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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:44:26 UTC
[06/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
deleted file mode 100644
index 7ca2578..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
+++ /dev/null
@@ -1,635 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-import javax.swing.ImageIcon;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JSeparator;
-import javax.swing.JTextField;
-import javax.swing.JTree;
-import javax.swing.ToolTipManager;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel;
-import net.sf.taverna.t2.activities.biomoby.datatypedescriptions.BiomobyDatatypeDescription;
-import net.sf.taverna.t2.activities.biomoby.edits.AddUpstreamObjectEdit;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-/**
- * Creates a Datatype tree for any BioMOBY registry. The tree allows the user to
- * add nodes to the workflow. Includes the ability to search for datatypes too.
- *
- * @author Eddie Kawas, The BioMoby Project
- *
- */
-public class BiomobyObjectTree {
-
- private static Logger logger = Logger
- .getLogger(BiomobyObjectTree.class);
-
- private JTree tree;
- private String registryEndpoint = "";
- private String registryNamespace = "";
- private static String SEARCH_DATATYPE_TEXT = "Type to search!";
- private FilterTreeModel model;
- private final EditManager editManager;
- private final FileManager fileManager;
-
- /**
- * Default constructor. Creates a BiomobyObjectTree for the default Biomoby
- * registry
- */
- public BiomobyObjectTree(EditManager editManager, FileManager fileManager) {
- this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager);
- }
-
- /**
- *
- * @param url
- * the Biomoby registry endpoint URL to build a tree for
- * @param uri
- * the Biomoby registry namespace URI to build a tree for
- */
- public BiomobyObjectTree(String url, String uri, EditManager editManager, FileManager fileManager) {
- this.registryEndpoint = url;
- this.registryNamespace = uri;
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- /*
- * method that inserts our BiomobyDatatypeDescription object into our tree
- */
- private void insertDescriptionIntoTree(
- BiomobyDatatypeDescription description,
- HashMap<String, FilterTreeNode> nodeMap,
- HashMap<String, BiomobyDatatypeDescription> descriptionMap) {
- FilterTreeNode node = nodeMap.containsKey(description.getName()) ? nodeMap
- .get(description.getName())
- : new FilterTreeNode(description);
-
- String parent = description.getParent();
- if (parent.equals(""))
- parent = "Object";
- FilterTreeNode pNode = nodeMap.containsKey(parent) ? nodeMap
- .get(parent) : new FilterTreeNode(descriptionMap.get(parent));
- pNode.add(node);
- nodeMap.put(description.getName(), node);
- nodeMap.put(parent, pNode);
- }
-
- /**
- *
- * @return a Tree containing the datatype ontology for the specified biomoby
- * registry
- * @throws MobyException
- * if there is a problem comunicating with the specified biomoby
- * registry
- */
- public Component getDatatypeTree() throws MobyException {
- BiomobyQueryHelper bqh = new BiomobyQueryHelper(getRegistryEndpoint(),
- getRegistryNamespace());
- List<BiomobyDatatypeDescription> descriptions = bqh
- .findDatatypeDescriptions();
-
- // create a tree from all of the nodes
- HashMap<String, BiomobyDatatypeDescription> descriptionMap = new HashMap<String, BiomobyDatatypeDescription>();
- HashMap<String, FilterTreeNode> nodeMap = new HashMap<String, FilterTreeNode>();
- for (BiomobyDatatypeDescription d : descriptions) {
- // PRECONDITION: datatype names are unique across the ontology
- descriptionMap.put(d.getDatatypeName(), d);
