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

Example 11 with Specimen

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

the class StudyImporterForGoMexSI2IT method assertThatSomeDataIsImported.

private static void assertThatSomeDataIsImported(NodeFactory nodeFactory, TaxonIndex taxonIndex) throws StudyImporterException, NodeFactoryException {
    Study study = nodeFactory.findStudy("Divita et al 1983");
    assertSpecimenProperties(((NodeBacked) study).getUnderlyingNode().getGraphDatabase());
    assertNotNull(study);
    assertThat(study.getTitle(), is("Divita et al 1983"));
    assertThat(study.getExternalId(), is(ExternalIdUtil.urlForExternalId("GAME:2689")));
    assertThat(study.getCitation(), is("Regina Divita, Mischelle Creel, Peter Sheridan. 1983. Foods of coastal fishes during brown shrimp Penaeus aztecus, migration from Texas estuaries (June - July 1981)."));
    assertNotNull(nodeFactory.findStudy("Beaumariage 1973"));
    assertNotNull(nodeFactory.findStudy("Baughman, 1943"));
    assertNotNull(taxonIndex.findTaxonByName("Chloroscombrus chrysurus"));
    assertNotNull(taxonIndex.findTaxonByName("Micropogonias undulatus"));
    assertNotNull(taxonIndex.findTaxonByName("Amphipoda"));
    assertNotNull(taxonIndex.findTaxonByName("Crustacea"));
    Taxon taxon = taxonIndex.findTaxonByName("Scomberomorus cavalla");
    List<String> preyList = new ArrayList<String>();
    final List<String> titles = new ArrayList<String>();
    Iterable<Relationship> classifiedAsRels = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    int count = 0;
    for (Relationship classifiedAsRel : classifiedAsRels) {
        Node predatorSpecimen = classifiedAsRel.getStartNode();
        Specimen predator = new SpecimenNode(predatorSpecimen);
        Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(predator);
        for (Relationship prey : stomachContents) {
            Relationship singleRelationship = prey.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
            preyList.add((String) singleRelationship.getEndNode().getProperty("name"));
        }
        count++;
        Relationship collectedBy = predatorSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat(collectedBy, is(notNullValue()));
        String title = (String) collectedBy.getStartNode().getProperty("title");
        titles.add(title);
    }
    assertThat(count > 7, is(true));
    assertThat(preyList, hasItem("Organic matter"));
    assertThat(preyList, hasItem("Triglidae"));
    assertThat(preyList, hasItem("Sparidae"));
    assertThat(titles, hasItem("Beaumariage 1973"));
    assertThat(titles, hasItem("Blanton et al 1972"));
    assertNotNull(taxon);
    final String footprintWKT = WKT_FOOTPRINT2;
    LocationImpl expectedLocation = new LocationImpl(29.346953, -92.980614, -13.641, footprintWKT);
    expectedLocation.setLocality("Louisiana inner continental shelf");
    Location location = nodeFactory.findLocation(expectedLocation);
    assertThat(location, is(notNullValue()));
    assertThat(location.getFootprintWKT(), is(footprintWKT));
    assertThat(location.getLocality(), is("Louisiana inner continental shelf"));
    assertNotNull(location);
    List<Environment> environments = location.getEnvironments();
    assertThat(environments.size(), not(is(0)));
    assertThat(environments.get(0).getExternalId(), is("http://cmecscatalog.org/classification/aquaticSetting/13"));
    assertThat(environments.get(0).getName(), is("Marine Nearshore Subtidal"));
    assertNotNull(nodeFactory.findStudy("GoMexSI"));
}

Example 12 with Specimen

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

the class ExportTestUtil method createTestData.

public static Study createTestData(Double length, NodeFactory factory) throws NodeFactoryException, ParseException {
    Study myStudy = factory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen1 = factory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:45634"));
    specimen1.setStomachVolumeInMilliLiter(666.0);
    specimen1.setLifeStage(new TermImpl("GLOBI:JUVENILE", "JUVENILE"));
    specimen1.setPhysiologicalState(new TermImpl("GLOBI:DIGESTATE", "DIGESTATE"));
    specimen1.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    factory.setUnixEpochProperty(specimen1, ExportTestUtil.utcTestDate());
    final Specimen specimen2 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen2.setVolumeInMilliLiter(124.0);
    specimen1.ate(specimen2);
    final Specimen specimen3 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen3.setVolumeInMilliLiter(18.0);
    specimen1.ate(specimen3);
    if (null != length) {
        specimen1.setLengthInMm(length);
    }
    Location location = factory.getOrCreateLocation(new LocationImpl(88.0, -120.0, -60.0, null));
    specimen1.caughtIn(location);
    return myStudy;
}

Example 13 with Specimen

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

the class ExporterAssociationAggregatesTest method exportNoMatchTaxa.

@Test
public void exportNoMatchTaxa() throws IOException, NodeFactoryException, ParseException {
    String[] studyTitles = { "myStudy1", "myStudy2" };
    for (String studyTitle : studyTitles) {
        Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl(studyTitle, "data source description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
        Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, null));
        specimen.ate(nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, null)));
    }
    resolveNames();
    ExporterAssociationAggregates exporter = new ExporterAssociationAggregates();
    StringWriter row = new StringWriter();
    for (String studyTitle : studyTitles) {
        Study myStudy1 = nodeFactory.findStudy(studyTitle);
        exporter.exportStudy(myStudy1, row, false);
    }
    assertThat(row.getBuffer().toString(), equalTo(""));
}

Example 14 with Specimen

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

the class ExporterAssociationAggregatesTest method createTestData.

private void createTestData(Double length, String studyTitle) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl(studyTitle, "data source description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, setPathAndId(new TaxonImpl("Homo sapiens", null)));
    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()));
    TaxonImpl taxon = new TaxonImpl("Canis lupus", null);
    Specimen otherSpecimen = nodeFactory.createSpecimen(myStudy, setPathAndId(taxon));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    specimen.ate(otherSpecimen);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(44.0, 120.0, -60.0, null));
    specimen.caughtIn(location);
}

Example 15 with Specimen

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

the class ExportUnmatchedTaxonNamesTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    String title = "my study\"";
    String citation = "citation my study";
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl(title, "my first source", null, citation));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null));
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, human());
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis lupus", null));
    Specimen preySpecimen6 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen6, InteractType.ATE);
    Specimen preySpecimen5 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen5, InteractType.ATE);
    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Caniz", null));
    predatorSpecimen.ate(preySpecimen);
    Specimen predatorSpecimen23 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen4 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen23.interactsWith(preySpecimen4, InteractType.ATE);
    Specimen predatorSpecimen22 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen3 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen22.interactsWith(preySpecimen3, InteractType.ATE);
    Study study2 = nodeFactory.getOrCreateStudy(new StudyImpl("my study2", "my source2", null, "citation study2"));
    Specimen predatorSpecimen21 = nodeFactory.createSpecimen(study2, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen2 = nodeFactory.createSpecimen(study2, dog());
    predatorSpecimen21.interactsWith(preySpecimen2, InteractType.ATE);
    Specimen predatorSpecimen2 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens3", PropertyAndValueDictionary.NO_MATCH));
    Specimen preySpecimen1 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen2.interactsWith(preySpecimen1, InteractType.ATE);
    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" + "\nCaniz\t\t\t\t\t\tcitation my study\tmy first source" + "\nHomo sapiens2\t\t\t\t\t\tcitation my study\tmy first source" + "\nHomo sapiens3\tno:match\t\t\t\t\tcitation my study\tmy first source"));
}