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

Example 11 with TaxonImpl

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

the class ExportTaxonMapTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    final PropertyEnricher taxonEnricher = new PropertyEnricher() {

        @Override
        public Map<String, String> enrich(Map<String, String> properties) {
            Taxon taxon = new TaxonImpl();
            TaxonUtil.mapToTaxon(properties, taxon);
            if ("Homo sapiens".equals(taxon.getName())) {
                taxon.setExternalId("homoSapiensId");
                taxon.setPath("one two three");
            } else if ("Canis lupus".equals(taxon.getName())) {
                taxon.setExternalId("canisLupusId");
                taxon.setPath("four\tfive six");
            }
            return TaxonUtil.taxonToMap(taxon);
        }

        @Override
        public void shutdown() {
        }
    };
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(taxonEnricher, getGraphDb());
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation"));
    Taxon taxon = new TaxonImpl("Homo sapiens");
    taxon.setExternalId("homoSapiensId");
    taxon.setPath("one two three");
    taxon.setExternalUrl("http://some/thing");
    taxon.setThumbnailUrl("http://thing/some");
    nodeFactory.createSpecimen(study, taxon);
    Taxon human = taxonIndex.getOrCreateTaxon(taxon);
    TaxonImpl dog = new TaxonImpl("Canis lupus");
    dog.setExternalId("canisLupusId");
    dog.setPath("four\tfive six");
    nodeFactory.createSpecimen(study, dog);
    final TaxonImpl altTaxonWithPath = new TaxonImpl("Alternate Homo sapiens", "alt:123");
    altTaxonWithPath.setPath("some path here");
    NodeUtil.connectTaxa(altTaxonWithPath, (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    NodeUtil.connectTaxa(new TaxonImpl("Alternate Homo sapiens no path", "alt:123"), (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    NodeUtil.connectTaxa(new TaxonImpl("Similar Homo sapiens", "alt:456"), (TaxonNode) human, getGraphDb(), RelTypes.SIMILAR_TO);
    resolveNames();
    StringWriter writer = new StringWriter();
    new ExportTaxonMap().exportStudy(study, writer, true);
    assertThat(writer.toString(), is("providedTaxonId\tprovidedTaxonName\tresolvedTaxonId\tresolvedTaxonName" + "\nhomoSapiensId\tHomo sapiens\thomoSapiensId\tHomo sapiens" + "\nhomoSapiensId\tHomo sapiens\talt:123\tAlternate Homo sapiens" + "\ncanisLupusId\tCanis lupus\tcanisLupusId\tCanis lupus"));
}

Example 12 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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"));
}