- }
-
- nodeMap.put("Object", new FilterTreeNode(descriptionMap.get("Object")));
- for (BiomobyDatatypeDescription d : descriptions) {
- if (!d.getName().equals("Object"))
- insertDescriptionIntoTree(d, nodeMap, descriptionMap);
- }
- // construct a new tree with our root node
- tree = new JTree(nodeMap.get("Object"));
-
- // only allow one node to be selected at once
- tree.getSelectionModel().setSelectionMode(
- TreeSelectionModel.SINGLE_TREE_SELECTION);
- model = new FilterTreeModel((FilterTreeNode) tree.getModel().getRoot());
- tree.setModel(model);
-
- // set up the icon and tooltips for the nodes in the tree
- ImageIcon icon = new ImageIcon(BiomobyObjectActivityItem.class
- .getResource("/biomoby_object.png"));
- if (icon != null) {
- DefaultTreeCellRenderer renderer = new DatatypeTreeRenderer();
- renderer.setLeafIcon(icon);
- renderer.setOpenIcon(icon);
- renderer.setClosedIcon(icon);
- renderer.setIcon(icon);
- tree.setCellRenderer(renderer);
- }
-
- // add a mouse listener to catch context clicks
- // the listener adds the selected datatype to the workflow
- // it also adds the datatype's container relationships
- tree.addMouseListener(new BiomobyObjectTreeMouseListener());
- // clear the hashmaps to clear some memory
- nodeMap.clear();
- descriptionMap.clear();
- // register our tree for tool tips
- ToolTipManager.sharedInstance().registerComponent(tree);
- // insert the tree into a scrollpane
- JScrollPane treeView = new JScrollPane(tree);
- treeView.setSize(getFrameSize());
-
- // create a new panel to hold the scrollpane and a search box
- JPanel panel = new JPanel(new BorderLayout());
- panel.add(treeView, BorderLayout.CENTER);
- JTextField search = new JTextField(SEARCH_DATATYPE_TEXT);
- panel.add(search, BorderLayout.PAGE_END);
- search.addKeyListener(new KeyListener() {
- public void keyPressed(KeyEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- field.setText("");
- }
- }
- }
-
- public void keyReleased(KeyEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (e.getKeyCode() == KeyEvent.VK_ESCAPE) {
- field.setText(SEARCH_DATATYPE_TEXT);
- model.setFilter(null);
- return;
- }
- // filter our tree
- if (!field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- // does our filter tree model exist yet?
- model.setFilter(field.getText().trim());
- }
- }
- }
-
- public void keyTyped(KeyEvent e) {
-
- }
- });
- search.addFocusListener(new FocusListener() {
-
- public void focusGained(FocusEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- field.setText("");
- }
- }
- }
-
- public void focusLost(FocusEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals("")) {
- field.setText(SEARCH_DATATYPE_TEXT);
- }
- }
- }
- });
- // done
- panel.setToolTipText("Datatype Viewer for " + getRegistryEndpoint().toString());
- return panel;
- }
-
- /**
- *
- * @param registryEndpoint
- * the endpoint to set
- */
- public void setRegistryEndpoint(String registryEndpoint) {
- this.registryEndpoint = registryEndpoint;
- }
-
- /**
- *
- * @param registryNamespace
- * the namespace to set
- */
- public void setRegistryNamespace(String registryNamespace) {
- this.registryNamespace = registryNamespace;
- }
-
- /**
- *
- * @return the registry endpoint that this tree is using
- */
- public String getRegistryEndpoint() {
- return registryEndpoint;
- }
-
- /**
- *
- * @return the registry namespace that this tree is using
- */
- public String getRegistryNamespace() {
- return registryNamespace;
- }
-
- /**
- * returns the frame size as a dimension for the content pane housing this
- * action
- */
- public Dimension getFrameSize() {
- return new Dimension(550, 450);
