[05/16] incubator-taverna-plugin-bioinformatics git commit: temporarily empty repository

[st...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
deleted file mode 100644
index e61406b..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
+++ /dev/null
@@ -1,1319 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceContext;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.service.dashboard.data.ParametersTable;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-import org.biomoby.shared.MobySecondaryData;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.Utils;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- * An Activity based on the Biomoby compliant web services. This activity
- * implementation will contact Biomoby registry in order to find the list of
- * extant ports at creation time.
- *
- * Copied from org.biomoby.client.taverna.plugin.BiomobyProcessor and
- * org.biomoby.client.taverna.plugin.BiomobyTask and converted to a Taverna 2
- * Activity.
- *
- * @author Martin Senger
- * @author Edward Kawas
- * @author Jose Maria Fernandez, INB
- * @author David Withers
- */
-public class BiomobyActivity extends
-		AbstractAsynchronousActivity<BiomobyActivityConfigurationBean> {
-
-	public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/service";
-
-	private static Logger logger = Logger.getLogger(BiomobyActivity.class);
-
-	protected BiomobyActivityConfigurationBean configurationBean = new BiomobyActivityConfigurationBean();
-
-	private URL endpoint;
-
-	private Central worker = null;
-
-	private MobyService mobyService = null;
-
-	private boolean containSecondary = false;
-
-	private ParametersTable parameterTable = null;
-
-
-
-	private boolean doInit = true;
-
-	@Override
-	public void configure(BiomobyActivityConfigurationBean configurationBean)
-			throws ActivityConfigurationException {
-		this.configurationBean = configurationBean;
-		if (doInit) {
-			init();
-			generatePorts();
-			configureSecondaries();
-			doInit = false;
-		} else {
-			configureSecondaries();
-		}
-	}
-
-	@Override
-	public BiomobyActivityConfigurationBean getConfiguration() {
-		return configurationBean;
-	}
-
-	@Override
-	public void executeAsynch(final Map<String, T2Reference> inputMap,
-			final AsynchronousActivityCallback callback) {
-		callback.requestRun(new Runnable() {
-			@SuppressWarnings("unchecked")
-			public void run() {
-				ReferenceService referenceService = callback.getContext()
-						.getReferenceService();
-
-				Map<String, T2Reference> outputMap = new HashMap<String, T2Reference>();
-
-				if (logger.isDebugEnabled()) {
-					logger.debug("Service " + mobyService.getUniqueName());
-					for (Iterator it = inputMap.keySet().iterator(); it
-							.hasNext();) {
-						String key = (String) it.next();
-						try {
-							Object input = referenceService.renderIdentifier(
-									inputMap.get(key), String.class, callback
-											.getContext());
-							if (input instanceof String) {
-								logger.debug("key " + key + "has value of\n"
-										+ input);
-								continue;
-							} else if (input instanceof List) {
-								List list = (List) input;
-								for (Iterator it2 = list.iterator(); it2
-										.hasNext();) {
-									logger.debug("List key " + key
-											+ "has value of\n" + it2.next());
-								}
-							}
-						} catch (ReferenceServiceException e) {
-							logger.debug(
-									"Error resolving data for port " + key, e);
-						}
-					}
-					logger.debug("Printing of ports complete.");
-				}
-				// invoke services with no defined input (as per BioMOBY API)
-				if (mobyService.getPrimaryInputs().length == 0) {
-					try {
-						String methodName = configurationBean.getServiceName();
-						String serviceEndpoint = endpoint.toExternalForm();
-						String serviceInput = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
-								+ "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">"
-								+ "  <moby:mobyContent>"
-								+ "    <moby:mobyData moby:queryID=\"sip_1_\" />"
-								+ "  </moby:mobyContent>" + "</moby:MOBY>";
-						String[] invocations = new String[] { serviceInput };
-						// add secondaries
-						if (containSecondary) {
-							@SuppressWarnings("unused")
-							ParametersTable pt = getParameterTable();
-							Element[] parameters = null;
-							parameters = getParameterTable().toXML();
-							serviceInput = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
-									+ "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">"
-									+ "  <moby:mobyContent>"
-									+ "    <moby:mobyData moby:queryID=\"sip_1_\">";
-							XMLOutputter out = new XMLOutputter(Format
-									.getCompactFormat());
-							Format format = out.getFormat();
-							format.setOmitDeclaration(true);
-							out.setFormat(format);
-							for (int i = 0; i < parameters.length; i++) {
-								serviceInput += out.outputString(parameters[i]);
-							}
-							serviceInput += "    </moby:mobyData>"
-									+ "  </moby:mobyContent>" + "</moby:MOBY>";
-							format = Format.getPrettyFormat();
-							format.setOmitDeclaration(false);
-							format.setIndent("   ");
-							serviceInput = new XMLOutputter(format)
-									.outputString(XMLUtilities
-											.getDOMDocument(serviceInput));
-							invocations = new String[] { serviceInput };
-						}
-
-						// execute the service that takes no Biomoby datatypes
-						// as input
-						for (int inCount = 0; inCount < invocations.length; inCount++) {
-							if (logger.isDebugEnabled())
-								logger.debug("input(" + inCount + "):\n"
-										+ invocations[inCount]);
-							// execute a 'moby' service
-							invocations[inCount] = executeService(
-									serviceEndpoint, methodName,
-									invocations[inCount]);
-							if (logger.isDebugEnabled())
-								logger.debug("output(" + inCount + "):\n"
-										+ invocations[inCount]);
-						}
-						String outputXML = XMLUtilities
-								.createMultipleInvokations(invocations);
-						// create the other ports
-						processOutputPorts(outputXML, outputMap,
-								referenceService, callback.getContext());
-
-						callback.receiveResult(outputMap, new int[0]);
-						return;
-					} catch (ReferenceServiceException e) {
-						callback.fail("Error accessing input/output data", e);
-					} catch (MobyException ex) {
-						// a MobyException should be already reasonably
-						// formatted
-						logger
-								.error(
-										"Error invoking biomoby service for biomoby. A MobyException caught",
-										ex);
-						callback.fail(
-								"Service failed due to problem invoking remote biomoby service.\n"
-										+ ex.getMessage(), ex);
-
-					} catch (Exception ex) {
-						logger.error(
-								"Error invoking biomoby service for biomoby",
-								ex);
-						callback
-								.fail(
-										"Task failed due to problem invoking biomoby service (see details in log)",
-										ex);
-					}
-				}
-
-				{
-					// now try other named ports
-					try {
-						String inputXML = null;
-						Element root = new Element("MOBY", XMLUtilities.MOBY_NS);
-						Element content = new Element("mobyContent",
-								XMLUtilities.MOBY_NS);
-						root.addContent(content);
-						int totalMobyDatas = 0;
-						Vector mobyDatas = new Vector(); // list of mobyData
-						// element
-						for (ActivityInputPort myInput : getInputPorts()) {
-							if (myInput.getName().equalsIgnoreCase("input")) {
-								continue;
-							}
-							// the port name
-							String portName = myInput.getName();
-							// the article name
-							String articleName = "";
-							String type = portName;
-							if (portName.indexOf("(") >= 0
-									&& portName.indexOf(")") > 0) {
-								articleName = portName.substring(portName
-										.indexOf("(") + 1, portName
-										.indexOf(")"));
-
-								if (articleName.indexOf("'") >= 0
-										&& articleName.lastIndexOf("'") > 0)
-									articleName = articleName.substring(
-											articleName.indexOf("'") + 1,
-											articleName.lastIndexOf("'"));
-
-								type = portName.substring(0, portName
-										.indexOf("("));
-							}
-
-							// String inputType = myInput.getSyntacticType();
-							Object input = referenceService.renderIdentifier(
-									inputMap.get(portName), myInput
-											.getTranslatedElementClass(),
-									callback.getContext());
-							if (myInput.getDepth() == 0) {
-								inputXML = (String) input;
-								Element inputElement = null;
-								try {
-									inputElement = XMLUtilities.getDOMDocument(
-											inputXML).getRootElement();
-
-								} catch (MobyException e) {
-									callback
-											.fail(XMLUtilities.newline
-													+ "There was an error parsing the input XML:"
-													+ XMLUtilities.newline
-													+ Utils.format(inputXML, 3)
-													+ XMLUtilities.newline
