Extractor Modules / Taverna Extractor / Diff of /src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java

Diff of /src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java [346c31] .. [c78deb]

Switch to unified view


...
import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
import net.sf.taverna.t2.activities.dataflow.DataflowActivity;
import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
import net.sf.taverna.t2.activities.rest.RESTActivity;
import net.sf.taverna.t2.activities.rshell.RshellActivity;
import net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean;
import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity;
import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity;
import net.sf.taverna.t2.activities.xpath.XPathActivity;
import net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean;
import net.sf.taverna.t2.commandline.CommandLineLauncher;
import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
...
    private IApplicationComponent workflowApplicationComponent = null;
    private IApplicationFunction callScriptApplicationFunction = null;
    private IApplicationFunction callXMLSplitterApplicationFunction = null;
    private IApplicationFunction callWebServiceApplicationFunction = null;
    private IApplicationFunction callToolInvocationFunction = null;
    private IApplicationFunction callXPathApplicationFunction = null;

    private Dataflow dataflow;
    private SSHManager sshManager;
    private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");

...
    }

    /*
     * // GETTER & SETTER ///////////////
     */
    public void setDotLocation(Path dotLocation) {
        TavernaExtractor.dotLocation = dotLocation;
    }

    public Path getDotLocation() {
        return dotLocation;
    }

    public Path getArchimateOutputPath() {
        return archimateOutputPath;
    }

    public void setArchimateOutputPath(Path archimateOutputPath) {
        TavernaExtractor.archimateOutputPath = archimateOutputPath;
    }

    public Path getInputFileName() {
        return inputFileName;
    }

    public void setInputFileName(Path inputFileName) {
        TavernaExtractor.inputFileName = inputFileName;
    }

    public Path getTavernaHome() {
        return tavernaHome;
    }

    public void setTavernaHome(Path tavernaHome) {

        TavernaExtractor.tavernaHome = tavernaHome;
    }

    public Path getTavernaHomeLib() {
        return tavernaHomeLib;
    }

    public void setTavernaHomeLib(Path tavernaHomeLib) {
        TavernaExtractor.tavernaHomeLib = tavernaHomeLib;
    }

    public Path getTavernaHomeRepo() {
        return tavernaHomeRepo;
    }

    public void setTavernaHomeRepo(Path tavernaHomeRepo) {
        TavernaExtractor.tavernaHomeRepo = tavernaHomeRepo;
    }


    public List<IRelationship> getRelations() {
...
            CMException, IOException, DeserializationException, IterationTypeMismatchException, TavernaExtractorException {

        LOGGER.info("Start Taverna Extractor ...");

        //setup
        this.setTavernaHomeLib(this.getTavernaHome().resolve("lib"));
        this.setTavernaHomeRepo(this.getTavernaHome().resolve("repository"));

        if (remote)
            validateRemoteDirectories(this.getTavernaHome(), this.getTavernaHomeLib(), this.getTavernaHomeRepo());
        else
            validateDirectories(this.getTavernaHome(), this.getTavernaHomeLib(), this.getTavernaHomeRepo());

        LOGGER.info("TavernaHome is set to [" + this.getTavernaHome() + "].");
        LOGGER.info("TavernaHomeLib is set to [" + this.getTavernaHomeLib() + "].");
        LOGGER.info("TavernaHomeRepo is set to [" + this.getTavernaHomeRepo() + "].");
        LOGGER.info("Workflow input file is [" + this.getInputFileName() + "].");
        LOGGER.info("Archimate output file is [" + this.getArchimateOutputPath() + "].");

        inputPorts = new Container(Orientation.VERTICAL);
        outputPorts = new Container(Orientation.VERTICAL);
        businessObjects = new Container(Orientation.HORIZONTAL);
        businessProcesses = new Container(Orientation.HORIZONTAL);
...
                workflowFile, applicationFolder, relations, IAccessRelationship.READ_ACCESS);

        ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, workflowFile, relationsFolder,
                relations);

        workflowFile.getProperties().add(createDepProperties(this.getInputFileName().toString()));

        // Orchestration Service
        parentProcessWorkflow = ArchiUtils.initElement(factory.createBusinessProcess(), dataflow.getLocalName()
                + " Process", businessFolder, businessProcesses);
        workflowApplicationComponent = ArchiUtils.initElement(factory.createApplicationComponent(),
...
                relationsFolder, relations);

        ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, repoBundle,
                relationsFolder, relations);

        if (this.getTavernaHomeRepo().toFile().isDirectory()) {

            final List<File> jarFiles = new ArrayList<>();
            final PathMatcher matcher = FileSystems.getDefault()
                    .getPathMatcher("glob:*.jar");
            Files.walkFileTree(this.getTavernaHomeRepo(), new FileVisitor<Path>() {
                @Override
                public FileVisitResult preVisitDirectory(Path path, BasicFileAttributes basicFileAttributes) throws IOException {
                    return CONTINUE;
                }

...
            for (File jarDep : jarFiles) {
                String jarLocation = jarDep.getAbsolutePath();
                repoBundle.getProperties().add(createDepProperties(jarLocation));
            }
        } else {
            LOGGER.error("ERROR: " + this.getTavernaHomeRepo().toFile() + " is not a directory. No further dependecies processing.");
        }
        // --- END Taverna ---

        // --- BEGIN Events ---
        // Start Event
...

