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 [ec30ce] .. [dc6df6]

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...

    private List<IArchimateElement> nodeElements;
    //private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");
    private LicenseCheck licenseCheck = new LicenseCheck();
    private IArtifact workflowFile;
    private ISystemSoftware taverna;
    private IApplicationComponent workflowApplicationComponent = null;
    private IApplicationFunction callScriptApplicationFunction = null;
    private IApplicationFunction callWebServiceApplicationFunction = null;
    private IApplicationFunction callToolInvocationFunction = null;

...

        infrastructure.getElements().add(desktop);

        // // BEGIN PATTERN v2.0 UPDATE
        // --- BEGIN Taverna ---
        taverna = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(), "Taverna 2.4", infrastructureFolder,
                nodeElements);
        IConstraint GNULicense = ArchiUtils.initElement(factory.createConstraint(),
                "GNU Lesser General Public License (LGPL) 2.1", motivationFolder, infrastructure);
        ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, GNULicense, relationsFolder,
                relations);
        ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, taverna, relationsFolder,
                relations);

        // Workflow file
        workflowFile = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Worfklow File",
                infrastructureFolder, nodeElements);
        ArchiUtils.initAccessRelation(factory.createAccessRelationship(), taverna,
                workflowFile, applicationFolder, relations, IAccessRelationship.READ_ACCESS);

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

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

        // Orchestration Service
...
        }

        // link relevant dependencies from taverna home to context model
        IArtifact repoBundle = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Repo Bundle", infrastructureFolder, nodeElements);
        ArchiUtils.initRelation(factory.createAssociationRelationship(), taverna, repoBundle,
                relationsFolder, relations);

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

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

            final List<File> jarFiles = new ArrayList<>();
...
        // --- END Events ---

        // --- BEGIN Java Runtime Environment ---
        ISystemSoftware java = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(), "JRE "
                + JAVA_VERSION + " (" + JAVA_VENDOR + ")", infrastructureFolder, nodeElements);

        // FIXME: this must not always be an ORACLE license
        IConstraint oracleLicense = ArchiUtils.initElement(factory.createConstraint(), "Oracle Binary Code License",
                motivationFolder, infrastructure);
        ArchiUtils.initRelation(factory.createRealisationRelationship(), java, oracleLicense, relationsFolder,
                relations);
        ArchiUtils.initRelation(factory.createUsedByRelationship(), java, taverna, relationsFolder, relations);
        ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, java, relationsFolder, relations);

        // --- BEGIN OS ---
        ISystemSoftware operatingSystem = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(),
                OS_SYSTEM_INFO, infrastructureFolder, nodeElements);
        ArchiUtils.initRelationNodeElement(factory.createUsedByRelationship(), operatingSystem, java, relationsFolder,
                nodeElements);
        ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, operatingSystem, relationsFolder, relations);
        // --- END CREATING DEFAULT ELEMENTS ---

        LOGGER.debug("Process Input ports");
        for (DataflowInputPort inputPort : dataflow.getInputPorts()) {
            IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(), inputPort.getName(),
...

            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,
                    relations);
            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,
                    relationsFolder, relations);

            ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, port_infrastructure,
                    relationsFolder, relations);
        }
        LOGGER.debug("Process Output ports");
        for (DataflowOutputPort outputPort : dataflow.getOutputPorts()) {
            IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(),
                    outputPort.getName(), businessFolder, outputPorts);
...

            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,
                    relations);
            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,
                    relationsFolder, relations);

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

        processorProcessMap = new HashMap<Processor, IBusinessProcess>();
        processorValueMap = new HashMap<Processor, IBusinessObject>();

...
                    infrastructureFolder, nodeElements);

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

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

            IProperty commandProperty = factory.createProperty();
            commandProperty.setKey("Command");
            commandProperty.setValue(externalInvocation.getConfiguration().getUseCaseDescription().getCommand());
            toolAsArtifact.getProperties().add(commandProperty);
        }
...

