.insert(0, '0');
+ }
+
+ // Place colons at every two hex characters
+ if (strBuff.length() > 2) {
+ for (int iCnt = 2; iCnt < strBuff.length(); iCnt += 3) {
+ strBuff.insert(iCnt, ':');
+ }
+ }
+
+ // Return the formatted message digest
+ return strBuff.toString();
+ }
+
+ /**
+ * Gets the intended certificate uses, i.e. Netscape Certificate Type
+ * extension (2.16.840.1.113730.1.1) value as a string
+ *
+ * @param value
+ * Extension value as a DER-encoded OCTET string
+ * @return Extension value as a string
+ */
+ private String getIntendedUses(byte[] value) {
+
+ // Netscape Certificate Types (2.16.840.1.113730.1.1)
+ int[] INTENDED_USES = new int[] { NetscapeCertType.sslClient,
+ NetscapeCertType.sslServer, NetscapeCertType.smime,
+ NetscapeCertType.objectSigning, NetscapeCertType.reserved,
+ NetscapeCertType.sslCA, NetscapeCertType.smimeCA,
+ NetscapeCertType.objectSigningCA, };
+
+ // Netscape Certificate Type strings (2.16.840.1.113730.1.1)
+ HashMap<String, String> INTENDED_USES_STRINGS = new HashMap<String, String>();
+ INTENDED_USES_STRINGS.put("128", "SSL Client");
+ INTENDED_USES_STRINGS.put("64", "SSL Server");
+ INTENDED_USES_STRINGS.put("32", "S/MIME");
+ INTENDED_USES_STRINGS.put("16", "Object Signing");
+ INTENDED_USES_STRINGS.put("8", "Reserved");
+ INTENDED_USES_STRINGS.put("4", "SSL CA");
+ INTENDED_USES_STRINGS.put("2", "S/MIME CA");
+ INTENDED_USES_STRINGS.put("1", "Object Signing CA");
+
+ // Get octet string from extension value
+ ASN1OctetString fromByteArray = new DEROctetString(value);
+ byte[] octets = fromByteArray.getOctets();
+ DERBitString fromByteArray2 = new DERBitString(octets);
+ int val = new NetscapeCertType(fromByteArray2).intValue();
+ StringBuffer strBuff = new StringBuffer();
+ for (int i = 0, len = INTENDED_USES.length; i < len; i++) {
+ int use = INTENDED_USES[i];
+ if ((val & use) == use) {
+ strBuff.append(INTENDED_USES_STRINGS.get(String.valueOf(use))
+ + ", \n");
+ }
+ }
+ // remove the last ", \n" from the end of the buffer
+ String str = strBuff.toString();
+ str = str.substring(0, str.length() - 3);
+ return str;
+ }
+
+ /**
+ * 'Trust' button pressed.
+ */
+ private void trustPressed() {
+ shouldTrust = true;
+ closeDialog();
+ }
+
+ /**
+ * 'Do not trust' button pressed.
+ */
+ private void dontTrustPressed() {
+ shouldTrust = false;
+ closeDialog();
+ }
+
+ /**
+ * Closes the dialog.
+ */
+ public void closeDialog() {
+ setVisible(false);
+ dispose();
+ }
+
+ public boolean shouldTrust() {
+ return shouldTrust;
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLActivityIcon.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLActivityIcon.java
new file mode 100644
index 0000000..79f8ccd
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLActivityIcon.java
@@ -0,0 +1,60 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+
+/**
+ *
+ * @author Alex Nenadic
+ * @author alanrw
+ *
+ */
+public class WSDLActivityIcon implements ActivityIconSPI {
+
+ private static Icon icon;
+
+ public int canProvideIconScore(URI activityType) {
+ if (activityType.equals(WSDLServiceDescription.ACTIVITY_TYPE))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getWSDLIcon();
+ }
+
+ public static Icon getWSDLIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(WSDLActivityIcon.class.getResource("/wsdl.png"));
+ }
+ return icon;
+ }
+}
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceDescription.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceDescription.java
new file mode 100644
index 0000000..faa3f8c
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceDescription.java
@@ -0,0 +1,154 @@
+/*********************************************************************
+ * Copyright (C) 2007-2009 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ **********************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class WSDLServiceDescription extends ServiceDescription {
+
+ public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/wsdl");
+ public static final URI INPUT_SPLITTER_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/xml-splitter/in");
+ public static final URI OUTPUT_SPLITTER_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/xml-splitter/out");
+
+ private static final String WSDL = "WSDL @ ";
+
+ private String use;
+ private URI uri;
+ private String style;
+ private String operation;
+ private final CredentialManager credentialManager;
+
+ private static Logger logger = Logger.getLogger(WSDLServiceDescription.class);
+
+ public WSDLServiceDescription(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+ public String getUse() {
+ return use;
+ }
+
+ public void setUse(String use) {
+ this.use = use;
+ }
+
+ public URI getURI() {
+ return uri;
+ }
+
+ public void setURI(URI url) {
+ this.uri = url;
+ }
+
+ public String getStyle() {
+ return style;
+ }
+
+ public void setStyle(String style) {
+ this.style = style;
+ }
+
+ public String getType() {
+ return "WSDL";
+ }
+
+ @Override
+ public String toString() {
+ return operation;
+ }
+
+ public String getOperation() {
+ return operation;
+ }
+
+ public void setOperation(String operation) {
+ this.operation = operation;
+ }
+
+ public Icon getIcon() {
+ return WSDLActivityIcon.getWSDLIcon();
+ }
+
+ @Override
+ public URI getActivityType() {
+ return ACTIVITY_TYPE;
+ }
+
+ @Override
+ public Configuration getActivityConfiguration() {
+ Configuration configuration = new Configuration();
+ configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+ ObjectNode json = (ObjectNode) configuration.getJson();
+ ObjectNode operation = json.objectNode();
+ json.put("operation", operation);
+ operation.put("wsdl", getURI().toString());
+ operation.put("name", getOperation());
+ return configuration;
+ }
+
+ public String getName() {
+ return getOperation();
+ }
+
+ public List<? extends Comparable<?>> getPath() {
+ return Collections.singletonList(WSDL + getURI());
+ }
+
+ protected List<Object> getIdentifyingData() {
+ return Arrays.<Object> asList(getURI(), getOperation());
+ }
+
+ @Override
+ public boolean isTemplateService() {
+ return needsSecurity();
+ }
+
+ protected boolean needsSecurity() {
+ if (credentialManager == null) {
+ // We don't know if it needs security or not
+ return false;
+ }
+ // A match is a good indicator that security configuration is needed
+ try {
+ return credentialManager.hasUsernamePasswordForService(getURI());
+ } catch (CMException e) {
+ logger.warn("Could not check if credential manager has username/password for " + getURI(), e);
+ return false;
+ }
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProvider.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProvider.java
new file mode 100644
index 0000000..daf0cad
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProvider.java
@@ -0,0 +1,206 @@
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.wsdl.Operation;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.activities.wsdl.WSDLActivityHealthChecker;
+import net.sf.taverna.t2.lang.observer.Observable;
+import net.sf.taverna.t2.lang.observer.Observer;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.CustomizedConfigurePanelProvider;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.servicedescriptions.events.RemovedProviderEvent;
+import net.sf.taverna.t2.servicedescriptions.events.ServiceDescriptionRegistryEvent;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+
+import org.apache.log4j.Logger;
+import org.xml.sax.SAXException;
+
+public class WSDLServiceProvider extends
+ AbstractConfigurableServiceProvider<WSDLServiceProviderConfig> implements
+ CustomizedConfigurePanelProvider<WSDLServiceProviderConfig> {
+
+ private static Logger logger = Logger.getLogger(WSDLServiceProvider.class);
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/wsdl");
+
+ private CredentialManager credentialManager;
+
+ public static class FlushWSDLCacheOnRemovalObserver implements
+ Observer<ServiceDescriptionRegistryEvent> {
+ public void notify(
+ Observable<ServiceDescriptionRegistryEvent> registry,
+ ServiceDescriptionRegistryEvent event) throws Exception {
+ if (!(event instanceof RemovedProviderEvent)) {
+ return;
+ }
+ RemovedProviderEvent removedProviderEvent = (RemovedProviderEvent) event;
+ if (!(removedProviderEvent.getProvider() instanceof WSDLServiceProvider)) {
+ return;
+ }
+ WSDLServiceProvider serviceProvider = (WSDLServiceProvider) removedProviderEvent
+ .getProvider();
+ URI wsdlLocation = serviceProvider.getConfiguration().getURI();
+ WSDLParser.flushCache(wsdlLocation.toASCIIString());
+ logger.info("Flushed cache for WSDL " + wsdlLocation);
+ }
+ }
+
+ private static final String WSDL_SERVICE = "WSDL service";
+
+ private static FlushWSDLCacheOnRemovalObserver flushObserver = new FlushWSDLCacheOnRemovalObserver();
+
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+
+ public WSDLServiceProvider() {
+ super(new WSDLServiceProviderConfig("http://somehost/service?wsdl"));
+ }
+
+ public String getName() {
+ return WSDL_SERVICE;
+ }
+
+ public List<WSDLServiceProviderConfig> getDefaultConfigurations() {
+
+ List<WSDLServiceProviderConfig> defaults = new ArrayList<WSDLServiceProviderConfig>();
+
+ // If defaults have failed to load from a configuration file then load them here.