        // create external application service for each business process/function
        if (callXMLSplitterApplicationFunction == null) {

            callXMLSplitterApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),
                    "XML Splitter Built-In Service", applicationFolder, applicationComponents);

            ArchiUtils.initRelation(factory.createAssignmentRelationship(), callXMLSplitterApplicationFunction,
                    workflowApplicationComponent, relationsFolder, relations);

            ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, callXMLSplitterApplicationFunction,
...
                relationsFolder, relations);

        ArchiUtils.initRelation(factory.createUsedByRelationship(), callXMLSplitterApplicationFunction,
                processorProcessMap.get(processor), relationsFolder, relations);

        LOGGER.debug("Get input elements of process "+ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
                relations).size());
        // creating request response data objects
        for (IArchimateElement inputElement : ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
                relations)) {

            LOGGER.debug("inputElement = "+inputElement.getName());

            if (!business2dataMap.containsKey(inputElement)) {

                IDataObject requestObject = ArchiUtils.initElement(factory.createDataObject(), inputElement.getName(),
                        applicationFolder, applicationComponents);

                business2dataMap.put((IBusinessObject) inputElement, requestObject);

                ArchiUtils.initRelation(factory.createRealisationRelationship(), requestObject, inputElement,
                        relationsFolder, relations);
            }
            ArchiUtils.initAccessRelation(factory.createAccessRelationship(), appService,
                    business2dataMap.get(inputElement), applicationFolder, relations, IAccessRelationship.READ_ACCESS);

        }

        LOGGER.debug("Get output elements of process "+ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
                relations).size());
        for (IArchimateElement outputElement : ArchiUtils.getOutputElementsOfProcess(
                processorProcessMap.get(processor), relations)) {

            LOGGER.debug("inputElement = "+outputElement.getName());

            if (!business2dataMap.containsKey(outputElement)) {

                IDataObject responseObject = ArchiUtils.initElement(factory.createDataObject(),
                        outputElement.getName(), applicationFolder, applicationComponents);

                ArchiUtils.initRelation(factory.createRealisationRelationship(), responseObject, outputElement,
                        relationsFolder, relations);

                business2dataMap.put((IBusinessObject) outputElement, responseObject);
            }

            ArchiUtils
                    .initAccessRelation(factory.createAccessRelationship(), appService,
                            business2dataMap.get(outputElement), applicationFolder, relations,
                            IAccessRelationship.WRITE_ACCESS);

        }
    }

    public void processXPathActivity(IFolder infrastructureFolder, IFolder motivationFolder,
                                         IFolder applicationFolder, IFolder relationsFolder, IApplicationComponent workflowApplicationComponent,
                                         HashMap<Processor, IBusinessProcess> processorProcessMap, Processor processor, Activity<?> a)
            throws IOException {

        //beanshellScripts.add((BeanshellActivity) a);

        LOGGER.debug("XPath script found = " + processor.getLocalName());

        //XPathActivity xPathActivity = (XPathActivity) a;

        // create external application service for each business process/function
        if (callXPathApplicationFunction == null) {

            callXPathApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),
                    "XPath Built-In Service", applicationFolder, applicationComponents);

            ArchiUtils.initRelation(factory.createAssignmentRelationship(), callXPathApplicationFunction,
                    workflowApplicationComponent, relationsFolder, relations);

            ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, callXPathApplicationFunction,
                    relationsFolder, relations);
        }

        IApplicationService appService = ArchiUtils.initElement(factory.createApplicationService(),
                processor.getLocalName(), applicationFolder, externalApplicationServices);

        appService.getProperties().add(createDepProperties(BeanshellActivity.class));

        ArchiUtils.initRelation(factory.createUsedByRelationship(), appService, processorProcessMap.get(processor),
                relationsFolder, relations);

        ArchiUtils.initRelation(factory.createUsedByRelationship(), callXPathApplicationFunction,
                processorProcessMap.get(processor), relationsFolder, relations);

        IArtifact script = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), processor.getLocalName()
                , infrastructureFolder, nodeElements);

       XPathActivityConfigurationBean c =  (XPathActivityConfigurationBean) a.getConfiguration();
       String ex = c.getXpathExpression() != null ? c.getXpathExpression() : "NO_EXPRESSION_AVAILABLE";
       String doc = c.getXmlDocument() != null ? c.getXmlDocument() : "NO_XML_DOCUMENT_AVAILABLE";

       IProperty property = factory.createProperty();
       property.setKey("expression");
       property.setValue(ex);
       script.getProperties().add(property);

       IProperty property_document = factory.createProperty();
       property_document.setKey("document");
       property_document.setValue(doc);
       script.getProperties().add(property_document);

       ArchiUtils.initRelation(factory.createCompositionRelationship(), workflowFile, script, relationsFolder,
                relations);

       ArchiUtils
                .initRelation(factory.createRealisationRelationship(), script, appService, relationsFolder, relations);

        // creating request response data objects
        for (IArchimateElement inputElement : ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
                relations)) {

...
                LOGGER.debug("\t Dependency for " + processor.getLocalName() + " [" + item + "]");

