You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by re...@apache.org on 2015/03/27 17:22:29 UTC
[16/23] incubator-taverna-workbench-common-activities git commit:
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/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
deleted file mode 100644
index ddcc4d6..0000000
--- a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
+++ /dev/null
@@ -1,302 +0,0 @@
-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 org.apache.taverna.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();
-
- }
-
- @Override
- public ServiceDescriptionProvider newInstance() {
- return new LocalworkerServiceProvider();
- }
-
- @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/163747de/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
deleted file mode 100644
index 41c7d25..0000000
--- a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
+++ /dev/null
@@ -1,42 +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
- ******************************************************************************/
-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 org.apache.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/163747de/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
deleted file mode 100644
index 461696d..0000000
--- a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
+++ /dev/null
@@ -1,115 +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
- ******************************************************************************/
-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 org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.configurations.Configuration;
-import org.apache.taverna.scufl2.api.port.InputActivityPort;
-import org.apache.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/163747de/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
deleted file mode 100644
index 3723215..0000000
--- a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
+++ /dev/null
@@ -1,82 +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
- ******************************************************************************/
-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 org.apache.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/actions/LocalworkerActivityConfigurationAction.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
new file mode 100644
index 0000000..d141ace
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/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 org.apache.taverna.activities.localworker.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+
+import org.apache.taverna.activities.localworker.views.LocalworkerActivityConfigView;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.actions.activity.ActivityConfigurationAction;
+import org.apache.taverna.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import org.apache.taverna.scufl2.api.activity.Activity;
+import org.apache.taverna.scufl2.api.common.Scufl2Tools;
+import org.apache.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/menu/ConfigureLocalworkerMenuAction.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
new file mode 100644
index 0000000..f344dd6
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
@@ -0,0 +1,62 @@
+package org.apache.taverna.activities.localworker.menu;
+
+import javax.swing.Action;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+
+import org.apache.taverna.activities.beanshell.actions.BeanshellActivityConfigurationAction;
+import org.apache.taverna.activities.localworker.actions.LocalworkerActivityConfigurationAction;
+import org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.ui.menu.ContextualMenuComponent;
+import org.apache.taverna.ui.menu.MenuComponent;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
new file mode 100644
index 0000000..f207aab
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/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 org.apache.taverna.activities.localworker.servicedescriptions;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import org.apache.taverna.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
new file mode 100644
index 0000000..73812d2
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
@@ -0,0 +1,105 @@
+package org.apache.taverna.activities.localworker.servicedescriptions;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import org.apache.taverna.servicedescriptions.ServiceDescription;
+import org.apache.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());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
new file mode 100644
index 0000000..86444e9
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
@@ -0,0 +1,302 @@
+package org.apache.taverna.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 org.apache.taverna.servicedescriptions.ServiceDescription;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider;
+import org.apache.taverna.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();
+
+ }
+
+ @Override
+ public ServiceDescriptionProvider newInstance() {
+ return new LocalworkerServiceProvider();
+ }
+
+ @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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityConfigView.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityConfigView.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityConfigView.java
new file mode 100644
index 0000000..7030d46
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/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 org.apache.taverna.activities.localworker.views;
+
+import org.apache.taverna.activities.beanshell.views.BeanshellConfigurationPanel;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import org.apache.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityContextualView.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityContextualView.java
new file mode 100644
index 0000000..2980c36
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/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 org.apache.taverna.activities.localworker.views;
+
+import java.awt.Frame;
+
+import javax.swing.Action;
+
+import org.apache.taverna.activities.localworker.actions.LocalworkerActivityConfigurationAction;
+import org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerServiceProvider;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.configuration.colour.ColourManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import org.apache.taverna.scufl2.api.activity.Activity;
+import org.apache.taverna.scufl2.api.configurations.Configuration;
+import org.apache.taverna.scufl2.api.port.InputActivityPort;
+import org.apache.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/163747de/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityViewFactory.java b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/activities/localworker/views/LocalworkerActivityViewFactory.java
new file mode 100644
index 0000000..ec48292
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/java/org/apache/taverna/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 org.apache.taverna.activities.localworker.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.configuration.colour.ColourManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
+import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import org.apache.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/163747de/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
deleted file mode 100644
index c3c01e0..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
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
deleted file mode 100644
index 5911ddf..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
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
deleted file mode 100644
