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

Example 11 with TaxonNode

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

the class ExporterRDF method taxonOfSpecimen.

public List<List<String>> taxonOfSpecimen(Node specimen) {
    List<List<String>> statements = new ArrayList<List<String>>();
    Relationship singleRelationship = specimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
    if (singleRelationship != null) {
        Node taxonNode = singleRelationship.getEndNode();
        List<String> sameAsTaxa = addSameAsTaxaFor(taxonNode);
        final String s = taxonIRI(taxonNode);
        final String taxon = iriNode(s);
        statements.add(Arrays.asList(blankNode(specimen), iriNode(MEMBER_OF), taxon));
        for (String sameAsTaxon : sameAsTaxa) {
            statements.add(Arrays.asList(taxon, iriNode(SAME_AS), iriNode(sameAsTaxon)));
        }
    }
    return statements;
}

Example 12 with TaxonNode

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

the class InteractionListenerImplTest method importAssociatedTaxa.

@Test
public void importAssociatedTaxa() throws StudyImporterException {
    final InteractionListenerImpl listener = new InteractionListenerImpl(nodeFactory, null, new ImportLogger() {

        @Override
        public void warn(LogContext study, String message) {
            fail("got message: " + message);
        }

        @Override
        public void info(LogContext study, String message) {
        }

        @Override
        public void severe(LogContext study, String message) {
            fail("got message: " + message);
        }
    });
    final HashMap<String, String> link = new HashMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(SOURCE_BODY_PART_ID, "bla:123");
    link.put(SOURCE_BODY_PART_NAME, "snout");
    link.put("associatedTaxa", "parasite of: Mini mouse");
    link.put(StudyImporterForMetaTable.EVENT_DATE, "20160404T21:31:40Z");
    link.put(StudyImporterForMetaTable.LATITUDE, "12.1");
    link.put(StudyImporterForMetaTable.LONGITUDE, "13.2");
    link.put(REFERENCE_ID, "123");
    link.put(STUDY_SOURCE_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:1234");
    listener.newLink(link);
    final List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(allStudies.size(), is(1));
    final Study study = allStudies.get(0);
    assertThat(study.getCitation(), is(""));
    boolean foundPair = false;
    for (Relationship specimenRel : NodeUtil.getSpecimens(study)) {
        final SpecimenNode predator = new SpecimenNode(specimenRel.getEndNode());
        for (Relationship hosts : ((NodeBacked) predator).getUnderlyingNode().getRelationships(NodeUtil.asNeo4j(InteractType.PARASITE_OF), Direction.OUTGOING)) {
            final SpecimenNode host = new SpecimenNode(hosts.getEndNode());
            final TaxonNode hostTaxon = getOrigTaxon(host);
            final TaxonNode predTaxon = getOrigTaxon(predator);
            assertThat(hostTaxon.getName(), is("Mini mouse"));
            assertThat(predTaxon.getName(), is("donald"));
            assertThat(predTaxon.getExternalId(), is("duck"));
            foundPair = true;
        }
    }
    assertThat(foundPair, is(true));
}

Example 13 with TaxonNode

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

the class ReportGenerator method countInteractionsAndTaxa.

private void countInteractionsAndTaxa(Iterable<Relationship> specimens, Set<Long> ids, Counter interactionCounter, Set<Long> idsNoMatch) {
    for (Relationship specimen : specimens) {
        Iterable<Relationship> relationships = specimen.getEndNode().getRelationships();
        for (Relationship relationship : relationships) {
            InteractType[] types = InteractType.values();
            for (InteractType type : types) {
                if (relationship.isType(NodeUtil.asNeo4j(type)) && !relationship.hasProperty(PropertyAndValueDictionary.INVERTED)) {
                    interactionCounter.count();
                    break;
                }
            }
        }
        Relationship classifiedAs = specimen.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
        if (classifiedAs != null) {
            Node taxonNode = classifiedAs.getEndNode();
            ids.add(taxonNode.getId());
            if (!TaxonUtil.isResolved(new TaxonNode(taxonNode))) {
                idsNoMatch.add(taxonNode.getId());
            }
        }
    }
}

Example 14 with TaxonNode

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

the class IndexInteractionsTest method indexInteractions.