+ if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()){
+ // 2009-12-16: 503 server error
+ defaults.add(new WSDLServiceProviderConfig(
+ "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl"));
+ defaults.add(new WSDLServiceProviderConfig(
+ "http://soap.bind.ca/wsdl/bind.wsdl"));
+ defaults.add(new WSDLServiceProviderConfig(
+ "http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl"));
+ } // else return an empty list
+
+ return defaults;
+ }
+
+ public void findServiceDescriptionsAsync(
+ FindServiceDescriptionsCallBack callBack) {
+
+ URI wsdl = serviceProviderConfig.getURI();
+
+ callBack.status("Parsing wsdl:" + wsdl);
+ WSDLParser parser = null;
+ try {
+ parser = new WSDLParser(wsdl.toASCIIString());
+ List<Operation> operations = parser.getOperations();
+ callBack.status("Found " + operations.size() + " WSDL operations:"
+ + wsdl);
+ List<WSDLServiceDescription> items = new ArrayList<WSDLServiceDescription>();
+ for (Operation op : operations) {
+ WSDLServiceDescription item = new WSDLServiceDescription(credentialManager);
+ try {
+ String name = op.getName();
+ item.setOperation(name);
+ String use = parser.getUse(name);
+ String style = parser.getStyle();
+ if (!WSDLActivityHealthChecker.checkStyleAndUse(style, use)) {
+ logger.warn("Unsupported style and use combination " + style + "/" + use + " for operation " + name + " from " + wsdl);
+ continue;
+ }
+ item.setUse(use);
+ item.setStyle(style);
+ item.setURI(wsdl);
+ item.setDescription(parser.getOperationDocumentation(name));
+ items.add(item);
+ } catch (UnknownOperationException e) {
+ String message = "Encountered an unexpected operation name:"
+ + item.getOperation();
+ callBack.fail(message, e);
+ }
+ }
+ callBack.partialResults(items);
+ callBack.finished();
+ } catch (ParserConfigurationException e) {
+ String message = "Error configuring the WSDL parser";
+ callBack.fail(message, e);
+ } catch (WSDLException e) {
+ String message = "There was an error with the wsdl: " + wsdl;
+ callBack.fail(message, e);
+ } catch (IOException e) {
+ String message = "There was an IO error parsing the wsdl: " + wsdl
+ + " Possible reason: the wsdl location was incorrect.";
+ callBack.fail(message, e);
+ } catch (SAXException e) {
+ String message = "There was an error with the XML in the wsdl: "
+ + wsdl;
+ callBack.fail(message, e);
+ } catch (IllegalArgumentException e) { // a problem with the wsdl url
+ String message = "There was an error with the wsdl: " + wsdl + " "
+ + "Possible reason: the wsdl location was incorrect.";
+ callBack.fail(message, e);
+ } catch (Exception e) { // anything else we did not expect
+ String message = "There was an error with the wsdl: " + wsdl;
+ callBack.fail(message, e);
+ }
+ }
+
+ @Override
+ public String toString() {
+ return getName() + " " + getConfiguration().getURI();
+ }
+
+ public Icon getIcon() {
+ return WSDLActivityIcon.getWSDLIcon();
+ }
+
+ @Override
+ protected List<? extends Object> getIdentifyingData() {
+ List<String> result;
+ result = Arrays.asList(getConfiguration().getURI().toString());
+ return result;
+ }
+
+ /**
+ * Will be set by ServiceDescriptionRegistryImpl
+ *
+ * @param registry Registry this provider has been added to
+ */
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ synchronized (flushObserver) {
+ // Add the (static common) observer if the registry does not have it
+ if (!serviceDescriptionRegistry.getObservers().contains(flushObserver)) {
+ serviceDescriptionRegistry.addObserver(flushObserver);
+ }
+ }
+ }
+
+ @SuppressWarnings("serial")
+ public void createCustomizedConfigurePanel(final CustomizedConfigureCallBack<WSDLServiceProviderConfig> callBack) {
+
+ AddWSDLServiceDialog addWSDLServiceDialog = new AddWSDLServiceDialog() {
+ @Override
+ protected void addRegistry(String wsdlURL) {
+
+ WSDLServiceProviderConfig providerConfig = new WSDLServiceProviderConfig(wsdlURL);
+ callBack.newProviderConfiguration(providerConfig);
+ }
+ };
+ addWSDLServiceDialog.setVisible(true);
+ }
+
+ public String getId() {
+ return providerId.toString();
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProviderConfig.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProviderConfig.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProviderConfig.java
new file mode 100644
index 0000000..9a63c03
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/WSDLServiceProviderConfig.java
@@ -0,0 +1,32 @@
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+
+public class WSDLServiceProviderConfig extends PropertyAnnotated {
+ private URI uri;
+
+ public WSDLServiceProviderConfig() {
+ }
+
+ public WSDLServiceProviderConfig(String uri) {
+ this.uri = URI.create(uri);
+ }
+
+ @PropertyAnnotation(displayName = "WSDL location", preferred = true)
+ public URI getURI() {
+ return uri;
+ }
+
+ public void setURI(URI uri) {
+ this.uri = uri;
+ }
+
+ @Override
+ public String toString() {
+ return getURI().toASCIIString();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLInputSplitterActivityIcon.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLInputSplitterActivityIcon.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLInputSplitterActivityIcon.java
new file mode 100644
index 0000000..cc92f3b
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLInputSplitterActivityIcon.java
@@ -0,0 +1,63 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+
+/**
+ *
+ * @author Alex Nenadic
+ *
+ */
+public class XMLInputSplitterActivityIcon implements ActivityIconSPI{
+
+ private static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/xml-splitter/in");
+
+ private static Icon icon = null;
+
+ public int canProvideIconScore(URI activityType) {
+ if (activityType.equals(ACTIVITY_TYPE))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getXMLOutputSplitterIcon();
+ }
+
+ public static Icon getXMLOutputSplitterIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(XMLOutputSplitterActivityIcon.class.getResource("/xml-splitter.png"));
+ }
+ return icon;
+ }
+
+}
+
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLOutputSplitterActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLOutputSplitterActivityIcon.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLOutputSplitterActivityIcon.java
new file mode 100644
index 0000000..73c9bcb
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/servicedescriptions/XMLOutputSplitterActivityIcon.java
@@ -0,0 +1,64 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+
+/**
+ *
+ * @author Alex Nenadic
+ *
+ */
+public class XMLOutputSplitterActivityIcon implements ActivityIconSPI{
+
+ private static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/xml-splitter/out");
+
+ private static Icon icon = null;
+
+ public int canProvideIconScore(URI activityType) {
+ if (activityType.equals(ACTIVITY_TYPE))
+ return DEFAULT_ICON + 1;
+ else
+ return NO_ICON;
+ }
+
+ public Icon getIcon(URI activityType) {
+ return getXMLOutputSplitterIcon();
+ }
+
+ public static Icon getXMLOutputSplitterIcon() {
+ if (icon == null) {
+ icon = new ImageIcon(XMLOutputSplitterActivityIcon.class.getResource("/xml-splitter.png"));
+ }
+ return icon;
+ }
+
+}
+
+
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/AbstractXMLSplitterActionView.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/AbstractXMLSplitterActionView.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/AbstractXMLSplitterActionView.java
new file mode 100644
index 0000000..0ca95e5
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/AbstractXMLSplitterActionView.java
@@ -0,0 +1,159 @@
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.io.IOException;
+import java.util.Map;
+
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.activities.wsdl.actions.AbstractAddXMLSplitterAction;
+import net.sf.taverna.t2.activities.wsdl.actions.AddXMLInputSplitterAction;
+import net.sf.taverna.t2.activities.wsdl.actions.AddXMLOutputSplitterAction;
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+import org.apache.log4j.Logger;
