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

Example 26 with TaxonNode

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

the class StudyImporterForLifeWatchGreeceTest method addTaxonNameForSpecimenNode.

private void addTaxonNameForSpecimenNode(Set<String> taxa, Node startNode) {
    Specimen predatorSpecimen = new SpecimenNode(startNode);
    Iterable<Relationship> classifications = NodeUtil.getClassifications(predatorSpecimen);
    for (Relationship classification : classifications) {
        taxa.add(new TaxonNode(classification.getEndNode()).getName());
    }
}

Example 27 with TaxonNode

use of org.eol.globi.domain.TaxonNode 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 28 with TaxonNode

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

the class NonResolvingTaxonIndexTest method createTaxon.

@Test
public final void createTaxon() throws NodeFactoryException {
    Taxon taxon1 = new TaxonImpl("bla bla", null);
    taxon1.setPath(null);
    TaxonNode taxon = taxonService.getOrCreateTaxon(taxon1);
    assertThat(taxon, is(notNullValue()));
    assertEquals("bla bla", taxon.getName());
}

Example 29 with TaxonNode

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

the class ResolvingTaxonIndexTest method indexResolvedOnly.

@Test
public void indexResolvedOnly() throws NodeFactoryException {
    TaxonNode unresolvedTaxon = getIndex().getOrCreateTaxon(new TaxonImpl("not resolved"));
    assertNotNull(unresolvedTaxon);
    assertFalse(TaxonUtil.isResolved(unresolvedTaxon));
    final ResolvingTaxonIndex indexResolvedOnly = getIndex();
    indexResolvedOnly.setIndexResolvedTaxaOnly(true);
    assertNull(indexResolvedOnly.getOrCreateTaxon(new TaxonImpl("no resolving either", null)));
}

Example 30 with TaxonNode

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

the class LinkerTaxonIndexTest method linking.

@Test
public void linking() throws NodeFactoryException {
    Taxon taxonFound = new TaxonImpl("Homo sapiens", "Bar:123");
    taxonFound.setPath("Animalia | Mammalia | Homo sapiens");
    Taxon taxon = taxonIndex.getOrCreateTaxon(taxonFound);
    TaxonImpl taxon1 = new TaxonImpl("Homo sapiens also", "FOO:444");
    taxon1.setPathIds("BARZ:111 | FOOZ:777");
    NodeUtil.connectTaxa(taxon1, (TaxonNode) taxon, getGraphDb(), RelTypes.SAME_AS);
    taxon = taxonIndex.getOrCreateTaxon(new TaxonImpl("Bla blaus", null));
    taxon.setExternalId("FOO 1234");
    resolveNames();
    new LinkerTaxonIndex(getGraphDb()).link();
    IndexHits<Node> hits = getGraphDb().index().forNodes(LinkerTaxonIndex.INDEX_TAXON_NAMES_AND_IDS).query("*:*");
    Node next = hits.next();
    assertThat(new TaxonNode(next).getName(), is("Homo sapiens"));
    assertThat(hits.hasNext(), is(true));
    hits.close();
    assertSingleHit(PropertyAndValueDictionary.PATH + ":BAR\\:123");
    assertSingleHit(PropertyAndValueDictionary.PATH + ":FOO\\:444");
    assertSingleHit(PropertyAndValueDictionary.PATH + ":FOO\\:444 " + PropertyAndValueDictionary.PATH + ":BAR\\:123");
    assertSingleHit(PropertyAndValueDictionary.PATH + ":BAR\\:*");
    assertSingleHit(PropertyAndValueDictionary.PATH + ":Homo");
    assertSingleHit(PropertyAndValueDictionary.PATH + ":\"Homo sapiens\"");
    Taxon node = taxonIndex.findTaxonByName("Homo sapiens");
    assertThat(((NodeBacked) node).getUnderlyingNode().getProperty(PropertyAndValueDictionary.EXTERNAL_IDS).toString(), is("Animalia | Mammalia | Homo sapiens | BARZ:111 | FOOZ:777 | Bar:123 | FOO:444"));
    assertThat(((NodeBacked) node).getUnderlyingNode().getProperty(PropertyAndValueDictionary.NAME_IDS).toString(), is("Bar:123 | FOO:444"));
    assertThat(new TaxonFuzzySearchIndex(getGraphDb()).query("name:sapienz~").size(), is(1));
    assertThat(new TaxonFuzzySearchIndex(getGraphDb()).query("name:sapienz").size(), is(0));
}