public void importGraph()

in taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/opm/OPMImporter.java [122:245]
71 lines of code
22 McCabe index (conditional complexity)

	public void importGraph(String XMLOPMGraphFilename) throws Exception,
			SQLException {
		try {
			logger.info("Importing OPM XML from file " + XMLOPMGraphFilename);

			// deserialize an XML OPM graph from file
			OPMDeserialiser deser = new OPMDeserialiser();
			graph = deser.deserialiseOPMGraph(new File(XMLOPMGraphFilename));

		} catch (Exception e) {
			logger.fatal("exception while deserializing -- unable to continue");
			logger.fatal(e.getMessage());
			return;
		}

		logger.debug("XML graph deserialized");

		/*
		 * generates one pair <workflowId, workflowRun> for each account in the
		 * graph
		 */
		try {
			Accounts accounts = graph.getAccounts();

			// use this global account alongside any other that may be defined in the graph
			generateWFFromAccount(OPM_DEF_ACCOUNT);

			if (accounts == null) {
				logger.warn("this graph contains no accounts -- using only the default");
			} else {
				for (Account acc:accounts.getAccount())
					// writes both workflow and instance into the DB, updates accountToWorkflow
					generateWFFromAccount(acc.getId());
			}
		} catch (Exception e) {
			logger.warn("exception while getting accounts for this graph");
		}

		// what have we got?
		// retrieve all OPM relations from the graph
		Dependencies dependencies = graph.getDependencies();

		/*
		 * associates processes and ports to workflows and varbindings to
		 * corresponding workflowRuns
		 */
		List<Object> allDeps = dependencies
				.getUsedOrWasGeneratedByOrWasTriggeredBy();
		// make sure these are processed in the right order: used, wgby, THEN wdf because this latter is derived from the first 2!
		// so collect them into sets and process them separately

		Set<WasGeneratedBy> wgbSet = new HashSet<>();
		Set<Used> usedSet = new HashSet<>();
		Set<WasDerivedFrom> wdfSet = new HashSet<>();
		Set<WasControlledBy> wcbSet = new HashSet<>();
		Set<WasTriggeredBy> wtbSet = new HashSet<>();

		for (Object dep : allDeps) {
			logger.info("dependency of type: " + dep.getClass().getName());

			if (dep instanceof org.openprovenance.model.WasGeneratedBy)
				wgbSet.add((WasGeneratedBy) dep);
			else if (dep instanceof org.openprovenance.model.Used)
				usedSet.add((Used) dep);
			else if (dep instanceof org.openprovenance.model.WasDerivedFrom)
				wdfSet.add((WasDerivedFrom) dep);
			else if (dep instanceof org.openprovenance.model.WasControlledBy)
				wcbSet.add((WasControlledBy) dep);
			else if (dep instanceof org.openprovenance.model.WasTriggeredBy)
				wtbSet.add((WasTriggeredBy) dep);
		}

		// process these in the correct order
		for (WasGeneratedBy dep: wgbSet)
			processWGBy(dep);

		for (Used dep : usedSet)
			processUsed(dep);

		for (WasDerivedFrom dep : wdfSet)
			processWDF(dep);

		// we actually ignore the others...

		// *********
		// complete the induced graph by building datalinks using the Artifact -> [Port] maps
		// *********

		List<String> accountNames = new ArrayList<>();

		accountNames.add(OPM_DEF_ACCOUNT);

		/* Disabled as allAccounts is never assigned to
		if (allAccounts != null)
			for (Account acc:allAccounts) { accountNames.add(acc.getId()); }
		*/

		for (String acc : accountNames) {
			String workflowId = accountToWorkflow.get(acc);

			Map<String, List<Port>> usedVars = usedVarsByAccount
					.get(workflowId);
			Map<String, List<Port>> wgbVars = wgbVarsByAccount.get(workflowId);

			if (usedVars == null || wgbVars == null)
				continue;

			// install an Datalink from each wgb var to each used var when the artifact is the same
			for (Map.Entry<String, List<Port>> entry : wgbVars.entrySet()) {
				// all Ports for this artifact get connected to all corresponding Ports in used
				List<Port> sourceVars = entry.getValue();
				List<Port> targetVars = usedVars.get(entry.getKey());

				if (sourceVars == null || targetVars == null)
					continue;

				// create an datalink from each sourceVar to each targetVar
				// note that we expect a single targetVar, but this is not guaranteed
				for (Port sourceVar : sourceVars)
					for (Port targetVar : targetVars)
						pw.addDataLink(sourceVar, targetVar, workflowId);
			}
		}
	}