                IArtifact beanshellScriptDep = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), item,
                        infrastructureFolder, nodeElements);

                ArchiUtils.initRelation(factory.createAssociationRelationship(), script, beanshellScriptDep,
                        relationsFolder);

                ArchiUtils.initRelation(factory.createCompositionRelationship(), beanshellScriptDep, desktop,
                        relationsFolder);

                // Do the license checking
                String fileName = this.getTavernaHomeLib() + File.separator + item;

                IProperty jarLocation = factory.createProperty();
                jarLocation.setKey("hasSourceLocation");
                jarLocation.setValue(fileName);
                beanshellScriptDep.getProperties().add(jarLocation);
...
            for (OutputPort outputPort : processor.getOutputPorts()) {
                outputPorts.add(outputPort);
            }
        }

        //TODO: needs improvements -> hasNoPrecedentProcessor not working if only one non-constant value processor exists!!
        List<Processor> startingProcessors = new ArrayList<Processor>();
        for (Processor processor : dataflow.getProcessors()) {

            if (ArchiUtils.isValueProcessor(processor)) {
                break;
            }
            else{
                startingProcessors.add(processor);
            }
        }
        if(startingProcessors.size() == 1){
            return startingProcessors;
        }

        startingProcessors = new ArrayList<Processor>();
        for (Processor processor : dataflow.getProcessors()) {

            if (ArchiUtils.isValueProcessor(processor)) {
                break;
            }

...
            fw.close();

            // Dot to SVG
            File svgTmp = new File(tmpDirPath + File.separator + "tavernaExtractorToArchimate.dot.svg");

            String[] COMMAND = {this.getDotLocation().toString(), "-Tsvg", dotTmp.getAbsolutePath(), "-o", svgTmp.getAbsolutePath()};

            LOGGER.debug("Running command '" + StringUtils.join(COMMAND, " ") + "'.");

            ProcessBuilder proc = new ProcessBuilder(COMMAND);
            Process process = proc.start();
...

                printPortInformation(processor);

                // TODO UnrecognizedActivity detected !!
                if (a instanceof UnrecognizedActivity) {
                    LOGGER.error("\tPROBLEM: UnrecognizedActivity detected! ");
                }
                // TODO DisabledActivity detected !!
                // From the javadoc: A disabled activity is a wrapper for an Activity that is offline or similarly
                // disabled
                else if (a instanceof DisabledActivity) {
                    LOGGER.error("\tPROBLEM: DisabledActivity detected! ");
                    // TODO: create a note element with information
                }

                // nested worklfow
                else if (a instanceof DataflowActivity) {
...
                            workflowApplicationComponent, processorProcessMap, callWebServiceApplicationFunction,
                            processor, processorName, a);
                }
                else if (a instanceof XMLInputSplitterActivity || a instanceof XMLOutputSplitterActivity) {
                    processXMLSplitterActivity(infrastructureFolder, motivationFolder, applicationFolder,
                            relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
                }
                else if (a instanceof XPathActivity){
                    LOGGER.info("XPathActivity has to be done");
                    processXPathActivity(infrastructureFolder, motivationFolder, applicationFolder,
                            relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
                }
                else if (a instanceof LocalworkerActivity){

                    /*
                          Localworker Activity equals BeanshellActivity ?!
                     */
                    processBeanshellActivity(infrastructureFolder, motivationFolder, applicationFolder,
                            relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
                }
                else{
                    LOGGER.debug("Unfortunately, we do not process that kind of activity.");
                }
...
                        // + ": " + sink.getClass());
                    }
                }
            }
        }

    }

    private Dataflow getDataflowRemote() throws TavernaExtractorException {

        try {
...


    private void saveRemote(IArchimateModel model) throws TavernaExtractorException {

        // Set new file
        File outFile = this.getArchimateOutputPath().toFile();
        model.setFile(outFile);

        // Set model version
        model.setVersion(ModelVersion.VERSION);

...
    }

    private void saveLocal(IArchimateModel model) throws IOException {

        // Set new file
        File outFile = this.getArchimateOutputPath().toFile();
        model.setFile(outFile);

        // Set model version
        model.setVersion(ModelVersion.VERSION);


