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

Example 1 with NodeBacked

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

the class StudyImporterForGoMexSI2IT method assertThatSomeDataIsImported.

private static void assertThatSomeDataIsImported(NodeFactory nodeFactory, TaxonIndex taxonIndex) throws StudyImporterException, NodeFactoryException {
    Study study = nodeFactory.findStudy("Divita et al 1983");
    assertSpecimenProperties(((NodeBacked) study).getUnderlyingNode().getGraphDatabase());
    assertNotNull(study);
    assertThat(study.getTitle(), is("Divita et al 1983"));
    assertThat(study.getExternalId(), is(ExternalIdUtil.urlForExternalId("GAME:2689")));
    assertThat(study.getCitation(), is("Regina Divita, Mischelle Creel, Peter Sheridan. 1983. Foods of coastal fishes during brown shrimp Penaeus aztecus, migration from Texas estuaries (June - July 1981)."));
    assertNotNull(nodeFactory.findStudy("Beaumariage 1973"));
    assertNotNull(nodeFactory.findStudy("Baughman, 1943"));
    assertNotNull(taxonIndex.findTaxonByName("Chloroscombrus chrysurus"));
    assertNotNull(taxonIndex.findTaxonByName("Micropogonias undulatus"));
    assertNotNull(taxonIndex.findTaxonByName("Amphipoda"));
    assertNotNull(taxonIndex.findTaxonByName("Crustacea"));
    Taxon taxon = taxonIndex.findTaxonByName("Scomberomorus cavalla");
    List<String> preyList = new ArrayList<String>();
    final List<String> titles = new ArrayList<String>();
    Iterable<Relationship> classifiedAsRels = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    int count = 0;
    for (Relationship classifiedAsRel : classifiedAsRels) {
        Node predatorSpecimen = classifiedAsRel.getStartNode();
        Specimen predator = new SpecimenNode(predatorSpecimen);
        Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(predator);
        for (Relationship prey : stomachContents) {
            Relationship singleRelationship = prey.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
            preyList.add((String) singleRelationship.getEndNode().getProperty("name"));
        }
        count++;
        Relationship collectedBy = predatorSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat(collectedBy, is(notNullValue()));
        String title = (String) collectedBy.getStartNode().getProperty("title");
        titles.add(title);
    }
    assertThat(count > 7, is(true));
    assertThat(preyList, hasItem("Organic matter"));
    assertThat(preyList, hasItem("Triglidae"));
    assertThat(preyList, hasItem("Sparidae"));
    assertThat(titles, hasItem("Beaumariage 1973"));
    assertThat(titles, hasItem("Blanton et al 1972"));
    assertNotNull(taxon);
    final String footprintWKT = WKT_FOOTPRINT2;
    LocationImpl expectedLocation = new LocationImpl(29.346953, -92.980614, -13.641, footprintWKT);
    expectedLocation.setLocality("Louisiana inner continental shelf");
    Location location = nodeFactory.findLocation(expectedLocation);
    assertThat(location, is(notNullValue()));
    assertThat(location.getFootprintWKT(), is(footprintWKT));
    assertThat(location.getLocality(), is("Louisiana inner continental shelf"));
    assertNotNull(location);
    List<Environment> environments = location.getEnvironments();
    assertThat(environments.size(), not(is(0)));
    assertThat(environments.get(0).getExternalId(), is("http://cmecscatalog.org/classification/aquaticSetting/13"));
    assertThat(environments.get(0).getName(), is("Marine Nearshore Subtidal"));
    assertNotNull(nodeFactory.findStudy("GoMexSI"));
}

Example 2 with NodeBacked

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