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

Example 81 with Specimen

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

the class StudyImporterForRaymond method parseDietObservation.

private void parseDietObservation(LabeledCSVParser dietParser, Study study) throws StudyImporterException {
    try {
        Specimen predator = getSpecimen(dietParser, "PREDATOR_NAME", "PREDATOR_LIFE_STAGE", study);
        dietParser.getValueByLabel("ALTITUDE_MIN");
        dietParser.getValueByLabel("ALTITUDE_MAX");
        dietParser.getValueByLabel("DEPTH_MIN");
        dietParser.getValueByLabel("DEPTH_MAX");
        Location sampleLocation = parseLocation(dietParser, study);
        predator.caughtIn(sampleLocation);
        Specimen prey = getSpecimen(dietParser, "PREY_NAME", "PREY_LIFE_STAGE", study);
        prey.caughtIn(sampleLocation);
        predator.ate(prey);
        Date date = parseCollectionDate(dietParser);
        nodeFactory.setUnixEpochProperty(prey, date);
        nodeFactory.setUnixEpochProperty(predator, date);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import data", e);
    }
}

Example 82 with Specimen

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

the class StudyImporterForLifeWatchGreeceTest method addTaxonNameForSpecimenNode.

private void addTaxonNameForSpecimenNode(Set<String> taxa, Node startNode) {
    Specimen predatorSpecimen = new SpecimenNode(startNode);
    Iterable<Relationship> classifications = NodeUtil.getClassifications(predatorSpecimen);
    for (Relationship classification : classifications) {
        taxa.add(new TaxonNode(classification.getEndNode()).getName());
    }
}

Example 83 with Specimen

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

the class StudyImporterForLifeWatchGreeceTest method readAssociations.

@Test
public void readAssociations() throws StudyImporterException {
    List<Study> studies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(studies.size(), is(0));
    ParserFactoryLocal parserFactory = new ParserFactoryLocal();
    StudyImporterForLifeWatchGreece importer = new StudyImporterForLifeWatchGreece(parserFactory, nodeFactory);
    importer.setDataset(new DatasetLocal());
    importStudy(importer);
    studies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(studies.size(), is(146));
    Set<String> taxa = new HashSet<String>();
    int totalPredatorPreyRelationships = 0;
    for (Study study : studies) {
        assertThat(study.getCitation(), is(notNullValue()));
        assertThat(study.getTitle(), containsString("greece"));
        Iterable<Relationship> specimens = NodeUtil.getSpecimens(study);
        for (Relationship collectedRel : specimens) {
            addTaxonNameForSpecimenNode(taxa, collectedRel.getEndNode());
            Specimen predatorSpecimen = new SpecimenNode(collectedRel.getEndNode());
            Iterable<Relationship> prey = NodeUtil.getStomachContents(predatorSpecimen);
            for (Relationship ateRel : prey) {
                totalPredatorPreyRelationships++;
                addTaxonNameForSpecimenNode(taxa, ateRel.getEndNode());
            }
        }
    }
    assertThat(taxa.contains("Aves"), is(true));
    assertThat(totalPredatorPreyRelationships, is(793));
}

Example 84 with Specimen

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

the class StudyImporterForRobledoTest method createAndPopulateStudy.

@Test
public void createAndPopulateStudy() throws StudyImporterException, NodeFactoryException {
    StudyImporterForRobledo importer = new StudyImporterForRobledo(new ParserFactoryLocal(), nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    assertNotNull(taxonIndex.findTaxonByName("Heliconia imbricata"));
    assertNotNull(taxonIndex.findTaxonByName("Renealmia alpinia"));
    assertNotNull(nodeFactory.findStudy(study.getTitle()));
    int count = 0;
    Iterable<Relationship> specimenRels = NodeUtil.getSpecimens(study);
    for (Relationship specimenRel : specimenRels) {
        Specimen specimen1 = new SpecimenNode(specimenRel.getEndNode());
        Location sampleLocation = specimen1.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getAltitude(), is(35.0));
        assertThat(Math.round(sampleLocation.getLongitude()), is(-84L));
        assertThat(Math.round(sampleLocation.getLatitude()), is(10L));
        count++;
    }
    assertThat(count, is(93));
}

Example 85 with Specimen

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