	a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java		b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java
	...		...
27	import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;	27	import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
28	import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;	28	import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
29	import net.sf.taverna.t2.activities.dataflow.DataflowActivity;	29	import net.sf.taverna.t2.activities.dataflow.DataflowActivity;
30	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;	30	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
31	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;	31	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
		32	import net.sf.taverna.t2.activities.localworker.LocalworkerActivity;
32	import net.sf.taverna.t2.activities.rest.RESTActivity;	33	import net.sf.taverna.t2.activities.rest.RESTActivity;
33	import net.sf.taverna.t2.activities.rshell.RshellActivity;	34	import net.sf.taverna.t2.activities.rshell.RshellActivity;
34	import net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean;	35	import net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean;
35	import net.sf.taverna.t2.activities.wsdl.WSDLActivity;	36	import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
36	import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity;	37	import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity;
37	import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity;	38	import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity;
		39	import net.sf.taverna.t2.activities.xpath.XPathActivity;
		40	import net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean;
38	import net.sf.taverna.t2.commandline.CommandLineLauncher;	41	import net.sf.taverna.t2.commandline.CommandLineLauncher;
39	import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;	42	import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
40	import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;	43	import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
41	import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;	44	import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
42	import net.sf.taverna.t2.commandline.exceptions.ReadInputException;	45	import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
	...		...
177	private IApplicationComponent workflowApplicationComponent = null;	180	private IApplicationComponent workflowApplicationComponent = null;
178	private IApplicationFunction callScriptApplicationFunction = null;	181	private IApplicationFunction callScriptApplicationFunction = null;
179	private IApplicationFunction callXMLSplitterApplicationFunction = null;	182	private IApplicationFunction callXMLSplitterApplicationFunction = null;
180	private IApplicationFunction callWebServiceApplicationFunction = null;	183	private IApplicationFunction callWebServiceApplicationFunction = null;
181	private IApplicationFunction callToolInvocationFunction = null;	184	private IApplicationFunction callToolInvocationFunction = null;
		185	private IApplicationFunction callXPathApplicationFunction = null;
182		186
183	private Dataflow dataflow;	187	private Dataflow dataflow;
184	private SSHManager sshManager;	188	private SSHManager sshManager;
185	private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");	189	private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");
186		190
	...		...
204	}	208	}
205		209
206	/*	210	/*
207	* // GETTER & SETTER ///////////////	211	* // GETTER & SETTER ///////////////
208	*/	212	*/
209	public static void setDotLocation(Path dotLocation) {	213	public void setDotLocation(Path dotLocation) {
210	TavernaExtractor.dotLocation = dotLocation;	214	TavernaExtractor.dotLocation = dotLocation;
211	}	215	}
212		216
213	public static Path getDotLocation() {	217	public Path getDotLocation() {
214	return dotLocation;	218	return dotLocation;
215	}	219	}
216		220
217	public static Path getArchimateOutputPath() {	221	public Path getArchimateOutputPath() {
218	return archimateOutputPath;	222	return archimateOutputPath;
219	}	223	}
220		224
221	public static void setArchimateOutputPath(Path archimateOutputPath) {	225	public void setArchimateOutputPath(Path archimateOutputPath) {
222	TavernaExtractor.archimateOutputPath = archimateOutputPath;	226	TavernaExtractor.archimateOutputPath = archimateOutputPath;
223	}	227	}
224		228
225	public static Path getInputFileName() {	229	public Path getInputFileName() {
226	return inputFileName;	230	return inputFileName;
227	}	231	}
228		232
229	public static void setInputFileName(Path inputFileName) {	233	public void setInputFileName(Path inputFileName) {
230	TavernaExtractor.inputFileName = inputFileName;	234	TavernaExtractor.inputFileName = inputFileName;
231	}	235	}
232		236
233	public static Path getTavernaHome() {	237	public Path getTavernaHome() {
234	return tavernaHome;	238	return tavernaHome;
235	}	239	}
236		240
237	public static void setTavernaHome(Path tavernaHome) {	241	public void setTavernaHome(Path tavernaHome) {
238		242
239	TavernaExtractor.tavernaHome = tavernaHome;	243	TavernaExtractor.tavernaHome = tavernaHome;
240	}	244	}
241		245
242	public static Path getTavernaHomeLib() {	246	public Path getTavernaHomeLib() {
243	return tavernaHomeLib;	247	return tavernaHomeLib;
244	}	248	}
245		249
246	public static void setTavernaHomeLib(Path tavernaHomeLib) {	250	public void setTavernaHomeLib(Path tavernaHomeLib) {
