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

Example 1 with StudyImporterForSPIRE

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

the class ExporterRDFTest method exportSPIRE.

@Test
public void exportSPIRE() throws IOException, StudyImporterException {
    StudyImporterForSPIRE importer = new StudyImporterForSPIRE(null, nodeFactory);
    importer.setFilter(recordNumber -> recordNumber < 5);
    importer.setDataset(new DatasetLocal());
    importStudy(importer);
    List<Study> studies = NodeUtil.findAllStudies(getGraphDb());
    Taxon taxon = taxonIndex.getOrCreateTaxon(new TaxonImpl("some taxon", null));
    Taxon sameAsTaxon = taxonIndex.getOrCreateTaxon(new TaxonImpl("bugus same as taxon", "EOL:123"));
    Transaction tx = getGraphDb().beginTx();
    try {
        assertThat(taxon, is(notNullValue()));
        ((NodeBacked) taxon).getUnderlyingNode().createRelationshipTo(((NodeBacked) sameAsTaxon).getUnderlyingNode(), NodeUtil.asNeo4j(RelTypes.SAME_AS));
        tx.success();
    } finally {
        tx.finish();
    }
    File file = File.createTempFile("spire-as-light-globi", ".nq");
    try {
        Writer writer = new FileWriter(file);
        ExporterRDF turtleExporter = new ExporterRDF();
        for (Study study : studies) {
            turtleExporter.exportStudy(study, writer, true);
        }
        writer.flush();
        writer.close();
        assertTrue(file.exists());
        String content = IOUtils.toString(new FileInputStream(file));
        assertThat(content, not(containsString("no:match")));
        assertThat(content, containsString("http://purl.obolibrary.org/obo/ENVO_"));
    } finally {
        FileUtils.deleteQuietly(file);
    }
}