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

Example 36 with TaxonImpl

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

the class LinkerTermMatcherTest method exactMatchMedicagoSativa.

@Test
public // see //see https://github.com/jhpoelen/eol-globi-data/issues/249
void exactMatchMedicagoSativa() throws NodeFactoryException, PropertyEnricherException {
    Taxon nbnTaxon = new TaxonImpl("Medicago sativa", "NBN:NBNSYS0000013971");
    nbnTaxon.setPath("Biota | Plantae | Tracheophyta | Magnoliopsida | Fabales | Fabaceae | Medicago | Medicago sativa");
    nbnTaxon.setPathNames("Unranked | Kingdom | Phylum | Class | Order | Family | Genus | Species");
    taxonIndex.getOrCreateTaxon(nbnTaxon);
    final Taxon taxonCreated = taxonIndex.getOrCreateTaxon(new TaxonImpl("Medicago sativa L.", null));
    assertThat(taxonCreated.getName(), is("Medicago sativa L."));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther(taxonCreated.getName(), 7, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItem("ITIS:183623"));
    assertThat(ids, hasItem("NCBI:3879"));
    assertThat(ids, not(hasItem("NCBI:56066")));
}

Example 37 with TaxonImpl

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

the class LinkerTermMatcherTest method exactMatchMonodelphisAmericana.

@Test
public void exactMatchMonodelphisAmericana() throws NodeFactoryException, PropertyEnricherException {
    final Taxon taxonCreated = taxonIndex.getOrCreateTaxon(new TaxonImpl("Monodelphis americana", null));
    assertThat(taxonCreated.getName(), is("Monodelphis americana"));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther(taxonCreated.getName(), 5, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItems("ITIS:552569", "NCBI:694061", "IRMNG:11060619", "GBIF:2439970", "OTT:446727"));
}

Example 38 with TaxonImpl

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

the class ReportGeneratorTest method createStudy.

protected Study createStudy(Study study1) throws NodeFactoryException {
    Study study = nodeFactory.getOrCreateStudy(study1);
    Specimen monkey = nodeFactory.createSpecimen(study, new TaxonImpl("Monkey"));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    TaxonImpl apple = new TaxonImpl("Apple", "some:id");
    apple.setPath("some | path");
    monkey.ate(nodeFactory.createSpecimen(study, apple));
    return study;
}

Example 39 with TaxonImpl

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

the class LinkerTermMatcherTest method threeTaxa.

@Test
public void threeTaxa() throws NodeFactoryException, PropertyEnricherException {
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Ariopsis felis", null));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis lupus", null));
    new LinkerTermMatcher(getGraphDb()).link();
    LinkerTestUtil.assertHasOther("Homo sapiens", 5, taxonIndex, RelTypes.SAME_AS);
    LinkerTestUtil.assertHasOther("Homo sapiens", 0, taxonIndex, RelTypes.SIMILAR_TO);
    LinkerTestUtil.assertHasOther("Canis lupus", 6, taxonIndex, RelTypes.SAME_AS);
    LinkerTestUtil.assertHasOther("Canis lupus", 0, taxonIndex, RelTypes.SIMILAR_TO);
    LinkerTestUtil.assertHasOther("Ariopsis felis", 8, taxonIndex, RelTypes.SAME_AS);
    LinkerTestUtil.assertHasOther("Ariopsis felis", 0, taxonIndex, RelTypes.SIMILAR_TO);
}

Example 40 with TaxonImpl

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

the class LinkerTermMatcherTest method hasSeaLifeBaseLinks.

@Test
public void hasSeaLifeBaseLinks() throws NodeFactoryException, PropertyEnricherException {
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Enhydra lutris", null));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther("Enhydra lutris", 8, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItem("FBC:SLB:SpecCode:69195"));
}