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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:49:39 UTC
[12/16] incubator-taverna-workbench-common-activities git commit:
Temporarily empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
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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 42345db..0000000
--- a/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
+++ /dev/null
@@ -1,297 +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 net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-import org.apache.log4j.Logger;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-public class LocalworkerServiceProvider implements ServiceDescriptionProvider {
-
- private static final String LOCALWORKER_NAMES = "/localworker_names";
-
- private static final String LOCALWORKER_SERVICE = "Local service";
-
- private static Logger logger = Logger.getLogger(Logger.class);
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/localworker");
-
- /** Used to deserialize the Activities stored on disk */
- private ObjectMapper objectMapper = new ObjectMapper();
-
- private static Map<String, String> localWorkerToScript = new HashMap<String, String>();
-
- static {
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
- "Byte Array To String");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
- "Decode Base 64 to byte Array");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EchoList", "Echo List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
- "Create Lots Of Strings");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
- "Encode Byte Array to Base 64");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
- "Get image URLs from HTTP document");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FilterStringList",
- "Filter List of Strings by regex");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FlattenList",
- "Flatten List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.PadNumber",
- "Pad numeral with leading 0s");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
- "Filter list of strings extracting match to a regex");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SendEmail",
- "Send an Email");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SliceList",
- "Extract Elements from a List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
- "Split string into string list by regular expression");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringConcat",
- "Concatenate two strings");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringListMerge",
- "Merge String List to a String");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
- "String List Difference");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
- "String List Intersection");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
- "String List Union");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
- "Remove String Duplicates");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
- "Always Fails");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
- "Sometimes Fails");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
- "Get Image From URL");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
- "Get Web Page from URL");
-
- // xml:XPathText
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
- "XPath From Text");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
- "Transform XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
- "Transform XML with parameters");
-
- // biojava
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
- "Read Gen Bank File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
- "Reverse Complement DNA");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
- "Read Swiss Prot File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
- "Transcribe DNA");
-
- // io
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileReader",
- "Read Text File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
- "Write Text File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.LocalCommand",
- "Execute Command Line App");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
- "List Files by Extension");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
- "List Files By Regex");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.DataRangeTask",
- "Select Data Range From File");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
- "Concatenate Files");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
- "Get Environment Variables as XML");
-
- // ui
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.AskWorker", "Ask");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectWorker", "Select");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.ChooseWorker", "Choose");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.TellWorker", "Tell");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.WarnWorker", "Warn");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
- "Select File");
- // ncbi
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
- "Get Nucleotide FASTA");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
- "Get Nucleotide GBSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
- "Get Nucleotide INSDSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
- "Get Nucleotide TinySeq XML");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
- "Get Protein FASTA");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
- "Get Protein INSDSeq XML");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
- "Get Protein GBSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
- "Get Protein TinySeq XML");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
- "Search PubMed XML");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
- "Get PubMed XML By PMID");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
- "Execute SQL Query");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
- "Execute SQL Update");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
- "Open web browser at a URL");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
- "Extract HTTP Header");
- }
-
- public String getName() {
- return LOCALWORKER_SERVICE;
- }
-
- /**
- * Use the {@link net.sf.taverna.t2.activities.localworker.translator.LocalworkerTranslator} to
- * get a {@link Map} of all the local workers. Use the keys in this map
- * to load all the serialized activities from disk by using
- * <code> getClass().getResourceAsStream("/" + className) </code> to get
- * them and then the {@link ActivityXMLDeserializer} to get the actual {@link Activity}. Create
- * the {@link LocalworkerActivityItem} by
- * populating them with the correct ports and depths. Sets the category to
- * match the T1 version so that a query by category will split the local
- * workers in to the correct place.
