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

Example 71 with StudyImpl

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

the class ExporterAssociationsTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl("myStudy", "data\tsource description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:123"));
    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()));
    eats(specimen, "Canis lupus", "EOL:456", myStudy);
    eats(specimen, "Felis whateverus", PropertyAndValueDictionary.NO_MATCH, myStudy);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(13.0, 45.9, -60.0, null));
    specimen.caughtIn(location);
}

Example 72 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 73 with StudyImpl

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

the class ExportFlatInteractionsTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = factory.createStudy(new StudyImpl("myStudy", null, null, null));
    specimenEatCatAndDog(length, myStudy, "Homo sapiens", "EOL:333");
    specimenEatCatAndDog(length, myStudy, "Homo sapiens", "EOL:333");
    specimenEatCatAndDog(length, myStudy, "Homo erectus", "EOL:123");
    specimenEatCatAndDog(length, myStudy, "Homo erectus", "EOL:123");
    specimenEatCatAndDog(length, factory.createStudy(new StudyImpl("yourStudy", null, null, null)), "Homo erectus", "EOL:888");
    specimenEatCatAndDog(length, factory.createStudy(new StudyImpl("yourStudy2", null, null, null)), "Homo erectus", "EOL:888");
    specimenEatCatAndDog(length, myStudy, "Blo blaaus", PropertyAndValueDictionary.NO_MATCH);
}

Example 74 with StudyImpl

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

the class ExportCitationsTest method exportCitations.

@Test
public void exportCitations() throws IOException, NodeFactoryException {
    StringWriter writer = new StringWriter();
    getNodeFactory().getOrCreateStudy(new StudyImpl("some title", "some source", "doi:some/doi", "some citation"));
    getNodeFactory().getOrCreateStudy(new StudyImpl("some other title", "some other source", "doi:some/otherdoi", "some other citation"));
    new ExportCitations().export(getGraphDb(), writer, "START study = node:studies('*:*') " + "RETURN study.externalId? as uri" + ", study.citation? as citation");
    assertThat(writer.toString(), Is.is("uri\tcitation" + "\nhttp://dx.doi.org/some/doi\tsome citation" + "\nhttp://dx.doi.org/some/otherdoi\tsome other citation"));
}

Example 75 with StudyImpl

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

the class ExporterOccurrenceAggregatesTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    specimenEatCatAndDog(length, myStudy, "Homo sapiens", "EOL:333");
    specimenEatCatAndDog(length, myStudy, "Homo sapiens", "EOL:333");
    specimenEatCatAndDog(length, myStudy, "Homo erectus", "EOL:123");
    specimenEatCatAndDog(length, myStudy, "Homo erectus", "EOL:123");
    specimenEatCatAndDog(length, nodeFactory.createStudy(new StudyImpl("yourStudy", null, null, null)), "Homo erectus", "EOL:888");
    specimenEatCatAndDog(length, nodeFactory.createStudy(new StudyImpl("yourStudy2", null, null, null)), "Homo erectus", "EOL:888");
    specimenEatCatAndDog(length, myStudy, "Blo blaaus", PropertyAndValueDictionary.NO_MATCH);
}