- }
-
- /*
- * A mouse listener for our datatype tree
- */
- private class BiomobyObjectTreeMouseListener implements MouseListener {
- public void mouseClicked(MouseEvent me) {
- }
-
- public void mousePressed(MouseEvent me) {
- mouseReleased(me);
- }
-
- public void mouseReleased(MouseEvent me) {
- if (me.isPopupTrigger()) // right click, show popup menu
- {
- TreePath path = tree.getPathForLocation(me.getX(), me.getY());
- if (path == null)
- return;
-
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
-
- final String selectedObject = node.toString();
- final BiomobyDatatypeDescription bdd = (BiomobyDatatypeDescription) node
- .getUserObject();
- final JPopupMenu menu = new JPopupMenu();
- // Create and add a menu item for adding to the
- // item to the workflow
- JMenuItem item = new JMenuItem("Add Datatype - '"
- + selectedObject + "' to the workflow?");
-
- item.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent ae) {
-
- try {
- Dataflow dataflow = fileManager.getCurrentDataflow();
- List<Edit<?>> compoundEdits = new ArrayList<Edit<?>>();
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
-
- String name = Tools.uniqueProcessorName(
- selectedObject, dataflow);
-
- BiomobyObjectActivityConfigurationBean configBean = new BiomobyObjectActivityConfigurationBean();
- configBean.setMobyEndpoint(bdd
- .getActivityConfiguration()
- .getMobyEndpoint());
- configBean.setAuthorityName("");
- configBean.setServiceName(selectedObject);
-
- Edits edits = editManager.getEdits();
- net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = edits
- .createProcessor(name);
- BiomobyObjectActivity boActivity = new BiomobyObjectActivity();
- Edit<?> configureActivityEdit = edits
- .getConfigureActivityEdit(boActivity,
- configBean);
- editList.add(configureActivityEdit);
-
- editList
- .add(edits
- .getDefaultDispatchStackEdit(sourceProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits
- .getAddActivityEdit(sourceProcessor,
- boActivity);
- editList.add(addActivityToProcessorEdit);
-
- editList.add(edits.getAddProcessorEdit(dataflow,
- sourceProcessor));
-
- CompoundEdit compoundEdit = new CompoundEdit(
- editList);
- compoundEdits.add(compoundEdit);
- compoundEdit.doEdit();
-
- // process relationships
- Edit<?> edit = new AddUpstreamObjectEdit(dataflow,
- sourceProcessor, boActivity, edits);
- editManager.doDataflowEdit(dataflow, edit);
-
- } catch (Exception e) {
- logger.error("Could not add datatype", e);
- }
- }
- });
- item.setIcon(MobyPanel.getIcon("/Add24.gif"));
-
- // add the components to the menus
- menu.add(new JLabel("Add to workflow ... ", JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- // show the window
- menu.show(me.getComponent(), me.getX(), me.getY());
- }
- }
-
- public void mouseEntered(MouseEvent me) {
- }
-
- public void mouseExited(MouseEvent me) {
- }
- }
-
- private static class DatatypeTreeRenderer extends DefaultTreeCellRenderer {
-
- private static final long serialVersionUID = 7287097980554656834L;
-
- // the max tool tip length
- private static int MAX_TOOLTIP_LENGTH = 300;
-
- @Override
- public Component getTreeCellRendererComponent(JTree tree, Object value,
- boolean sel, boolean expanded, boolean leaf, int row,
- boolean hasFocus) {
- if (value instanceof DefaultMutableTreeNode) {
- if (((DefaultMutableTreeNode) value).getUserObject() instanceof BiomobyDatatypeDescription) {
- BiomobyDatatypeDescription desc = (BiomobyDatatypeDescription) ((DefaultMutableTreeNode) value)
- .getUserObject();
- String d = desc.getDescription().trim();
- // we only keep MAX_TOOLTIP_LENGTH characters of the string
- if (d.length() > MAX_TOOLTIP_LENGTH)