- */
- public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
-
- List<ServiceDescription> items = new ArrayList<ServiceDescription>();
-
- InputStream inputStream = getClass().getResourceAsStream(LOCALWORKER_NAMES);
- if (inputStream == null) {
- logger.error("Could not find resource " + LOCALWORKER_NAMES);
- return;
- }
- BufferedReader inputReader = new BufferedReader(new InputStreamReader(inputStream));
- String line = "";
- String category = null;
- try {
- while ((line = inputReader.readLine()) != null) {
- if (line.startsWith("category")) {
- String[] split = line.split(":");
- category = split[1];
- } else {
- LocalworkerServiceDescription createItem;
- try {
- createItem = createItem(line);
- } catch (ItemCreationException e) {
- logger.warn("Could not create item for: " + line, e);
- continue;
- }
- createItem.setCategory(category);
- createItem.setProvider("myGrid");
- items.add(createItem);
- }
- }
- } catch (IOException e1) {
- logger.warn("Could not read local worker definitions from " + LOCALWORKER_NAMES);
- }
- callBack.partialResults(items);
- callBack.finished();
-
- }
-
- @SuppressWarnings("serial")
- public class ItemCreationException extends Exception {
-
- public ItemCreationException() {
- super();
- }
-
- public ItemCreationException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public ItemCreationException(String message) {
- super(message);
- }
-
- public ItemCreationException(Throwable cause) {
- super(cause);
- }
-
- }
-
- /**
- * Loads the deserialised local worker from disk and creates a {@link LocalworkerActivityItem}
- * with the correct ports and script from it
- *
- * @param line
- * @return a LocalWorker with the appropriate Input/Output ports and script
- * @throws ItemCreationException
- */
- private LocalworkerServiceDescription createItem(String line) throws ItemCreationException {
- // get the file from disk
- String resource = "/" + line + ".json";
- InputStream resourceAsStream = getClass().getResourceAsStream(resource);
- if (resourceAsStream == null) {
- throw new ItemCreationException("Could not find resource " + resource);
- }
-
- JsonNode json;
- try {
- json = objectMapper.readTree(resourceAsStream);
- } catch (IOException e) {
- throw new ItemCreationException("Could not read resource " + resource, e);
- }
-
- LocalworkerServiceDescription item = new LocalworkerServiceDescription();
- item.setJson(json);
- item.setLocalworkerName(line);
- item.setOperation(localWorkerToScript.get(line));
- return item;
-
- }
-
- public Icon getIcon() {
- return LocalworkerActivityIcon.getLocalworkerIcon();
- }
-
- @Override
- public String toString() {
- return "Local workers provider";
- }
-
- public static String getServiceNameFromClassname(String classname) {
- return (localWorkerToScript.get(classname));
- }
-
- public String getId() {
- return providerId.toString();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
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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 155c631..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 uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class LocalworkerActivityConfigView extends BeanshellConfigurationPanel {
-
- public LocalworkerActivityConfigView(Activity activity, ApplicationConfiguration applicationConfiguration) {
- super(activity, applicationConfiguration);
- }
-
- public boolean isConfigurationChanged() {
- boolean configurationChanged = super.isConfigurationChanged();
- if (configurationChanged) {
- getJson().put("isAltered", true);
- }
- return configurationChanged;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
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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 fc09d57..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 uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-import uk.org.taverna.scufl2.api.port.InputActivityPort;
-import uk.org.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-@SuppressWarnings("serial")
-public class LocalworkerActivityContextualView extends HTMLBasedActivityContextualView {
-
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- private final ApplicationConfiguration applicationConfiguration;
-
- public LocalworkerActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ColourManager colourManager,
- ActivityIconManager activityIconManager,
- ServiceDescriptionRegistry serviceDescriptionRegistry,
- ApplicationConfiguration applicationConfiguration) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- this.applicationConfiguration = applicationConfiguration;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- StringBuilder html = new StringBuilder();
- html.append("<tr><th>Input Port Name</th><th>Depth</th></tr>");
- for (InputActivityPort inputActivityPort : getActivity().getInputPorts()) {
- html.append("<tr><td>" + inputActivityPort.getName() + "</td><td>");
- html.append(inputActivityPort.getDepth() + "</td></tr>");
- }
- html.append("<tr><th>Output Port Name</th><th>Depth</th></tr>");
- for (OutputActivityPort outputActivityPort : getActivity().getOutputPorts()) {
- html.append("<tr><td>" + outputActivityPort.getName() + "</td><td>");
- html.append(outputActivityPort.getDepth() + "</td></tr>");
- }
- return html.toString();
- }
-
- @Override
- public String getViewTitle() {
- String result = "";
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(json.get(
- "localworkerName").textValue());