+import org.jdom.JDOMException;
+import org.xml.sax.SAXException;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.port.DepthPort;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+@SuppressWarnings("serial")
+public abstract class AbstractXMLSplitterActionView extends HTMLBasedActivityContextualView {
+
+ private static Logger logger = Logger.getLogger(AbstractXMLSplitterActionView.class);
+ protected final EditManager editManager;
+ protected final SelectionManager selectionManager;
+ protected AbstractAddXMLSplitterAction splitterAction;
+
+ public AbstractXMLSplitterActionView(Activity activity, EditManager editManager,
+ SelectionManager selectionManager, ColourManager colourManager) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ if (getActivity().getType().equals(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE)) {
+ splitterAction = new AddXMLOutputSplitterAction(getActivity(),
+ null, editManager, selectionManager);
+ } else if (getActivity().getType().equals(WSDLServiceDescription.INPUT_SPLITTER_TYPE)) {
+ splitterAction = new AddXMLInputSplitterAction(getActivity(),
+ null, editManager, selectionManager);
+ }
+ super.initView();
+ }
+
+ @Override
+ public void initView() {
+ }
+
+ protected void addOutputSplitter(final JComponent mainFrame, JPanel flowPanel) {
+ if (getActivity().getType().equals(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE)) {
+ try {
+ Map<String, TypeDescriptor> descriptors = splitterAction.getTypeDescriptors();
+ if (!AbstractAddXMLSplitterAction.filterDescriptors(descriptors).isEmpty()) {
+ flowPanel.add(new JButton(splitterAction));
+ }
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ logger.warn("Could not find type descriptors for " + getActivity(), e);
+ }
+ }
+ }
+
+ protected void addInputSplitter(final JComponent mainFrame, JPanel flowPanel) {
+ if (getActivity().getType().equals(WSDLServiceDescription.INPUT_SPLITTER_TYPE)) {
+ try {
+ Map<String, TypeDescriptor> descriptors = splitterAction.getTypeDescriptors();
+ if (!AbstractAddXMLSplitterAction.filterDescriptors(descriptors).isEmpty()) {
+ splitterAction.setOwner(mainFrame);
+ flowPanel.add(new JButton(splitterAction));
+ }
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ logger.warn("Could not find type descriptors for " + getActivity(), e);
+ }
+ }
+ }
+
+ protected String describePorts() {
+ StringBuilder html = new StringBuilder();
+
+ if (!getActivity().getInputPorts().isEmpty()) {
+ html.append("<tr><th colspan='2' align='left'>Inputs</th></tr>");
+ for (InputActivityPort port : getActivity().getInputPorts()) {
+ TypeDescriptor descriptor = null;
+ if (getActivity().getType().equals(WSDLServiceDescription.INPUT_SPLITTER_TYPE)) {
+ try {
+ descriptor = splitterAction.getTypeDescriptors().get(port.getName());
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ logger.warn("Could not find type descriptors for " + getActivity(), e);
+ }
+ }
+ if (descriptor == null) {
+ html.append(describePort(port));
+ } else {
+ html.append(describePort(port, descriptor));
+ }
+
+ }
+ }
+
+ if (!getActivity().getOutputPorts().isEmpty()) {
+ html.append("<tr><th colspan='2' align='left'>Outputs</th></tr>");
+ for (OutputActivityPort port : getActivity().getOutputPorts()) {
+ TypeDescriptor descriptor = null;
+ if (getActivity().getType().equals(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE)) {
+ try {
+ descriptor = splitterAction.getTypeDescriptors().get(port.getName());
+ } catch (UnknownOperationException | IOException | ParserConfigurationException
+ | WSDLException | SAXException | JDOMException e) {
+ logger.warn("Could not find type descriptors for " + getActivity(), e);
+ }
+ }
+ if (descriptor == null) {
+ html.append(describePort(port));
+ } else {
+ html.append(describePort(port, descriptor));
+ }
+ }
+ }
+
+ return html.toString();
+ }
+
+ private String describePort(DepthPort port, TypeDescriptor descriptor) {
+ String html = "<tr><td>" + port.getName() + "</td><td>";
+ if (descriptor != null && descriptor.isOptional()) {
+ html += "<em>optional</em><br>";
+ }
+ html+="Depth:"+port.getDepth()+"<br>";
+ if (descriptor != null ) {
+ html+="<code>"+descriptor.getQname().toString()+"</code><br>";
+// if (descriptor.getDocumentation() != null && !descriptor.getDocumentation().isEmpty()){
+// html += "<p>"+descriptor.getDocumentation()+"</p>";
+// }
+ }
+
+ html+="</td></tr>";
+ return html;
+ }
+
+ private String describePort(DepthPort port) {
+ String html = "<tr><td>" + port.getName() + "</td><td>";
+ html += "Depth:" + port.getDepth() + "<br>";
+ html += "</td></tr>";
+ return html;
+ }
+
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityConfigurationView.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityConfigurationView.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityConfigurationView.java
new file mode 100644
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+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.net.URI;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import javax.swing.plaf.basic.BasicComboBoxRenderer;
+
+import net.sf.taverna.t2.activities.wsdl.security.SecurityProfiles;
+import net.sf.taverna.t2.lang.ui.DialogTextArea;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.workbench.ui.credentialmanager.CredentialManagerUI;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+/**
+ * Configuration dialog for WSDL activity.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class WSDLActivityConfigurationView extends ActivityConfigurationPanel implements ItemListener {
+
+ private CredentialManager credentialManager;
+ private CredentialManagerUI credManagerUI;
+
+ private ButtonGroup buttonGroup;
+ private JRadioButton noSecurityRadioButton;
+ private JLabel noSecurityLabel;
+ private JRadioButton httpSecurityAuthNRadioButton;
+ private JLabel httpSecurityAuthNLabel;
+ private JRadioButton wsSecurityAuthNRadioButton;
+ private JLabel wsSecurityAuthNLabel;
+
+ // Password types
+ private final String PLAINTEXT_PASSWORD = "Plaintext password";
+ private final String DIGEST_PASSWORD = "Digest password";
+ private String[] passwordTypes = new String[] { PLAINTEXT_PASSWORD, DIGEST_PASSWORD };
+ private String[] tooltips = new String[] {
+ "Password will be sent in plaintext (which is OK if service is using HTTPS)",
+ "Password will be digested (cryptographically hashed) before sending" };
+ private JComboBox<String> passwordTypeComboBox;
+ private JCheckBox addTimestampCheckBox;
+ private JButton setHttpUsernamePasswordButton;
+ private JButton setWsdlUsernamePasswordButton;
+
+ // private Logger logger = Logger.getLogger(WSDLActivityConfigurationView.class);
+
+ public WSDLActivityConfigurationView(Activity activity, CredentialManager credentialManager) {
+ super(activity);
+ this.credentialManager = credentialManager;
+ initialise();
+ }
+
+ @Override
+ protected void initialise() {
+ super.initialise();
+
+ int gridy = 0;
+
+ // title panel
+ JPanel titlePanel = new JPanel(new BorderLayout());
+ titlePanel.setBackground(Color.WHITE);
+ JLabel titleLabel = new JLabel("Security configuration");
+ titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD, 13.5f));
+ titleLabel.setBorder(new EmptyBorder(10, 10, 0, 10));
+ DialogTextArea titleMessage = new DialogTextArea(
+ "Select a security profile for the service");
+ titleMessage.setMargin(new Insets(5, 20, 10, 10));
+ titleMessage.setFont(titleMessage.getFont().deriveFont(11f));
+ titleMessage.setEditable(false);
+ titleMessage.setFocusable(false);
+ titlePanel.setBorder(new EmptyBorder(10, 10, 0, 10));
+ titlePanel.add(titleLabel, BorderLayout.NORTH);
+ titlePanel.add(titleMessage, BorderLayout.CENTER);
+ addDivider(titlePanel, SwingConstants.BOTTOM, true);
+
+ // Main panel
+ JPanel mainPanel = new JPanel();
+ mainPanel.setLayout(new GridBagLayout());
+ mainPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
+
+ // Create the radio buttons
+ noSecurityRadioButton = new JRadioButton("None");
+ noSecurityRadioButton.addItemListener(this);
