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 [55846c] .. [d30f7f]

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import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
import net.sf.taverna.t2.workflowmodel.processor.activity.UnrecognizedActivity;
import net.sf.taverna.t2.workflowmodel.processor.iteration.IterationTypeMismatchException;
import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;

import net.timbusproject.extractors.modules.tavernaextractor.utils.*;
import net.timbusproject.extractors.modules.tavernaextractor.utils.Container;
import net.timbusproject.extractors.modules.tavernaextractor.utils.Container.Orientation;
import org.apache.batik.swing.JSVGCanvas;
import org.apache.commons.lang.StringUtils;
...
import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.eclipse.emf.common.util.URI;
import org.eclipse.emf.ecore.resource.Resource;
import org.eclipse.emf.ecore.resource.ResourceSet;


import org.osgi.service.log.LogService;
import org.sbaresearch.licensecheck.LicenseCheck;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
import uk.ac.bolton.archimate.editor.model.viewpoints.IViewpoint;
import uk.ac.bolton.archimate.model.*;
import uk.ac.bolton.archimate.model.impl.BusinessEvent;
...

/**
 * @author Rudolf Mayer (rmayer@sba-research.org)
 * @author Marco Unterberger (munterberger@sba-research.org)
 */
public class TavernaExtractor extends CommandLineLauncher {

    private IArchimateFactory factory;
    private Map<String, IDiagramModelArchimateObject> elementModelObjectMap;
    private List<IRelationship> relations;
    private IArchimateDiagramModel layeredView;
...
    private IApplicationFunction callScriptApplicationFunction = null;
    private IApplicationFunction callWebServiceApplicationFunction = null;
    private IApplicationFunction callToolInvocationFunction = null;

    private Dataflow dataflow;

    private SSHManager sshManager;
    private Logger LOGGER = LoggerFactory.getLogger(TavernaExtractor.class);






    public TavernaExtractor(){}

    public TavernaExtractor(boolean verbose) {

    }

    public TavernaExtractor(SSHManager sshManager) {
        this.sshManager = sshManager;
    }
...
        return this.businessProcesses.getElements();
    }

    public List<IArchimateElement> getBusinessObjects() {
        return this.businessObjects.getElements();







































































    }

    /*
     * // Transform a Taverna (t2flow) file to an Archimate file ///////////////
     */
    public void process() throws EditException, OpenDataflowException, InvalidOptionException,
            InvalidDataflowException, TokenOrderException, ReadInputException, DatabaseConfigurationException,
            CMException, IOException, DeserializationException, IterationTypeMismatchException {

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

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

        validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());

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

        inputPorts = new Container(Orientation.VERTICAL);
        outputPorts = new Container(Orientation.VERTICAL);
        businessObjects = new Container(Orientation.HORIZONTAL);
        businessProcesses = new Container(Orientation.HORIZONTAL);
...

            if (file.exists()) {
                    workflowURL = file.toURI().toURL();
            }

            LOGGER.info( "Reading workflow from " + workflowURL);
            dataflow = openDataflow(workflowURL);
        } catch (NullPointerException npe) {
            npe.printStackTrace();
            LOGGER.error( "ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());
            return;
        }

        // current classpath
        String classpath = System.getProperty("java.class.path");
...
                String jarLocation = jarDep.getAbsolutePath();
                repoBundle.getProperties().add(createDepProperties(jarLocation));
            }
         }
        else{
            LOGGER.error( "ERROR: "+TavernaExtractor.getTavernaHomeRepo().toFile()+" is not a directory. No further dependecies processing.");
        }
        // --- END Taverna ---

        // --- BEGIN Events ---
        // Start Event
...
                OS_SYSTEM_INFO, infrastructureFolder, nodeElements);
        ArchiUtils.initRelationNodeElement(factory.createUsedByRelationship(), operatingSystem, java, relationsFolder,
                nodeElements);
        // --- END CREATING DEFAULT ELEMENTS ---

        LOGGER.debug("Process Input ports");
        for (DataflowInputPort inputPort : dataflow.getInputPorts()) {
            IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(), inputPort.getName(),
                    businessFolder, inputPorts);
            IDataObject port_data = ArchiUtils.initElement(factory.createDataObject(), inputPort.getName(),
                    applicationFolder, dataObjects);
...
            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_data, port_business, relationsFolder,
                    relations);
            ArchiUtils.initRelation(factory.createRealisationRelationship(), port_infrastructure, port_data,
                    relationsFolder, relations);
        }
        LOGGER.debug("Process Output ports");
        for (DataflowOutputPort outputPort : dataflow.getOutputPorts()) {
            IBusinessObject port_business = ArchiUtils.initElement(factory.createBusinessObject(),
                    outputPort.getName(), businessFolder, outputPorts);
            IDataObject port_data = ArchiUtils.initElement(factory.createDataObject(), outputPort.getName(),
                    applicationFolder, dataObjects);
...
        //sshManager.send(...);

        resource.getContents().add(model);
        resource.save(null);