-													+ e.getLocalizedMessage());
-									return;
-								}
-								// determine whether we have a multiple
-								// invocation message
-								if (XMLUtilities
-										.isMultipleInvocationMessage(inputElement)) {
-									// multiple invocations
-									Element[] invocations = XMLUtilities
-											.getSingleInvokationsFromMultipleInvokations(inputElement);
-									ArrayList list = new ArrayList();
-									for (int j = 0; j < invocations.length; j++) {
-										Element[] elements = XMLUtilities
-												.getListOfCollections(invocations[j]);
-										if (elements.length == 0) {
-											// single simple
-											inputElement = XMLUtilities
-													.renameSimple(articleName,
-															type,
-															invocations[j]);
-											Element md = XMLUtilities
-													.extractMobyData(inputElement);
-											list.add(md);
-										} else {
-											// collection of simples => create
-											// multiple
-											// invocation message
-											String queryID = XMLUtilities
-													.getQueryID(invocations[j]);
-											Element[] simples = XMLUtilities
-													.getSimplesFromCollection(invocations[j]);
-											for (int k = 0; k < simples.length; k++) {
-												Element wrappedSimple = XMLUtilities
-														.createMobyDataElementWrapper(simples[k]);
-												wrappedSimple = XMLUtilities
-														.renameSimple(
-																articleName,
-																type,
-																wrappedSimple);
-												wrappedSimple = XMLUtilities
-														.setQueryID(
-																wrappedSimple,
-																queryID );
-												list
-														.add(XMLUtilities
-																.extractMobyData(wrappedSimple));
-											}
-										}
-									}
-									if (list.isEmpty())
-										continue;
-									if (totalMobyDatas < 1)
-										totalMobyDatas = 1;
-									totalMobyDatas *= list.size();
-									mobyDatas.add(list);
-								} else {
-									// single invocation
-									// is this a collection
-									Element[] elements = XMLUtilities
-											.getListOfCollections(inputElement);
-									if (elements.length == 0) {
-										// single simple
-										inputElement = XMLUtilities
-												.renameSimple(articleName,
-														type, inputElement);
-										ArrayList list = new ArrayList();
-										Element md = XMLUtilities
-												.extractMobyData(inputElement);
-										list.add(md);
-										mobyDatas.add(list);
-										if (totalMobyDatas < 1)
-											totalMobyDatas = 1;
-									} else {
-										// collection of simples => create
-										// multiple
-										// invocation message
-										String queryID = XMLUtilities
-												.getQueryID(inputElement);
-										Element[] simples = XMLUtilities
-												.getSimplesFromCollection(inputElement);
-
-										ArrayList list = new ArrayList();
-										for (int j = 0; j < simples.length; j++) {
-											Element wrappedSimple = XMLUtilities
-													.createMobyDataElementWrapper(simples[j]);
-											wrappedSimple = XMLUtilities
-													.renameSimple(articleName,
-															type, wrappedSimple);
-											wrappedSimple = XMLUtilities
-													.setQueryID(wrappedSimple,
-															queryID );
-											list
-													.add(XMLUtilities
-															.extractMobyData(wrappedSimple));
-										}
-										if (list.isEmpty())
-											continue;
-										mobyDatas.add(list);
-										if (totalMobyDatas < 1)
-											totalMobyDatas = 1 * list.size();
-										else {
-											totalMobyDatas *= list.size();
-										}
-									}
-
-								}
-							} else {
-								// we have a collection!
-								// inputThing is a list of Strings
-								List list = (List) input;
-								/*
-								 * need this map in cases where simples are
-								 * passed into a service that wants a
-								 * collection. each simple is then added into
-								 * the same collection
-								 */
-								Map collectionMap = new HashMap();
-								for (Iterator it = list.iterator(); it
-										.hasNext();) {
-									Element inputElement = null;
-									String next = (String) it.next();
-									try {
-										inputElement = XMLUtilities
-												.getDOMDocument(next)
-												.getRootElement();
-
-									} catch (MobyException e) {
-										callback
-												.fail(XMLUtilities.newline
-														+ "There was an error parsing the input XML:"
-														+ XMLUtilities.newline
-														+ Utils.format(
-																inputXML, 3)
-														+ XMLUtilities.newline
-														+ e
-																.getLocalizedMessage());
-										return;
-									}
-									// determine whether we have a multiple
-									// invocation message
-									if (XMLUtilities
-											.isMultipleInvocationMessage(inputElement)) {
-										// multiple invocations (update
-										// totalMobyDatas)
-										Element[] invocations = XMLUtilities
-												.getSingleInvokationsFromMultipleInvokations(inputElement);
-										ArrayList mdList = new ArrayList();
-										// this is here for mim messages of
-										// simples
-										Element mimCollection = null;
-										String mimQueryID = "";
-										for (int j = 0; j < invocations.length; j++) {
-											Element[] elements = XMLUtilities
-													.getListOfCollections(invocations[j]);
-											mimQueryID = XMLUtilities
-													.getQueryID(invocations[j]);
-											if (elements.length == 0) {
-												if (mimCollection == null)
-													mimCollection = new Element(
-															"Collection",
-															XMLUtilities.MOBY_NS);
-
-												Element theSimple = XMLUtilities
-														.extractMobyData(invocations[j]);
-												if (theSimple
-														.getChild("Simple") != null)
-													theSimple = theSimple
-															.getChild("Simple");
-												else if (theSimple.getChild(
-														"Simple",
-														XMLUtilities.MOBY_NS) != null)
-													theSimple = theSimple
-															.getChild(
-																	"Simple",
-																	XMLUtilities.MOBY_NS);
-												mimCollection
-														.addContent(theSimple
-																.detach());
-											} else {
-												// collection passed in (always
-												// 1 passed in)
-												Element collection = invocations[j];
-												collection = XMLUtilities
-														.renameCollection(
-																articleName,
-																collection);
-												collection = XMLUtilities
-														.createMobyDataElementWrapper(
-																collection,
-																XMLUtilities
-																		.getQueryID(invocations[j]),
-																null);
-												mdList
-														.add(XMLUtilities
-																.extractMobyData(collection));
-											}
-										}
-										if (mimCollection != null) {
-											mimCollection = XMLUtilities
-													.createMobyDataElementWrapper(
-															mimCollection,
-															mimQueryID, null);
-											mimCollection = XMLUtilities
-													.renameCollection(
-															articleName,
-															mimCollection);
-											mimCollection = XMLUtilities
-													.createMobyDataElementWrapper(
-															mimCollection,
-															mimQueryID, null);
-											mdList
-													.add(XMLUtilities
-															.extractMobyData(mimCollection));
-										}
-
-										if (mdList.isEmpty())
-											continue;
-
-										mobyDatas.add(mdList);
-										if (totalMobyDatas < 1)
-											totalMobyDatas = 1;
-										totalMobyDatas *= mdList.size();
-									} else {
-										// single invocation
-										Element[] elements = XMLUtilities
-												.getListOfCollections(inputElement);
-										if (elements.length == 0) {
-											// simple was passed in so wrap it
-											Element collection = new Element(
-													"Collection",
-													XMLUtilities.MOBY_NS);
-											collection.addContent(XMLUtilities
-													.extractMobyData(
-															inputElement)
-													.cloneContent());
-											collection = XMLUtilities
-													.createMobyDataElementWrapper(
-															collection,
-															XMLUtilities
-																	.getQueryID(inputElement),
-															null);
-											collection = XMLUtilities
-													.renameCollection(
-															articleName,
-															collection);
-											collection = XMLUtilities
-													.createMobyDataElementWrapper(
-															collection,
-															XMLUtilities
-																	.getQueryID(inputElement),
-															null);
-											if (collectionMap
-													.containsKey(articleName)) {
-												// add the simple to a
-												// pre-existing