+
+ wsSecurityAuthNRadioButton = new JRadioButton(
+ "WS-Security username and password authentication");
+ wsSecurityAuthNRadioButton.addItemListener(this);
+
+ httpSecurityAuthNRadioButton = new JRadioButton("HTTP username and password authentication");
+ httpSecurityAuthNRadioButton.addItemListener(this);
+
+ // Group the radio buttons
+ buttonGroup = new ButtonGroup();
+ buttonGroup.add(noSecurityRadioButton);
+ buttonGroup.add(wsSecurityAuthNRadioButton);
+ buttonGroup.add(httpSecurityAuthNRadioButton);
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 1.0;
+ gbc.weighty = 0.0;
+
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 0);
+ mainPanel.add(noSecurityRadioButton, gbc);
+
+ noSecurityLabel = new JLabel("Service requires no security");
+ noSecurityLabel.setFont(noSecurityLabel.getFont().deriveFont(11f));
+ // addDivider(noSecurityLabel, SwingConstants.BOTTOM, false);
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(0, 40, 10, 10);
+ mainPanel.add(noSecurityLabel, gbc);
+
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 0);
+ mainPanel.add(httpSecurityAuthNRadioButton, gbc);
+
+ ActionListener usernamePasswordListener = new ActionListener() {
+
+ public void actionPerformed(ActionEvent e) {
+ // Get Credential Manager UI to get the username and password for the service
+ if (credManagerUI == null) {
+ credManagerUI = new CredentialManagerUI(credentialManager);
+ }
+ credManagerUI.newPasswordForService(URI.create(getJson().get("operation")
+ .get("wsdl").textValue()));
+ }
+ };
+
+ httpSecurityAuthNLabel = new JLabel(
+ "Service requires HTTP username and password in order to authenticate the user");
+ httpSecurityAuthNLabel.setFont(httpSecurityAuthNLabel.getFont().deriveFont(11f));
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(0, 40, 10, 10);
+ mainPanel.add(httpSecurityAuthNLabel, gbc);
+
+ // Set username and password button;
+ setHttpUsernamePasswordButton = new JButton("Set username and password");
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.EAST;
+ gbc.insets = new Insets(0, 40, 10, 10);
+ gbc.weightx = 1.0;
+ gbc.weighty = 1.0; // add any vertical space to this component
+ mainPanel.add(setHttpUsernamePasswordButton, gbc);
+ setHttpUsernamePasswordButton.addActionListener(usernamePasswordListener);
+
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 10, 0, 0);
+ mainPanel.add(wsSecurityAuthNRadioButton, gbc);
+
+ wsSecurityAuthNLabel = new JLabel(
+ "Service requires WS-Security username and password in order to authenticate the user");
+ wsSecurityAuthNLabel.setFont(wsSecurityAuthNLabel.getFont().deriveFont(11f));
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(0, 40, 0, 0);
+ mainPanel.add(wsSecurityAuthNLabel, gbc);
+
+ // Password type list
+ passwordTypeComboBox = new JComboBox<>(passwordTypes);
+ passwordTypeComboBox.setRenderer(new ComboBoxTooltipRenderer());
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(10, 40, 0, 0);
+ mainPanel.add(passwordTypeComboBox, gbc);
+
+ // 'Add timestamp' checkbox
+ addTimestampCheckBox = new JCheckBox("Add a timestamp to SOAP message");
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 40, 10, 10);
+ mainPanel.add(addTimestampCheckBox, gbc);
+
+ // Set username and password button;
+ setWsdlUsernamePasswordButton = new JButton("Set username and password");
+ gbc.gridx = 0;
+ gbc.gridy = gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.EAST;
+ gbc.insets = new Insets(0, 40, 10, 10);
+ gbc.weightx = 1.0;
+ gbc.weighty = 1.0; // add any vertical space to this component
+ mainPanel.add(setWsdlUsernamePasswordButton, gbc);
+ setWsdlUsernamePasswordButton.addActionListener(usernamePasswordListener);
+
+ addDivider(mainPanel, SwingConstants.BOTTOM, true);
+
+ // Enable/disable controls based on what is the current security profiles
+ if (!getJson().has("securityProfile")) {
+ noSecurityRadioButton.setSelected(true);
+ } else {
+ URI securityProfile = URI.create(getJson().get("securityProfile").textValue());
+ if (securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) {
+ wsSecurityAuthNRadioButton.setSelected(true);
+ }
+ if (securityProfile.equals(SecurityProfiles.HTTP_BASIC_AUTHN)
+ || securityProfile.equals(SecurityProfiles.HTTP_DIGEST_AUTHN)) {
+ httpSecurityAuthNRadioButton.setSelected(true);
+ }
+ if (securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)) {
+ passwordTypeComboBox.setSelectedItem(PLAINTEXT_PASSWORD);
+ } else if (securityProfile
+ .equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) {
+ passwordTypeComboBox.setSelectedItem(DIGEST_PASSWORD);
+ }
+ if (securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)
+ || securityProfile
+ .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)) {
+ addTimestampCheckBox.setSelected(true);
+ } else {
+ addTimestampCheckBox.setSelected(false);
+ }
+ }
+
+ // Put everything together
+ JPanel layoutPanel = new JPanel(new BorderLayout());
+ layoutPanel.add(titlePanel, BorderLayout.NORTH);
+ layoutPanel.add(mainPanel, BorderLayout.CENTER);
+ layoutPanel.setPreferredSize(new Dimension(550, 400));
+
+ add(layoutPanel);
+ }
+
+ @Override
+ public boolean checkValues() {
+ return true;
+ }
+
+ @Override
+ public void noteConfiguration() {
+
+ if (noSecurityRadioButton.isSelected()) {
+ getJson().remove("securityProfile"); // no security required
+ } else if (httpSecurityAuthNRadioButton.isSelected()) {
+ getJson().put("securityProfile", SecurityProfiles.HTTP_BASIC_AUTHN.toString());
+ } else if (wsSecurityAuthNRadioButton.isSelected()) { // plaintext password
+ if (passwordTypeComboBox.getSelectedItem().equals(PLAINTEXT_PASSWORD)) {
+ if (addTimestampCheckBox.isSelected()) {
+ getJson().put(
+ "securityProfile",
+ SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD
+ .toString());
+ } else {
+ getJson().put("securityProfile",
+ SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD.toString());
+ }
+ } else { // digest password
+ if (addTimestampCheckBox.isSelected()) {
+ getJson().put(
+ "securityProfile",
+ SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD
+ .toString());
+ } else {
+ getJson().put("securityProfile",
+ SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD.toString());
+ }
+ }
+ }
+ }
+
+ /**
+ * Disable/enable items on the panel based on this radio button
+ * has been selected.
+ */
+ public void itemStateChanged(ItemEvent e) {
+
+ Object source = e.getItemSelectable();
+ if (source == noSecurityRadioButton) {
+ httpSecurityAuthNLabel.setEnabled(false);
+ wsSecurityAuthNLabel.setEnabled(false);
+ passwordTypeComboBox.setEnabled(false);
+ setHttpUsernamePasswordButton.setEnabled(false);
+ setWsdlUsernamePasswordButton.setEnabled(false);
+ addTimestampCheckBox.setEnabled(false);
+
+ noSecurityLabel.setEnabled(true);
+ } else if (source == httpSecurityAuthNRadioButton) {
+ noSecurityLabel.setEnabled(false);
+ httpSecurityAuthNLabel.setEnabled(true);
+ wsSecurityAuthNLabel.setEnabled(false);
+ passwordTypeComboBox.setEnabled(false);
+ setHttpUsernamePasswordButton.setEnabled(true);
+ setWsdlUsernamePasswordButton.setEnabled(false);
+ addTimestampCheckBox.setEnabled(false);
+ } else if (source == wsSecurityAuthNRadioButton) {
+ noSecurityLabel.setEnabled(false);
+ httpSecurityAuthNLabel.setEnabled(false);
+ wsSecurityAuthNLabel.setEnabled(true);
+ passwordTypeComboBox.setEnabled(true);
+ setHttpUsernamePasswordButton.setEnabled(false);
+ setWsdlUsernamePasswordButton.setEnabled(true);
+ addTimestampCheckBox.setEnabled(true);
+ }
+ }
+
+ /**
+ * A renderer for JComboBox that will display a tooltip for
+ * the selected item.
+ */
+ class ComboBoxTooltipRenderer extends BasicComboBoxRenderer {
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ if (-1 < index) {
+ list.setToolTipText(tooltips[index]);
+ }
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+ setFont(list.getFont());
+ setText((value == null) ? "" : value.toString());
+ return this;
+ }
+ }
+
+ /**
+ * Adds a light gray or etched border to the top or bottom of a JComponent.
