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(); - } - -}