247	TavernaExtractor.tavernaHomeLib = tavernaHomeLib;	251	TavernaExtractor.tavernaHomeLib = tavernaHomeLib;
248	}	252	}
249		253
250	public static Path getTavernaHomeRepo() {	254	public Path getTavernaHomeRepo() {
251	return tavernaHomeRepo;	255	return tavernaHomeRepo;
252	}	256	}
253		257
254	public static void setTavernaHomeRepo(Path tavernaHomeRepo) {	258	public void setTavernaHomeRepo(Path tavernaHomeRepo) {
255	TavernaExtractor.tavernaHomeRepo = tavernaHomeRepo;	259	TavernaExtractor.tavernaHomeRepo = tavernaHomeRepo;
256	}	260	}
257		261
258		262
259	public List<IRelationship> getRelations() {	263	public List<IRelationship> getRelations() {
	...		...
279	CMException, IOException, DeserializationException, IterationTypeMismatchException, TavernaExtractorException {	283	CMException, IOException, DeserializationException, IterationTypeMismatchException, TavernaExtractorException {
280		284
281	LOGGER.info("Start Taverna Extractor ...");	285	LOGGER.info("Start Taverna Extractor ...");
282		286
283	//setup	287	//setup
284	TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));	288	this.setTavernaHomeLib(this.getTavernaHome().resolve("lib"));
285	TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));	289	this.setTavernaHomeRepo(this.getTavernaHome().resolve("repository"));
286		290
287	if (remote)	291	if (remote)
288	validateRemoteDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());	292	validateRemoteDirectories(this.getTavernaHome(), this.getTavernaHomeLib(), this.getTavernaHomeRepo());
289	else	293	else
290	validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());	294	validateDirectories(this.getTavernaHome(), this.getTavernaHomeLib(), this.getTavernaHomeRepo());
291		295
292	LOGGER.info("TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");	296	LOGGER.info("TavernaHome is set to [" + this.getTavernaHome() + "].");
293	LOGGER.info("TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");	297	LOGGER.info("TavernaHomeLib is set to [" + this.getTavernaHomeLib() + "].");
294	LOGGER.info("TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");	298	LOGGER.info("TavernaHomeRepo is set to [" + this.getTavernaHomeRepo() + "].");
295	LOGGER.info("Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");	299	LOGGER.info("Workflow input file is [" + this.getInputFileName() + "].");
296	LOGGER.info("Archimate output file is [" + TavernaExtractor.getArchimateOutputPath() + "].");	300	LOGGER.info("Archimate output file is [" + this.getArchimateOutputPath() + "].");
297		301
298	inputPorts = new Container(Orientation.VERTICAL);	302	inputPorts = new Container(Orientation.VERTICAL);
299	outputPorts = new Container(Orientation.VERTICAL);	303	outputPorts = new Container(Orientation.VERTICAL);
300	businessObjects = new Container(Orientation.HORIZONTAL);	304	businessObjects = new Container(Orientation.HORIZONTAL);
301	businessProcesses = new Container(Orientation.HORIZONTAL);	305	businessProcesses = new Container(Orientation.HORIZONTAL);
	...		...
395	workflowFile, applicationFolder, relations, IAccessRelationship.READ_ACCESS);	399	workflowFile, applicationFolder, relations, IAccessRelationship.READ_ACCESS);
396		400
397	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, workflowFile, relationsFolder,	401	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, workflowFile, relationsFolder,
398	relations);	402	relations);
399		403
400	workflowFile.getProperties().add(createDepProperties(TavernaExtractor.getInputFileName().toString()));	404	workflowFile.getProperties().add(createDepProperties(this.getInputFileName().toString()));
401		405
402	// Orchestration Service	406	// Orchestration Service
403	parentProcessWorkflow = ArchiUtils.initElement(factory.createBusinessProcess(), dataflow.getLocalName()	407	parentProcessWorkflow = ArchiUtils.initElement(factory.createBusinessProcess(), dataflow.getLocalName()
404	+ " Process", businessFolder, businessProcesses);	408	+ " Process", businessFolder, businessProcesses);
405	workflowApplicationComponent = ArchiUtils.initElement(factory.createApplicationComponent(),	409	workflowApplicationComponent = ArchiUtils.initElement(factory.createApplicationComponent(),
	...		...
419	relationsFolder, relations);	423	relationsFolder, relations);
420		424
421	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, repoBundle,	425	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, repoBundle,
422	relationsFolder, relations);	426	relationsFolder, relations);
423		427
424	if (TavernaExtractor.getTavernaHomeRepo().toFile().isDirectory()) {	428	if (this.getTavernaHomeRepo().toFile().isDirectory()) {
425		429
426	final List<File> jarFiles = new ArrayList<>();	430	final List<File> jarFiles = new ArrayList<>();
427	final PathMatcher matcher = FileSystems.getDefault()	431	final PathMatcher matcher = FileSystems.getDefault()
428	.getPathMatcher("glob:*.jar");	432	.getPathMatcher("glob:*.jar");
429	Files.walkFileTree(TavernaExtractor.getTavernaHomeRepo(), new FileVisitor<Path>() {	433	Files.walkFileTree(this.getTavernaHomeRepo(), new FileVisitor<Path>() {
430	@Override	434	@Override
431	public FileVisitResult preVisitDirectory(Path path, BasicFileAttributes basicFileAttributes) throws IOException {	435	public FileVisitResult preVisitDirectory(Path path, BasicFileAttributes basicFileAttributes) throws IOException {
432	return CONTINUE;	436	return CONTINUE;
