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

Example 21 with Specimen

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

the class StudyImporterForGoMexSI2 method createSpecimen.

private Specimen createSpecimen(Study study, Map<String, String> properties) throws StudyImporterException {
    Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(properties.get(PropertyAndValueDictionary.NAME), null));
    specimen.setLengthInMm(doubleValueOrNull(properties, SpecimenConstant.LENGTH_IN_MM));
    specimen.setFrequencyOfOccurrence(doubleValueOrNull(properties, SpecimenConstant.FREQUENCY_OF_OCCURRENCE));
    setSpecimenProperty(specimen, SpecimenConstant.FREQUENCY_OF_OCCURRENCE_PERCENT, properties);
    specimen.setTotalCount(integerValueOrNull(properties, SpecimenConstant.TOTAL_COUNT));
    setSpecimenProperty(specimen, SpecimenConstant.TOTAL_COUNT_PERCENT, properties);
    specimen.setTotalVolumeInMl(doubleValueOrNull(properties, SpecimenConstant.TOTAL_VOLUME_IN_ML));
    setSpecimenProperty(specimen, SpecimenConstant.TOTAL_VOLUME_PERCENT, properties);
    addLifeStage(properties, specimen);
    addPhysiologicalState(properties, specimen);
    addBodyPart(properties, specimen);
    // add all original GoMexSI properties for completeness
    for (Map.Entry<String, String> entry : properties.entrySet()) {
        if (entry.getKey().startsWith(GOMEXSI_NAMESPACE)) {
            specimen.setProperty(entry.getKey(), entry.getValue());
        }
    }
    return specimen;
}

Example 22 with Specimen

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

the class StudyImporterForINaturalist method createAssociation.

private Specimen createAssociation(long observationId, String interactionDataType, InteractType interactType, JsonNode observation, Taxon targetTaxon, Taxon sourceTaxonName, Study study, Date observationDate) throws StudyImporterException, NodeFactoryException {
    Specimen sourceSpecimen = getSourceSpecimen(observationId, interactionDataType, sourceTaxonName, study);
    setBasisOfRecord(sourceSpecimen);
    Specimen targetSpecimen = nodeFactory.createSpecimen(study, targetTaxon);
    setBasisOfRecord(targetSpecimen);
    sourceSpecimen.interactsWith(targetSpecimen, interactType);
    setCollectionDate(sourceSpecimen, targetSpecimen, observationDate);
    setCollectionDate(sourceSpecimen, sourceSpecimen, observationDate);
    Location location = parseLocation(observation);
    sourceSpecimen.caughtIn(location);
    targetSpecimen.caughtIn(location);
    return sourceSpecimen;
}

Example 23 with Specimen

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

the class ExporterOccurrenceAggregatesTest method collectSpecimen.

private Specimen collectSpecimen(Study myStudy, String scientificName, String externalId) throws NodeFactoryException {
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(scientificName, externalId));
    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()));
    return specimen;
}

Example 24 with Specimen

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

the class ExporterOccurrenceAggregatesTest method eatPrey.

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

Example 25 with Specimen

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