- d = d.substring(0, MAX_TOOLTIP_LENGTH) + "...";
- setToolTipText("<html><body><div style='width:200px;'><span>"
- + d + "</span></div></body></html>");
-
- ToolTipManager.sharedInstance().setDismissDelay(
- Integer.MAX_VALUE);
- }
- }
- return super.getTreeCellRendererComponent(tree, value, sel,
- expanded, leaf, row, hasFocus);
- }
- }
-
- /*
- * Shamelessly stolen from t2. Made the Filter a simple string filter and
- * modified the code a bit to make it relevant to my tree
- */
- private final class FilterTreeModel extends DefaultTreeModel {
-
- private static final long serialVersionUID = 8446366558654481274L;
- String currentFilter;
-
- /**
- *
- * @param node
- * the node to apply filtering to
- */
- public FilterTreeModel(FilterTreeNode node) {
- this(node, null);
- }
-
- /**
- *
- * @param node
- * the node to apply filtering to
- * @param filter
- * the actual filter we will apply
- */
- public FilterTreeModel(FilterTreeNode node, String filter) {
- super(node);
- currentFilter = filter;
- node.setFilter(filter);
- }
-
- /**
- *
- * @param filter
- * the filter to set and apply to our node
- */
- public void setFilter(String filter) {
- if (root != null) {
- currentFilter = filter;
- ((FilterTreeNode) root).setFilter(filter);
- Object[] path = { root };
- fireTreeStructureChanged(this, path, null, null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * javax.swing.tree.DefaultTreeModel#getChildCount(java.lang.Object)
- */
- public int getChildCount(Object parent) {
- if (parent instanceof FilterTreeNode) {
- return (((FilterTreeNode) parent).getChildCount());
- }
- return 0;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultTreeModel#getChild(java.lang.Object,
- * int)
- */
- public Object getChild(Object parent, int index) {
- if (parent instanceof FilterTreeNode) {
- return (((FilterTreeNode) parent).getChildAt(index));
- }
- return null;
- }
-
- /**
- * Getter
- *
- * @return the filter that we are currently using
- */
- public String getCurrentFilter() {
- return currentFilter;
- }
- }
-
- private class FilterTreeNode extends DefaultMutableTreeNode {
-
- private static final long serialVersionUID = -5269485070471940445L;
- private String filter;
- private boolean passed = true;
- private List<FilterTreeNode> filteredChildren = new ArrayList<FilterTreeNode>();
-
- public FilterTreeNode(Object userObject) {
- super(userObject);
- }
-
- public String getFilter() {
- return filter;
- }
-
- public void setFilter(String filter) {
- this.filter = filter == null ? "" : filter;
- passed = false;
- filteredChildren.clear();
- if (filter == null) {
- passed = true;
- passFilterDown(null);
- } else if (pass(this)) {
- passed = true;
- passFilterDown(filter);
- } else {
- passFilterDown(filter);
- passed = filteredChildren.size() != 0;
- }
- }
-
- private boolean pass(FilterTreeNode node) {
- if (getFilter().trim().equals("")) {
- return true;
- }
- return node.getUserObject().toString().toLowerCase().trim()
- .contains(getFilter().toLowerCase().trim());
- }
-
- private void passFilterDown(String filter) {
- int realChildCount = super.getChildCount();
- for (int i = 0; i < realChildCount; i++) {
- FilterTreeNode realChild = (FilterTreeNode) super.getChildAt(i);
- realChild.setFilter(filter);
- if (realChild.isPassed()) {
- filteredChildren.add(realChild);
- }
- }
- }
-
- public void add(FilterTreeNode node) {
- super.add(node);
- node.setFilter(filter);
- if (node.isPassed()) {
- filteredChildren.add(node);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#remove(int)
- */
- public void remove(int childIndex) {
- if (filter != null) {
- // as child indexes might be inconsistent..
