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

Example 16 with TermImpl

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

the class InteractionListenerImpl method setBodyPartIfAvailable.

private void setBodyPartIfAvailable(Map<String, String> link, Specimen specimen, String name, String id) {
    final String bodyPartName = link.get(name);
    final String bodyPartId = link.get(id);
    if (StringUtils.isNotBlank(bodyPartName) || StringUtils.isNotBlank(bodyPartId)) {
        specimen.setBodyPart(new TermImpl(bodyPartId, bodyPartName));
    }
}

Example 17 with TermImpl

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

the class ExporterAssociationsTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl("myStudy", "data\tsource description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:123"));
    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, new Date(ExportTestUtil.utcTestTime()));
    eats(specimen, "Canis lupus", "EOL:456", myStudy);
    eats(specimen, "Felis whateverus", PropertyAndValueDictionary.NO_MATCH, myStudy);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(13.0, 45.9, -60.0, null));
    specimen.caughtIn(location);
}

Example 18 with TermImpl

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

the class ExportFlatInteractionsTest method collectSpecimen.

private Specimen collectSpecimen(Study myStudy, String scientificName, String externalId) throws NodeFactoryException {
    final TaxonImpl taxon = new TaxonImpl(scientificName, externalId);
    taxon.setPath("pathElem1 | pathElem 2");
    Specimen specimen = factory.createSpecimen(myStudy, taxon);
    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"));
    factory.setUnixEpochProperty(specimen, new Date(ExportTestUtil.utcTestTime()));
    return specimen;
}

Example 19 with TermImpl

use of org.eol.globi.domain.TermImpl 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();
}