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