-												// collection
-												ArrayList mdList = (ArrayList) collectionMap
-														.remove(articleName);
-												mdList
-														.add(XMLUtilities
-																.extractMobyData(collection));
-												collectionMap.put(articleName,
-														mdList);
-											} else {
-												// new collection - add element
-												// and
-												// increment count
-												ArrayList mdList = new ArrayList();
-												mdList
-														.add(XMLUtilities
-																.extractMobyData(collection));
-												collectionMap.put(articleName,
-														mdList);
-												// totalMobyDatas++;
-												if (totalMobyDatas < 1)
-													totalMobyDatas = 1;
-											}
-										} else {
-											// we have a collection
-											Element collection = inputElement;
-											collection = XMLUtilities
-													.renameCollection(
-															articleName,
-															collection);
-											ArrayList mdList = new ArrayList();
-											collection = XMLUtilities
-													.createMobyDataElementWrapper(
-															collection,
-															XMLUtilities
-																	.getQueryID(inputElement),
-															null);
-											mdList
-													.add(XMLUtilities
-															.extractMobyData(collection));
-											mobyDatas.add(mdList);
-											if (totalMobyDatas < 1)
-												totalMobyDatas = 1;
-
-										}
-									} // end if SIM
-								} // end iteration over inputThing list
-								Iterator collectionIterator = collectionMap
-										.keySet().iterator();
-								while (collectionIterator.hasNext()) {
-									String key = (String) collectionIterator
-											.next();
-									List theList = (List) collectionMap
-											.get(key);
-									theList = XMLUtilities.mergeCollections(
-											theList, key);
-									List unwrappedList = new ArrayList();
-									for (Iterator it = theList.iterator(); it
-											.hasNext();) {
-										Element e = (Element) it.next();
-										if (XMLUtilities.isWrapped(e))
-											unwrappedList.add(XMLUtilities
-													.extractMobyData(e));
-										else
-											unwrappedList.add(e);
-									}
-									mobyDatas.add(unwrappedList);
-								}
-							}
-						}
-
-						if (logger.isDebugEnabled()) {
-							logger.debug("Before MobyData aggregation");
-							for (Iterator itr = mobyDatas.iterator(); itr
-									.hasNext();) {
-								List eList = (List) itr.next();
-								for (int x = 0; x < eList.size(); x++) {
-									logger.debug(new XMLOutputter(Format
-											.getPrettyFormat())
-											.outputString((Element) eList
-													.get(x)));
-								}
-							}
-							logger.debug("******* End ******");
-						}
-						/*
-						 * ports have been processed -> vector contains a list
-						 * of all the different types of inputs with their
-						 * article names set correctly. The elements are from
-						 * mobyData down. Moreover, there are totalMobyData
-						 * number of invocations in the output moby message
-						 */
-						if (logger.isDebugEnabled()) {
-							logger.debug("TotalMobyDatas: " + totalMobyDatas);
-						}
-						Element[] mds = new Element[totalMobyDatas];
-						// initialize the mobydata blocks
-						for (int x = 0; x < mds.length; x++) {
-							mds[x] = new Element("mobyData",
-									XMLUtilities.MOBY_NS);
-							String queryID = "_";
-							// add the content
-							for (Iterator iter = mobyDatas.iterator(); iter
-									.hasNext();) {
-								ArrayList list = (ArrayList) iter.next();
-								int index = x % list.size();
-								Element next = ((Element) list.get(index));
-								logger.debug(new XMLOutputter(Format
-										.getPrettyFormat()).outputString(next));
-								// queryID += "_" +
-								// XMLUtilities.getQueryID(next);
-								queryID = XMLUtilities.getQueryID(next);
-								mds[x].addContent(next.cloneContent());
-
-							}
-							// remove the first _
-							// if (queryID != null && queryID.length() > 1)
-							// queryID = queryID.substring(1);
-							mds[x].setAttribute("queryID", queryID,
-									XMLUtilities.MOBY_NS);
-							// if secondarys exist add them here
-							if (containSecondary) {
-								@SuppressWarnings("unused")
-								ParametersTable pt = parameterTable;
-								Element[] parameters = null;
-								parameters = parameterTable.toXML();
-								for (int i = 0; i < parameters.length; i++) {
-									mds[x].addContent((parameters[i]).detach());
-								}
-							}
-							content.addContent(mds[x].detach());
-						}
-
-						if (logger.isDebugEnabled()) {
-							logger.debug("After MobyData aggregation");
-							logger.debug(new XMLOutputter(Format
-									.getPrettyFormat()).outputString(root));
-							logger.debug("******* End ******");
-						}
-						// do the task and populate outputXML
-
-						String methodName = configurationBean.getServiceName();
-						String serviceEndpoint = endpoint.toExternalForm();
-
-						String serviceInput = new XMLOutputter(Format
-								.getPrettyFormat()).outputString(root);
-						String[] invocations = XMLUtilities
-								.getSingleInvokationsFromMultipleInvokations(serviceInput);
-						// logger.debug(serviceInput);
-						// going to iterate over all invocations so that
-						// messages with
-						// many mobyData blocks dont timeout.
-						logger.debug("Total invocations " + invocations.length);
-						if (invocations.length > 0)
-							logger.debug("invocation 00");
-						for (int inCount = 0; inCount < invocations.length; inCount++) {
-							if (logger.isDebugEnabled())
-								logger.info("input(" + inCount + "):\n"
-										+ invocations[inCount]);
-							if (!XMLUtilities.isEmpty(invocations[inCount]))
-								invocations[inCount] = executeService(
-										serviceEndpoint, methodName,
-										invocations[inCount]);
-							if (logger.isDebugEnabled())
-								logger.info("output(" + inCount + "):\n"
-										+ invocations[inCount]);
-						}
-
-						String outputXML = XMLUtilities
-								.createMultipleInvokations(invocations);
-						// create the other ports
-						processOutputPorts(outputXML, outputMap,
-								referenceService, callback.getContext());
-
-						callback.receiveResult(outputMap, new int[0]);
-
-					} catch (ReferenceServiceException e) {
-						callback.fail("Error accessing input/output data", e);
-					} catch (MobyException ex) {
-						// a MobyException should be already reasonably
-						// formatted
-						logger
-								.error(
-										"Error invoking biomoby service for biomoby. A MobyException caught",
-										ex);
-						callback.fail(
-								"Service failed due to exception invoking remote biomoby service.\n"
-										+ ex.getMessage(), ex);
-
-					} catch (Exception ex) {
-						// details of other exceptions will appear only in a log
-//						ex.();
-						logger.error(
-								"Error invoking biomoby service for biomoby",
-								ex);
-						callback
-								.fail(
-										"Task failed due to problem invoking biomoby service (see details in log)",
-										ex);
-					}
-
-				}
-			}
-
-		});
-
-	}
-
-	private void init() throws ActivityConfigurationException {
-		// Find the service endpoint (by calling Moby registry)
-		try {
-			if (mobyService == null) {
-				worker = new CentralImpl(configurationBean.getMobyEndpoint());
-
-				MobyService pattern = new MobyService(configurationBean
-						.getServiceName());
-				pattern.setAuthority(configurationBean.getAuthorityName());
-				pattern.setCategory("");
-				MobyService[] services = worker.findService(pattern);
-				if (services == null || services.length == 0)
-					throw new ActivityConfigurationException(
-							formatError("I cannot find the service."));
-				mobyService = services[0];
-			}
-			String serviceEndpoint = mobyService.getURL();
-			if (serviceEndpoint == null || serviceEndpoint.equals(""))
-				throw new ActivityConfigurationException(
-						formatError("Service has an empty endpoint."));
-			try {
-				endpoint = new URL(serviceEndpoint);
-			} catch (MalformedURLException e2) {
-				throw new ActivityConfigurationException(
-						formatError("Service has malformed endpoint: '"
-								+ serviceEndpoint + "'."));
-			}
-
-		} catch (Exception e) {
-			if (e instanceof ActivityConfigurationException) {
-				throw (ActivityConfigurationException) e;
-			}
-			throw new ActivityConfigurationException(formatError(e.toString()));
-		}
-		// here we make sure that we have downloaded the ontology for the
-		// registry that we got this service from
-		try {
-			new GetOntologyThread(worker.getRegistryEndpoint()).start();
-		} catch (Exception e) {
-			/* don't care if an exception occurs here ... */
-		}
-
-	}
-
-	/**
-	 * Use the endpoint data to create new ports and attach them to the
-	 * processor.