- if (json.get("isAltered").booleanValue()) {
- result = "Altered local worker service";
- if ((workerName != null) && !workerName.equals("")) {
- result += " - originally " + workerName;
- }
- } else {
- result = "Local worker service";
- if ((workerName != null) && !workerName.equals("")) {
- result += " - " + workerName;
- }
- }
- return result;
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new LocalworkerActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, serviceDescriptionRegistry,
- applicationConfiguration);
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
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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 4fec0a2..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 uk.org.taverna.scufl2.api.activity.Activity;
-
-public class LocalworkerActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ApplicationConfiguration applicationConfiguration;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity
- && ((Activity) object).getType()
- .equals(LocalworkerServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new LocalworkerActivityContextualView(activity,
- editManager, fileManager, colourManager, activityIconManager,
- serviceDescriptionRegistry, applicationConfiguration) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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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
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-net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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--- 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/b4725724/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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--- 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
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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-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/b4725724/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
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--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
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@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="LocalworkerActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="LocalworkerServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
-
- <service ref="ConfigureLocalworkerMenuAction" auto-export="interfaces" />
-
- <service ref="LocalworkerActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
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diff --git a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml b/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
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--- a/taverna-localworker-activity-ui/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
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-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="LocalworkerActivityIcon" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon" />
-
- <bean id="LocalworkerServiceProvider" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
-
- <bean id="ConfigureLocalworkerMenuAction" class="net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- </bean>
-
- <bean id="LocalworkerActivityViewFactory" class="net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/localworker.png
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diff --git a/taverna-localworker-activity-ui/src/main/resources/localworker_names b/taverna-localworker-activity-ui/src/main/resources/localworker_names
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--- a/taverna-localworker-activity-ui/src/main/resources/localworker_names
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-category:biojava
-net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
-net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
-net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
-net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
-category:io
-net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
-net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
-net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
-net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
-net.sourceforge.taverna.scuflworkers.io.LocalCommand
-net.sourceforge.taverna.scuflworkers.io.TextFileReader
-net.sourceforge.taverna.scuflworkers.io.TextFileWriter
-category:ui
-net.sourceforge.taverna.scuflworkers.ui.AskWorker
-net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
-net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
-net.sourceforge.taverna.scuflworkers.ui.SelectWorker
-net.sourceforge.taverna.scuflworkers.ui.TellWorker
-net.sourceforge.taverna.scuflworkers.ui.WarnWorker
-category:xml
-net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
-net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
-net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
-category:list
-org.embl.ebi.escience.scuflworkers.java.EchoList
-org.embl.ebi.escience.scuflworkers.java.FlattenList
-org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
-org.embl.ebi.escience.scuflworkers.java.StringListMerge
-category:test
-org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
-org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
-org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
-category:text
-org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
