Examples with GraphService org.eol.globi.db.GraphService used on opensource projects

Example 1 with GraphService

use of org.eol.globi.db.GraphService in project eol-globi-data by jhpoelen.

the class NanoPress method createLinkers.

public static List<Linker> createLinkers(CommandLine cmdLine, GraphDatabaseService graphService, File pubDir) {
    List<Linker> linkers = new ArrayList<>();
    if (!cmdLine.hasOption("nanoOnly")) {
        String batchSize = cmdLine.getOptionValue("batchSize", "1000");
        linkers.add(new IndexInteractions(graphService, Integer.parseInt(batchSize)));
    }
    linkers.add(new LinkerTrustyNanoPubs(graphService, nanopub -> {
        String code = TrustyUriUtils.getArtifactCode(nanopub.getUri().toString());
        OutputStream os = null;
        if (StringUtils.isNotBlank(code)) {
            try {
                os = new GZIPOutputStream(new FileOutputStream(new File(pubDir, code + ".trig.gz")));
            } catch (IOException e) {
                LOG.error("failed to produce nanopub file for [" + code + "]", e);
            }
        }
        return os == null ? new NullOutputStream() : os;
    }));
    return linkers;
}

Example 2 with GraphService

use of org.eol.globi.db.GraphService in project eol-globi-data by jhpoelen.

the class Normalizer method importData.

void importData(GraphDatabaseService graphService, String cacheDir) {
    NodeFactoryNeo4j factory = new NodeFactoryNeo4j(graphService);
    factory.setEcoregionFinder(getEcoregionFinder());
    factory.setDoiResolver(new DOIResolverImpl());
    try {
        CacheFactory cacheFactory = dataset -> new CacheLocalReadonly(dataset.getNamespace(), cacheDir);
        DatasetFinder finder = new DatasetFinderLocal(cacheDir, cacheFactory);
        StudyImporter importer = new StudyImporterForGitHubData(new ParserFactoryLocal(), factory, finder);
        importer.setDataset(new DatasetLocal());
        importer.setLogger(new StudyImportLogger());
        importer.importStudy();
    } catch (StudyImporterException e) {
        LOG.error("problem encountered while importing [" + StudyImporterForGitHubData.class.getName() + "]", e);
    }
    EcoregionFinder regionFinder = getEcoregionFinder();
    if (regionFinder != null) {
        regionFinder.shutdown();
    }
}