-	 */
-	private void generatePorts() {
-
-		// inputs TODO - find a better way to deal with collections
-		MobyData[] serviceInputs = this.mobyService.getPrimaryInputs();
-		int inputDepth = 0;
-		for (int x = 0; x < serviceInputs.length; x++) {
-			if (serviceInputs[x] instanceof MobyPrimaryDataSimple) {
-				MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) serviceInputs[x];
-
-				// retrieve the simple article name
-				String simpleName = simple.getName();
-				if (simpleName.equals("")) {
-					simpleName = "_ANON_";
-				}
-				simpleName = "(" + simpleName + ")";
-
-				String portName = simple.getDataType().getName() + simpleName;
-				addInput(portName, inputDepth, true,
-						new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-						String.class);
-			} else {
-				// collection of items
-				inputDepth = 1;
-				MobyPrimaryDataSet collection = (MobyPrimaryDataSet) serviceInputs[x];
-				String collectionName = collection.getName();
-				if (collectionName.equals(""))
-					collectionName = "MobyCollection";
-				MobyPrimaryDataSimple[] simples = collection.getElements();
-				for (int y = 0; y < simples.length; y++) {
-					// collection port
-					String portName = simples[y].getDataType().getName()
-							+ "(Collection - '" + collectionName + "')";
-					addInput(
-							portName,
-							inputDepth,
-							true,
-							new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-							String.class);
-
-				}
-			}
-		}
-		/*addInput("input", inputDepth, true,
-				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-				String.class);*/
-
-		MobyData[] secondaries = this.mobyService.getSecondaryInputs();
-
-		if (secondaries.length > 0) {
-			MobySecondaryData[] msd = new MobySecondaryData[secondaries.length];
-			for (int i = 0; i < secondaries.length; i++) {
-				msd[i] = (MobySecondaryData) secondaries[i];
-			}
-			containSecondary = true;
-			this.parameterTable = new org.biomoby.service.dashboard.data.ParametersTable(
-					msd);
-			updateConfigBeanSecondaries();
-		}
-
-		// outputs
-		MobyData[] serviceOutputs = this.mobyService.getPrimaryOutputs();
-		int outputDepth = 0;
-		for (int x = 0; x < serviceOutputs.length; x++) {
-			if (serviceOutputs[x] instanceof MobyPrimaryDataSimple) {
-				MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) serviceOutputs[x];
-
-				// retrieve the simple article name
-				String simpleName = simple.getName();
-				if (simpleName.equals("")) {
-					simpleName = "_ANON_";
-				}
-				simpleName = "(" + simpleName + ")";
-
-				String outputName = simple.getDataType().getName() + simpleName;
-				addOutput(outputName, outputDepth, "text/xml");
-			} else {
-				outputDepth = 1;
-				// collection of items
-				MobyPrimaryDataSet collection = (MobyPrimaryDataSet) serviceOutputs[x];
-				String collectionName = collection.getName();
-				if (collectionName.equals(""))
-					collectionName = "MobyCollection";
-				MobyPrimaryDataSimple[] simples = collection.getElements();
-				for (int y = 0; y < simples.length; y++) {
-					String outputName = simples[y].getDataType().getName()
-							+ "(Collection - '" + collectionName + "')";
-					addOutput(outputName, outputDepth, "text/xml");
-
-					outputName = simples[y].getDataType().getName()
-							+ "(Collection - '" + collectionName
-							+ "' As Simples)";
-					addOutput(outputName, outputDepth, "text/xml");
-				}
-			}
-		}
-
-//		addOutput("output", outputDepth, "text/xml");
-
-	}
-
-	/**
-	 * Updates config bean secondaries for those that aren't already defined so
-	 * this only records new ones, but doesn't overwrite existing ones.
-	 */
-	private void updateConfigBeanSecondaries() {
-		ParametersTable table = getParameterTable();
-		int rows = table.getModel().getRowCount();
-		Map<String, String> secondaries = getConfiguration().getSecondaries();
-		for (int i = 0; i < rows; i++) {
-			String key = (String) table.getModel().getValueAt(i, 0);
-			String value = table.getModel().getValueAt(i, 1).toString();
-			if (!secondaries.containsKey(key)) {
-				secondaries.put(key, value);
-			}
-		}
-
-	}
-
-	public ParametersTable getParameterTable() {
-		return parameterTable;
-	}
-
-	public boolean containsSecondaries() {
-		return containSecondary;
-	}
-
-	public MobyService getMobyService() {
-		return mobyService;
-	}
-
-	@SuppressWarnings("unchecked")
-	private void processOutputPorts(String outputXML, Map outputMap,
-			ReferenceService referenceService, ReferenceContext context)
-			throws MobyException, ReferenceServiceException {
-		boolean isMIM = XMLUtilities.isMultipleInvocationMessage(outputXML);
-		for (OutputPort outputPort : getOutputPorts()) {
-			String name = outputPort.getName();
-			if (!name.equalsIgnoreCase("output")) {
-				if (outputPort.getDepth() == 1) {
-					// collection - list of strings
-					String articleName = "";
-					if (name.indexOf("MobyCollection") > 0) {
-						// un-named collection -> ignore it as it is illegal
-						// in the api
-						// TODO could throw exception
-
-						List innerList = new ArrayList();
-						outputMap.put(name, referenceService
-								.register(innerList, outputPort.getDepth(),
-										true, context));
-						continue;
-					} else {
-						articleName = name.substring(name.indexOf("'") + 1,
-								name.lastIndexOf("'"));
-						if (name.indexOf("' As Simples)") > 0) {
-							// list of simples wanted
-							if (isMIM) {
-								String[] invocations = XMLUtilities
-										.getSingleInvokationsFromMultipleInvokations(outputXML);
-
-								List innerList = new ArrayList();
-								Element serviceNotesElement = XMLUtilities
-										.getServiceNotesAsElement(outputXML);
-								for (int i = 0; i < invocations.length; i++) {
-									try {
-										String collection = XMLUtilities
-												.getWrappedCollection(
-														articleName,
-														invocations[i]);
-										String[] simples = XMLUtilities
-												.getSimplesFromCollection(
-														articleName, collection);
-										for (int j = 0; j < simples.length; j++) {
-											innerList
-													.add(XMLUtilities
-															.createMobyDataElementWrapper(
-																	simples[j],
-																	XMLUtilities
-																			.getQueryID(collection)
-																	/*
-																	 * + "_+_s"
-																	 * +
-																	 * qCounter
-																	 * ++
-																	 */,
-																	serviceNotesElement));
-										}
-									} catch (MobyException e) {
-										// collection didnt exist, so put an
-										// empty
-										// mobyData
-										// TODO keep the original wrapper
-										/*
-										 * String qID =
-										 * XMLUtilities.getQueryID(invocations
-										 * [i]); Element empty =
-										 * XMLUtilities.createMobyDataWrapper
-										 * (qID,
-										 * XMLUtilities.getServiceNotesAsElement
-										 * (outputXML)); XMLOutputter output =
-										 * new XMLOutputter(Format
-										 * .getPrettyFormat());
-										 * innerList.add(output
-										 * .outputString(empty));
-										 */
-									}
-								}
-								outputMap.put(name, referenceService.register(
-										innerList, outputPort.getDepth(), true,
-										context));
-							} else {
-								// process the single invocation and put string
-								// into
-								// a
-								// list
-								try {
-
-									List innerList = new ArrayList();
-									String collection = XMLUtilities
-											.getWrappedCollection(articleName,
-													outputXML);
-
-									String[] simples = XMLUtilities
-											.getSimplesFromCollection(
-													articleName, collection);
-									Element serviceNotesElement = XMLUtilities
-											.getServiceNotesAsElement(outputXML);
-									for (int i = 0; i < simples.length; i++) {
-										innerList
-												.add(XMLUtilities
-														.createMobyDataElementWrapper(
-																simples[i],
-																XMLUtilities
-																		.getQueryID(collection),
-																serviceNotesElement));
-									}
-
-									outputMap
-											.put(
-													name,
-													referenceService
-															.register(
-																	innerList,
-																	outputPort
-																			.getDepth(),
-																	true,
-																	context));
-								} catch (MobyException e) {
-									List innerList = new ArrayList();
-									outputMap
-											.put(
-													name,
-													referenceService
-															.register(
-																	innerList,
-																	outputPort
-																			.getDepth(),
-																	true,
-																	context));
-								}
-							}
-						} else {
-							if (isMIM) {
-								// process each invocation and then merge them
-								// into
-								// a
-								// single string
-								String[] invocations = XMLUtilities
-										.getSingleInvokationsFromMultipleInvokations(outputXML);
-
-								List innerList = new ArrayList();
-								for (int i = 0; i < invocations.length; i++) {
-									try {
-										String collection = XMLUtilities
-												.getWrappedCollection(
-														articleName,
-														invocations[i]);
-										innerList.add(collection);
-									} catch (MobyException e) {
-
-									}
-								}
-
-								outputMap.put(name, referenceService.register(
-										innerList, outputPort.getDepth(), true,
-										context));
-							} else {
-
-								try {
-
-									List innerList = new ArrayList();
-									String collection = XMLUtilities
-											.getWrappedCollection(articleName,
-													outputXML);
-									innerList.add(collection);
-									outputMap
-											.put(
-													name,
-													referenceService
-															.register(
-																	innerList,
-																	outputPort
-																			.getDepth(),
-																	true,
-																	context));
-								} catch (MobyException e) {
-									List innerList = new ArrayList();
-									outputMap
-											.put(
-													name,
-													referenceService
-															.register(
-																	innerList,
-																	outputPort
-																			.getDepth(),
-																	true,
-																	context));
-								}
-							}
-						}
-					}
-				} else {
-					// simple - single string
-					if (name.indexOf("_ANON_") > 0) {
-						// un-named simple -> ignore it as it is illegal in the
-						// api
-						// TODO could throw exception
-
-						String empty = new XMLOutputter()
-								.outputString(XMLUtilities
-										.createMobyDataWrapper(
-												XMLUtilities
-														.getQueryID(outputXML),
-												XMLUtilities
-														.getServiceNotesAsElement(outputXML)));
-						List innerList = new ArrayList();
-						innerList.add(empty);
-						outputMap.put(name, referenceService.register(empty,
-								outputPort.getDepth(), true, context));
-						// FIXME outputMap.put(name, new
-						// DataThing((Object)null));
-						continue;
-					} else {
-						// TODO what if you make mim messages a single string
-						// and then simples always output 'text/xml'?