433	}	437	}
434		438
	...		...
455	for (File jarDep : jarFiles) {	459	for (File jarDep : jarFiles) {
456	String jarLocation = jarDep.getAbsolutePath();	460	String jarLocation = jarDep.getAbsolutePath();
457	repoBundle.getProperties().add(createDepProperties(jarLocation));	461	repoBundle.getProperties().add(createDepProperties(jarLocation));
458	}	462	}
459	} else {	463	} else {
460	LOGGER.error("ERROR: " + TavernaExtractor.getTavernaHomeRepo().toFile() + " is not a directory. No further dependecies processing.");	464	LOGGER.error("ERROR: " + this.getTavernaHomeRepo().toFile() + " is not a directory. No further dependecies processing.");
461	}	465	}
462	// --- END Taverna ---	466	// --- END Taverna ---
463		467
464	// --- BEGIN Events ---	468	// --- BEGIN Events ---
465	// Start Event	469	// Start Event
	...		...
928		932
929	// create external application service for each business process/function	933	// create external application service for each business process/function
930	if (callXMLSplitterApplicationFunction == null) {	934	if (callXMLSplitterApplicationFunction == null) {
931		935
932	callXMLSplitterApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),	936	callXMLSplitterApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),
933	"XML Splitter", applicationFolder, applicationComponents);	937	"XML Splitter Built-In Service", applicationFolder, applicationComponents);
934		938
935	ArchiUtils.initRelation(factory.createAssignmentRelationship(), callXMLSplitterApplicationFunction,	939	ArchiUtils.initRelation(factory.createAssignmentRelationship(), callXMLSplitterApplicationFunction,
936	workflowApplicationComponent, relationsFolder, relations);	940	workflowApplicationComponent, relationsFolder, relations);
937		941
938	ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, callXMLSplitterApplicationFunction,	942	ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, callXMLSplitterApplicationFunction,
	...		...
948	relationsFolder, relations);	952	relationsFolder, relations);
949		953
950	ArchiUtils.initRelation(factory.createUsedByRelationship(), callXMLSplitterApplicationFunction,	954	ArchiUtils.initRelation(factory.createUsedByRelationship(), callXMLSplitterApplicationFunction,
951	processorProcessMap.get(processor), relationsFolder, relations);	955	processorProcessMap.get(processor), relationsFolder, relations);
952		956
		957	LOGGER.debug("Get input elements of process "+ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
		958	relations).size());
		959	// creating request response data objects
		960	for (IArchimateElement inputElement : ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
		961	relations)) {
		962
		963	LOGGER.debug("inputElement = "+inputElement.getName());
		964
		965	if (!business2dataMap.containsKey(inputElement)) {
		966
		967	IDataObject requestObject = ArchiUtils.initElement(factory.createDataObject(), inputElement.getName(),
		968	applicationFolder, applicationComponents);
		969
		970	business2dataMap.put((IBusinessObject) inputElement, requestObject);
		971
		972	ArchiUtils.initRelation(factory.createRealisationRelationship(), requestObject, inputElement,
		973	relationsFolder, relations);
		974	}
		975	ArchiUtils.initAccessRelation(factory.createAccessRelationship(), appService,
		976	business2dataMap.get(inputElement), applicationFolder, relations, IAccessRelationship.READ_ACCESS);
		977
		978	}
		979
		980	LOGGER.debug("Get output elements of process "+ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
		981	relations).size());
		982	for (IArchimateElement outputElement : ArchiUtils.getOutputElementsOfProcess(
		983	processorProcessMap.get(processor), relations)) {
		984
		985	LOGGER.debug("inputElement = "+outputElement.getName());
		986
		987	if (!business2dataMap.containsKey(outputElement)) {
		988
		989	IDataObject responseObject = ArchiUtils.initElement(factory.createDataObject(),
		990	outputElement.getName(), applicationFolder, applicationComponents);
		991
		992	ArchiUtils.initRelation(factory.createRealisationRelationship(), responseObject, outputElement,
		993	relationsFolder, relations);
		994
		995	business2dataMap.put((IBusinessObject) outputElement, responseObject);
		996	}
		997
		998	ArchiUtils
		999	.initAccessRelation(factory.createAccessRelationship(), appService,
		1000	business2dataMap.get(outputElement), applicationFolder, relations,
		1001	IAccessRelationship.WRITE_ACCESS);
		1002
		1003	}
		1004	}
		1005
		1006	public void processXPathActivity(IFolder infrastructureFolder, IFolder motivationFolder,
		1007	IFolder applicationFolder, IFolder relationsFolder, IApplicationComponent workflowApplicationComponent,
		1008	HashMap<Processor, IBusinessProcess> processorProcessMap, Processor processor, Activity<?> a)
		1009	throws IOException {
		1010
		1011	//beanshellScripts.add((BeanshellActivity) a);
		1012
		1013	LOGGER.debug("XPath script found = " + processor.getLocalName());
		1014
		1015	//XPathActivity xPathActivity = (XPathActivity) a;
		1016
		1017	// create external application service for each business process/function
		1018	if (callXPathApplicationFunction == null) {
		1019
		1020	callXPathApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),
		1021	"XPath Built-In Service", applicationFolder, applicationComponents);
		1022
		1023	ArchiUtils.initRelation(factory.createAssignmentRelationship(), callXPathApplicationFunction,