-org.embl.ebi.escience.scuflworkers.java.StringSetDifference
-org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
-org.embl.ebi.escience.scuflworkers.java.StringSetUnion
-org.embl.ebi.escience.scuflworkers.java.PadNumber
-org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
-org.embl.ebi.escience.scuflworkers.java.SplitByRegex
-org.embl.ebi.escience.scuflworkers.java.StringConcat
-org.embl.ebi.escience.scuflworkers.java.FilterStringList
-category:net
-org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
-org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
-org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
-org.embl.ebi.escience.scuflworkers.java.SendEmail
-net.sourceforge.taverna.scuflworkers.net.BrowseUrl
-net.sourceforge.taverna.scuflworkers.net.ExtractHeader
-category:base64
-org.embl.ebi.escience.scuflworkers.java.EncodeBase64
-org.embl.ebi.escience.scuflworkers.java.DecodeBase64
-category:ncbi
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
-net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
-category:jdbc
-net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
-net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
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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
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--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
+++ /dev/null
@@ -1,74 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
-
-
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.Sequence;
-import org.biojava.bio.seq.SequenceIterator;
-import org.biojava.bio.seq.io.SeqIOTools;
-import org.biojava.bio.seq.io.agave.AgaveWriter;
-
-BufferedReader getReader (String fileUrl) throws IOException {
- InputStreamReader reader;
- try {
- reader = new FileReader(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
- }
- return new BufferedReader(reader);
- }
-
-if ((fileUrl == void) || (fileUrl == null)) {
- throw new RuntimeException("The fileUrl must be specified");
-}
-
-BufferedReader br = getReader(fileUrl);
-
-// read the GenBank File
-SequenceIterator sequences = SeqIOTools.readGenbank(br);
-
-// iterate through the sequences
-ByteArrayOutputStream os = new ByteArrayOutputStream();
-StringBuffer sb = new StringBuffer();
-AgaveWriter writer = new AgaveWriter();
-PrintStream ps = new PrintStream(os);
-
-while (sequences.hasNext()) {
- Sequence seq = sequences.nextSequence();
- writer.writeSequence(seq, ps);
- sb.append(os.toString());
-}
-
-genbankdata = sb.toString();
-br.close();
-ps.close();
-
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileUrl</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>genbankdata</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
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--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
+++ /dev/null
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-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\nBufferedReader br = getReader(fileUrl);\n\n// read the GenBank File\nSequenceIterator sequences = SeqIOTools.readGenbank(br);\n\n// iterate through the sequences\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nAgaveWriter writer = new AgaveWriter();\nPrintStrea
m ps = new PrintStream(os);\n\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\n\ngenbankdata = sb.toString();\nbr.close();\nps.close();\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
- "inputPorts" : [ {
- "name" : "fileUrl",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "genbankdata",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
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--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
+++ /dev/null
@@ -1,43 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.DNATools;
-import org.biojava.bio.symbol.SymbolList;
-
-if ((rawSeq == void) || (rawSeq == null)) {
- throw new RuntimeException("The rawSeq must be specified");
-}
-
-// make a DNA SymbolListbena
-SymbolList symL = DNATools.createDNA(rawSeq);
-
-// reverse complement it
-symL = DNATools.reverseComplement(symL);
-
-// prove that it worked
-revSeq = symL.seqString();
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>rawSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>revSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
deleted file mode 100644
index c214819..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((rawSeq == void) || (rawSeq == null)) {\n throw new RuntimeException(\"The rawSeq must be specified\");\n}\n\n// make a DNA SymbolListbena\nSymbolList symL = DNATools.createDNA(rawSeq);\n\n// reverse complement it\nsymL = DNATools.reverseComplement(symL);\n\n// prove that it worked\nrevSeq = symL.seqString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
- "inputPorts" : [ {
- "name" : "rawSeq",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "revSeq",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
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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
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index 7f64778..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
+++ /dev/null
@@ -1,72 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.Sequence;
-import org.biojava.bio.seq.SequenceIterator;
-import org.biojava.bio.seq.io.SeqIOTools;
-import org.biojava.bio.seq.io.agave.AgaveWriter;
-
-BufferedReader getReader (String fileUrl) throws IOException {
- InputStreamReader reader;
- try {