-						String articleName = name.substring(
-								name.indexOf("(") + 1, name.indexOf(")"));
-						if (isMIM) {
-
-							String[] invocations = XMLUtilities
-									.getSingleInvokationsFromMultipleInvokations(outputXML);
-
-							ArrayList innerList = new ArrayList();
-
-							for (int i = 0; i < invocations.length; i++) {
-								try {
-									String simple = XMLUtilities
-											.getWrappedSimple(articleName,
-													invocations[i]);
-									innerList.add(simple);
-								} catch (MobyException e) {
-									// simple didnt exist, so put an empty
-									// mobyData
-									// TODO keep the original wrapper
-									String qID = XMLUtilities
-											.getQueryID(invocations[i]);
-
-									Element empty = XMLUtilities
-											.createMobyDataWrapper(
-													qID,
-													XMLUtilities
-															.getServiceNotesAsElement(outputXML));
-									XMLOutputter output = new XMLOutputter(
-											Format.getPrettyFormat());
-									// invocations[i] =
-									// output.outputString(empty);
-									innerList.add(output.outputString(empty));
-									// FIXME outputMap.put(name, new
-									// DataThing(""));
-								}
-							}
-							String[] s = new String[innerList.size()];
-							s = (String[]) innerList.toArray(s);
-							try {
-								outputMap.put(name, referenceService.register(
-										XMLUtilities
-												.createMultipleInvokations(s),
-										outputPort.getDepth(), true, context));
-							} catch (MobyException e) {
-								logger
-										.error("Error creating output for service: "
-												+ "."
-												+ System
-														.getProperty("line.separator")
-												+ e.getMessage());
-								outputMap.put(name, referenceService.register(
-										"", outputPort.getDepth(), true,
-										context));
-							}
-						} else {
-							// process the single invocation and put into a
-							// string
-							try {
-								String simple = XMLUtilities.getWrappedSimple(
-										articleName, outputXML);
-								ArrayList innerList = new ArrayList();
-								innerList.add(simple);
-								outputMap.put(name, referenceService.register(
-										simple, outputPort.getDepth(), true,
-										context));
-							} catch (MobyException e) {
-								// simple didnt exist, so put an empty mobyData
-								// TODO keep the original wrapper
-								String qID = XMLUtilities.getQueryID(outputXML);
-								Element empty = XMLUtilities
-										.createMobyDataWrapper(
-												qID,
-												XMLUtilities
-														.getServiceNotesAsElement(outputXML));
-								XMLOutputter output = new XMLOutputter(Format
-										.getPrettyFormat());
-								ArrayList innerList = new ArrayList();
-								innerList.add(output.outputString(empty));
-								outputMap.put(name, referenceService.register(
-										output.outputString(empty), outputPort
-												.getDepth(), true, context));
-								// FIXME outputMap.put(name, new DataThing(""));
-
-							}
-						}
-					}
-				}
-			}
-		}
-	}
-
-	protected String formatError(String msg) {
-		// Removed references to the authority, some errors
-		// were causing it to be null which in turn threw
-		// a NPE from here, breaking Taverna's error handlers
-		return ("Problems with service '" + configurationBean.getServiceName()
-				+ "' provided by authority '"
-				+ configurationBean.getAuthorityName()
-				+ "'\nfrom Moby registry at "
-				+ configurationBean.getMobyEndpoint() + ":\n\n" + msg);
-	}
-
-	protected ActivityInputPort getInputPort(String name) {
-		for (ActivityInputPort port : getInputPorts()) {
-			if (port.getName().equals(name)) {
-				return port;
-			}
-		}
-		return null;
-	}
-
-	protected OutputPort getOutputPort(String name) {
-		for (OutputPort port : getOutputPorts()) {
-			if (port.getName().equals(name)) {
-				return port;
-			}
-		}
-		return null;
-	}
-
-	protected void addOutput(String portName, int portDepth, String type) {
-		OutputPort port = edits.createActivityOutputPort(
-				portName, portDepth, portDepth);
-		MimeType mimeType = new MimeType();
-		mimeType.setText(type);
-		try {
-			edits.getAddAnnotationChainEdit(port, mimeType)
-					.doEdit();
-		} catch (EditException e) {
-			logger.debug("Error adding MimeType annotation to port", e);
-		}
-		outputPorts.add(port);
-	}
-
-	private void configureSecondaries() {
-		if (configurationBean.getSecondaries().size() > 0
-				&& containsSecondaries()) {
-			MobyData[] datas = getMobyService().getSecondaryInputs();
-			for (Entry<String, String> entry : configurationBean
-					.getSecondaries().entrySet()) {
-				String name = entry.getKey();
-				String value = entry.getValue();
-				for (int i = 0; i < datas.length; i++) {
-					if (datas[i].getName().equals(name)) {
-						((MobySecondaryData) datas[i]).setDefaultValue(value);
-						break;
-					}
-				}
-			}
-			MobySecondaryData[] msd = new MobySecondaryData[datas.length];
-			for (int i = 0; i < datas.length; i++) {
-				msd[i] = (MobySecondaryData) datas[i];
-			}
-			setParameterTable(new ParametersTable(msd));
-		}
-	}
-
-	private void setParameterTable(ParametersTable table) {
-		parameterTable = table;
-	}
-
-	private String executeService(String url, String serviceName, String xml)
-			throws MobyException {
-		// here we get the wsdl before calling the service, as the biomoby api assumes ...
-		try {
-			new RetrieveWsdlThread(worker, mobyService).start();
-		} catch (Exception e) {
-			/* don't care if an exception occurs here ... */
-			logger.info("Problem getting the biomoby wsdl for " + mobyService.getUniqueName() + ".\n" + e.getLocalizedMessage());
-		}
-		String serviceCategory = mobyService.getCategory();
-		if (serviceCategory.equalsIgnoreCase(MobyService.CATEGORY_MOBY)) {
-			return ExecuteMobyService.executeMobyService(url, serviceName, xml);
-		} else if (serviceCategory.equalsIgnoreCase("cgi")) {
-			return ExecuteCgiService.executeCgiService(url, xml);
-		} else if (serviceCategory.equalsIgnoreCase(MobyService.CATEGORY_MOBY_ASYNC)) {
-			return ExecuteAsyncMobyService.executeMobyAsyncService(url, serviceName, xml);
-		} else if (serviceCategory.equalsIgnoreCase("cgi-async")) {
-			return ExecuteAsyncCgiService.executeMobyCgiAsyncService(url, serviceName, xml);
-		}
-		// TODO should we throw an exception here?
-		return "";
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
deleted file mode 100644
index 03abb6e..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
+++ /dev/null
@@ -1,142 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to the Biomoby activity.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = BiomobyActivity.URI + "#Config")
-public class BiomobyActivityConfigurationBean {
-
-	private String mobyEndpoint="";
-
-	private String serviceName="";
-
-	private String authorityName="";
-
-	@Deprecated
-	private String category = "";
-	@Deprecated
-	private String serviceType = "";
-
-	private Map<String,String> secondaries=new HashMap<String,String>();
-
-	/**
-	 * Returns the mobyEndpoint.
