Examples with CmdGenerateReport org.eol.globi.tool.CmdGenerateReport used on opensource projects

Example 1 with CmdGenerateReport

use of org.eol.globi.tool.CmdGenerateReport in project eol-globi-data by jhpoelen.

the class Elton4N method importWithVersion.

private void importWithVersion(CommandLine cmdLine, String neo4jVersion) throws StudyImporterException {
    final String graphDbDirPath = cmdLine.getOptionValue(CmdOptionConstants.OPTION_GRAPHDB_DIR, "graph.db");
    Factories factoriesNeo4j = new Factories() {

        final GraphServiceFactory factory = new GraphServiceFactoryImpl(new File(graphDbDirPath));

        final NodeFactoryFactory nodeFactoryFactory = StringUtils.equals("2", neo4jVersion) ? new NodeFactoryFactoryTransactingOnDatasetNeo4j2(factory) : new NodeFactoryFactoryTransactingOnDatasetNeo4j3(factory);

        @Override
        public GraphServiceFactory getGraphServiceFactory() {
            return factory;
        }

        @Override
        public NodeFactoryFactory getNodeFactoryFactory() {
            return nodeFactoryFactory;
        }
    };
    try {
        String datasetDir = CmdUtil.getDatasetDir(cmdLine);
        GraphServiceFactory graphServiceFactory = factoriesNeo4j.getGraphServiceFactory();
        List<Cmd> steps = new ArrayList<>();
        LOG.info("processing steps: [" + StringUtils.join(cmdLine.getArgList(), ", ") + "]");
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_COMPILE)) {
            steps.add(new CmdImportDatasets(factoriesNeo4j.getNodeFactoryFactory(), graphServiceFactory, datasetDir));
        }
        String exportDir = cmdLine.getOptionValue(CmdOptionConstants.OPTION_EXPORT_DIR, ".");
        CmdInterpretTaxa interpretTaxa = createInterpretTaxaCmd(cmdLine, graphServiceFactory, exportDir);
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_LINK_NAMES)) {
            steps.add(interpretTaxa);
        }
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_LINK)) {
            if (!steps.contains(interpretTaxa)) {
                steps.add(interpretTaxa);
            }
            steps.addAll(Arrays.asList(new CmdIndexTaxa(graphServiceFactory), new CmdIndexTaxonStrings(graphServiceFactory), new CmdGenerateReport(graphServiceFactory.getGraphService())));
        }
        CmdExportInteractionsTSV interactionsTSVExporter = new CmdExportInteractionsTSV(graphServiceFactory, new File(exportDir));
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_PACKAGE_INTERACTIONS_TSV)) {
            steps.add(interactionsTSVExporter);
        }
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_PACKAGE)) {
            if (!steps.contains(interactionsTSVExporter)) {
                steps.add(interactionsTSVExporter);
            }
            steps.add(new CmdExport(graphServiceFactory, new File(exportDir)));
        }
        for (Cmd step : steps) {
            step.run();
        }
    } finally {
        HttpUtil.shutdown();
    }
}

Example 2 with CmdGenerateReport

use of org.eol.globi.tool.CmdGenerateReport in project eol-globi-data by jhpoelen.

the class CypherTestUtil method validate.

public static void validate(CypherQuery cypherQuery, GraphDatabaseService graphDatabaseService) {
    try (Transaction tx = graphDatabaseService.beginTx()) {
        new NodeFactoryNeo4j2(graphDatabaseService);
        new NonResolvingTaxonIndex(graphDatabaseService);
        new LinkerTaxonIndex(new GraphServiceFactoryProxy(graphDatabaseService)).index();
        CacheService cacheService = new CacheService();
        File cacheDir = new File("target/reportGeneration" + UUID.randomUUID());
        cacheService.setCacheDir(cacheDir);
        CmdGenerateReport reportGenerator = new CmdGenerateReport(graphDatabaseService, cacheService);
        reportGenerator.run(NOPLogger.NOP_LOGGER);
        Map<String, Object> params = cypherQuery.getParams() == null ? Collections.emptyMap() : new HashMap<>(cypherQuery.getParams());
        try {
            graphDatabaseService.execute(cypherQuery.getVersionedQuery(), params);
        } catch (NullPointerException ex) {
            // encountered nullpointer exceptions were caused by initialization of graph database
            throw ex;
        } catch (RuntimeException ex) {
            // work fine in cypher query, but cause parse exception when running programatically
            if (!ex.getMessage().contains("Encountered \" \":\" \": \"\"")) {
                throw ex;
            }
        } finally {
            FileUtils.deleteQuietly(cacheDir);
        }
    }
}