- reader = new FileReader(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
- }
- return new BufferedReader(reader);
- }
-
-if ((fileUrl == void) || (fileUrl == null)) {
- throw new RuntimeException("The fileUrl must be specified");
-}
-
-BufferedReader br = getReader(fileUrl);
-
-// read the EMBL File
-SequenceIterator sequences = SeqIOTools.readSwissprot(br);
-
-// Prepare the writer
-AgaveWriter writer = new AgaveWriter();
-ByteArrayOutputStream os = new ByteArrayOutputStream();
-StringBuffer sb = new StringBuffer();
-PrintStream ps = new PrintStream(os);
-
-// iterate through the sequences
-while (sequences.hasNext()) {
- Sequence seq = sequences.nextSequence();
- writer.writeSequence(seq, ps);
- sb.append(os.toString());
-}
-results = sb.toString();
-
-br.close();
-ps.close();
-
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileUrl</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>results</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
deleted file mode 100644
index 929c316..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\t\nBufferedReader br = getReader(fileUrl);\n\n// read the EMBL File\nSequenceIterator sequences = SeqIOTools.readSwissprot(br);\n\n// Prepare the writer\nAgaveWriter writer = new AgaveWriter();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nPrintStream ps = ne
w PrintStream(os);\n\n// iterate through the sequences\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\nresults = sb.toString();\n\nbr.close();\nps.close();\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
- "inputPorts" : [ {
- "name" : "fileUrl",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "results",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
deleted file mode 100644
index e46e219..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
+++ /dev/null
@@ -1,48 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.DNATools;
-import org.biojava.bio.seq.RNATools;
-import org.biojava.bio.symbol.SymbolList;
-
-if ((dna_seq == void) || (dna_seq == null)) {
- throw new RuntimeException("The dna_seq must be specified");
-}
-
-// make a DNA SymbolList
-SymbolList symL = DNATools.createDNA(dna_seq);
-
-// transcribe it to RNA (after BioJava 1.4 this method is
-// deprecated)
-symL = RNATools.transcribe(symL);
-
-// (after BioJava 1.4 use this method instead)
-// symL = DNATools.toRNA(symL);
-
-// just to prove it worked
-rna_seq = symL.seqString();
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>dna_seq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>rna_seq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
deleted file mode 100644
index 767852c..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.seq.RNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((dna_seq == void) || (dna_seq == null)) {\n\tthrow new RuntimeException(\"The dna_seq must be specified\");\n}\n\n// make a DNA SymbolList\nSymbolList symL = DNATools.createDNA(dna_seq);\n\n// transcribe it to RNA (after BioJava 1.4 this method is\n// deprecated)\nsymL = RNATools.transcribe(symL);\n\n// (after BioJava 1.4 use this method instead)\n// symL = DNATools.toRNA(symL);\n\n// just to prove it worked\nrna_seq = symL.seqString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
- "inputPorts" : [ {
- "name" : "dna_seq",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "rna_seq",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
deleted file mode 100644
index 9ed72e4..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
+++ /dev/null
@@ -1,101 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>BufferedReader getReader (String fileUrl) throws IOException {
- InputStreamReader reader;
- try {
- reader = new FileReader(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
- }
- return new BufferedReader(reader);
- }
-
-String NEWLINE = System.getProperty("line.separator");
-
-boolean displayResults = false;
-if (displayresults != void) {
- displayResults = Boolean.valueOf(displayresults).booleanValue();
-}
-
-StringBuffer sb = new StringBuffer(2000);
-
-if (outputfile == void) {
- throw new RuntimeException("The 'outputfile' parameter cannot be null");
-}
-
-if (filelist == null) {
- throw new RuntimeException("The 'filelist' parameter cannot be null");
-}
-
-String str = null;
-
-Writer writer = new FileWriter(outputfile);
-for (int i = 0; i < filelist.size(); i++) {
- BufferedReader reader = getReader(filelist.get(i));
- while ((str = reader.readLine()) != null) {
- writer.write(str);
- writer.write(NEWLINE);
-
- if (displayResults) {
- sb.append(str);
- sb.append(NEWLINE);
- }
- }
-
- reader.close();
-
-}
-writer.flush();
-writer.close();
-
-if (displayResults) {
- results= sb.toString();
-}
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>filelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>outputfile</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>displayresults</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>results</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
deleted file mode 100644
index d91d466..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "BufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nString NEWLINE = System.getProperty(\"line.separator\");\n\nboolean displayResults = false;\nif (displayresults != void) {\n\tdisplayResults = Boolean.valueOf(displayresults).booleanValue();\n}\n\nStringBuffer sb = new StringBuffer(2000);\n\nif (outputfile == void) {\n\tthrow new RuntimeException(\"The 'outputfile' parameter cannot be null\");\n}\n\nif (filelist == null) {\n\tthrow new RuntimeException(\"The 'filelist' parameter cannot be null\");\n}\n\nString str = null;\n\nWriter writer = new FileWriter(outputfile);\nfor (int i = 0; i < filelist.size(); i++) {\n\tBufferedReader reader = getReader(file
