Examples with RelationshipListener org.eol.globi.util.RelationshipListener used on opensource projects

Example 1 with RelationshipListener

use of org.eol.globi.util.RelationshipListener in project eol-globi-data by jhpoelen.

the class ExporterMeasurementOrFact method doExportStudy.

@Override
public void doExportStudy(StudyNode study, ExportUtil.Appender writer, boolean includeHeader) throws IOException {
    Map<String, String> properties = new TreeMap<String, String>();
    AtomicReference<IOException> lastException = new AtomicReference<>();
    RelationshipListener handler = collectedRel -> {
        Node specimenNode = collectedRel.getEndNode();
        if (isSpecimenClassified(specimenNode)) {
            try {
                writeMeasurements(writer, properties, specimenNode, collectedRel, study);
            } catch (IOException ex) {
                lastException.set(ex);
            }
        }
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), handler);
    if (lastException.get() != null) {
        throw lastException.get();
    }
}

Example 2 with RelationshipListener

use of org.eol.globi.util.RelationshipListener 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/globalbioticinteractions/globalbioticinteractions/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", new DOI("123.23", "222"), "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, new DatasetImpl("some/namespace", URI.create("https://some.uri"), inStream -> inStream));
    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(new GraphServiceFactoryProxy(getGraphDb())).index();
    NodeFactoryNeo4j nodeFactoryNeo4j = new NodeFactoryNeo4j2(getGraphDb());
    StudyImpl study1 = new StudyImpl("some study", new DOI("123.23", "222"), "come citation");
    study1.setOriginatingDataset(new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream));
    StudyNode someStudy = nodeFactoryNeo4j.getOrCreateStudy(study1);
    assertThat(interaction.getOriginatingDataset().getNamespace(), is(someStudy.getOriginatingDataset().getNamespace()));
    assertThat(interaction.getTitle(), is(someStudy.getTitle()));
    RelationshipType hasParticipant = NodeUtil.asNeo4j(RelTypes.HAS_PARTICIPANT);
    Set<Long> ids = new HashSet<>();
    List<Long> idList = new ArrayList<>();
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(someStudy.getUnderlyingNode()), new RelationshipListener() {

        @Override
        public void on(Relationship specimen) {
            assertThat(specimen.getEndNode().hasRelationship(Direction.INCOMING, hasParticipant), Is.is(true));
            Iterable<Relationship> relationships = specimen.getEndNode().getRelationships(hasParticipant, Direction.INCOMING);
            for (Relationship relationship : relationships) {
                long id = relationship.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 3 with RelationshipListener

use of org.eol.globi.util.RelationshipListener in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importWithLocalityAndLatLng.

@Test
public void importWithLocalityAndLatLng() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(LOCALITY_ID, "back:yard");
    link.put(LOCALITY_NAME, "my back yard");
    link.put(DECIMAL_LATITUDE, "12.2");
    link.put(DECIMAL_LONGITUDE, "13.2");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:10.12/34");
    listener.on(link);
    AtomicBoolean foundSpecimen = new AtomicBoolean(false);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        LocationNode sampleLocation = someSpecimen.getSampleLocation();
        assertThat(sampleLocation.getLatitude(), is(12.2d));
        assertThat(sampleLocation.getLongitude(), is(13.2d));
        assertThat(sampleLocation.getLocality(), is("my back yard"));
        assertThat(sampleLocation.getLocalityId(), is("back:yard"));
        foundSpecimen.set(true);
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(true));
}

Example 4 with RelationshipListener

use of org.eol.globi.util.RelationshipListener in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importRefutingClaim.

@Test
public void importRefutingClaim() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(ARGUMENT_TYPE_ID, "https://en.wiktionary.org/wiki/refute");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:10.12/34");
    listener.on(link);
    AtomicBoolean foundSpecimen = new AtomicBoolean(false);
    RelationshipListener relHandler = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.REFUTES)));
        assertFalse(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        foundSpecimen.set(true);
    };
    handleRelations(relHandler, RelTypes.REFUTES);
    assertThat(foundSpecimen.get(), is(true));
}

Example 5 with RelationshipListener

use of org.eol.globi.util.RelationshipListener in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importWithSex.

@Test
public void importWithSex() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_SEX_NAME, "female");
    link.put(SOURCE_SEX_ID, "some:female");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, InteractType.ATE.getIRI());
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_SEX_NAME, "male");
    link.put(TARGET_SEX_ID, "some:male");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_ID, "123");
    link.put(REFERENCE_CITATION, "");
    listener.on(link);
    AtomicInteger foundSpecimen = new AtomicInteger(0);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(NodeUtil.asNeo4j(InteractType.ATE)));
        if (someSpecimen.getUnderlyingNode().hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE))) {
            assertThat(someSpecimen.getSex().getName(), is("female"));
            assertThat(someSpecimen.getSex().getId(), is("some:female"));
        } else {
            assertThat(someSpecimen.getSex().getName(), is("male"));
            assertThat(someSpecimen.getSex().getId(), is("some:male"));
        }
        foundSpecimen.incrementAndGet();
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(2));
}