- throw new IllegalStateException(
- "Can't remove while the filter is active");
- }
- super.remove(childIndex);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#getChildCount()
- */
- public int getChildCount() {
- if (filter == null) {
- return super.getChildCount();
- }
- return (filteredChildren.size());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#getChildAt(int)
- */
- public FilterTreeNode getChildAt(int index) {
- if (filter == null) {
- return (FilterTreeNode) super.getChildAt(index);
- }
- return filteredChildren.get(index);
- }
-
- /**
- *
- * @return
- */
- public boolean isPassed() {
- return passed;
- }
- }
-
- public static void main(String[] args) throws Exception {
- // Create a frame
- String title = "TeST";
- JFrame frame = new JFrame(title);
-
- // Create a component to add to the frame
-/* Component comp = new BiomobyObjectTree(CentralImpl.DEFAULT_ENDPOINT,
- CentralImpl.DEFAULT_NAMESPACE).getDatatypeTree();*/
-
- Component comp = new BiomobyObjectTree("http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl",
- CentralImpl.DEFAULT_NAMESPACE, null, null).getDatatypeTree();
-
- // Add the component to the frame's content pane;
- // by default, the content pane has a border layout
- frame.getContentPane().add(comp, BorderLayout.CENTER);
-
- // Show the frame
- int width = 300;
- int height = 300;
- frame.setSize(width, height);
- frame.setVisible(true);
-
- // Set to exit on close
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
deleted file mode 100644
index c5a7468..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.ImageIcon;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-
-import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem;
-import net.sf.taverna.t2.workbench.MainWindow;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-import com.sun.java.help.impl.SwingWorker;
-
-/**
- * DatatypeMenuItem is a JMenuItem that onClick produces a biomoby datatype tree
- * that workbench users can utilize to add datatypes to any workflow.
- *
- * @author Edward Kawas
- *
- */
-public class DatatypeMenuItem extends JMenuItem {
-
- private static Logger logger = Logger.getLogger(DatatypeMenuItem.class);
- private static final long serialVersionUID = -1010828167358361441L;
-
- private String endpoint;
- private String namespace;
-
- private final EditManager editManager;
- private final FileManager fileManager;
-
- /**
- * Default constructor; Creates a menu item for the default registry
- */
- public DatatypeMenuItem(EditManager editManager, FileManager fileManager) {
- this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager);
- }
-
- /**
- * Create a Datatype menu item for a biomoby registry given a specific
- * endpoint and namespace
- *
- * @param endpoint
- * the registry endpoint
- * @param namespace
- * the registry namespace
- */
- public DatatypeMenuItem(String endpoint, String namespace, EditManager editManager, FileManager fileManager) {
- this(endpoint, namespace, endpoint, editManager, fileManager);
- }
-
- /*
- * A private constructor. Every constructor ends up here
- */
- private DatatypeMenuItem(String endpoint, String namespace, String label, EditManager editManager, FileManager fileManager) {
- // set up some specifics
- this.endpoint = endpoint;
- this.namespace = namespace;
- this.editManager = editManager;
- this.fileManager = fileManager;
- // set up the name, label and icon for this menu item
- setName(label);
- setText(label);
- setIcon(new ImageIcon(BiomobyObjectActivityItem.class
- .getResource("/biomoby_object.png")));
- // enable the item
- setEnabled(true);
- // create an action listener to catch clicks
- addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- if (e.getSource() instanceof DatatypeMenuItem) {
- final DatatypeMenuItem item = (DatatypeMenuItem) e
- .getSource();
- // create a swing worker that creates our tree
- SwingWorker worker = new SwingWorker() {
- @Override
- public Object construct() {
- // create a progress bar ...
- JProgressBar bar = new JProgressBar();
- bar.setIndeterminate(true);
- bar.setString("Creating datatype tree ...");
- bar.setStringPainted(true);
- // a dialog frame hold the bar
- String title = "Datatype Tree Builder";
- JDialog frame = new HelpEnabledDialog(MainWindow.getMainWindow(), title, false, null);
- JLabel label = new JLabel(
- "Constructing tree for:\n\t"
- + item.getEndpoint());
- JPanel panel = new JPanel();
- panel.add(bar);
- // the panel that holds the label and bar
- JPanel panel1 = new JPanel();
- panel1.setLayout(new BorderLayout());
- panel1.add(panel, BorderLayout.NORTH);
- panel1.add(label, BorderLayout.CENTER);
- panel1.setBorder(BorderFactory.createEmptyBorder(
- 20, 20, 20, 20));
- frame.setContentPane(panel1);
- frame.setResizable(false);
- frame.pack();
- frame.setVisible(true);
- // do our task
- getTreeForRegistry(item.getEndpoint(), item
- .getNamespace());
- // hide the progress bar ...