list.get(i));\n\twhile ((str = reader.readLine()) != null) {\n\t\twriter.write(str);\n\t\twriter.write(NEWLINE);\n\n\t\tif (displayResults) {\n\t\t\tsb.append(str);\n\t\t\tsb.append(NEWLINE);\n\t\t}\n\t}\n\n\treader.close();\n\n}\nwriter.flush();\nwriter.close();\n\nif (displayResults) {\n\tresults= sb.toString();\n}\n\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
- "inputPorts" : [ {
- "name" : "filelist",
- "depth" : 1,
- "type" : "String"
- }, {
- "name" : "outputfile",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "displayresults",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "results",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
deleted file mode 100644
index 410ceb0..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
+++ /dev/null
@@ -1,33 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="properties" to="properties" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import java.net.URLEncoder;
-
-Properties sysProps = System.getProperties();
-Set keys = sysProps.keySet();
-Iterator it = keys.iterator();
-String currKey = null;
-StringBuffer sb = new StringBuffer();
-sb.append("<?xml version=\"1.0\"?>\n");
-sb.append("<property-list>\n");
-while (it.hasNext()) {
- currKey = (String) it.next();
- sb.append("<property ");
- sb.append(" name=\"" + URLEncoder.encode(currKey) + "\"");
- sb.append(" value=\"" + URLEncoder.encode(sysProps.getProperty(currKey)) + "\"/>\n");
-}
-sb.append("</property-list>");
-
-properties = sb.toString();
-</script>
- <dependencies />
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>properties</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
deleted file mode 100644
index 5dc2349..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import java.net.URLEncoder;\n\nProperties sysProps = System.getProperties();\nSet keys = sysProps.keySet();\nIterator it = keys.iterator();\nString currKey = null;\nStringBuffer sb = new StringBuffer();\nsb.append(\"<?xml version=\\\"1.0\\\"?>\\n\");\nsb.append(\"<property-list>\\n\");\nwhile (it.hasNext()) {\n\tcurrKey = (String) it.next();\n\tsb.append(\"<property \");\n\tsb.append(\" name=\\\"\" + URLEncoder.encode(currKey) + \"\\\"\");\n\tsb.append(\" value=\\\"\" + URLEncoder.encode(sysProps.getProperty(currKey)) + \"\\\"/>\\n\");\n}\nsb.append(\"</property-list>\");\n\nproperties = sb.toString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
- "outputPorts" : [ {
- "name" : "properties",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
deleted file mode 100644
index 910d0d6..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
+++ /dev/null
@@ -1,73 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>class FileExtFilter implements FileFilter {
-
- public FileExtFilter(String ext) {
- this.ext = ext;
- }
-
- public boolean accept(File file) {
- return file.getName().endsWith(ext);
- }
-
- String ext = null;
-}
-
-if (extension == void || extension.equals("")) {
- throw new RuntimeException(
- "The 'extension' parameter cannot be null. Please enter a valid file extension.");
-}
-
-if (directory == void || directory.equals("")) {
- throw new RuntimeException(
- "The 'directory' parameter cannot be null. Please enter a valid file directory.");
-}
-
-File dirObj = new File(directory);
-
-if (!dirObj.exists()) {
- throw new RuntimeException("The 'directory' parameter specified:" + directory
- + "does not exist. Please enter a valid file directory.");
-}
-
-File[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));
-List filelist = new ArrayList();
-for (int i = 0; i < fileObjList.length; i++) {
- filelist.add(fileObjList[i].getAbsolutePath());
-}
-
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>directory</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>extension</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>filelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
deleted file mode 100644
index 656453e..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByExtTask.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "class FileExtFilter implements FileFilter {\n\n\tpublic FileExtFilter(String ext) {\n\t\tthis.ext = ext;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().endsWith(ext);\n\t}\n\n\tString ext = null;\n}\n\nif (extension == void || extension.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'extension' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObj
List[i].getAbsolutePath());\n}\n\n\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
- "inputPorts" : [ {
- "name" : "directory",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "extension",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "filelist",
- "depth" : 1,
- "granularDepth" : 1
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
deleted file mode 100644
index 06906b6..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
+++ /dev/null
@@ -1,71 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>class FileRegexFilter implements FileFilter {
-
- public FileRegexFilter(String regex) {
- this.regex = regex;
- }
-
- public boolean accept(File file) {
- return file.getName().matches(regex);
- }
-
- String regex = null;
-}
-
-if (regex == void || regex.equals("")) {