index 720a022..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-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/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
----------------------------------------------------------------------
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
deleted file mode 100644
index f1d2c0d..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-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/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.servicedescriptions.ServiceDescriptionProvider b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.servicedescriptions.ServiceDescriptionProvider
new file mode 100644
index 0000000..7a2e65b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.servicedescriptions.ServiceDescriptionProvider
@@ -0,0 +1 @@
+org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.ui.menu.MenuComponent b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.ui.menu.MenuComponent
new file mode 100644
index 0000000..98f48fe
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.ui.menu.MenuComponent
@@ -0,0 +1 @@
+org.apache.taverna.activities.localworker.menu.ConfigureLocalworkerMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.activityicons.ActivityIconSPI b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.activityicons.ActivityIconSPI
new file mode 100644
index 0000000..990d212
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.activityicons.ActivityIconSPI
@@ -0,0 +1 @@
+org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory
new file mode 100644
index 0000000..f1d1fe0
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory
@@ -0,0 +1 @@
+org.apache.taverna.activities.localworker.views.LocalworkerActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
----------------------------------------------------------------------
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
index dd4c7a8..a8c3ab7 100644
--- 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
@@ -6,19 +6,19 @@
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="LocalworkerActivityIcon" interface="org.apache.taverna.workbench.activityicons.ActivityIconSPI" />
- <service ref="LocalworkerServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+ <service ref="LocalworkerServiceProvider" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionProvider" />
<service ref="ConfigureLocalworkerMenuAction" auto-export="interfaces" />
- <service ref="LocalworkerActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+ <service ref="LocalworkerActivityViewFactory" interface="org.apache.taverna.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="editManager" interface="org.apache.taverna.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="org.apache.taverna.workbench.file.FileManager" />
+ <reference id="activityIconManager" interface="org.apache.taverna.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="org.apache.taverna.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="org.apache.taverna.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/163747de/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
----------------------------------------------------------------------
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
index edcd6be..4c1bc28 100644
--- 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
@@ -3,11 +3,11 @@
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="LocalworkerActivityIcon" class="org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerActivityIcon" />
- <bean id="LocalworkerServiceProvider" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
+ <bean id="LocalworkerServiceProvider" class="org.apache.taverna.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
- <bean id="ConfigureLocalworkerMenuAction" class="net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction">
+ <bean id="ConfigureLocalworkerMenuAction" class="org.apache.taverna.activities.localworker.menu.ConfigureLocalworkerMenuAction">
<property name="editManager" ref="editManager" />
<property name="fileManager" ref="fileManager" />
<property name="activityIconManager" ref="activityIconManager" />
@@ -15,7 +15,7 @@
<property name="applicationConfiguration" ref="applicationConfiguration" />
</bean>
- <bean id="LocalworkerActivityViewFactory" class="net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory">
+ <bean id="LocalworkerActivityViewFactory" class="org.apache.taverna.activities.localworker.views.LocalworkerActivityViewFactory">
<property name="editManager" ref="editManager" />
<property name="fileManager" ref="fileManager" />
<property name="activityIconManager" ref="activityIconManager" />
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/163747de/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
index d6c62b2..c491c54 100644
--- 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
@@ -1,7 +1,7 @@
<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="">
+<class>org.apache.taverna.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><org.apache.taverna.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
<script>import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;
@@ -50,7 +50,7 @@ ps.close();
<element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
</dependencies>
<inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
@@ -59,16 +59,16 @@ ps.close();
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <org.apache.taverna.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>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
+</org.apache.taverna.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/163747de/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
----------------------------------------------------------------------
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
index 0044c82..68aba93 100644
--- 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
@@ -1,4 +1,4 @@
-<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="">
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>org.apache.taverna.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><org.apache.taverna.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
<script>import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.SymbolList;
@@ -19,7 +19,7 @@ revSeq = symL.seqString();
<element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
</dependencies>
<inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
@@ -28,16 +28,16 @@ revSeq = symL.seqString();
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <org.apache.taverna.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>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
+</org.apache.taverna.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/163747de/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
index 7f64778..60a7e25 100644
--- 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
@@ -1,4 +1,4 @@
-<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="">
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>org.apache.taverna.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><org.apache.taverna.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
<script>import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;
@@ -48,7 +48,7 @@ ps.close();
<element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
</dependencies>
<inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
@@ -57,16 +57,16 @@ ps.close();
<mimeTypes>
<string>'text/plain</string>
</mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+ <org.apache.taverna.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>
+ </org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
+</org.apache.taverna.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file