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

                ArchiUtils.initRelationNodeElement(factory.createAssociationRelationship(), script, beanshellScriptDep,
                        relationsFolder, nodeElements);

                ArchiUtils.initRelationNodeElement(factory.createCompositionRelationship(), beanshellScriptDep,desktop,
                        relationsFolder, nodeElements);

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

...
        }
    }

    private List<Processor> findStartingProcessors(Dataflow dataflow) {

        LOGGER.debug("find starting processors");

        List<OutputPort> outputPorts = new ArrayList<OutputPort>();
        for (Processor processor : dataflow.getProcessors()) {
            for (OutputPort outputPort : processor.getOutputPorts()) {
                outputPorts.add(outputPort);
            }
...
            if (hasNoPrecedentProcessor(processor, outputPorts)) {
                LOGGER.debug("Processor '" + processor.getLocalName() + "' has no precendent processors.");
                startingProcessors.add(processor);
            }
        }

        LOGGER.debug(startingProcessors.size()+" starting processors found");

        return startingProcessors;
    }

    private List<Processor> findEndProcessors(Dataflow dataflow) {


	a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java		b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java
	...		...
169		169
170	private List<IArchimateElement> nodeElements;	170	private List<IArchimateElement> nodeElements;
171	//private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");	171	//private static Logger LOGGER = LogManager.getLogger("TavernaExtractor");
172	private LicenseCheck licenseCheck = new LicenseCheck();	172	private LicenseCheck licenseCheck = new LicenseCheck();
173	private IArtifact workflowFile;	173	private IArtifact workflowFile;
174	private IArtifact taverna;	174	private ISystemSoftware taverna;
175	private IApplicationComponent workflowApplicationComponent = null;	175	private IApplicationComponent workflowApplicationComponent = null;
176	private IApplicationFunction callScriptApplicationFunction = null;	176	private IApplicationFunction callScriptApplicationFunction = null;
177	private IApplicationFunction callWebServiceApplicationFunction = null;	177	private IApplicationFunction callWebServiceApplicationFunction = null;
178	private IApplicationFunction callToolInvocationFunction = null;	178	private IApplicationFunction callToolInvocationFunction = null;
179		179
	...		...
374		374
375	infrastructure.getElements().add(desktop);	375	infrastructure.getElements().add(desktop);
376		376
377	// // BEGIN PATTERN v2.0 UPDATE	377	// // BEGIN PATTERN v2.0 UPDATE
378	// --- BEGIN Taverna ---	378	// --- BEGIN Taverna ---
379	taverna = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Taverna 2.4", infrastructureFolder,	379	taverna = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(), "Taverna 2.4", infrastructureFolder,
380	nodeElements);	380	nodeElements);
381	IConstraint GNULicense = ArchiUtils.initElement(factory.createConstraint(),	381	IConstraint GNULicense = ArchiUtils.initElement(factory.createConstraint(),
382	"GNU Lesser General Public License (LGPL) 2.1", motivationFolder, infrastructure);	382	"GNU Lesser General Public License (LGPL) 2.1", motivationFolder, infrastructure);
383	ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, GNULicense, relationsFolder,	383	ArchiUtils.initRelation(factory.createRealisationRelationship(), taverna, GNULicense, relationsFolder,
384	relations);	384	relations);
		385	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, taverna, relationsFolder,
		386	relations);
385		387
386	// Workflow file	388	// Workflow file
387	workflowFile = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Worfklow File",	389	workflowFile = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Worfklow File",
388	infrastructureFolder, nodeElements);	390	infrastructureFolder, nodeElements);
		391	ArchiUtils.initAccessRelation(factory.createAccessRelationship(), taverna,
		392	workflowFile, applicationFolder, relations, IAccessRelationship.READ_ACCESS);
		393
389	ArchiUtils.initRelation(factory.createAssociationRelationship(), workflowFile, taverna, relationsFolder,	394	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, workflowFile, relationsFolder,
390	relations);	395	relations);
391		396
392	workflowFile.getProperties().add(createDepProperties(TavernaExtractor.getInputFileName().toString()));	397	workflowFile.getProperties().add(createDepProperties(TavernaExtractor.getInputFileName().toString()));
