src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java - incubator-taverna-workbench-common-activities - Git at Google

 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.LinkedHashSet;
 import java.util.List;
 import java.util.Map;

 import javax.swing.Icon;

 import net.sf.taverna.raven.repository.BasicArtifact;
 import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
 import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
 import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
 import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
 import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
 import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
 import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
 import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
 import net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer;

 import org.apache.log4j.Logger;
 import org.jdom.Element;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;

 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 ActivityXMLDeserializer deserializer = ActivityXMLDeserializer.getInstance();;

 	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");

 		// 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");
 	}

 	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")
 	private 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 {
 		//String[] split = line.split("[.]");
 		// get the file from disk
 		String resource = "/" + line;
 		InputStream resourceAsStream = getClass().getResourceAsStream(resource);
 		if (resourceAsStream == null) {
 			throw new ItemCreationException("Could not find resource "
 					+ resource);
 		}

 		SAXBuilder builder = new SAXBuilder();
 		Element detachRootElement = null;
 		try {
 			detachRootElement = builder.build(resourceAsStream)
 					.detachRootElement();
 		} catch (JDOMException e) {
 			throw new ItemCreationException("Could not parse resource "
 					+ resource, e);
 		} catch (IOException e) {
 			throw new ItemCreationException("Could not read resource "
 					+ resource, e);
 		}
 		LocalworkerActivity activity = null;
 		try {
 			activity = (LocalworkerActivity) deserializer
 					.deserializeActivity(detachRootElement,
 							new HashMap<String, Element>(), getClass()
 									.getClassLoader());
 		} catch (Exception e) {
 			logger.error("Could not create LocalWorkerServiceDescription", e);
 			throw new ItemCreationException(e);
 		}
 		List<ActivityInputPortDefinitionBean> inputPortBeans = new ArrayList<ActivityInputPortDefinitionBean>();
 		LocalworkerActivityConfigurationBean configuration = (LocalworkerActivityConfigurationBean) activity
 				.getConfiguration();

 		// Translate the old dependencies field into artifactDependencies field
 		// The local worker definition xml files still have the old dependencies field
 		LinkedHashSet<BasicArtifact> artifactDependencies = new LinkedHashSet<BasicArtifact>();
 		for (String dep : configuration.getDependencies()){
 			String[] artifactParts = dep.split(":");
 			if (artifactParts.length == 3) {
 				artifactDependencies.add(new BasicArtifact(artifactParts[0], artifactParts[1],
 						artifactParts[2]));
 			}
 		}
 		configuration.setArtifactDependencies(artifactDependencies);

 		for (ActivityInputPortDefinitionBean bean : configuration
 				.getInputPortDefinitions()) {
 			bean.setDepth(bean.getDepth());
 			bean.setName(bean.getName());
 			bean.setHandledReferenceSchemes(bean.getHandledReferenceSchemes());
 			bean.setTranslatedElementType(bean.getTranslatedElementType());
 			// bean.setMimeTypes(bean.getMimeTypes());
 			inputPortBeans.add(bean);
 		}
 		List<ActivityOutputPortDefinitionBean> outputPortBeans = new ArrayList<ActivityOutputPortDefinitionBean>();
 		for (ActivityOutputPortDefinitionBean bean : configuration
 				.getOutputPortDefinitions()) {
 			bean.setDepth(bean.getDepth());
 			bean.setGranularDepth(bean.getGranularDepth());
 			bean.setName(bean.getName());
 			bean.setMimeTypes(bean.getMimeTypes());
 			outputPortBeans.add(bean);
 		}

 		String script = ((BeanshellActivity) activity).getConfiguration()
 				.getScript();

 		LocalworkerServiceDescription item = new LocalworkerServiceDescription();
 		item.setScript(script);
 		item.setOutputPorts(outputPortBeans);
 		item.setInputPorts(inputPortBeans);
 		item.setLocalworkerName(line);
 		// name is last part of the class name that was split
 		//String operation = split[split.length - 1];
 		String operationName = localWorkerToScript.get(line);
 		item.setOperation(operationName);
 		item.setDependencies(((BeanshellActivity) activity).getConfiguration()
 				.getDependencies()); // this property is not in use any more
 		item.setArtifactDependencies(configuration.getArtifactDependencies());
 //		item.setOperation(operation);
 		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();
 	}