        LOGGER.info( "Wrote model successfully to " + outFile.getAbsolutePath());
    }

    public void processWebServiceActivity(IFolder businessFolder, IFolder infrastructureFolder,
                                          IFolder applicationFolder, IFolder relationsFolder, IApplicationComponent workflowApplicationComponent,
                                          HashMap<Processor, IBusinessProcess> processorProcessMap,
...
        String type = null;
        IProperty prop = factory.createProperty();
        IProperty locationProp = factory.createProperty();
        if (a instanceof WSDLActivity) {

            LOGGER.debug("WSDL Service found = " + processor.getLocalName());
            type = "SOAP";
            WSDLActivity wsdlActivity = (WSDLActivity) a;
            prop.setKey("WSDL_Location");
            prop.setValue(wsdlActivity.getConfiguration().getWsdl());
            externalNode.getProperties().add(prop);
...
            locationProp = createDepProperties(WSDLActivity.class);
        }

        if (a instanceof RESTActivity) {

            LOGGER.debug("RESTful Service found = " + processor.getLocalName());
            type = "HTTP";
            RESTActivity restActivity = (RESTActivity) a;
            prop.setKey("URL");
            prop.setValue(restActivity.getConfiguration().getUrlSignature());
            externalNode.getProperties().add(prop);
...
                                      HashMap<Processor, IBusinessProcess> processorProcessMap,
                                      IApplicationFunction callWebServiceApplicationFunction, Processor processor, String processorName,
                                      Activity<?> a) {

        if (!(a instanceof RshellActivity)) {
            LOGGER.info( "Activity [" + a + "] is not an instance of RshellActivity. Stop further processing!");
            return;
        }

        RshellActivity rshellActivity = (RshellActivity) a;

...
                                    HashMap<Processor, IBusinessProcess> processorProcessMap,
                                    IApplicationFunction callWebServiceApplicationFunction, Processor processor, String processorName,
                                    Activity<?> a, boolean isExternal) {

        if (!(a instanceof ExternalToolActivity)) {
            LOGGER.info( "Activity [" + a + "] is not an instance of ExternalToolActivity. Stop further processing!");
            return;
        }

        ExternalToolActivity externalInvocation = (ExternalToolActivity) a;

...
                                         IFolder applicationFolder, IFolder relationsFolder, IApplicationComponent workflowApplicationComponent,
                                         HashMap<Processor, IBusinessProcess> processorProcessMap, Processor processor, Activity<?> a)
            throws IOException {
        beanshellScripts.add((BeanshellActivity) a);

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

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

            callScriptApplicationFunction = ArchiUtils.initElement(factory.createApplicationFunction(),
...
            Iterator<String> iter = conf.getLocalDependencies().iterator();
            while (iter.hasNext()) {

                String item = iter.next();

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

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

                ArchiUtils.initRelationNodeElement(factory.createAssociationRelationship(), script, beanshellScriptDep,
...
                Path pathToDep = Paths.get(fileName);
                if (Files.exists(pathToDep)) {
                    String license = licenseCheck.extract(pathToDep.toAbsolutePath().toString());

                    if (license.equals("Unknown license")) {
                        LOGGER.debug("\t Unknown license for dependency [" + item + "].");
                    }

                    if (license != null && !license.equals("Unknown license")) {

                        LOGGER.debug("\t Found license [" + license + "] for dependency [" + item + "].");

                        // create constraint element for dependency
                        IConstraint licenseConstraint = ArchiUtils.initElement(factory.createConstraint(), license,
                                motivationFolder, infrastructure);

                        ArchiUtils.initRelation(factory.createRealisationRelationship(), beanshellScriptDep,
                                licenseConstraint, relationsFolder, relations);
                    }
                } else {
                    LOGGER.error( "\t ERROR: Jar file [" + fileName + "] not found!");
                }
            }
        }
    }

...
        }

        externalInfrastructureModelGroup.setBounds(0, starting_y, overall_X, 150);
        overall_Y += 150;

        LOGGER.debug("drawExternalInfrastructureServices.getElements().size() = "
                + infrastructureServices.getElements().size());

        Map<String, int[]> boundsMap = ArchiLayoutUtils.getBoundsForElements(infrastructureServices.getElements(),
                infrastructureServices.orientation);
        for (IArchimateElement element : infrastructureServices.getElements()) {
...
            }
            if (relation.getTarget() == null) {
                return;
            }