-	 *
-	 * @return the mobyEndpoint
-	 */
-	public String getMobyEndpoint() {
-		return mobyEndpoint;
-	}
-
-	/**
-	 * Sets the mobyEndpoint.
-	 *
-	 * @param mobyEndpoint the new mobyEndpoint
-	 */
-	@ConfigurationProperty(name = "mobyEndpoint", label = "Moby Endpoint")
-	public void setMobyEndpoint(String mobyEndpoint) {
-		this.mobyEndpoint = mobyEndpoint;
-	}
-
-	/**
-	 * Returns the serviceName.
-	 *
-	 * @return the serviceName
-	 */
-	public String getServiceName() {
-		return serviceName;
-	}
-
-	/**
-	 * Sets the serviceName.
-	 *
-	 * @param serviceName the new serviceName
-	 */
-	@ConfigurationProperty(name = "serviceName", label = "Service Name")
-	public void setServiceName(String serviceName) {
-		this.serviceName = serviceName;
-	}
-
-	/**
-	 * Returns the authorityName.
-	 *
-	 * @return the authorityName
-	 */
-	public String getAuthorityName() {
-		return authorityName;
-	}
-
-	/**
-	 * Sets the authorityName.
-	 *
-	 * @param authorityName the new authorityName
-	 */
-	@ConfigurationProperty(name = "authorityName", label = "Authority Name")
-	public void setAuthorityName(String authorityName) {
-		this.authorityName = authorityName;
-	}
-
-	/**
-	 * Returns the secondaries
-	 *
-	 * @return secondaries as a HashMap
-	 */
-	public Map<String,String> getSecondaries() {
-		return secondaries;
-	}
-
-	/**
-	 *
-	 * @param secondaries
-	 */
-	public void setSecondaries(Map<String,String> secondaries) {
-		this.secondaries=secondaries;
-	}
-
-	@ConfigurationProperty(name = "secondaries", label = "Secondaries", required=false)
-	public void setSecondaries(Set<Secondary> secondaries) {
-		Map<String,String> secondariesMap = new HashMap<String,String>();
-		for (Secondary secondary : secondaries) {
-			secondariesMap.put(secondary.getKey(), secondary.getValue());
-		}
-		this.secondaries=secondariesMap;
-	}
-
-	@ConfigurationBean(uri = BiomobyActivity.URI + "#Secondary")
-	public static class Secondary {
-		private String key, value;
-
-		public String getKey() {
-			return key;
-		}
-
-		@ConfigurationProperty(name = "key", label = "Key")
-		public void setKey(String key) {
-			this.key = key;
-		}
-
-		public String getValue() {
-			return value;
-		}
-
-		@ConfigurationProperty(name = "value", label = "Value")
-		public void setValue(String value) {
-			this.value = value;
-		}
-
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
deleted file mode 100644
index 9a7bdf0..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 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.biomoby;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-
-/**
- * An {@link ActivityFactory} for creating <code>BiomobyActivity</code>.
- * 
- * @author David Withers
- */
-public class BiomobyActivityFactory implements ActivityFactory {
-
-	@Override
-	public BiomobyActivity createActivity() {
-		return new BiomobyActivity();
-	}
-
-	@Override
-	public URI getActivityURI() {
-		return URI.create(BiomobyActivity.URI);
-	}
-
-	@Override
-	public Object createActivityConfiguration() {
-		return new BiomobyActivityConfigurationBean();
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
deleted file mode 100644
index aec3d1a..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.visit.VisitReport;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-/**
- * A health checker for the Biomoby activity.
- * 
- * @author David Withers
- */
-public class BiomobyActivityHealthChecker extends RemoteHealthChecker {
-	
-	public boolean canVisit(Object subject) {
-		if (subject == null) {
-			return false;
-		}
-		if (subject instanceof BiomobyActivity) {
-			return true;
-		}
-		if (subject instanceof DisabledActivity) {
-			return (((DisabledActivity) subject).getActivity() instanceof BiomobyActivity);
-		}
-		return false;
-	}
-
-	public VisitReport visit(Object o, List<Object> ancestors) {
-		Activity activity = (Activity) o;
-		BiomobyActivityConfigurationBean configuration = null;
-		if (activity instanceof BiomobyActivity) {
-			configuration = (BiomobyActivityConfigurationBean) activity.getConfiguration();
-		} else if (activity instanceof DisabledActivity) {
-			configuration = (BiomobyActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration();
-		}
-		return contactEndpoint(activity, configuration.getMobyEndpoint());
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
deleted file mode 100644
index 288e654..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralDigestCachedImpl;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-
-/**
- * A utility class that handles triggering JMoby to cache for a given {@link Registry} for a given registry
- *
- * @author Stuart Owen
- * @author Eddie Kawas
- */
-
-public class BiomobyCache {
-
-    private static Logger logger = Logger.getLogger(BiomobyCache.class);
-
-	private static Map<String,Object> cached = new HashMap<String, Object>();
-
-    /**
-	 * If necessary caches the Ontology and namespace information.
-     * This call immediately returns if the cache has been previously called for this endpoint
-     *
-	 * @param reg - the Registry instance
-	 *
-	 */
-	public static synchronized void cacheForRegistry(Registry reg) {
-		if (cached.get(reg.getEndpoint()) == null) {
-			logger.info("Caching started for Biomoby registry"
-					+ reg.getEndpoint());
-
-			Central c;
-			try {
-				c = CentralImpl.getDefaultCentral(reg);
-				if (c instanceof CentralDigestCachedImpl)
-					((CentralDigestCachedImpl) c)
-							.updateCache(CentralDigestCachedImpl.CACHE_PART_DATATYPES);
-				MobyDataType.getDataType("Object", reg);
-				MobyNamespace.getNamespace("foo", reg);
-
-				cached.put(reg.getEndpoint(), new Boolean(true));
-				logger.info("Caching complete for Biomoby registry"
-						+ reg.getEndpoint());
-
-			} catch (MobyException e) {
-				logger.error("Error whilst caching for Biomoby registry",e);
-			}
-
-		}
-	}
-
-    /**
-	 * If necessary caches the Ontology and namespace information.
-     * This call immediately returns if the cache has been previously called for this endpoint url.
-     *
-	 * @param endpointUrl - the Registry endpoint Url
-	 *
-	 */
-    public static synchronized void cacheForRegistryEndpoint(String endpointUrl) {
-        Registry registry = new Registry(endpointUrl, endpointUrl,
-					"http://domain.com/MOBY/Central");
-        cacheForRegistry(registry);
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
deleted file mode 100644
index 41e8c4f..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
+++ /dev/null
@@ -1,545 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyRelationship;
-import org.biomoby.shared.NoSuccessException;
-import org.biomoby.shared.data.MobyDataBoolean;
-import org.biomoby.shared.data.MobyDataComposite;
-import org.biomoby.shared.data.MobyDataDateTime;
-import org.biomoby.shared.data.MobyDataFloat;
-import org.biomoby.shared.data.MobyDataInstance;
-import org.biomoby.shared.data.MobyDataInt;
-import org.biomoby.shared.data.MobyDataString;
-import org.jdom.Element;
-
-/**
- * An Activity providing Biomoby Object functionality.
- *
- * Copied from org.biomoby.client.taverna.plugin.BiomobyObjectProcessor and
- * org.biomoby.client.taverna.plugin.BiomobyObjectTask and converted to a Taverna 2
- * Activity.