+ *
+ * @author David Withers
+ * @param component
+ */
+ protected void addDivider(JComponent component, final int position, final boolean etched) {
+ component.setBorder(new Border() {
+ private final Color borderColor = new Color(.6f, .6f, .6f);
+
+ public Insets getBorderInsets(Component c) {
+ if (position == SwingConstants.TOP) {
+ return new Insets(5, 0, 0, 0);
+ } else {
+ return new Insets(0, 0, 5, 0);
+ }
+ }
+
+ public boolean isBorderOpaque() {
+ return false;
+ }
+
+ public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
+ if (position == SwingConstants.TOP) {
+ if (etched) {
+ g.setColor(borderColor);
+ g.drawLine(x, y, x + width, y);
+ g.setColor(Color.WHITE);
+ g.drawLine(x, y + 1, x + width, y + 1);
+ } else {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(x, y, x + width, y);
+ }
+ } else {
+ if (etched) {
+ g.setColor(borderColor);
+ g.drawLine(x, y + height - 2, x + width, y + height - 2);
+ g.setColor(Color.WHITE);
+ g.drawLine(x, y + height - 1, x + width, y + height - 1);
+ } else {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(x, y + height - 1, x + width, y + height - 1);
+ }
+ }
+ }
+
+ });
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityContextualView.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityContextualView.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityContextualView.java
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@@ -0,0 +1,108 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.activities.wsdl.actions.WSDLActivityConfigureAction;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+@SuppressWarnings("serial")
+public class WSDLActivityContextualView extends AbstractXMLSplitterActionView {
+
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final CredentialManager credentialManager;
+ private final FileManager fileManager;
+
+ public WSDLActivityContextualView(Activity activity, EditManager editManager, FileManager fileManager,
+ SelectionManager selectionManager, ActivityIconManager activityIconManager,
+ ColourManager colourManager, CredentialManager credentialManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ super(activity, editManager, selectionManager, colourManager);
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.credentialManager = credentialManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ /**
+ * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
+ * allowing XML splitters to be added
+ */
+ @Override
+ public JComponent getMainFrame() {
+ final JComponent mainFrame = super.getMainFrame();
+ JPanel flowPanel = new JPanel(new FlowLayout());
+
+ addInputSplitter(mainFrame, flowPanel);
+ addOutputSplitter(mainFrame, flowPanel);
+
+ mainFrame.add(flowPanel, BorderLayout.SOUTH);
+ return mainFrame;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "WSDL-based service";
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ JsonNode operation = getConfigBean().getJson().get("operation");
+ String summary = "<tr><td>WSDL</td><td>" + operation.get("wsdl").textValue();
+ summary += "</td></tr><tr><td>Operation</td><td>" + operation.get("name").textValue()
+ + "</td></tr>";
+ boolean securityConfigured = getConfigBean().getJson().has("securityProfile");
+ summary += "<tr><td>Secure</td><td>" + securityConfigured + "</td></tr>";
+ summary += "</tr>";
+ summary += describePorts();
+ return summary;
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new WSDLActivityConfigureAction(getActivity(), owner, editManager, fileManager,
+ activityIconManager, serviceDescriptionRegistry, credentialManager);
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityViewFactory.java
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diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityViewFactory.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/WSDLActivityViewFactory.java
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@@ -0,0 +1,88 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class WSDLActivityViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private SelectionManager selectionManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private CredentialManager credentialManager;
+ private FileManager fileManager;
+
+ public boolean canHandle(Object object) {
+ return object instanceof Activity
+ && ((Activity) object).getType().equals(WSDLServiceDescription.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays
+ .asList(new ContextualView[] { new WSDLActivityContextualView(activity,
+ editManager, fileManager, selectionManager, activityIconManager, colourManager,
+ credentialManager, serviceDescriptionRegistry) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterContextualView.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterContextualView.java
new file mode 100644
index 0000000..228edd4
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterContextualView.java
@@ -0,0 +1,78 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class XMLSplitterContextualView extends AbstractXMLSplitterActionView {
+
+ public XMLSplitterContextualView(Activity activity,
+ EditManager editManager, SelectionManager selectionManager, ColourManager colourManager) {
+ super(activity, editManager, selectionManager, colourManager);
+ }
+
+ static Logger logger = Logger.getLogger(XMLSplitterContextualView.class);
+
+ /**
+ * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
+ * allowing XML splitters to be added
+ */
+ @Override
+ public JComponent getMainFrame() {
+ final JComponent mainFrame = super.getMainFrame();
+ JPanel flowPanel = new JPanel(new FlowLayout());
+
+ addInputSplitter(mainFrame, flowPanel);
+ addOutputSplitter(mainFrame, flowPanel);
+ mainFrame.add(flowPanel, BorderLayout.SOUTH);
+ return mainFrame;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "XML splitter";
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ return describePorts();
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterViewFactory.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterViewFactory.java
new file mode 100644
index 0000000..d0d5f8f
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/views/XMLSplitterViewFactory.java
@@ -0,0 +1,66 @@
+/*******************************************************************************
+ * Copyright (C) 2007-2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceDescription;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity;
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class XMLSplitterViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private SelectionManager selectionManager;
+ private ColourManager colourManager;
+
+ public boolean canHandle(Object object) {
+
+ return object instanceof Activity
+ && (((Activity) object).getType().equals(WSDLServiceDescription.INPUT_SPLITTER_TYPE)
+ || ((Activity) object).getType().equals(WSDLServiceDescription.OUTPUT_SPLITTER_TYPE));
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new XMLSplitterContextualView(activity,
+ editManager, selectionManager, colourManager) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setSelectionManager(SelectionManager selectionManager) {
+ this.selectionManager = selectionManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..3bf8341
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..7b0e040
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1,5 @@
+net.sf.taverna.t2.activities.wsdl.menu.AddXMLInputSplitterForWSDLActivityMenuAction
+net.sf.taverna.t2.activities.wsdl.menu.AddXMLInputSplitterForXMLInputSplitterMenuAction
+net.sf.taverna.t2.activities.wsdl.menu.AddXMLOutputSplitterForWSDLActivityMenuAction
+net.sf.taverna.t2.activities.wsdl.menu.AddXMLOutputSplitterForXMLOutputSplitterMenuAction
+net.sf.taverna.t2.activities.wsdl.menu.ConfigureWSDLMenuAction
[12/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
new file mode 100644
index 0000000..42345db
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
@@ -0,0 +1,297 @@
+package net.sf.taverna.t2.activities.localworker.servicedescriptions;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.Icon;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+import org.apache.log4j.Logger;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class LocalworkerServiceProvider implements ServiceDescriptionProvider {
+
+ private static final String LOCALWORKER_NAMES = "/localworker_names";
+
+ private static final String LOCALWORKER_SERVICE = "Local service";
+
+ private static Logger logger = Logger.getLogger(Logger.class);
+
+ private static final URI providerId = URI
+ .create("http://taverna.sf.net/2010/service-provider/localworker");
+
+ /** Used to deserialize the Activities stored on disk */
+ private ObjectMapper objectMapper = new ObjectMapper();
+
+ private static Map<String, String> localWorkerToScript = new HashMap<String, String>();
+
+ static {
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
+ "Byte Array To String");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
+ "Decode Base 64 to byte Array");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EchoList", "Echo List");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
+ "Create Lots Of Strings");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
+ "Encode Byte Array to Base 64");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
+ "Get image URLs from HTTP document");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FilterStringList",
+ "Filter List of Strings by regex");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FlattenList",
+ "Flatten List");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.PadNumber",
+ "Pad numeral with leading 0s");
+ localWorkerToScript.put(
+ "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
+ "Filter list of strings extracting match to a regex");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SendEmail",
+ "Send an Email");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SliceList",
+ "Extract Elements from a List");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
+ "Split string into string list by regular expression");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringConcat",
+ "Concatenate two strings");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringListMerge",
+ "Merge String List to a String");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
+ "String List Difference");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
+ "String List Intersection");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
+ "String List Union");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
+ "Remove String Duplicates");
+ localWorkerToScript.put(
+ "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
+ "Always Fails");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
+ "Sometimes Fails");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
+ "Get Image From URL");
+ localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
+ "Get Web Page from URL");
+
+ // xml:XPathText
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
+ "XPath From Text");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
+ "Transform XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
+ "Transform XML with parameters");
+
+ // biojava
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
+ "Read Gen Bank File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
+ "Reverse Complement DNA");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
+ "Read Swiss Prot File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
+ "Transcribe DNA");
+
+ // io
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileReader",
+ "Read Text File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
+ "Write Text File");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.LocalCommand",
+ "Execute Command Line App");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
+ "List Files by Extension");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
+ "List Files By Regex");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.DataRangeTask",
+ "Select Data Range From File");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
+ "Concatenate Files");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
+ "Get Environment Variables as XML");
+
+ // ui
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.AskWorker", "Ask");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectWorker", "Select");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.ChooseWorker", "Choose");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.TellWorker", "Tell");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.WarnWorker", "Warn");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
+ "Select File");
+ // ncbi
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
+ "Get Nucleotide FASTA");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
+ "Get Nucleotide GBSeq XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
+ "Get Nucleotide INSDSeq XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
+ "Get Nucleotide TinySeq XML");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
+ "Get Protein FASTA");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
+ "Get Protein INSDSeq XML");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
+ "Get Protein GBSeq XML");
+ localWorkerToScript.put(
+ "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
+ "Get Protein TinySeq XML");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
+ "Search PubMed XML");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
+ "Get PubMed XML By PMID");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
+ "Execute SQL Query");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
+ "Execute SQL Update");
+
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
+ "Open web browser at a URL");
+ localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
+ "Extract HTTP Header");
+ }
+
+ public String getName() {
+ return LOCALWORKER_SERVICE;
+ }
+
+ /**
+ * Use the {@link net.sf.taverna.t2.activities.localworker.translator.LocalworkerTranslator} to
+ * get a {@link Map} of all the local workers. Use the keys in this map
+ * to load all the serialized activities from disk by using
+ * <code> getClass().getResourceAsStream("/" + className) </code> to get
+ * them and then the {@link ActivityXMLDeserializer} to get the actual {@link Activity}. Create
+ * the {@link LocalworkerActivityItem} by
+ * populating them with the correct ports and depths. Sets the category to
+ * match the T1 version so that a query by category will split the local
+ * workers in to the correct place.
