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

Example 6 with StudyImporterException

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

the class GraphExporterImpl method export.

@Override
public void export(GraphDatabaseService graphService, String baseDir) throws StudyImporterException {
    try {
        FileUtils.forceMkdir(new File(baseDir));
    } catch (IOException e) {
        throw new StudyImporterException("failed to create output dir [" + baseDir + "]", e);
    }
    LOG.info("site maps generating... ");
    File siteMapDir = new File(baseDir, "sitemap");
    final File citations = new File(siteMapDir, "citations");
    LOG.info("site maps at [" + citations.getAbsolutePath() + "] generating... ");
    new ExporterSiteMapForCitations().export(graphService, citations.getAbsolutePath());
    LOG.info("site maps at [" + citations.getAbsolutePath() + "] generated.");
    final File names = new File(siteMapDir, "names");
    LOG.info("site maps at [" + names.getAbsolutePath() + "] generating... ");
    final GraphExporter exporter = new ExporterSiteMapForNames();
    exporter.export(graphService, names.getAbsolutePath());
    LOG.info("site maps at [" + names.getAbsolutePath() + "] generated.");
    LOG.info("site maps generated... ");
    List<Study> studies = NodeUtil.findAllStudies(graphService);
    exportNames(baseDir, studies);
    // export to taxa for now, to avoid additional assemblies
    new ExportFlatInteractions().export(graphService, "tsv");
    new ExportCitations().export(graphService, "tsv");
    exportNCBILinkOut(graphService, baseDir, studies);
    exportDataOntology(studies, baseDir);
    exportDarwinCoreAggregatedByStudy(baseDir, studies);
    exportDarwinCoreAll(baseDir, studies);
}

Example 7 with StudyImporterException

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

the class SiteMapUtils method generateSiteMap.

public static void generateSiteMap(Set<String> names, String baseDirPath, String queryParamName, String siteMapLocation) throws StudyImporterException {
    try {
        final File baseDir = new File(baseDirPath);
        FileUtils.forceMkdir(baseDir);
        generateSiteMapFor(queryParamName, names, baseDir, siteMapLocation);
    } catch (IOException e) {
        throw new StudyImporterException("failed to generate site map", e);
    }
}

Example 8 with StudyImporterException

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

the class ExportNCBIResourceFile method export.

protected void export(GraphDatabaseService graphService, OutputStreamFactory fileFactory) throws StudyImporterException {
    String query = "START taxon = node:taxons('*:*') " + "MATCH taxon-[?:SAME_AS*0..1]->linkedTaxon " + "WHERE has(linkedTaxon.externalId) AND linkedTaxon.externalId =~ 'NCBI:.*'" + "RETURN distinct(linkedTaxon.externalId) as id";
    ExecutionResult rows = new ExecutionEngine(graphService).execute(query, new HashMap<String, Object>());
    int rowCount = 0;
    OutputStream os = null;
    try {
        List<String> columns = rows.columns();
        for (Map<String, Object> row : rows) {
            if (rowCount % getLinksPerResourceFile() == 0) {
                close(os);
                os = null;
            }
            for (String column : columns) {
                String taxonId = row.get(column).toString();
                String ncbiTaxonId = StringUtils.replace(taxonId, TaxonomyProvider.ID_PREFIX_NCBI, "");
                String aLink = String.format("         <ObjId>%s</ObjId>\n", ncbiTaxonId);
                IOUtils.write(aLink, os == null ? (os = open(fileFactory, rowCount)) : os);
            }
            rowCount++;
        }
        close(os);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export ncbi resources", e);
    }
}

Example 9 with StudyImporterException

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

the class ExportCitations method export.

public static void export(GraphDatabaseService graphService, String baseDir, String tsvFilename, String cypherQuery) throws StudyImporterException {
    try {
        ExportUtil.mkdirIfNeeded(baseDir);
        final FileOutputStream out = new FileOutputStream(baseDir + tsvFilename);
        GZIPOutputStream os = new GZIPOutputStream(out);
        final Writer writer = new BufferedWriter(new OutputStreamWriter(os, "UTF-8"));
        export(graphService, writer, cypherQuery);
        writer.flush();
        os.finish();
        IOUtils.closeQuietly(writer);
        IOUtils.closeQuietly(os);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export citations", e);
    }
}