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

Example 1 with CmdInterpretTaxa

use of org.eol.globi.tool.CmdInterpretTaxa 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 CmdInterpretTaxa

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

the class Elton4N method createInterpretTaxaCmd.

private CmdInterpretTaxa createInterpretTaxaCmd(CommandLine cmdLine, GraphServiceFactory graphServiceFactory, String exportDir) {
    String taxonCachePath = cmdLine.getOptionValue(CmdOptionConstants.OPTION_TAXON_CACHE_PATH, "taxonCache.tsv.gz");
    String taxonMapPath = cmdLine.getOptionValue(CmdOptionConstants.OPTION_TAXON_MAP_PATH, "taxonMap.tsv.gz");
    return new CmdInterpretTaxa(graphServiceFactory, taxonCachePath, taxonMapPath, new File(exportDir));
}