- frame.setVisible(false);
- frame.removeAll();
- frame = null;
- return null;
- }
- };
- worker.start();
- }
- }
- });
- }
-
- /**
- * Set the registry namespace
- *
- * @param namespace
- * the registry namespace that this menu item will use
- */
- public void setNamespace(String namespace) {
- this.namespace = namespace;
- }
-
- /**
- * Set the registry endpoint
- *
- * @param endpoint
- * the registry endpoint that this menu item will use
- */
- public void setEndpoint(String endpoint) {
- this.endpoint = endpoint;
- }
-
- /**
- * Get the registry endpoint
- *
- * @return the registry endpoint that this menu item is using
- */
- public String getEndpoint() {
- return endpoint;
- }
-
- /**
- * Get the registry namespace
- *
- * @return the registry namespace that this menu item is using
- */
- public String getNamespace() {
- return namespace;
- }
-
- /*
- * Creates a tree for a given registry
- */
- private void getTreeForRegistry(String endpoint, String namespace) {
- Frame f = MobyPanel.CreateFrame("Datatype Viewer for " + endpoint);
- try {
- Component c = new BiomobyObjectTree(endpoint, namespace, editManager, fileManager)
- .getDatatypeTree();
- f.add(c);
- f.setPreferredSize(c.getPreferredSize());
- f.setMinimumSize(c.getPreferredSize());
- f.pack();
- } catch (MobyException e) {
- logger.error(
- "Error encountered while constructing datatype viewer:\n",
- e);
- }
- f.setVisible(true);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
deleted file mode 100644
index 4911721..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.Frame;
-import java.util.Map.Entry;
-
-import javax.swing.Action;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction;
-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;
-
-@SuppressWarnings("serial")
-public class BiomobyActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
-
- @Override
- public Action getConfigureAction(Frame owner) {
- BiomobyActivity activity = (BiomobyActivity) getActivity();
- if (activity.getMobyService() != null && activity.containsSecondaries()) {
- return new BiomobyActivityConfigurationAction((BiomobyActivity) getActivity(), owner,
- editManager, fileManager, activityIconManager);
- } else {
- return null;
- }
- }
-
- public BiomobyActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Service</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- if (getConfigBean().getSecondaries().size() > 0) {
- html += "<tr><th colspan='2' align='left'>Secondaries</th></tr>";
- for (Entry<String, String> entry : getConfigBean().getSecondaries().entrySet()) {
- html += "<tr><td>" + entry.getKey() + "</td><td>" + entry.getValue() + "</td></tr>";
- }
- }
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby service details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- JPanel flowPanel = new JPanel(new FlowLayout());
-
- BiomobyActivity activity = (BiomobyActivity) getActivity();
-
- JButton button = new JButton(new MobyServiceDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- if (activity.getMobyService() != null) {
- JButton button2 = new JButton(new MobyParserAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button2);
- }
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
deleted file mode 100644
index 942e52c..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-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;
-
-public class BiomobyActivityContextualViewFactory implements ContextualViewFactory<BiomobyActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyActivity;
- }
-
- public List<ContextualView> getViews(BiomobyActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager) });
- }
-
- 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-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
deleted file mode 100644
index 0e08e0b..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.util.Map;
-
-import javax.swing.JComponent;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-
-import org.apache.log4j.Logger;
-import org.biomoby.service.dashboard.data.ParametersTable;
-
-/**
- * @author alanrw
- *
- */
-public class BiomobyConfigView extends ActivityConfigurationPanel<BiomobyActivity, BiomobyActivityConfigurationBean> {
-
- private BiomobyActivity activity;
- private BiomobyActivityConfigurationBean configuration;
- private boolean changed = false;
-
- private static Logger logger = Logger
- .getLogger(BiomobyConfigView.class);
- private ParametersTable parameterTable;
-
- public BiomobyConfigView(BiomobyActivity activity) {
- this.activity = activity;
- initialise();
- }
-
- private void initialise() {
- configuration = activity.getConfiguration();
- this.setLayout(new BorderLayout());
- parameterTable = activity.getParameterTable();
- JComponent component = parameterTable.scrollable();
- this.add(component, BorderLayout.NORTH);
- validate();
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#getConfiguration()
- */
- @Override
- public BiomobyActivityConfigurationBean getConfiguration() {
- return configuration;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#isConfigurationChanged()
- */
- @Override
- public boolean isConfigurationChanged() {
- Map<String,String> secondaries = configuration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String newValue = parameterTable.getModel().getValueAt(i,1).toString();
- String currentValue = secondaries.get(key);
- if (!currentValue.equals(newValue)) {
- return true;