+ */
+ public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
+
+ List<ServiceDescription> items = new ArrayList<ServiceDescription>();
+
+ InputStream inputStream = getClass().getResourceAsStream(LOCALWORKER_NAMES);
+ if (inputStream == null) {
+ logger.error("Could not find resource " + LOCALWORKER_NAMES);
+ return;
+ }
+ BufferedReader inputReader = new BufferedReader(new InputStreamReader(inputStream));
+ String line = "";
+ String category = null;
+ try {
+ while ((line = inputReader.readLine()) != null) {
+ if (line.startsWith("category")) {
+ String[] split = line.split(":");
+ category = split[1];
+ } else {
+ LocalworkerServiceDescription createItem;
+ try {
+ createItem = createItem(line);
+ } catch (ItemCreationException e) {
+ logger.warn("Could not create item for: " + line, e);
+ continue;
+ }
+ createItem.setCategory(category);
+ createItem.setProvider("myGrid");
+ items.add(createItem);
+ }
+ }
+ } catch (IOException e1) {
+ logger.warn("Could not read local worker definitions from " + LOCALWORKER_NAMES);
+ }
+ callBack.partialResults(items);
+ callBack.finished();
+
+ }
+
+ @SuppressWarnings("serial")
+ public class ItemCreationException extends Exception {
+
+ public ItemCreationException() {
+ super();
+ }
+
+ public ItemCreationException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+ public ItemCreationException(String message) {
+ super(message);
+ }
+
+ public ItemCreationException(Throwable cause) {
+ super(cause);
+ }
+
+ }
+
+ /**
+ * Loads the deserialised local worker from disk and creates a {@link LocalworkerActivityItem}
+ * with the correct ports and script from it
+ *
+ * @param line
+ * @return a LocalWorker with the appropriate Input/Output ports and script
+ * @throws ItemCreationException
+ */
+ private LocalworkerServiceDescription createItem(String line) throws ItemCreationException {
+ // get the file from disk
+ String resource = "/" + line + ".json";
+ InputStream resourceAsStream = getClass().getResourceAsStream(resource);
+ if (resourceAsStream == null) {
+ throw new ItemCreationException("Could not find resource " + resource);
+ }
+
+ JsonNode json;
+ try {
+ json = objectMapper.readTree(resourceAsStream);
+ } catch (IOException e) {
+ throw new ItemCreationException("Could not read resource " + resource, e);
+ }
+
+ LocalworkerServiceDescription item = new LocalworkerServiceDescription();
+ item.setJson(json);
+ item.setLocalworkerName(line);
+ item.setOperation(localWorkerToScript.get(line));
+ return item;
+
+ }
+
+ public Icon getIcon() {
+ return LocalworkerActivityIcon.getLocalworkerIcon();
+ }
+
+ @Override
+ public String toString() {
+ return "Local workers provider";
+ }
+
+ public static String getServiceNameFromClassname(String classname) {
+ return (localWorkerToScript.get(classname));
+ }
+
+ public String getId() {
+ return providerId.toString();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
new file mode 100644
index 0000000..155c631
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
@@ -0,0 +1,42 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.localworker.views;
+
+import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigurationPanel;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class LocalworkerActivityConfigView extends BeanshellConfigurationPanel {
+
+ public LocalworkerActivityConfigView(Activity activity, ApplicationConfiguration applicationConfiguration) {
+ super(activity, applicationConfiguration);
+ }
+
+ public boolean isConfigurationChanged() {
+ boolean configurationChanged = super.isConfigurationChanged();
+ if (configurationChanged) {
+ getJson().put("isAltered", true);
+ }
+ return configurationChanged;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
new file mode 100644
index 0000000..fc09d57
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
@@ -0,0 +1,115 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.localworker.views;
+
+import java.awt.Frame;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
+import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.port.InputActivityPort;
+import uk.org.taverna.scufl2.api.port.OutputActivityPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+@SuppressWarnings("serial")
+public class LocalworkerActivityContextualView extends HTMLBasedActivityContextualView {
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+
+ private final ApplicationConfiguration applicationConfiguration;
+
+ public LocalworkerActivityContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ColourManager colourManager,
+ ActivityIconManager activityIconManager,
+ ServiceDescriptionRegistry serviceDescriptionRegistry,
+ ApplicationConfiguration applicationConfiguration) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ StringBuilder html = new StringBuilder();
+ html.append("<tr><th>Input Port Name</th><th>Depth</th></tr>");
+ for (InputActivityPort inputActivityPort : getActivity().getInputPorts()) {
+ html.append("<tr><td>" + inputActivityPort.getName() + "</td><td>");
+ html.append(inputActivityPort.getDepth() + "</td></tr>");
+ }
+ html.append("<tr><th>Output Port Name</th><th>Depth</th></tr>");
+ for (OutputActivityPort outputActivityPort : getActivity().getOutputPorts()) {
+ html.append("<tr><td>" + outputActivityPort.getName() + "</td><td>");
+ html.append(outputActivityPort.getDepth() + "</td></tr>");
+ }
+ return html.toString();
+ }
+
+ @Override
+ public String getViewTitle() {
+ String result = "";
+ Configuration configuration = getConfigBean();
+ JsonNode json = configuration.getJson();
+ String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(json.get(
+ "localworkerName").textValue());
+ if (json.get("isAltered").booleanValue()) {
+ result = "Altered local worker service";
+ if ((workerName != null) && !workerName.equals("")) {
+ result += " - originally " + workerName;
+ }
+ } else {
+ result = "Local worker service";
+ if ((workerName != null) && !workerName.equals("")) {
+ result += " - " + workerName;
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new LocalworkerActivityConfigurationAction(getActivity(), owner, editManager,
+ fileManager, activityIconManager, serviceDescriptionRegistry,
+ applicationConfiguration);
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
new file mode 100644
index 0000000..4fec0a2
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
@@ -0,0 +1,82 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.localworker.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class LocalworkerActivityViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ApplicationConfiguration applicationConfiguration;
+
+ public boolean canHandle(Object object) {
+ return object instanceof Activity
+ && ((Activity) object).getType()
+ .equals(LocalworkerServiceDescription.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new LocalworkerActivityContextualView(activity,
+ editManager, fileManager, colourManager, activityIconManager,
+ serviceDescriptionRegistry, applicationConfiguration) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..c3c01e0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
new file mode 100644
index 0000000..5911ddf
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..720a022
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..f1d2c0d
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
new file mode 100644
index 0000000..dd4c7a8
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="LocalworkerActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="LocalworkerServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+
+ <service ref="ConfigureLocalworkerMenuAction" auto-export="interfaces" />
+
+ <service ref="LocalworkerActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
new file mode 100644
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--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="LocalworkerActivityIcon" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon" />
+
+ <bean id="LocalworkerServiceProvider" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
+
+ <bean id="ConfigureLocalworkerMenuAction" class="net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+ <bean id="LocalworkerActivityViewFactory" class="net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/localworker.png
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diff --git a/taverna-localworker-activity-ui/src/main/resources/localworker.png b/taverna-localworker-activity-ui/src/main/resources/localworker.png
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index 0000000..758a457
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/localworker_names
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diff --git a/taverna-localworker-activity-ui/src/main/resources/localworker_names b/taverna-localworker-activity-ui/src/main/resources/localworker_names
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+++ b/taverna-localworker-activity-ui/src/main/resources/localworker_names
@@ -0,0 +1,67 @@
+category:biojava
+net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
+net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
+net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
+net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
+category:io
+net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
+net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
+net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
+net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
+net.sourceforge.taverna.scuflworkers.io.LocalCommand
+net.sourceforge.taverna.scuflworkers.io.TextFileReader
+net.sourceforge.taverna.scuflworkers.io.TextFileWriter
+category:ui
+net.sourceforge.taverna.scuflworkers.ui.AskWorker
+net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
+net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
+net.sourceforge.taverna.scuflworkers.ui.SelectWorker
+net.sourceforge.taverna.scuflworkers.ui.TellWorker
+net.sourceforge.taverna.scuflworkers.ui.WarnWorker
+category:xml
+net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
+net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
+net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
+category:list
+org.embl.ebi.escience.scuflworkers.java.EchoList
+org.embl.ebi.escience.scuflworkers.java.FlattenList
+org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
+org.embl.ebi.escience.scuflworkers.java.StringListMerge
+category:test
+org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
+org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
+org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
+category:text
+org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
+org.embl.ebi.escience.scuflworkers.java.StringSetDifference
+org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
+org.embl.ebi.escience.scuflworkers.java.StringSetUnion
+org.embl.ebi.escience.scuflworkers.java.PadNumber
+org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
