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

Example 46 with Study

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

the class ExporterOccurrencesTest method dontExportToCSVSpecimenEmptyStomach.

@Test
public void dontExportToCSVSpecimenEmptyStomach() throws NodeFactoryException, IOException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:123"));
    specimen.setBasisOfRecord(new TermImpl("test:123", "aBasisOfRecord"));
    resolveNames();
    StringWriter row = new StringWriter();
    exportOccurrences().exportStudy(myStudy, row, true);
    String expected = "";
    expected += getExpectedHeader();
    expected += "\nglobi:occur:2\tEOL:123\t\t\t\t\t\t\t\t\t\t\t\t\taBasisOfRecord\t\t\t\t\t\t\t\t\t\t\t\t\t\t";
    assertThat(row.getBuffer().toString(), equalTo(expected));
}

Example 47 with Study

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

the class ExporterOccurrencesTest method exportNoHeader.

@Test
public void exportNoHeader() throws IOException, NodeFactoryException, ParseException {
    createTestData(null);
    resolveNames();
    String expected = getExpectedData();
    Study myStudy1 = nodeFactory.findStudy("myStudy");
    StringWriter row = new StringWriter();
    exportOccurrences().exportStudy(myStudy1, row, false);
    assertThat(row.getBuffer().toString(), equalTo(expected));
}

Example 48 with Study

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

the class ExporterOccurrencesTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:327955"));
    specimen.setStomachVolumeInMilliLiter(666.0);
    specimen.setLifeStage(new TermImpl("GLOBI:JUVENILE", "JUVENILE"));
    specimen.setPhysiologicalState(new TermImpl("GLOBI:DIGESTATE", "DIGESTATE"));
    specimen.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    nodeFactory.setUnixEpochProperty(specimen, ExportTestUtil.utcTestDate());
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(12.0, -1.0, -60.0, null));
    specimen.caughtIn(location);
    Specimen wolf1 = eatWolf(specimen, myStudy);
    wolf1.caughtIn(location);
    Specimen wolf2 = eatWolf(specimen, myStudy);
    wolf2.caughtIn(location);
}

Example 49 with Study

use of org.eol.globi.domain.Study 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 50 with Study

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