            LOGGER.debug("drawing relation [" + relation.getSource().getName() + "("
                    + relation.getSource().eClass().getName() + ")] --> [" + relation.getTarget().getName() + "("
                    + relation.getTarget().eClass().getName() + ")]");

            IDiagramModelArchimateObject source = elementModelObjectMap.get(relation.getSource().getId());
            IDiagramModelArchimateObject target = elementModelObjectMap.get(relation.getTarget().getId());
...

        for (IArchimateElement element : layout.getGraph().getVertices()) {

            int x = (int) ((AbstractLayout<IArchimateElement, IArchimateElement>) layout).getX(element);
            int y = (int) ((AbstractLayout<IArchimateElement, IArchimateElement>) layout).getY(element);
            LOGGER.debug(element.getName() + "[" + x + "][" + y + "]");
            items.put(element, new Point(x, y));
        }
        return items;
    }

...
            portProperty.setKey("Port");
            portProperty.setValue(document.selectSingleNode("//port").getText());
            props.add(portProperty);

        } catch (DocumentException e) {
            LOGGER.error( "ERROR parsing external tool invocation mechanism. " + e.getMessage());
        }

        IProperty commandProperty = factory.createProperty();
        commandProperty.setKey("Command");
        commandProperty.setValue(configuration.getUseCaseDescription().getCommand());
...

    private void printPortInformation(Processor processor) {

        if (processor != null) {
            for (ProcessorInputPort inputPort : processor.getInputPorts()) {
                LOGGER.debug("--> Port = " + inputPort.getName() + "[depth = " + inputPort.getDepth() + "]");
            }
            for (ProcessorOutputPort outputPort : processor.getOutputPorts()) {
                LOGGER.debug("<-- Port = " + outputPort.getName() + "[depth = " + outputPort.getDepth() + "]");
            }
        }
    }

    private List<Processor> findStartingProcessors(Dataflow dataflow) {
...
            if (ArchiUtils.isValueProcessor(processor)) {
                break;
            }

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

            // detect if first step processor
            if (hasNoSucceedProcessor(processor, inputPorts)) {
                LOGGER.debug("Processor '" + processor.getLocalName() + "' has no succeed processors.");
                endingProcessors.add(processor);
            }
        }
        return endingProcessors;
    }
...
            // Dot to SVG
            File svgTmp = new File(tmpDirPath + File.separator + "tavernaExtractorToArchimate.dot.svg");

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

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

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

            InputStream stderr = process.getErrorStream();
...
            try {
                Integer x = (int) Math.abs(Double.parseDouble(nodeList.item(i).getTextContent()));
                Integer y = (int) Math.abs(Double.parseDouble(nodeList.item(i + 1).getTextContent()));
                map.put(key, new Point(x, y));
            } catch (NumberFormatException nfe) {
                LOGGER.error( "ERROR: Unable to convert to integer. " + nfe.getMessage());
                map.put(key, new Point(1, 1));
            }
        }

        for (Entry<String, Point> entry : map.entrySet()) {
...

            String processorName = processor.getLocalName();

            for (Activity<?> a : processor.getActivityList()) {

                LOGGER.debug(processorName + " [" + processor.getActivityList().size() + "] -> "
                        + a.getClass().getName());

                printPortInformation(processor);

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

                // nested worklfow
                if (a instanceof DataflowActivity) {
...
        for (Processor processor : dataflow.getProcessors()) {
            boolean isValueProcessor = ArchiUtils.isValueProcessor(processor);

            for (ProcessorOutputPort processorOutputPort : processor.getOutputPorts()) {

                LOGGER.debug("Process processorOutputPort = '" + processorOutputPort.getName() + "'");

                for (Datalink datalink : processorOutputPort.getOutgoingLinks()) {

                    EventHandlingInputPort sink = datalink.getSink();

...
                                IOrJunction mergeJunction = loopsJunctions.get(processor);

                                ArchiUtils.initRelation(factory.createTriggeringRelationship(), mergeJunction,
                                        splitJunction, relationsFolder, relations);

                                LOGGER.debug("loop detected between [" + startProcessor.getLocalName() + "] --> ["
                                        + processor.getLocalName() + "]");
                            }
                        }

                        Processor targetProcessor = ((ProcessorInputPortImpl) sink).getProcessor();
...

                            // 2. create business object
                            IBusinessObject businessObject = ArchiUtils.initElement(factory.createBusinessObject(),
                                    sink.getName(), businessFolder, businessObjects);

                            LOGGER.debug("\t BusinessObject for datalink '" + datalink.getSource().getName() + " -> "
                                    + sink.getName() + "' created.");

                            if (processorObjectMapping.get(processor) == null) {
                                processorObjectMapping.put(processor, new ArrayList<IBusinessObject>());
                            }