+org.embl.ebi.escience.scuflworkers.java.SplitByRegex
+org.embl.ebi.escience.scuflworkers.java.StringConcat
+org.embl.ebi.escience.scuflworkers.java.FilterStringList
+category:net
+org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
+org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
+org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
+org.embl.ebi.escience.scuflworkers.java.SendEmail
+net.sourceforge.taverna.scuflworkers.net.BrowseUrl
+net.sourceforge.taverna.scuflworkers.net.ExtractHeader
+category:base64
+org.embl.ebi.escience.scuflworkers.java.EncodeBase64
+org.embl.ebi.escience.scuflworkers.java.DecodeBase64
+category:ncbi
+net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
+net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
+net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
+net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
+net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
+net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
+net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
+net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
+net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
+net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
+category:jdbc
+net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
+net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
new file mode 100644
index 0000000..d6c62b2
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
@@ -0,0 +1,74 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
+
+
+<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.biojava.bio.seq.Sequence;
+import org.biojava.bio.seq.SequenceIterator;
+import org.biojava.bio.seq.io.SeqIOTools;
+import org.biojava.bio.seq.io.agave.AgaveWriter;
+
+BufferedReader getReader (String fileUrl) throws IOException {
+ InputStreamReader reader;
+ try {
+ reader = new FileReader(fileUrl);
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ reader = new InputStreamReader (url.openStream());
+ }
+ return new BufferedReader(reader);
+ }
+
+if ((fileUrl == void) || (fileUrl == null)) {
+ throw new RuntimeException("The fileUrl must be specified");
+}
+
+BufferedReader br = getReader(fileUrl);
+
+// read the GenBank File
+SequenceIterator sequences = SeqIOTools.readGenbank(br);
+
+// iterate through the sequences
+ByteArrayOutputStream os = new ByteArrayOutputStream();
+StringBuffer sb = new StringBuffer();
+AgaveWriter writer = new AgaveWriter();
+PrintStream ps = new PrintStream(os);
+
+while (sequences.hasNext()) {
+ Sequence seq = sequences.nextSequence();
+ writer.writeSequence(seq, ps);
+ sb.append(os.toString());
+}
+
+genbankdata = sb.toString();
+br.close();
+ps.close();
+
+</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>fileUrl</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>genbankdata</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/xml'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
new file mode 100644
index 0000000..452850f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\nBufferedReader br = getReader(fileUrl);\n\n// read the GenBank File\nSequenceIterator sequences = SeqIOTools.readGenbank(br);\n\n// iterate through the sequences\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nAgaveWriter writer = new AgaveWriter();\nPrintStrea
m ps = new PrintStream(os);\n\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\n\ngenbankdata = sb.toString();\nbr.close();\nps.close();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
+ "inputPorts" : [ {
+ "name" : "fileUrl",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "genbankdata",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
new file mode 100644
index 0000000..0044c82
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
@@ -0,0 +1,43 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.biojava.bio.seq.DNATools;
+import org.biojava.bio.symbol.SymbolList;
+
+if ((rawSeq == void) || (rawSeq == null)) {
+ throw new RuntimeException("The rawSeq must be specified");
+}
+
+// make a DNA SymbolListbena
+SymbolList symL = DNATools.createDNA(rawSeq);
+
+// reverse complement it
+symL = DNATools.reverseComplement(symL);
+
+// prove that it worked
+revSeq = symL.seqString();
+</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>rawSeq</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>revSeq</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
new file mode 100644
index 0000000..c214819
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((rawSeq == void) || (rawSeq == null)) {\n throw new RuntimeException(\"The rawSeq must be specified\");\n}\n\n// make a DNA SymbolListbena\nSymbolList symL = DNATools.createDNA(rawSeq);\n\n// reverse complement it\nsymL = DNATools.reverseComplement(symL);\n\n// prove that it worked\nrevSeq = symL.seqString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
+ "inputPorts" : [ {
+ "name" : "rawSeq",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "revSeq",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
new file mode 100644
index 0000000..7f64778
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
@@ -0,0 +1,72 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.biojava.bio.seq.Sequence;
+import org.biojava.bio.seq.SequenceIterator;
+import org.biojava.bio.seq.io.SeqIOTools;
+import org.biojava.bio.seq.io.agave.AgaveWriter;
+
+BufferedReader getReader (String fileUrl) throws IOException {
+ InputStreamReader reader;
+ try {
+ reader = new FileReader(fileUrl);
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ reader = new InputStreamReader (url.openStream());
+ }
+ return new BufferedReader(reader);
+ }
+
+if ((fileUrl == void) || (fileUrl == null)) {
+ throw new RuntimeException("The fileUrl must be specified");
+}
+
+BufferedReader br = getReader(fileUrl);
+
+// read the EMBL File
+SequenceIterator sequences = SeqIOTools.readSwissprot(br);
+
+// Prepare the writer
+AgaveWriter writer = new AgaveWriter();
+ByteArrayOutputStream os = new ByteArrayOutputStream();
+StringBuffer sb = new StringBuffer();
+PrintStream ps = new PrintStream(os);
+
+// iterate through the sequences
+while (sequences.hasNext()) {
+ Sequence seq = sequences.nextSequence();
+ writer.writeSequence(seq, ps);
+ sb.append(os.toString());
+}
+results = sb.toString();
+
+br.close();
+ps.close();
+
+</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>fileUrl</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>results</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
new file mode 100644
index 0000000..929c316
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\t\nBufferedReader br = getReader(fileUrl);\n\n// read the EMBL File\nSequenceIterator sequences = SeqIOTools.readSwissprot(br);\n\n// Prepare the writer\nAgaveWriter writer = new AgaveWriter();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nPrintStream ps = ne
w PrintStream(os);\n\n// iterate through the sequences\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\nresults = sb.toString();\n\nbr.close();\nps.close();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
+ "inputPorts" : [ {
+ "name" : "fileUrl",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "results",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
new file mode 100644
index 0000000..e46e219
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
@@ -0,0 +1,48 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import org.biojava.bio.seq.DNATools;
+import org.biojava.bio.seq.RNATools;
+import org.biojava.bio.symbol.SymbolList;
+
+if ((dna_seq == void) || (dna_seq == null)) {
+ throw new RuntimeException("The dna_seq must be specified");
+}
+
+// make a DNA SymbolList
+SymbolList symL = DNATools.createDNA(dna_seq);
+
+// transcribe it to RNA (after BioJava 1.4 this method is
+// deprecated)
+symL = RNATools.transcribe(symL);
+
+// (after BioJava 1.4 use this method instead)
+// symL = DNATools.toRNA(symL);
+
+// just to prove it worked
+rna_seq = symL.seqString();
+</script>
+ <dependencies class="java.util.Collections$SingletonList">
+ <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
+ </dependencies>
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>dna_seq</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>rna_seq</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
new file mode 100644
index 0000000..767852c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
@@ -0,0 +1,16 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.seq.RNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((dna_seq == void) || (dna_seq == null)) {\n\tthrow new RuntimeException(\"The dna_seq must be specified\");\n}\n\n// make a DNA SymbolList\nSymbolList symL = DNATools.createDNA(dna_seq);\n\n// transcribe it to RNA (after BioJava 1.4 this method is\n// deprecated)\nsymL = RNATools.transcribe(symL);\n\n// (after BioJava 1.4 use this method instead)\n// symL = DNATools.toRNA(symL);\n\n// just to prove it worked\nrna_seq = symL.seqString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
+ "inputPorts" : [ {
+ "name" : "dna_seq",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "rna_seq",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
new file mode 100644
index 0000000..9ed72e4
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
@@ -0,0 +1,101 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>BufferedReader getReader (String fileUrl) throws IOException {
+ InputStreamReader reader;
+ try {
+ reader = new FileReader(fileUrl);
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ reader = new InputStreamReader (url.openStream());
+ }
+ return new BufferedReader(reader);
+ }
+
+String NEWLINE = System.getProperty("line.separator");
+
+boolean displayResults = false;
+if (displayresults != void) {
+ displayResults = Boolean.valueOf(displayresults).booleanValue();
+}
+
+StringBuffer sb = new StringBuffer(2000);
+
+if (outputfile == void) {
+ throw new RuntimeException("The 'outputfile' parameter cannot be null");
+}
+
+if (filelist == null) {
+ throw new RuntimeException("The 'filelist' parameter cannot be null");
+}
+
+String str = null;
+
+Writer writer = new FileWriter(outputfile);
+for (int i = 0; i < filelist.size(); i++) {
+ BufferedReader reader = getReader(filelist.get(i));
+ while ((str = reader.readLine()) != null) {
+ writer.write(str);
+ writer.write(NEWLINE);
+
+ if (displayResults) {
+ sb.append(str);
+ sb.append(NEWLINE);
+ }
+ }
+
+ reader.close();
+
+}
+writer.flush();
+writer.close();
+
+if (displayResults) {
+ results= sb.toString();
+}
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>filelist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>outputfile</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>displayresults</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>results</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
new file mode 100644
index 0000000..d91d466
