Examples with TaxonImpl org.eol.globi.domain.TaxonImpl used on opensource projects

Example 96 with TaxonImpl

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

the class TaxonUtilTest method copyTaxon.

@Test
public void copyTaxon() {
    Taxon src = new TaxonImpl("name", "id");
    src.setStatus(new TermImpl("statusId", "statusLabel"));
    Taxon target = new TaxonImpl();
    TaxonUtil.copy(src, target);
    assertThat(target.getStatus().getId(), is("statusId"));
    assertThat(target.getStatus().getName(), is("statusLabel"));
}

Example 97 with TaxonImpl

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

the class ExporterTaxaDistinctTest method exportMissingLength.

@Test
public void exportMissingLength() throws IOException, NodeFactoryException, ParseException {
    ExportTestUtil.createTestData(null, nodeFactory);
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis lupus", "EOL:123"));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis", "EOL:126"));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("ThemFishes", "no:match"));
    resolveNames();
    Study myStudy1 = nodeFactory.findStudy("myStudy");
    String actual = exportStudy(myStudy1);
    assertThat(actual, containsString("EOL:123\tCanis lupus\t\t\t\t\t\t\t\t\thttp://eol.org/pages/123\t\t\t\t"));
    assertThat(actual, containsString("EOL:45634\tHomo sapiens\t\t\t\t\t\t\t\t\thttp://eol.org/pages/45634\t\t\t\t"));
    assertThat(actual, not(containsString("no:match\tThemFishes\t\t\t\t\t\t\t\t\t\t\t\t\t")));
    assertThatNoTaxaAreExportedOnMissingHeader(myStudy1, new StringWriter());
}

Example 98 with TaxonImpl

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

the class ExporterTaxaDistinctTest method excludeNoMatchNames.

@Test
public void excludeNoMatchNames() throws NodeFactoryException, IOException {
    Study study = nodeFactory.createStudy(new StudyImpl("bla", null, null, null));
    Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, "EOL:1234"));
    Specimen prey = nodeFactory.createSpecimen(study, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, "EOL:122"));
    predator.ate(prey);
    assertThat(exportStudy(study), not(containsString(PropertyAndValueDictionary.NO_MATCH)));
}

Example 99 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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);
    }
}

Example 100 with TaxonImpl

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

the class TaxonCacheServiceIT method init10k.

@Test
public void init10k() throws PropertyEnricherException {
    final TaxonCacheService cacheService = new TaxonCacheService("/org/eol/globi/taxon/taxonCache10k.tsv.gz", "/org/eol/globi/taxon/taxonMap10k.tsv.gz");
    cacheService.setCacheDir(mapdbDir);
    StopWatch watch = new StopWatch();
    final TaxonImpl taxon = new TaxonImpl();
    taxon.setExternalId("EOL:1049789");
    watch.start();
    final Map<String, String> enriched = cacheService.enrich(TaxonUtil.taxonToMap(taxon));
    assertThat(TaxonUtil.mapToTaxon(enriched).getPath(), is("Animalia | Chordata | Aves | Columbiformes | Columbidae | Turtur | Turtur tympanistria"));
    watch.stop();
}