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

Example 21 with Study

use of org.eol.globi.domain.Study 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 22 with Study

use of org.eol.globi.domain.Study 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 23 with Study

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

the class ExporterAssociationsTest method exportWithoutHeader.

@Test
public void exportWithoutHeader() throws IOException, NodeFactoryException, ParseException {
    createTestData(null);
    resolveNames();
    String expected = "\nglobi:assoc:4\tglobi:occur:2\thttp://purl.obolibrary.org/obo/RO_0002470\tglobi:occur:4\t\t\t\t\tdata source description\t\t\tglobi:ref:1" + "\nglobi:assoc:6\tglobi:occur:2\thttp://purl.obolibrary.org/obo/RO_0002470\tglobi:occur:4\t\t\t\t\tdata source description\t\t\tglobi:ref:1";
    Study myStudy1 = nodeFactory.findStudy("myStudy");
    StringWriter row = new StringWriter();
    new ExporterAssociations().exportStudy(myStudy1, row, false);
    assertThat(row.getBuffer().toString(), equalTo(expected));
}

Example 24 with Study

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

Example 25 with Study

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

the class InteractionListenerImpl method importValidLink.

private void importValidLink(Map<String, String> link) throws StudyImporterException, IOException {
    Study study = nodeFactory.getOrCreateStudy(studyFromLink(link));
    Specimen source = createSpecimen(link, study, SOURCE_TAXON_NAME, SOURCE_TAXON_ID, SOURCE_BODY_PART_NAME, SOURCE_BODY_PART_ID);
    Specimen target = createSpecimen(link, study, TARGET_TAXON_NAME, TARGET_TAXON_ID, TARGET_BODY_PART_NAME, TARGET_BODY_PART_ID);
    String interactionTypeId = link.get(INTERACTION_TYPE_ID);
    InteractType type = InteractType.typeOf(interactionTypeId);
    source.interactsWith(target, type, getOrCreateLocation(study, link));
}