@Test
public void indexInteractions() throws NodeFactoryException {
    TaxonIndex taxonIndex = getOrCreateTaxonIndex();
    // see https://github.com/jhpoelen/eol-globi-data/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", "some source", "http://doi.org/123.23/222", "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, new DatasetImpl("some/namespace", URI.create("https://some.uri")));
    Study interaction = factory.getOrCreateStudy(study);
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    TaxonImpl mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonNCBI = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonNCBI, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxon);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxon));
    donald.ate(mickey);
    new IndexInteractions(getGraphDb()).link();
    NodeFactoryNeo4j nodeFactoryNeo4j = new NodeFactoryNeo4j(getGraphDb());
    StudyImpl study1 = new StudyImpl("some study", "some source", null, "come citation");
    study1.setOriginatingDataset(new DatasetImpl("some/namespace", URI.create("some:uri")));
    StudyNode someStudy = nodeFactoryNeo4j.getOrCreateStudy(study1);
    assertThat(interaction.getOriginatingDataset().getNamespace(), is(someStudy.getOriginatingDataset().getNamespace()));
    assertThat(interaction.getTitle(), is(someStudy.getTitle()));
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(someStudy);
    RelationshipType hasParticipant = NodeUtil.asNeo4j(RelTypes.HAS_PARTICIPANT);
    Set<Long> ids = new HashSet<>();
    List<Long> idList = new ArrayList<>();
    for (Relationship specimen : specimens) {
        assertThat(specimen.getEndNode().hasRelationship(Direction.INCOMING, hasParticipant), Is.is(true));
        Relationship singleRelationship = specimen.getEndNode().getSingleRelationship(hasParticipant, Direction.INCOMING);
        long id = singleRelationship.getStartNode().getId();
        ids.add(id);
        idList.add(id);
    }
    assertThat(ids.size(), Is.is(1));
    assertThat(idList.size(), Is.is(2));
    Node interactionNode = getGraphDb().getNodeById(idList.get(0));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.DERIVED_FROM)));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.ACCESSED_AT)));
}

Example 15 with TaxonNode

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

the class ResolvingTaxonIndexTest method synonymsAddedToIndexOnce.

@Test
public final void synonymsAddedToIndexOnce() throws NodeFactoryException {
    ResolvingTaxonIndex taxonService = createTaxonService(getGraphDb());
    taxonService.setEnricher(new PropertyEnricher() {

        private boolean firstTime = true;

        @Override
        public Map<String, String> enrich(Map<String, String> properties) throws PropertyEnricherException {
            Taxon taxon = TaxonUtil.mapToTaxon(properties);
            if ("not pref".equals(taxon.getName())) {
                if (!firstTime) {
                    fail("should already have indexed [" + taxon.getName() + "]...");
                }
                taxon.setName("preferred");
                taxon.setExternalId("bla:123");
                taxon.setPath("one | two | three");
                taxon.setPathIds("1 | 2 | 3");
                firstTime = false;
            }
            return TaxonUtil.taxonToMap(taxon);
        }

        @Override
        public void shutdown() {
        }
    });
    this.taxonService = taxonService;
    Taxon taxon2 = new TaxonImpl("not pref", null);
    taxon2.setPath(null);
    TaxonNode first = this.taxonService.getOrCreateTaxon(taxon2);
    assertThat(first.getName(), is("preferred"));
    assertThat(first.getPath(), is("one | two | three"));
    assertThat(first.getPathIds(), is("1 | 2 | 3"));
    Taxon taxon1 = new TaxonImpl("not pref", null);
    taxon1.setPath(null);
    TaxonNode second = this.taxonService.getOrCreateTaxon(taxon1);
    assertThat(second.getNodeID(), is(first.getNodeID()));
    TaxonNode third = this.taxonService.getOrCreateTaxon(new TaxonImpl("not pref"));
    assertThat(third.getNodeID(), is(first.getNodeID()));
    TaxonNode foundTaxon = this.taxonService.findTaxonByName("not pref");
    assertThat(foundTaxon.getNodeID(), is(first.getNodeID()));
    foundTaxon = this.taxonService.findTaxonByName("preferred");
    assertThat(foundTaxon.getNodeID(), is(first.getNodeID()));
}