393		398
394	// Orchestration Service	399	// Orchestration Service
	...		...
406	}	411	}
407		412
408	// link relevant dependencies from taverna home to context model	413	// link relevant dependencies from taverna home to context model
409	IArtifact repoBundle = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Repo Bundle", infrastructureFolder, nodeElements);	414	IArtifact repoBundle = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), "Repo Bundle", infrastructureFolder, nodeElements);
410	ArchiUtils.initRelation(factory.createAssociationRelationship(), taverna, repoBundle,	415	ArchiUtils.initRelation(factory.createAssociationRelationship(), taverna, repoBundle,
		416	relationsFolder, relations);
		417
		418	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, repoBundle,
411	relationsFolder, relations);	419	relationsFolder, relations);
412		420
413	if(TavernaExtractor.getTavernaHomeRepo().toFile().isDirectory()){	421	if(TavernaExtractor.getTavernaHomeRepo().toFile().isDirectory()){
414		422
415	final List<File> jarFiles = new ArrayList<>();	423	final List<File> jarFiles = new ArrayList<>();
	...		...
462	// --- END Events ---	470	// --- END Events ---
463		471
464	// --- BEGIN Java Runtime Environment ---	472	// --- BEGIN Java Runtime Environment ---
465	ISystemSoftware java = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(), "JRE "	473	ISystemSoftware java = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(), "JRE "
466	+ JAVA_VERSION + " (" + JAVA_VENDOR + ")", infrastructureFolder, nodeElements);	474	+ JAVA_VERSION + " (" + JAVA_VENDOR + ")", infrastructureFolder, nodeElements);
		475
467	// FIXME: this must not always be an ORACLE license	476	// FIXME: this must not always be an ORACLE license
468	IConstraint oracleLicense = ArchiUtils.initElement(factory.createConstraint(), "Oracle Binary Code License",	477	IConstraint oracleLicense = ArchiUtils.initElement(factory.createConstraint(), "Oracle Binary Code License",
469	motivationFolder, infrastructure);	478	motivationFolder, infrastructure);
470	ArchiUtils.initRelation(factory.createRealisationRelationship(), java, oracleLicense, relationsFolder,	479	ArchiUtils.initRelation(factory.createRealisationRelationship(), java, oracleLicense, relationsFolder,
471	relations);	480	relations);
472	ArchiUtils.initRelation(factory.createUsedByRelationship(), java, taverna, relationsFolder, relations);	481	ArchiUtils.initRelation(factory.createUsedByRelationship(), java, taverna, relationsFolder, relations);
		482	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, java, relationsFolder, relations);
473		483
474	// --- BEGIN OS ---	484	// --- BEGIN OS ---
475	ISystemSoftware operatingSystem = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(),	485	ISystemSoftware operatingSystem = (ISystemSoftware) ArchiUtils.initElement(factory.createSystemSoftware(),
476	OS_SYSTEM_INFO, infrastructureFolder, nodeElements);	486	OS_SYSTEM_INFO, infrastructureFolder, nodeElements);
477	ArchiUtils.initRelationNodeElement(factory.createUsedByRelationship(), operatingSystem, java, relationsFolder,	487	ArchiUtils.initRelationNodeElement(factory.createUsedByRelationship(), operatingSystem, java, relationsFolder,
478	nodeElements);	488	nodeElements);
		489	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, operatingSystem, relationsFolder, relations);
479	// --- END CREATING DEFAULT ELEMENTS ---	490	// --- END CREATING DEFAULT ELEMENTS ---
480		491
481	LOGGER.debug("Process Input ports");	492	LOGGER.debug("Process Input ports");
482	for (DataflowInputPort inputPort : dataflow.getInputPorts()) {	493	for (DataflowInputPort inputPort : dataflow.getInputPorts()) {
483	IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(), inputPort.getName(),	494	IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(), inputPort.getName(),
	...		...
491		502
492	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,	503	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,
493	relations);	504	relations);
494	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,	505	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,
495	relationsFolder, relations);	506	relationsFolder, relations);
		507
		508	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, port_infrastructure,
		509	relationsFolder, relations);
496	}	510	}
497	LOGGER.debug("Process Output ports");	511	LOGGER.debug("Process Output ports");
498	for (DataflowOutputPort outputPort : dataflow.getOutputPorts()) {	512	for (DataflowOutputPort outputPort : dataflow.getOutputPorts()) {