 }
	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.LinkedHashSet;
	import java.util.List;
	import java.util.Map;

	import javax.swing.Icon;

	import net.sf.taverna.raven.repository.BasicArtifact;
	import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
	import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
	import net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean;
	import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
	import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
	import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
	import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
	import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
	import net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer;

	import org.apache.log4j.Logger;
	import org.jdom.Element;
	import org.jdom.JDOMException;
	import org.jdom.input.SAXBuilder;

	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 ActivityXMLDeserializer deserializer = ActivityXMLDeserializer.getInstance();;

	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");

	// 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");
	}

	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")
	private 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 {
	//String[] split = line.split("[.]");
	// get the file from disk
	String resource = "/" + line;
	InputStream resourceAsStream = getClass().getResourceAsStream(resource);
	if (resourceAsStream == null) {
	throw new ItemCreationException("Could not find resource "
	+ resource);
	}

	SAXBuilder builder = new SAXBuilder();
	Element detachRootElement = null;
	try {
	detachRootElement = builder.build(resourceAsStream)
	.detachRootElement();
	} catch (JDOMException e) {
	throw new ItemCreationException("Could not parse resource "
	+ resource, e);
	} catch (IOException e) {
	throw new ItemCreationException("Could not read resource "
	+ resource, e);
	}
	LocalworkerActivity activity = null;
	try {
	activity = (LocalworkerActivity) deserializer
	.deserializeActivity(detachRootElement,
	new HashMap<String, Element>(), getClass()
	.getClassLoader());
	} catch (Exception e) {
	logger.error("Could not create LocalWorkerServiceDescription", e);
	throw new ItemCreationException(e);
	}
	List<ActivityInputPortDefinitionBean> inputPortBeans = new ArrayList<ActivityInputPortDefinitionBean>();
	LocalworkerActivityConfigurationBean configuration = (LocalworkerActivityConfigurationBean) activity
	.getConfiguration();

	// Translate the old dependencies field into artifactDependencies field
	// The local worker definition xml files still have the old dependencies field
	LinkedHashSet<BasicArtifact> artifactDependencies = new LinkedHashSet<BasicArtifact>();
	for (String dep : configuration.getDependencies()){
	String[] artifactParts = dep.split(":");
	if (artifactParts.length == 3) {
	artifactDependencies.add(new BasicArtifact(artifactParts[0], artifactParts[1],
	artifactParts[2]));
	}
	}
	configuration.setArtifactDependencies(artifactDependencies);

	for (ActivityInputPortDefinitionBean bean : configuration
	.getInputPortDefinitions()) {
	bean.setDepth(bean.getDepth());
	bean.setName(bean.getName());
	bean.setHandledReferenceSchemes(bean.getHandledReferenceSchemes());
	bean.setTranslatedElementType(bean.getTranslatedElementType());
	// bean.setMimeTypes(bean.getMimeTypes());
	inputPortBeans.add(bean);
	}
	List<ActivityOutputPortDefinitionBean> outputPortBeans = new ArrayList<ActivityOutputPortDefinitionBean>();
	for (ActivityOutputPortDefinitionBean bean : configuration
	.getOutputPortDefinitions()) {
	bean.setDepth(bean.getDepth());
	bean.setGranularDepth(bean.getGranularDepth());
	bean.setName(bean.getName());
	bean.setMimeTypes(bean.getMimeTypes());
	outputPortBeans.add(bean);
	}

	String script = ((BeanshellActivity) activity).getConfiguration()
	.getScript();

	LocalworkerServiceDescription item = new LocalworkerServiceDescription();
	item.setScript(script);
	item.setOutputPorts(outputPortBeans);
	item.setInputPorts(inputPortBeans);
	item.setLocalworkerName(line);
	// name is last part of the class name that was split
	//String operation = split[split.length - 1];
	String operationName = localWorkerToScript.get(line);
	item.setOperation(operationName);
	item.setDependencies(((BeanshellActivity) activity).getConfiguration()
	.getDependencies()); // this property is not in use any more
	item.setArtifactDependencies(configuration.getArtifactDependencies());
	// item.setOperation(operation);
	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();
	}

	}