- *
- * @author Edward Kawas
- * @author David Withers
- */
-public class BiomobyObjectActivity extends AbstractAsynchronousActivity<BiomobyObjectActivityConfigurationBean> {
-
-	public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/object";
-
-	private static Logger logger = Logger.getLogger(BiomobyObjectActivity.class);
-
-    private BiomobyObjectActivityConfigurationBean configurationBean = new BiomobyObjectActivityConfigurationBean();
-
-    private Central worker = null;
-
-    private MobyDataType mobyObject = null;
-
-    @Override
-	public void configure(BiomobyObjectActivityConfigurationBean configurationBean) throws ActivityConfigurationException {
-		this.configurationBean = configurationBean;
-		init();
-		generatePorts();
-	}
-
-	@Override
-	public void executeAsynch(final Map<String, T2Reference> data,
-			final AsynchronousActivityCallback callback) {
-		callback.requestRun(new Runnable() {
-
-			public void run() {
-				ReferenceService referenceService = callback.getContext().getReferenceService();
-
-				Map<String, T2Reference> outputMap = new HashMap<String, T2Reference>();
-
-				// initialize the namespace and id fields
-				String namespace = "";
-				String id = "";
-				String article = "";
-				boolean isPrimitiveType = getInputPort("value")!=null;
-				String objectName = configurationBean.getServiceName();
-				// would like to use the MobyObjectClass to generate a skeleton
-
-				String registryEndpoint = worker.getRegistryEndpoint();
-				Registry mRegistry = new Registry(registryEndpoint,registryEndpoint,"http://domain.com/MOBY/Central");
-
-                BiomobyCache.cacheForRegistry(mRegistry);
-
-				if (isPrimitiveType) {
-					try {
-
-						T2Reference inputId;
-						try {
-							inputId = data.get("namespace");
-							namespace = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						try {
-							inputId = data.get("id");
-							id = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						try {
-							inputId = data.get("article name");
-							article = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						inputId = data.get("value");
-						String value = null;
-						try {
-							value = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						}
-						catch(NullPointerException e) {
-							//means the value hasn't been set and is handled below
-						}
-
-						if (objectName.equals("String")) {
-							if (value == null) {
-								value = "";
-							}
-							MobyDataString d = new MobyDataString(value,mRegistry);
-							d.setId(id);
-							MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-							if (mNamespace != null)
-								d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-							d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-							outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-									"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-						} else if (objectName.equals("Float")) {
-							if (value == null || value.trim().equals("")) {
-								MobyDataComposite d = new MobyDataComposite(
-										MobyDataType.getDataType("Float", mRegistry));
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							} else {
-								MobyDataFloat d = new MobyDataFloat(value,mRegistry);
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							}
-						} else if (objectName.equals("Integer")) {
-
-							try {
-								int val = 0;
-								val = Integer.parseInt(value);
-								MobyDataInt d = new MobyDataInt(val,mRegistry);
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							} catch (Exception e) {
-								MobyDataComposite d = new MobyDataComposite(
-										MobyDataType.getDataType("Integer", mRegistry));
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							}
-						}else if (objectName.equals("Boolean")) {
-							if (value == null || value.trim().equals("")) {
-								MobyDataComposite d = new MobyDataComposite(MobyDataType.getDataType("Boolean", mRegistry));
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							} else {
-								MobyDataBoolean d = new MobyDataBoolean(value,mRegistry);
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							}
-						} else if (objectName.equals("DateTime")) {
-							if (value == null || value.trim().equals("")) {
-								MobyDataComposite d = new MobyDataComposite(MobyDataType.getDataType("DateTime", mRegistry));
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							} else {
-								MobyDataDateTime d = new MobyDataDateTime("", value,mRegistry);
-								d.setId(id);
-								MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-								if (mNamespace != null)
-									d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-								d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-								outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
-										"<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
-							}
-						}
-						callback.receiveResult(outputMap, new int[0]);
-					} catch (Exception ex) {
-						// details of other exceptions will appear only in a log
-						logger.error("Error creating biomoby object for biomoby", ex);
-						callback.fail("Service failed due to problem creating biomoby object (see details in log)", ex);
-					}
-				} else {
-					// Situation where simples are feeding into this non primitive type
-					try {
-						T2Reference inputId;
-						try {
-							inputId = data.get("namespace");
-							namespace = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						try {
-							inputId = data.get("id");
-							id = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						try {
-							inputId = data.get("article name");
-							article = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-						} catch (Exception e) {
-						}
-
-						//Element mobyObjectElement = mo.createObject(objectName,namespace, id, article);
-
-						MobyDataComposite composite = new MobyDataComposite(MobyDataType.getDataType(objectName, mRegistry));
-						composite.setId(id);
-						MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
-						if (mNamespace != null)
-							composite.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
-						composite.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-
-						// Element mobyObjectElement = XMLUtilities.getDOMDocument(XMLUtilities.createMobyDataElementWrapper( "<Simple articleName=\""+article+"\">" + composite.toXML() +"</Simple>" )).detachRootElement();
-						Element mobyObjectElement = XMLUtilities.getDOMDocument(( composite.toXML() )).detachRootElement();
-
-						// using the inputs, iterate through and fill in data
-						for (ActivityInputPort inputPort : getInputPorts()) {
-							String portName = inputPort.getName();
-							if (!(portName.equalsIgnoreCase("namespace")
-									|| portName.equalsIgnoreCase("id") || portName
-									.equalsIgnoreCase("article name"))) {
-								String type = portName.substring(0, portName
-										.indexOf("("));
-								String articleName = portName.substring(
-										type.length() + 1, portName.length() - 1);
-								inputId = null;
-								try {
-									inputId = data.get(portName);
-								} catch (Exception e) {
-
-								}
-								if (inputId != null) {
-									String value = (String) referenceService.renderIdentifier(inputId, inputPort.getTranslatedElementClass(), callback.getContext());
-									Element valueElement = (XMLUtilities.getDOMDocument(value)).getRootElement();
-									if (valueElement.getChild("mobyContent",XMLUtilities.MOBY_NS) != null) {
-										valueElement = valueElement.getChild("mobyContent",XMLUtilities.MOBY_NS);
-									} else {
-										valueElement = valueElement.getChild("mobyContent");
-									}
-									if (valueElement.getChild("mobyData",XMLUtilities.MOBY_NS) != null ) {
-										valueElement = valueElement.getChild("mobyData",XMLUtilities.MOBY_NS);
-									} else {
-										valueElement = valueElement.getChild("mobyData");
-									}
-									if (valueElement.getChild("Simple",XMLUtilities.MOBY_NS) != null ) {
-										valueElement = valueElement.getChild("Simple",XMLUtilities.MOBY_NS);
-									} else {
-										valueElement = valueElement.getChild("Simple");
-									}
-									if (valueElement.getChild(type,XMLUtilities.MOBY_NS) != null ) {
-										valueElement = valueElement.getChild(type,XMLUtilities.MOBY_NS);
-									} else {
-										valueElement = valueElement.getChild(type);
-									}
-									// Element _child = mo.getObject(mobyObjectElement,type, articleName);
-
-									valueElement.removeAttribute("articleName");
-									valueElement.removeAttribute("articleName", XMLUtilities.MOBY_NS);
-									valueElement.setAttribute("articleName", articleName, XMLUtilities.MOBY_NS);
-//									Element _newChild = mo.createObject(type, _ns, _id,
-//									articleName);
-//									_newChild.setText(valueElement
-//									.getText());
-//									_newChild.addContent(_child.cloneContent());
-									// import and replace the node
-									// mobyObjectElement.removeContent(_child);
-									mobyObjectElement.addContent(valueElement.detach());
-								}
-							}
-						}
-						Element simple = new Element("Simple", XMLUtilities.MOBY_NS);
-						simple.setAttribute("articleName", article, XMLUtilities.MOBY_NS);
-						simple.addContent(mobyObjectElement);
-
-						org.jdom.output.XMLOutputter outputter = new org.jdom.output.XMLOutputter(org.jdom.output.Format.getPrettyFormat());
-						String mobyDataString = outputter.outputString(XMLUtilities.createMobyDataElementWrapper(simple));
-						outputMap.put("mobyData", referenceService.register(mobyDataString, 0, true, callback.getContext()));
-
-						callback.receiveResult(outputMap, new int[0]);
-					} catch (Exception ex) {
-						// details of other exceptions will appear only in a log
-						logger.error("Error creating biomoby object for biomoby", ex);
-						callback.fail("Service failed due to problem creating biomoby object (see details in log)", ex);