- }
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#noteConfiguration()
- */
- @Override
- public void noteConfiguration() {
- BiomobyActivityConfigurationBean newConfiguration =
- (BiomobyActivityConfigurationBean) cloneBean(configuration);
- Map<String,String> secondaries = newConfiguration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String value = parameterTable.getModel().getValueAt(i,1).toString();
- secondaries.put(key, value);
- }
-// logger.info(convertBeanToString(configuration));
-// logger.info("COnfiguration was " + configuration.hashCode());
-// logger.info(convertBeanToString(newConfiguration));
-// logger.info("New configuration is " + newConfiguration.hashCode());
- configuration = newConfiguration;
- }
-
- @Override
- public void refreshConfiguration() {
- logger.info(convertBeanToString(activity.getConfiguration()));
- removeAll();
- initialise();
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet implemented
- return true;
- }
-
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
deleted file mode 100644
index 4ceed9b..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * 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
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyObjectDetailsAction;
-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;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class BiomobyObjectActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyObjectActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
-
- public BiomobyObjectActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby Object service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby object details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- BiomobyObjectActivity activity = (BiomobyObjectActivity) getActivity();
- if (activity.getMobyObject() != null) {
- JPanel flowPanel = new JPanel(new FlowLayout());
- JButton button = new JButton(new MobyObjectDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- }
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
deleted file mode 100644
index 0e6ea55..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/**
- * 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
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-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;
-
-/**
- * @author Stuart Owen
- *
- */
-public class BiomobyObjectActivityContextualViewFactory implements
- ContextualViewFactory<BiomobyObjectActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyObjectActivity;
- }
-
- public List<ContextualView> getViews(BiomobyObjectActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyObjectActivityContextualView(
- activity, editManager, fileManager, colourManager) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
deleted file mode 100644
index 91d4cd6..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/**
- * 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
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyParseDatatypeContextualView extends
- HTMLBasedActivityContextualView<MobyParseDatatypeActivityConfigurationBean> {
-
- public MobyParseDatatypeContextualView(Activity<?> activity, ColourManager colourManager) {
- super(activity, colourManager);
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Article name used by service</td><td>"
- + getConfigBean().getArticleNameUsedByService() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getDatatypeName() + "</td></tr>";
- html += "<tr><td>Registry endpoint</td><td>" + getConfigBean().getRegistryEndpoint()
- + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Moby parse datatype service";
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
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-/**
- * 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
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-/**
- * @author Stuart Owen
- *
- */
-public class MobyParseDatatypeContextualViewFactory implements
- ContextualViewFactory<MobyParseDatatypeActivity> {
-
- private ColourManager colourManager;
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#canHandle
- * (java.lang.Object)
- */
- public boolean canHandle(Object activity) {
- return activity instanceof MobyParseDatatypeActivity;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#getView
- * (java.lang.Object)
- */
- public List<ContextualView> getViews(MobyParseDatatypeActivity activity) {
- return Arrays.asList(new ContextualView[] { new MobyParseDatatypeContextualView(activity,
- colourManager) });
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
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-net.sf.taverna.t2.activities.biomoby.partition.BiomobyPartitionAlgorithmSetSPI
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-net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryFactory
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-net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider
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-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction
-#net.sf.taverna.t2.activities.biomoby.actions.BiomobyAdvancedMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction
-
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-net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon
-net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon
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-net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory
-net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory
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-<?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="BiomobyActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
- <service ref="BiomobyObjectActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="BiomobyServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
-
- <service ref="BiomobyActivityDetailsMenuAction" auto-export="interfaces" />
- <service ref="BiomobyActivityParserMenuAction" auto-export="interfaces" />
- <service ref="ConfigureBiomobyMenuAction" auto-export="interfaces" />
-
- <service ref="BiomobyActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="BiomobyObjectActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="MobyParseDatatypeContextualViewFactory" 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" />
-
-</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="BiomobyActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon" />
- <bean id="BiomobyObjectActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon" />
-
- <bean id="BiomobyServiceProvider" class="net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="BiomobyActivityDetailsMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="BiomobyActivityParserMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="ConfigureBiomobyMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- </bean>
-
- <bean id="BiomobyActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="BiomobyObjectActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="MobyParseDatatypeContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory">
- <property name="colourManager" ref="colourManager" />
- </bean>
-
-</beans>
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-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiomobyContextualViewFactoryTest {
- BiomobyActivity activity;
- @Before
- public void setup() throws ActivityConfigurationException {
- activity=new BiomobyActivity() { //need to prevent the activity trying to configure itself, but store a copy of the config bean
-
- @Override
- public void configure(
- BiomobyActivityConfigurationBean configurationBean)
- throws ActivityConfigurationException {
- this.configurationBean=configurationBean;
- }
-
- };
- BiomobyActivityConfigurationBean b = new BiomobyActivityConfigurationBean();
- b.setAuthorityName("a");
- b.setMobyEndpoint("e");
- b.setServiceName("s");
- activity.configure(b);
- }
-
- @Test
- public void testGetConfigureAction() throws Exception {
- ContextualView view = new BiomobyActivityContextualView(activity, null, null, null, null);
- //will be null because its not a valid activity so therefore has no secondaries
- assertNull("The action should be null",view.getConfigureAction(null));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/pom.xml b/taverna-biomoby-activity/pom.xml
deleted file mode 100644
index 21f220e..0000000
--- a/taverna-biomoby-activity/pom.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?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.activities</groupId>
- <artifactId>biomoby-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomoby Activity</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <configuration>
- <instructions>
- <Embed-Transitive>true</Embed-Transitive>
- <Embed-Dependency>jmoby;jmoby-dashboard</Embed-Dependency>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>org.biomoby</groupId>
- <artifactId>jmoby</artifactId>
- <version>${jmoby.version}</version>
- <exclusions>
- <exclusion>
- <groupId>org.biomoby</groupId>
- <artifactId>taverna-for-moby</artifactId>
- </exclusion>
- <exclusion>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xml-apis</groupId>
- <artifactId>xml-apis</artifactId>
- </exclusion>
- <exclusion>
- <groupId>stax</groupId>
- <artifactId>stax-api</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xerces</groupId>
- <artifactId>xmlParserAPIs</artifactId>
- </exclusion>
- <exclusion>
- <groupId>javax.xml.ws</groupId>
- <artifactId>jaxws-api</artifactId>
- </exclusion>
- <exclusion>
- <groupId>javax.xml.soap</groupId>
- <artifactId>saaj-api</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
- <groupId>org.biomoby</groupId>
- <artifactId>jmoby-dashboard</artifactId>
- <version>${jmoby.version}</version>
- </dependency>
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>${jdom.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
- <version>${commons.httpclient.version}</version>
- </dependency>
- <!--<dependency> <groupId>org.apache.xmlcommons</groupId> <artifactId>com.springsource.org.apache.xmlcommons</artifactId>
- <version>1.3.4</version> </dependency> -->
- <!--<dependency> <groupId>javax.xml.ws</groupId> <artifactId>jaxws-api</artifactId>
- <version>2.1</version> </dependency> -->
- <!--<dependency> <groupId>com.sun.org.apache</groupId> <artifactId>jaxp-ri</artifactId>
- <version>1.4</version> </dependency> -->
- <dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>activity-test-utils</artifactId>
- <version>${t2.activities.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>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomoby-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-biomoby-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomoby-activity/</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>