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

Example 76 with StudyImpl

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

the class ExporterOccurrenceAggregatesTest method exportNoMatchName.

@Test
public void exportNoMatchName() throws NodeFactoryException, IOException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, "some externalid"));
    resolveNames();
    StringWriter row = new StringWriter();
    new ExporterOccurrenceAggregates().exportDistinct(myStudy, row);
    assertThat(row.toString(), equalTo(""));
}

Example 77 with StudyImpl

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

the class ExporterMeasurementOrFactTest method createTestData.

private void createTestData(Double length, String targetTaxonName, String sourceTaxonName) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(sourceTaxonName, "externalId1"));
    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());
    Specimen otherSpecimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(targetTaxonName, "externalId2"));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    otherSpecimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(targetTaxonName, "externalId2"));
    otherSpecimen.setVolumeInMilliLiter(18.0);
    specimen.ate(otherSpecimen);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(22.0, 129.9, -60.0, null));
    specimen.caughtIn(location);
    resolveNames();
}

Example 78 with StudyImpl

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

the class ExportNCBIResourceFileTest method init.

@Before
public void init() throws NodeFactoryException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation"));
    Taxon taxon = new TaxonImpl("Homo sapiens", TaxonomyProvider.NCBI.getIdPrefix() + "9606");
    taxon.setPath("some path");
    taxonIndex.getOrCreateTaxon(taxon);
    taxon = new TaxonImpl("Homo sapiens", "foo:123");
    taxon.setPath("some path");
    taxonIndex.getOrCreateTaxon(taxon);
    taxon = new TaxonImpl("Enhydra lutris", "NCBI:34882");
    taxon.setPath("some path");
    taxonIndex.getOrCreateTaxon(taxon);
}

Example 79 with StudyImpl

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

the class LinkerDOITest method createStudyDOIlookupCitationWithURL.

@Test
public void createStudyDOIlookupCitationWithURL() throws NodeFactoryException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", "some source", null, "http://bla"));
    new LinkerDOI(getGraphDb()).linkStudy(new DOIResolverThatFails(), study);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getCitation(), is("http://bla"));
    assertThat(study.getTitle(), is("title"));
}

Example 80 with StudyImpl

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

the class LinkerDOITest method createStudyDOIlookupCitationEnabled.

@Test
public void createStudyDOIlookupCitationEnabled() throws NodeFactoryException {
    StudyImpl title = new StudyImpl("title", "some source", null, "some citation");
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, true);
    originatingDataset.setConfig(objectNode);
    title.setOriginatingDataset(originatingDataset);
    StudyNode study = getNodeFactory().getOrCreateStudy(title);
    new LinkerDOI(getGraphDb()).linkStudy(new TestDOIResolver(), study);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getDOI(), is("doi:some citation"));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
}