-					}
-				}
-			}
-		});
-
-	}
-
-	@Override
-	public BiomobyObjectActivityConfigurationBean getConfiguration() {
-		return configurationBean;
-	}
-
-    private void init() throws ActivityConfigurationException {
-        // Find the service endpoint (by calling Moby registry)
-        try {
-            if (mobyObject == null) {
-                worker = new CentralImpl(configurationBean.getMobyEndpoint());
-                mobyObject = worker.getDataType(configurationBean.getServiceName());
-            }
-
-        } catch (Exception e) {
-            if (e instanceof ActivityConfigurationException) {
-                throw (ActivityConfigurationException) e;
-            }
-            throw new ActivityConfigurationException(formatError(e.toString()));
-        }
-        // here we make sure that we have downloaded the ontology for the
-		// registry that we got this service from
-        try {
-			new GetOntologyThread(worker.getRegistryEndpoint()).start();
-		} catch (Exception e) {
-			/* don't care if an exception occurs here ... */
-		}
-    }
-
-    private void generatePorts() {
-    	removeInputs();
-    	removeOutputs();
-
-    	//inputs
-		addInput("namespace", 0, true,
-				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-				String.class);
-
-		addInput("id", 0, true,
-				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-				String.class);
-
-		addInput("article name", 0, true,
-				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-				String.class);
-
-    	try {
-    		String serviceName = configurationBean.getServiceName();
-    		MobyDataType datatype = worker.getDataType(serviceName);
-    		MobyRelationship[] relations = datatype.getChildren();
-    		processRelationships(relations);
-    		String parent = "Object";
-    		try {
-    			parent = datatype.getParentNames()[0];
-    			if (parent.indexOf(":") > 0) {
-    				parent = parent.substring(parent.lastIndexOf(":") + 1);
-    			}
-    		} catch (ArrayIndexOutOfBoundsException e) {
-    			// parent is then by default object
-    		}
-    		if (parent.equalsIgnoreCase("String")
-    				|| parent.equalsIgnoreCase("Integer")
-    				|| parent.equalsIgnoreCase("float")
-    				|| parent.equalsIgnoreCase("DateTime")
-    				|| parent.equalsIgnoreCase("Boolean")
-    				|| serviceName.equalsIgnoreCase("String")
-    				|| serviceName.equalsIgnoreCase("Boolean")
-    				|| serviceName.equalsIgnoreCase("Integer")
-    				|| serviceName.equalsIgnoreCase("float")
-    				|| serviceName.equalsIgnoreCase("DateTime")) {
-    			addInput("value", 0, true,
-    					new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-    					String.class);
-    		} else {
-    			if (!parent.equalsIgnoreCase("Object"))
-    				extractParentContainerRelationships(parent);
-    		}
-    	} catch (MobyException e) {
-    	} catch (NoSuccessException e) {
-    	}
-
-    	//outputs
-		addOutput("mobyData", 0, "text/xml");
-    }
-
-    private void extractParentContainerRelationships(String string) {
-        try {
-            MobyDataType datatype = worker.getDataType(string);
-            // need to propagate the isa up to Object to get all of the has/hasa
-            MobyRelationship[] relations = datatype.getChildren();
-            processRelationships(relations);
-            String parent = "Object";
-            try {
-                parent = datatype.getParentNames()[0];
-                if (parent.indexOf(":") > 0) {
-                    parent = parent.substring(parent.lastIndexOf(":") + 1);
-                }
-            } catch (ArrayIndexOutOfBoundsException e) {
-                // parent is then by default object
-            }
-    		String serviceName = configurationBean.getServiceName();
-            if (parent.equalsIgnoreCase("String")
-                    || parent.equalsIgnoreCase("Integer")
-                    || parent.equalsIgnoreCase("float")
-                    || serviceName.equalsIgnoreCase("String")
-                     || parent.equalsIgnoreCase("Boolean")
-                    || serviceName.equalsIgnoreCase("Boolean")
-                    || serviceName.equalsIgnoreCase("Integer")
-                    || serviceName.equalsIgnoreCase("float")) {
-        		addInput("value", 0, true,
-        				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-        				String.class);
-            } else {
-                if (!parent.equalsIgnoreCase("Object"))
-                    extractParentContainerRelationships(parent);
-            }
-        } catch (MobyException e) {
-        } catch (NoSuccessException e) {
-        }
-    }
-
-    private void processRelationships(MobyRelationship[] relations) {
-        for (int x = 0; x < relations.length; x++) {
-            MobyRelationship relationship = relations[x];
-
-            // strip urn:lsid:...
-            String name = relationship.getDataTypeName();
-            if (name.indexOf(":") > 0) {
-                name = name.substring(name.lastIndexOf(":") + 1);
-            }
-            // port name == DataType(articleName)
-            name = name + "(" + relationship.getName() + ")";
-            switch (relationship.getRelationshipType()) {
-            case (Central.iHAS): {
-                // TODO - not really supported
-        		addInput(name, 0, true,
-        				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-        				String.class);
-                break;
-            }
-            case (Central.iHASA): {
-        		addInput(name, 0, true,
-        				new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-        				String.class);
-                break;
-            }
-            default:
-                break;
-            }
-        }
-    }
-
-
-	protected String formatError(String msg) {
-		// Removed references to the authority, some errors
-		// were causing it to be null which in turn threw
-		// a NPE from here, breaking Taverna's error handlers
-		return ("Problems with service '" + configurationBean.getServiceName()
-				+ "' provided by authority '"
-				+ configurationBean.getAuthorityName()
-				+ "'\nfrom Moby registry at "
-				+ configurationBean.getMobyEndpoint() + ":\n\n" + msg);
-	}
-
-	protected ActivityInputPort getInputPort(String name) {
-		for (ActivityInputPort port : getInputPorts()) {
-			if (port.getName().equals(name)) {
-				return port;
-			}
-		}
-		return null;
-	}
-
-	protected OutputPort getOutputPort(String name) {
-		for (OutputPort port : getOutputPorts()) {
-			if (port.getName().equals(name)) {
-				return port;
-			}
-		}
-		return null;
-	}
-
-	protected void addOutput(String portName, int portDepth, String type) {
-		OutputPort port = edits.createActivityOutputPort(
-				portName, portDepth, portDepth);
-		MimeType mimeType = new MimeType();
-		mimeType.setText(type);
-		try {
-			edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
-		} catch (EditException e) {
-			logger.debug("Error adding MimeType annotation to port", e);
-		}
-		outputPorts.add(port);
-	}
-
-	public Central getCentral() {
-        if (worker != null)
-            return worker;
-        else
-            try {
-                return new CentralImpl(getConfiguration().getMobyEndpoint());
-            } catch (MobyException e) {
-                return null;
-            }
-    }
-
-	public MobyDataType getMobyObject() {
-        return mobyObject;
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
deleted file mode 100644
index ab26b32..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed  under the
- *  GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to the Biomoby Object activity.
- * 
- * @author David Withers
- */
-@ConfigurationBean(uri = BiomobyObjectActivity.URI + "#Config")
-public class BiomobyObjectActivityConfigurationBean {
-
-	private String mobyEndpoint="";
-
-	private String serviceName="";
-
-	private String authorityName="";
-
-	/**
-	 * Returns the mobyEndpoint.
-	 *
-	 * @return the mobyEndpoint
-	 */
-	public String getMobyEndpoint() {
-		return mobyEndpoint;
-	}
-
-	/**
-	 * Sets the mobyEndpoint.
-	 *
-	 * @param mobyEndpoint the new mobyEndpoint
-	 */
-	@ConfigurationProperty(name = "mobyEndpoint", label = "Moby Endpoint", description = "")
-	public void setMobyEndpoint(String mobyEndpoint) {
-		this.mobyEndpoint = mobyEndpoint;
-	}
-
-	/**
-	 * Returns the serviceName.
-	 *
-	 * @return the serviceName
-	 */
-	public String getServiceName() {
-		return serviceName;
-	}
-
-	/**
-	 * Sets the serviceName.
-	 *
-	 * @param serviceName the new serviceName
-	 */
-	@ConfigurationProperty(name = "serviceName", label = "Service Name", description = "")
-	public void setServiceName(String serviceName) {
-		this.serviceName = serviceName;
-	}
-
-	/**
-	 * Returns the authorityName.
-	 *
-	 * @return the authorityName
-	 */
-	public String getAuthorityName() {
-		return authorityName;
-	}
-
-	/**
-	 * Sets the authorityName.
-	 *
-	 * @param authorityName the new authorityName
-	 */
-	@ConfigurationProperty(name = "authorityName", label = "Authority Name", description = "")
-	public void setAuthorityName(String authorityName) {
-		this.authorityName = authorityName;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
deleted file mode 100644
index 955b808..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 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.biomoby;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-
-/**
- * An {@link ActivityFactory} for creating <code>BiomobyObjectActivity</code>.
- * 
- * @author David Withers
- */
-public class BiomobyObjectActivityFactory implements ActivityFactory {
-
-	@Override
-	public BiomobyObjectActivity createActivity() {
-		return new BiomobyObjectActivity();
-	}
-
-	@Override
-	public URI getActivityURI() {
-		return URI.create(BiomobyObjectActivity.URI);
-	}
-
-	@Override
-	public Object createActivityConfiguration() {
-		return new BiomobyObjectActivityConfigurationBean();
-	}
-
-}