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "BufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nString NEWLINE = System.getProperty(\"line.separator\");\n\nboolean displayResults = false;\nif (displayresults != void) {\n\tdisplayResults = Boolean.valueOf(displayresults).booleanValue();\n}\n\nStringBuffer sb = new StringBuffer(2000);\n\nif (outputfile == void) {\n\tthrow new RuntimeException(\"The 'outputfile' parameter cannot be null\");\n}\n\nif (filelist == null) {\n\tthrow new RuntimeException(\"The 'filelist' parameter cannot be null\");\n}\n\nString str = null;\n\nWriter writer = new FileWriter(outputfile);\nfor (int i = 0; i < filelist.size(); i++) {\n\tBufferedReader reader = getReader(file
list.get(i));\n\twhile ((str = reader.readLine()) != null) {\n\t\twriter.write(str);\n\t\twriter.write(NEWLINE);\n\n\t\tif (displayResults) {\n\t\t\tsb.append(str);\n\t\t\tsb.append(NEWLINE);\n\t\t}\n\t}\n\n\treader.close();\n\n}\nwriter.flush();\nwriter.close();\n\nif (displayResults) {\n\tresults= sb.toString();\n}\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
+ "inputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "type" : "String"
+ }, {
+ "name" : "outputfile",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "displayresults",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "results",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
new file mode 100644
index 0000000..410ceb0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
@@ -0,0 +1,33 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="properties" to="properties" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>import java.net.URLEncoder;
+
+Properties sysProps = System.getProperties();
+Set keys = sysProps.keySet();
+Iterator it = keys.iterator();
+String currKey = null;
+StringBuffer sb = new StringBuffer();
+sb.append("<?xml version=\"1.0\"?>\n");
+sb.append("<property-list>\n");
+while (it.hasNext()) {
+ currKey = (String) it.next();
+ sb.append("<property ");
+ sb.append(" name=\"" + URLEncoder.encode(currKey) + "\"");
+ sb.append(" value=\"" + URLEncoder.encode(sysProps.getProperty(currKey)) + "\"/>\n");
+}
+sb.append("</property-list>");
+
+properties = sb.toString();
+</script>
+ <dependencies />
+ <inputs />
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>properties</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/xml'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
new file mode 100644
index 0000000..5dc2349
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
@@ -0,0 +1,11 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.net.URLEncoder;\n\nProperties sysProps = System.getProperties();\nSet keys = sysProps.keySet();\nIterator it = keys.iterator();\nString currKey = null;\nStringBuffer sb = new StringBuffer();\nsb.append(\"<?xml version=\\\"1.0\\\"?>\\n\");\nsb.append(\"<property-list>\\n\");\nwhile (it.hasNext()) {\n\tcurrKey = (String) it.next();\n\tsb.append(\"<property \");\n\tsb.append(\" name=\\\"\" + URLEncoder.encode(currKey) + \"\\\"\");\n\tsb.append(\" value=\\\"\" + URLEncoder.encode(sysProps.getProperty(currKey)) + \"\\\"/>\\n\");\n}\nsb.append(\"</property-list>\");\n\nproperties = sb.toString();\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
+ "outputPorts" : [ {
+ "name" : "properties",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
new file mode 100644
index 0000000..910d0d6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
@@ -0,0 +1,73 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>class FileExtFilter implements FileFilter {
+
+ public FileExtFilter(String ext) {
+ this.ext = ext;
+ }
+
+ public boolean accept(File file) {
+ return file.getName().endsWith(ext);
+ }
+
+ String ext = null;
+}
+
+if (extension == void || extension.equals("")) {
+ throw new RuntimeException(
+ "The 'extension' parameter cannot be null. Please enter a valid file extension.");
+}
+
+if (directory == void || directory.equals("")) {
+ throw new RuntimeException(
+ "The 'directory' parameter cannot be null. Please enter a valid file directory.");
+}
+
+File dirObj = new File(directory);
+
+if (!dirObj.exists()) {
+ throw new RuntimeException("The 'directory' parameter specified:" + directory
+ + "does not exist. Please enter a valid file directory.");
+}
+
+File[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));
+List filelist = new ArrayList();
+for (int i = 0; i < fileObjList.length; i++) {
+ filelist.add(fileObjList[i].getAbsolutePath());
+}
+
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>directory</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>extension</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>filelist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
new file mode 100644
index 0000000..656453e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "class FileExtFilter implements FileFilter {\n\n\tpublic FileExtFilter(String ext) {\n\t\tthis.ext = ext;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().endsWith(ext);\n\t}\n\n\tString ext = null;\n}\n\nif (extension == void || extension.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'extension' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObj
List[i].getAbsolutePath());\n}\n\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
+ "inputPorts" : [ {
+ "name" : "directory",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "extension",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
new file mode 100644
index 0000000..06906b6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
@@ -0,0 +1,71 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>class FileRegexFilter implements FileFilter {
+
+ public FileRegexFilter(String regex) {
+ this.regex = regex;
+ }
+
+ public boolean accept(File file) {
+ return file.getName().matches(regex);
+ }
+
+ String regex = null;
+}
+
+if (regex == void || regex.equals("")) {
+ throw new RuntimeException(
+ "The 'regex' parameter cannot be null. Please enter a valid file extension.");
+}
+
+if (directory == void || directory.equals("")) {
+ throw new RuntimeException(
+ "The 'directory' parameter cannot be null. Please enter a valid file directory.");
+}
+
+File dirObj = new File(directory);
+
+if (!dirObj.exists()) {
+ throw new RuntimeException("The 'directory' parameter specified:" + directory
+ + "does not exist. Please enter a valid file directory.");
+}
+
+File[] fileObjList = dirObj.listFiles(new FileRegexFilter(regex));
+List filelist = new ArrayList();
+for (int i = 0; i < fileObjList.length; i++) {
+ filelist.add(fileObjList[i].getAbsolutePath());
+}
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>directory</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>regex</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>1</granularDepth>
+ <name>filelist</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
new file mode 100644
index 0000000..35cdb01
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "class FileRegexFilter implements FileFilter {\n\n\tpublic FileRegexFilter(String regex) {\n\t\tthis.regex = regex;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().matches(regex);\n\t}\n\n\tString regex = null;\n}\n\nif (regex == void || regex.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'regex' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileRegexFilter(regex));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObjL
ist[i].getAbsolutePath());\n}\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
+ "inputPorts" : [ {
+ "name" : "directory",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "regex",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filelist",
+ "depth" : 1,
+ "granularDepth" : 1
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
new file mode 100644
index 0000000..c0adc09
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
@@ -0,0 +1,80 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <script>if (command == void || command.equals("")) {
+ throw new RuntimeException("The 'command' port cannot be null.");
+}
+Process proc = null;
+Runtime rt = Runtime.getRuntime();
+
+String osName = System.getProperty("os.name");
+String[] cmdArray = null;
+if (osName.contains("Windows")) {
+ cmdArray = new String[] { "cmd.exe", "/c", command };
+} else {// TODO: investigate if this will work in Linux and OSX
+ cmdArray = new String[] { command };
+}
+
+// concatenate the arrays
+if ((args == void) || (args == null)) {
+ args = new ArrayList();
+}
+
+int argSize = cmdArray.length + args.size();
+ArrayList appArray = new ArrayList(argSize);
+for (int i = 0; i < cmdArray.length; i++) {
+ appArray.add(cmdArray[i]);
+}
+
+for (int i = 0; i < args.size(); i++) {
+ appArray.add(args.get(i));
+}
+
+String[] applist = new String[argSize];
+appArray.toArray(applist);
+proc = rt.exec(applist);
+
+// Get the input stream and read from it
+InputStream in = proc.getInputStream();
+
+int c;
+StringBuffer sb = new StringBuffer();
+while ((c = in.read()) != -1) {
+ sb.append((char) c);
+}
+in.close();
+result = sb.toString();
+
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>command</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>args</name>
+ <depth>1</depth>
+ <mimeTypes>
+ <string>l('text/plain')</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </inputs>
+ <outputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <granularDepth>0</granularDepth>
+ <name>result</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'text/plain'</string>
+ </mimeTypes>
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
new file mode 100644
index 0000000..f6ddf4f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "if (command == void || command.equals(\"\")) {\n\tthrow new RuntimeException(\"The 'command' port cannot be null.\");\n}\nProcess proc = null;\nRuntime rt = Runtime.getRuntime();\n\nString osName = System.getProperty(\"os.name\");\nString[] cmdArray = null;\nif (osName.contains(\"Windows\")) {\n\tcmdArray = new String[] { \"cmd.exe\", \"/c\", command };\n} else {// TODO: investigate if this will work in Linux and OSX\n\tcmdArray = new String[] { command };\n}\n\n// concatenate the arrays\nif ((args == void) || (args == null)) {\n\targs = new ArrayList();\n}\n\nint argSize = cmdArray.length + args.size();\nArrayList appArray = new ArrayList(argSize);\nfor (int i = 0; i < cmdArray.length; i++) {\n\tappArray.add(cmdArray[i]);\n}\n\nfor (int i = 0; i < args.size(); i++) {\n\tappArray.add(args.get(i));\n}\n\nString[] applist = new String[argSize];\nappArray.toArray(applist);\nproc = rt.exec(applist);\n\n// Get the input stream and read from it\nInputStream in = proc.getInpu
tStream();\n\nint c;\nStringBuffer sb = new StringBuffer();\nwhile ((c = in.read()) != -1) {\n\tsb.append((char) c);\n}\nin.close();\nresult = sb.toString();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.LocalCommand",
+ "inputPorts" : [ {
+ "name" : "command",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "args",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "result",
+ "depth" : 0,
+ "granularDepth" : 0
+ } ],
+ "isAltered" : false
+}
\ No newline at end of file