- throw new RuntimeException(
- "The 'regex' parameter cannot be null. Please enter a valid file extension.");
-}
-
-if (directory == void || directory.equals("")) {
- throw new RuntimeException(
- "The 'directory' parameter cannot be null. Please enter a valid file directory.");
-}
-
-File dirObj = new File(directory);
-
-if (!dirObj.exists()) {
- throw new RuntimeException("The 'directory' parameter specified:" + directory
- + "does not exist. Please enter a valid file directory.");
-}
-
-File[] fileObjList = dirObj.listFiles(new FileRegexFilter(regex));
-List filelist = new ArrayList();
-for (int i = 0; i < fileObjList.length; i++) {
- filelist.add(fileObjList[i].getAbsolutePath());
-}
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>directory</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>regex</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>filelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
deleted file mode 100644
index 35cdb01..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "class FileRegexFilter implements FileFilter {\n\n\tpublic FileRegexFilter(String regex) {\n\t\tthis.regex = regex;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\treturn file.getName().matches(regex);\n\t}\n\n\tString regex = null;\n}\n\nif (regex == void || regex.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'regex' parameter cannot be null. Please enter a valid file extension.\");\n}\n\nif (directory == void || directory.equals(\"\")) {\n\tthrow new RuntimeException(\n\t\t\t\"The 'directory' parameter cannot be null. Please enter a valid file directory.\");\n}\n\nFile dirObj = new File(directory);\n\nif (!dirObj.exists()) {\n\tthrow new RuntimeException(\"The 'directory' parameter specified:\" + directory\n\t\t\t+ \"does not exist. Please enter a valid file directory.\");\n}\n\nFile[] fileObjList = dirObj.listFiles(new FileRegexFilter(regex));\nList filelist = new ArrayList();\nfor (int i = 0; i < fileObjList.length; i++) {\n\tfilelist.add(fileObjL
ist[i].getAbsolutePath());\n}\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
- "inputPorts" : [ {
- "name" : "directory",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "regex",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "filelist",
- "depth" : 1,
- "granularDepth" : 1
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
deleted file mode 100644
index c0adc09..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand
+++ /dev/null
@@ -1,80 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>if (command == void || command.equals("")) {
- throw new RuntimeException("The 'command' port cannot be null.");
-}
-Process proc = null;
-Runtime rt = Runtime.getRuntime();
-
-String osName = System.getProperty("os.name");
-String[] cmdArray = null;
-if (osName.contains("Windows")) {
- cmdArray = new String[] { "cmd.exe", "/c", command };
-} else {// TODO: investigate if this will work in Linux and OSX
- cmdArray = new String[] { command };
-}
-
-// concatenate the arrays
-if ((args == void) || (args == null)) {
- args = new ArrayList();
-}
-
-int argSize = cmdArray.length + args.size();
-ArrayList appArray = new ArrayList(argSize);
-for (int i = 0; i < cmdArray.length; i++) {
- appArray.add(cmdArray[i]);
-}
-
-for (int i = 0; i < args.size(); i++) {
- appArray.add(args.get(i));
-}
-
-String[] applist = new String[argSize];
-appArray.toArray(applist);
-proc = rt.exec(applist);
-
-// Get the input stream and read from it
-InputStream in = proc.getInputStream();
-
-int c;
-StringBuffer sb = new StringBuffer();
-while ((c = in.read()) != -1) {
- sb.append((char) c);
-}
-in.close();
-result = sb.toString();
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>command</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>args</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>result</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
deleted file mode 100644
index f6ddf4f..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.LocalCommand.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if (command == void || command.equals(\"\")) {\n\tthrow new RuntimeException(\"The 'command' port cannot be null.\");\n}\nProcess proc = null;\nRuntime rt = Runtime.getRuntime();\n\nString osName = System.getProperty(\"os.name\");\nString[] cmdArray = null;\nif (osName.contains(\"Windows\")) {\n\tcmdArray = new String[] { \"cmd.exe\", \"/c\", command };\n} else {// TODO: investigate if this will work in Linux and OSX\n\tcmdArray = new String[] { command };\n}\n\n// concatenate the arrays\nif ((args == void) || (args == null)) {\n\targs = new ArrayList();\n}\n\nint argSize = cmdArray.length + args.size();\nArrayList appArray = new ArrayList(argSize);\nfor (int i = 0; i < cmdArray.length; i++) {\n\tappArray.add(cmdArray[i]);\n}\n\nfor (int i = 0; i < args.size(); i++) {\n\tappArray.add(args.get(i));\n}\n\nString[] applist = new String[argSize];\nappArray.toArray(applist);\nproc = rt.exec(applist);\n\n// Get the input stream and read from it\nInputStream in = proc.getInpu
tStream();\n\nint c;\nStringBuffer sb = new StringBuffer();\nwhile ((c = in.read()) != -1) {\n\tsb.append((char) c);\n}\nin.close();\nresult = sb.toString();\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.LocalCommand",
- "inputPorts" : [ {
- "name" : "command",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "args",
- "depth" : 1,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "result",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file