Examples with StudyImporterException org.eol.globi.data.StudyImporterException used on opensource projects

Example 1 with StudyImporterException

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

the class GraphExporterImpl method exportDataOntology.

private void exportDataOntology(List<Study> studies, String baseDir) throws StudyImporterException {
    try {
        ExporterRDF studyExporter = new ExporterRDF();
        OutputStreamWriter writer = openStream(baseDir + "globi.nq.gz");
        int total = studies.size();
        int count = 1;
        for (Study study : studies) {
            studyExporter.exportStudy(study, writer, true);
            if (count % 50 == 0) {
                LOG.info("added triples for [" + count + "] of [" + total + "] studies...");
            }
            count++;
        }
        LOG.info("adding triples for [" + total + "] of [" + total + "] studies.");
        LOG.info("writing nquads archive...");
        closeStream(baseDir + "globi.nq.gz", writer);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export as owl", e);
    }
}

Example 2 with StudyImporterException

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

the class GraphExporterImpl method exportNames.

private void exportNames(List<Study> studies, String baseDir, StudyExporter exporter, String filename) throws StudyImporterException {
    try {
        String filePath = baseDir + filename;
        OutputStreamWriter writer = openStream(filePath);
        for (Study study : studies) {
            boolean includeHeader = studies.indexOf(study) == 0;
            exporter.exportStudy(study, writer, includeHeader);
        }
        closeStream(filePath, writer);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export unmatched source taxa", e);
    }
}

Example 3 with StudyImporterException

use of org.eol.globi.data.StudyImporterException 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();
    }
}

Example 4 with StudyImporterException

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

the class GitHubImporterFactory method createImporter.

public StudyImporter createImporter(Dataset dataset, final NodeFactory nodeFactory) throws StudyImporterException {
    Class<? extends StudyImporter> anImporter = findImporterFor(dataset);
    try {
        Constructor<? extends StudyImporter> constructor = anImporter.getConstructor(ParserFactory.class, NodeFactory.class);
        ParserFactoryForDataset parserFactory = new ParserFactoryForDataset(dataset);
        StudyImporter studyImporter = constructor.newInstance(parserFactory, new NodeFactoryWithDatasetContext(nodeFactory, dataset));
        studyImporter.setDataset(dataset);
        return studyImporter;
    } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException | InstantiationException e) {
        throw new StudyImporterException("failed to instantiate importer for [" + dataset.getNamespace() + "]", e);
    }
}

Example 5 with StudyImporterException

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

the class GraphExporterImpl method exportDarwinCoreArchive.

private void exportDarwinCoreArchive(List<Study> studies, String pathPrefix, Map<String, DarwinCoreExporter> exporters) throws StudyImporterException {
    try {
        FileUtils.forceMkdir(new File(pathPrefix));
        FileWriter darwinCoreMeta = writeMetaHeader(pathPrefix);
        for (Map.Entry<String, DarwinCoreExporter> exporter : exporters.entrySet()) {
            export(studies, pathPrefix, exporter.getKey(), exporter.getValue(), darwinCoreMeta);
        }
        writeMetaFooter(darwinCoreMeta);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export result to csv file", e);
    }
}