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

Example 86 with Specimen

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

the class ExportUnmatchedTaxonNamesTest method exportOnePredatorNoPathButWithSameAs.

@Test
public void exportOnePredatorNoPathButWithSameAs() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    String citation = "cite, study";
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("my, study", "my first, source", null, citation));
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapienz", null));
    Taxon humanz = taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapienz", null));
    TaxonImpl taxon = new TaxonImpl("Homo sapiens", "TESTING:123");
    taxon.setPath("one | two | Homo sapiens");
    NodeUtil.connectTaxa(taxon, (TaxonNode) humanz, getGraphDb(), RelTypes.SIMILAR_TO);
    assertNotNull(humanz);
    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Caniz", null));
    predatorSpecimen.interactsWith(preySpecimen, InteractType.ATE);
    predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens", null));
    Node synonymNode = ((NodeBacked) taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens Synonym", null))).getUnderlyingNode();
    Node node = ((NodeBacked) taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null))).getUnderlyingNode();
    Transaction tx = getGraphDb().beginTx();
    try {
        node.createRelationshipTo(synonymNode, NodeUtil.asNeo4j(RelTypes.SAME_AS));
        tx.success();
    } finally {
        tx.finish();
    }
    preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Canis", null));
    predatorSpecimen.ate(preySpecimen);
    resolveNames();
    StringWriter writer = new StringWriter();
    new ExportUnmatchedTaxonNames().exportStudy(study, writer, true);
    assertThat(writer.toString(), is("unmatched taxon name\tunmatched taxon id\tname status\tsimilar to taxon name\tsimilar to taxon path\tsimilar to taxon id\tstudy\tsource" + "\nHomo sapienz\t\t\tHomo sapiens\tone | two | Homo sapiens\tTESTING:123\tcite, study\tmy first, source" + "\nCaniz\t\t\t\t\t\tcite, study\tmy first, source" + "\nCanis\t\t\t\t\t\tcite, study\tmy first, source"));
}

Example 87 with Specimen

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

the class ExportFlatInteractionsTest method eatPrey.

private Specimen eatPrey(Specimen specimen, String scientificName, String externalId, Study study) throws NodeFactoryException {
    final TaxonImpl preyTaxon = new TaxonImpl(scientificName, externalId);
    preyTaxon.setPath("preyPathElem1 | preyPathElem2");
    Specimen otherSpecimen = factory.createSpecimen(study, preyTaxon);
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    return otherSpecimen;
}

Example 88 with Specimen

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

the class ExportFlatInteractionsTest method specimenEatCatAndDog.

private void specimenEatCatAndDog(Double length, Study myStudy, String scientificName, String externalId) throws NodeFactoryException {
    Specimen specimen = collectSpecimen(myStudy, scientificName, externalId);
    eatPrey(specimen, "Canis lupus", "EOL:555", myStudy);
    eatPrey(specimen, "Felis domesticus", "EOL:666", myStudy);
    eatPrey(specimen, "Blah blahuuuu", PropertyAndValueDictionary.NO_MATCH, myStudy);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    LocationImpl location1 = new LocationImpl(12.0, -45.9, -60.0, null);
    location1.setLocality("some locale");
    location1.setLocalityId("some:localeid");
    Location location = factory.getOrCreateLocation(location1);
    specimen.caughtIn(location);
}

Example 89 with Specimen

use of org.eol.globi.domain.Specimen 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 90 with Specimen

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