		1024	workflowApplicationComponent, relationsFolder, relations);
		1025
		1026	ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, callXPathApplicationFunction,
		1027	relationsFolder, relations);
		1028	}
		1029
		1030	IApplicationService appService = ArchiUtils.initElement(factory.createApplicationService(),
		1031	processor.getLocalName(), applicationFolder, externalApplicationServices);
		1032
		1033	appService.getProperties().add(createDepProperties(BeanshellActivity.class));
		1034
		1035	ArchiUtils.initRelation(factory.createUsedByRelationship(), appService, processorProcessMap.get(processor),
		1036	relationsFolder, relations);
		1037
		1038	ArchiUtils.initRelation(factory.createUsedByRelationship(), callXPathApplicationFunction,
		1039	processorProcessMap.get(processor), relationsFolder, relations);
		1040
953	// IArtifact script = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), processor.getLocalName()	1041	IArtifact script = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), processor.getLocalName()
954	// + "Script", infrastructureFolder, nodeElements);	1042	, infrastructureFolder, nodeElements);
955		1043
		1044	XPathActivityConfigurationBean c = (XPathActivityConfigurationBean) a.getConfiguration();
		1045	String ex = c.getXpathExpression() != null ? c.getXpathExpression() : "NO_EXPRESSION_AVAILABLE";
		1046	String doc = c.getXmlDocument() != null ? c.getXmlDocument() : "NO_XML_DOCUMENT_AVAILABLE";
		1047
		1048	IProperty property = factory.createProperty();
		1049	property.setKey("expression");
		1050	property.setValue(ex);
		1051	script.getProperties().add(property);
		1052
		1053	IProperty property_document = factory.createProperty();
		1054	property_document.setKey("document");
		1055	property_document.setValue(doc);
		1056	script.getProperties().add(property_document);
		1057
956	// ArchiUtils.initRelation(factory.createCompositionRelationship(), workflowFile, script, relationsFolder,	1058	ArchiUtils.initRelation(factory.createCompositionRelationship(), workflowFile, script, relationsFolder,
957	// relations);	1059	relations);
958		1060
959	// ArchiUtils	1061	ArchiUtils
960	// .initRelation(factory.createRealisationRelationship(), script, appService, relationsFolder, relations);	1062	.initRelation(factory.createRealisationRelationship(), script, appService, relationsFolder, relations);
961		1063
962	// creating request response data objects	1064	// creating request response data objects
963	for (IArchimateElement inputElement : ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),	1065	for (IArchimateElement inputElement : ArchiUtils.getInputElementsOfProcess(processorProcessMap.get(processor),
964	relations)) {	1066	relations)) {
965		1067
	...		...
1095	LOGGER.debug("\t Dependency for " + processor.getLocalName() + " [" + item + "]");	1197	LOGGER.debug("\t Dependency for " + processor.getLocalName() + " [" + item + "]");
1096		1198
1097	IArtifact beanshellScriptDep = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), item,	1199	IArtifact beanshellScriptDep = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), item,
1098	infrastructureFolder, nodeElements);	1200	infrastructureFolder, nodeElements);
1099		1201
1100	ArchiUtils.initRelationNodeElement(factory.createAssociationRelationship(), script, beanshellScriptDep,	1202	ArchiUtils.initRelation(factory.createAssociationRelationship(), script, beanshellScriptDep,
1101	relationsFolder, nodeElements);	1203	relationsFolder);
1102		1204
1103	ArchiUtils.initRelationNodeElement(factory.createCompositionRelationship(), beanshellScriptDep, desktop,	1205	ArchiUtils.initRelation(factory.createCompositionRelationship(), beanshellScriptDep, desktop,
1104	relationsFolder, nodeElements);	1206	relationsFolder);
1105		1207
1106	// Do the license checking	1208	// Do the license checking
1107	String fileName = TavernaExtractor.getTavernaHomeLib() + File.separator + item;	1209	String fileName = this.getTavernaHomeLib() + File.separator + item;
1108		1210
1109	IProperty jarLocation = factory.createProperty();	1211	IProperty jarLocation = factory.createProperty();
1110	jarLocation.setKey("hasSourceLocation");	1212	jarLocation.setKey("hasSourceLocation");
1111	jarLocation.setValue(fileName);	1213	jarLocation.setValue(fileName);
1112	beanshellScriptDep.getProperties().add(jarLocation);	1214	beanshellScriptDep.getProperties().add(jarLocation);
	...		...
1757	for (OutputPort outputPort : processor.getOutputPorts()) {	1859	for (OutputPort outputPort : processor.getOutputPorts()) {
1758	outputPorts.add(outputPort);	1860	outputPorts.add(outputPort);
1759	}	1861	}
1760	}	1862	}
1761		1863
		1864	//TODO: needs improvements -> hasNoPrecedentProcessor not working if only one non-constant value processor exists!!
1762	List<Processor> startingProcessors = new ArrayList<Processor>();	1865	List<Processor> startingProcessors = new ArrayList<Processor>();
1763	for (Processor processor : dataflow.getProcessors()) {	1866	for (Processor processor : dataflow.getProcessors()) {
1764		1867
1765	// detect if first step processor	1868	if (ArchiUtils.isValueProcessor(processor)) {
		1869	break;
		1870	}
		1871	else{
		1872	startingProcessors.add(processor);
		1873	}
		1874	}
		1875	if(startingProcessors.size() == 1){
		1876	return startingProcessors;
		1877	}
		1878
		1879	startingProcessors = new ArrayList<Processor>();
		1880	for (Processor processor : dataflow.getProcessors()) {
1766		1881
