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

Example 26 with TaxonImpl

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

the class ExporterOccurrencesTest method eatWolf.

private Specimen eatWolf(Specimen specimen, Study study) throws NodeFactoryException {
    Specimen otherSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Canis lupus", "EOL:328607"));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    nodeFactory.setUnixEpochProperty(otherSpecimen, ExportTestUtil.utcTestDate());
    specimen.ate(otherSpecimen);
    return otherSpecimen;
}

Example 27 with TaxonImpl

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

the class ExporterAssociationsTest method eats.

private void eats(Specimen specimen, String scientificName, String taxonExternalId, Study study) throws NodeFactoryException {
    Specimen otherSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(scientificName, taxonExternalId));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    specimen.ate(otherSpecimen);
}

Example 28 with TaxonImpl

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

the class ExporterMeasurementOrFactTest method noMatchNames.

@Test
public void noMatchNames() throws IOException, NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_NAME, "externalId1"));
    nodeFactory.createSpecimen(myStudy, new TaxonImpl("Some namus", PropertyAndValueDictionary.NO_MATCH));
    Study myStudy1 = nodeFactory.findStudy("myStudy");
    StringWriter row = new StringWriter();
    new ExporterMeasurementOrFact().exportStudy(myStudy1, row, false);
    assertThat(row.getBuffer().toString(), equalTo(""));
}

Example 29 with TaxonImpl

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

the class GraphExporterImplTest method exportAll.

@Test
public void exportAll() throws StudyImporterException, IOException {
    File tmpDir = FileUtils.getTempDirectory();
    File tmpDirPath = new File(tmpDir, "test" + new Random().nextLong());
    FileUtils.forceMkdir(tmpDirPath);
    assertThat(tmpDirPath.list().length, is(0));
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("a study", "a source", "doi:12345L", null));
    Specimen human = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens", "NCBI:123"));
    human.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Canis familiaris", "BLA:444")));
    resolveNames();
    try {
        new GraphExporterImpl().export(getGraphDb(), tmpDirPath.getAbsolutePath() + "/");
        assertThat(tmpDirPath.list().length, is(6));
    } finally {
        FileUtils.deleteQuietly(tmpDirPath);
    }
}

Example 30 with TaxonImpl

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

the class ExporterSiteMapForNamesTest method writeSiteMapWithNames.

@Test
public void writeSiteMapWithNames() throws StudyImporterException, IOException {
    taxonIndex = new NonResolvingTaxonIndex(getGraphDb());
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation 123"));
    TaxonImpl homoSapiens = new TaxonImpl("Homo sapiens", "homoSapiensId");
    homoSapiens.setPath("one two three");
    final Specimen human = nodeFactory.createSpecimen(study, homoSapiens);
    TaxonImpl dogTaxon = new TaxonImpl("Canis familiaris", null);
    final Specimen dog = nodeFactory.createSpecimen(study, dogTaxon);
    human.ate(dog);
    resolveNames();
    final File baseDirNames = createBaseDir("target/sitemap/names");
    final GraphExporter siteMapForNames = new ExporterSiteMapForNames();
    siteMapForNames.export(getGraphDb(), baseDirNames.getAbsolutePath());
    assertSiteMap(baseDirNames, "http://www.globalbioticinteractions.org/?interactionType=interactsWith&sourceTaxon=Homo%20sapiens", "https://depot.globalbioticinteractions.org/snapshot/target/data/sitemap/names/sitemap.xml.gz");
}