499	IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(),	513	IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(),
500	outputPort.getName(), businessFolder, outputPorts);	514	outputPort.getName(), businessFolder, outputPorts);
	...		...
507		521
508	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,	522	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,
509	relations);	523	relations);
510	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,	524	ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,
511	relationsFolder, relations);	525	relationsFolder, relations);
		526
		527	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, port_infrastructure,
		528	relationsFolder, relations);
512	}	529	}
513		530
514	processorProcessMap = new HashMap<Processor, IBusinessProcess>();	531	processorProcessMap = new HashMap<Processor, IBusinessProcess>();
515	processorValueMap = new HashMap<Processor, IBusinessObject>();	532	processorValueMap = new HashMap<Processor, IBusinessObject>();
516		533
	...		...
888	infrastructureFolder, nodeElements);	905	infrastructureFolder, nodeElements);
889		906
890	ArchiUtils.initRelation(factory.createRealisationRelationship(), toolAsArtifact, appService,	907	ArchiUtils.initRelation(factory.createRealisationRelationship(), toolAsArtifact, appService,
891	relationsFolder, relations);	908	relationsFolder, relations);
892		909
		910	ArchiUtils.initRelation(factory.createCompositionRelationship(), desktop, toolAsArtifact,
		911	relationsFolder, relations);
		912
893	IProperty commandProperty = factory.createProperty();	913	IProperty commandProperty = factory.createProperty();
894	commandProperty.setKey("Command");	914	commandProperty.setKey("Command");
895	commandProperty.setValue(externalInvocation.getConfiguration().getUseCaseDescription().getCommand());	915	commandProperty.setValue(externalInvocation.getConfiguration().getUseCaseDescription().getCommand());
896	toolAsArtifact.getProperties().add(commandProperty);	916	toolAsArtifact.getProperties().add(commandProperty);
897	}	917	}
	...		...
993		1013
994	IArtifact beanshellScriptDep = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), item,	1014	IArtifact beanshellScriptDep = (IArtifact) ArchiUtils.initElement(factory.createArtifact(), item,
995	infrastructureFolder, nodeElements);	1015	infrastructureFolder, nodeElements);
996		1016
997	ArchiUtils.initRelationNodeElement(factory.createAssociationRelationship(), script, beanshellScriptDep,	1017	ArchiUtils.initRelationNodeElement(factory.createAssociationRelationship(), script, beanshellScriptDep,
		1018	relationsFolder, nodeElements);
		1019
		1020	ArchiUtils.initRelationNodeElement(factory.createCompositionRelationship(), beanshellScriptDep,desktop,
998	relationsFolder, nodeElements);	1021	relationsFolder, nodeElements);
999		1022
1000	// Do the license checking	1023	// Do the license checking
1001	String fileName = TavernaExtractor.getTavernaHomeLib() + File.separator + item;	1024	String fileName = TavernaExtractor.getTavernaHomeLib() + File.separator + item;
1002		1025
	...		...
1642	}	1665	}
1643	}	1666	}
1644		1667
1645	private List<Processor> findStartingProcessors(Dataflow dataflow) {	1668	private List<Processor> findStartingProcessors(Dataflow dataflow) {
1646		1669
		1670	LOGGER.debug("find starting processors");
		1671
1647	List<OutputPort> outputPorts = new ArrayList<OutputPort>();	1672	List<OutputPort> outputPorts = new ArrayList<OutputPort>();
1648	for (Processor processor : dataflow.getProcessors()) {	1673	for (Processor processor : dataflow.getProcessors()) {
1649	for (OutputPort outputPort : processor.getOutputPorts()) {	1674	for (OutputPort outputPort : processor.getOutputPorts()) {
1650	outputPorts.add(outputPort);	1675	outputPorts.add(outputPort);
1651	}	1676	}
	...		...
1663	if (hasNoPrecedentProcessor(processor, outputPorts)) {	1688	if (hasNoPrecedentProcessor(processor, outputPorts)) {
1664	LOGGER.debug("Processor '" + processor.getLocalName() + "' has no precendent processors.");	1689	LOGGER.debug("Processor '" + processor.getLocalName() + "' has no precendent processors.");
1665	startingProcessors.add(processor);	1690	startingProcessors.add(processor);
1666	}	1691	}
1667	}	1692	}
		1693
		1694	LOGGER.debug(startingProcessors.size()+" starting processors found");
		1695
1668	return startingProcessors;	1696	return startingProcessors;
1669	}	1697	}
1670		1698
1671	private List<Processor> findEndProcessors(Dataflow dataflow) {	1699	private List<Processor> findEndProcessors(Dataflow dataflow) {
1672		1700