1767	if (ArchiUtils.isValueProcessor(processor)) {	1882	if (ArchiUtils.isValueProcessor(processor)) {
1768	break;	1883	break;
1769	}	1884	}
1770		1885
	...		...
1842	fw.close();	1957	fw.close();
1843		1958
1844	// Dot to SVG	1959	// Dot to SVG
1845	File svgTmp = new File(tmpDirPath + File.separator + "tavernaExtractorToArchimate.dot.svg");	1960	File svgTmp = new File(tmpDirPath + File.separator + "tavernaExtractorToArchimate.dot.svg");
1846		1961
1847	String[] COMMAND = {TavernaExtractor.getDotLocation().toString(), "-Tsvg", dotTmp.getAbsolutePath(), "-o", svgTmp.getAbsolutePath()};	1962	String[] COMMAND = {this.getDotLocation().toString(), "-Tsvg", dotTmp.getAbsolutePath(), "-o", svgTmp.getAbsolutePath()};
1848		1963
1849	LOGGER.debug("Running command '" + StringUtils.join(COMMAND, " ") + "'.");	1964	LOGGER.debug("Running command '" + StringUtils.join(COMMAND, " ") + "'.");
1850		1965
1851	ProcessBuilder proc = new ProcessBuilder(COMMAND);	1966	ProcessBuilder proc = new ProcessBuilder(COMMAND);
1852	Process process = proc.start();	1967	Process process = proc.start();
	...		...
1965		2080
1966	printPortInformation(processor);	2081	printPortInformation(processor);
1967		2082
1968	// TODO UnrecognizedActivity detected !!	2083	// TODO UnrecognizedActivity detected !!
1969	if (a instanceof UnrecognizedActivity) {	2084	if (a instanceof UnrecognizedActivity) {
1970	LOGGER.error("PROBLEM: UnrecognizedActivity detected! ");	2085	LOGGER.error("\tPROBLEM: UnrecognizedActivity detected! ");
1971	}	2086	}
1972	// TODO DisabledActivity detected !!	2087	// TODO DisabledActivity detected !!
1973	// From the javadoc: A disabled activity is a wrapper for an Activity that is offline or similarly	2088	// From the javadoc: A disabled activity is a wrapper for an Activity that is offline or similarly
1974	// disabled	2089	// disabled
1975	else if (a instanceof DisabledActivity) {	2090	else if (a instanceof DisabledActivity) {
1976	LOGGER.error("PROBLEM: DisabledActivity detected! ");	2091	LOGGER.error("\tPROBLEM: DisabledActivity detected! ");
1977	// TODO: create a note element with information	2092	// TODO: create a note element with information
1978	}	2093	}
1979		2094
1980	// nested worklfow	2095	// nested worklfow
1981	else if (a instanceof DataflowActivity) {	2096	else if (a instanceof DataflowActivity) {
	...		...
2034	workflowApplicationComponent, processorProcessMap, callWebServiceApplicationFunction,	2149	workflowApplicationComponent, processorProcessMap, callWebServiceApplicationFunction,
2035	processor, processorName, a);	2150	processor, processorName, a);
2036	}	2151	}
2037	else if (a instanceof XMLInputSplitterActivity \|\| a instanceof XMLOutputSplitterActivity) {	2152	else if (a instanceof XMLInputSplitterActivity \|\| a instanceof XMLOutputSplitterActivity) {
2038	processXMLSplitterActivity(infrastructureFolder, motivationFolder, applicationFolder,	2153	processXMLSplitterActivity(infrastructureFolder, motivationFolder, applicationFolder,
		2154	relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
		2155	}
		2156	else if (a instanceof XPathActivity){
		2157	LOGGER.info("XPathActivity has to be done");
		2158	processXPathActivity(infrastructureFolder, motivationFolder, applicationFolder,
		2159	relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
		2160	}
		2161	else if (a instanceof LocalworkerActivity){
		2162
		2163	/*
		2164	Localworker Activity equals BeanshellActivity ?!
		2165	*/
		2166	processBeanshellActivity(infrastructureFolder, motivationFolder, applicationFolder,
2039	relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);	2167	relationsFolder, workflowApplicationComponent, processorProcessMap, processor, a);
2040	}	2168	}
2041	else{	2169	else{
2042	LOGGER.debug("Unfortunately, we do not process that kind of activity.");	2170	LOGGER.debug("Unfortunately, we do not process that kind of activity.");
2043	}	2171	}
	...		...
2300	// + ": " + sink.getClass());	2428	// + ": " + sink.getClass());
2301	}	2429	}
2302	}	2430	}
2303	}	2431	}
2304	}	2432	}
2305
2306	}	2433	}
2307		2434
2308	private Dataflow getDataflowRemote() throws TavernaExtractorException {	2435	private Dataflow getDataflowRemote() throws TavernaExtractorException {
2309		2436
2310	try {	2437	try {
	...		...
2353		2480
2354		2481
2355	private void saveRemote(IArchimateModel model) throws TavernaExtractorException {	2482	private void saveRemote(IArchimateModel model) throws TavernaExtractorException {
2356		2483
2357	// Set new file	2484	// Set new file
2358	File outFile = TavernaExtractor.getArchimateOutputPath().toFile();	2485	File outFile = this.getArchimateOutputPath().toFile();
2359	model.setFile(outFile);	2486	model.setFile(outFile);
2360		2487
2361	// Set model version	2488	// Set model version
2362	model.setVersion(ModelVersion.VERSION);	2489	model.setVersion(ModelVersion.VERSION);
2363		2490
	...		...
2402	}	2529	}
2403		2530
2404	private void saveLocal(IArchimateModel model) throws IOException {	2531	private void saveLocal(IArchimateModel model) throws IOException {
2405		2532
2406	// Set new file	2533	// Set new file
2407	File outFile = TavernaExtractor.getArchimateOutputPath().toFile();	2534	File outFile = this.getArchimateOutputPath().toFile();
2408	model.setFile(outFile);	2535	model.setFile(outFile);
2409		2536
2410	// Set model version	2537	// Set model version
2411	model.setVersion(ModelVersion.VERSION);	2538	model.setVersion(ModelVersion.VERSION);
2412		2539