Examples with GraphServiceFactoryProxy org.eol.globi.db.GraphServiceFactoryProxy used on opensource projects

Example 1 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class ResolvingTaxonIndexTest method ensureThatEnrichedPropertiesAreLinked.

@Test
public void ensureThatEnrichedPropertiesAreLinked() throws NodeFactoryException {
    this.taxonService = new ResolvingTaxonIndex(new PropertyEnricher() {

        @Override
        public Map<String, String> enrichFirstMatch(Map<String, String> properties) throws PropertyEnricherException {
            return enrichAllMatches(properties).get(0);
        }

        @Override
        public List<Map<String, String>> enrichAllMatches(Map<String, String> properties) throws PropertyEnricherException {
            Taxon taxon1 = enrichTaxonWithSuffix(properties, "1");
            Taxon taxon2 = enrichTaxonWithSuffix(properties, "2");
            return Arrays.asList(TaxonUtil.taxonToMap(taxon1), TaxonUtil.taxonToMap(taxon2));
        }

        Taxon enrichTaxonWithSuffix(Map<String, String> properties, String suffix) {
            Taxon taxon = TaxonUtil.mapToTaxon(properties);
            taxon.setPathNames("kingdom" + suffix + CharsetConstant.SEPARATOR + "phylum" + CharsetConstant.SEPARATOR + "etc" + CharsetConstant.SEPARATOR);
            taxon.setPath("a kingdom name" + suffix + CharsetConstant.SEPARATOR + "a phylum name" + CharsetConstant.SEPARATOR + "a etc name" + CharsetConstant.SEPARATOR);
            taxon.setPathIds("a kingdom id" + suffix + CharsetConstant.SEPARATOR + "a phylum id" + CharsetConstant.SEPARATOR + "a etc id" + CharsetConstant.SEPARATOR);
            taxon.setExternalId("anExternalId" + suffix);
            taxon.setCommonNames(EXPECTED_COMMON_NAMES);
            return taxon;
        }

        @Override
        public void shutdown() {
        }
    }, getGraphDb());
    assertThat(getGraphDb().index().existsForNodes("taxons"), is(false));
    assertThat(getGraphDb().index().existsForNodes("thisDoesnoTExist"), is(false));
    TaxonNode indexedTaxonNode = taxonService.getOrCreateTaxon(new TaxonImpl("some name1"));
    assertThat(getGraphDb().index().existsForNodes("taxons"), is(true));
    assertEnrichedPropertiesSet(indexedTaxonNode, "1");
    TaxonNode someFoundTaxonNode = taxonService.findTaxonByName("some name1");
    assertThat(someFoundTaxonNode.getNodeID(), is(indexedTaxonNode.getNodeID()));
    assertEnrichedPropertiesSet(someFoundTaxonNode, "1");
    {
        Index<Node> ids = getGraphDb().index().forNodes(INDEX_TAXON_NAMES_AND_IDS, MapUtil.stringMap(IndexManager.PROVIDER, "lucene", "type", "fulltext"));
        assertThat(ids.query("path:\"some name2\"").size(), is(0));
    }
    LinkerTaxonIndex linkerTaxonIndex = new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb()));
    linkerTaxonIndex.index();
    {
        Index<Node> ids = getGraphDb().index().forNodes(INDEX_TAXON_NAMES_AND_IDS, MapUtil.stringMap(IndexManager.PROVIDER, "lucene", "type", "fulltext"));
        IndexHits<Node> hits = ids.query("path:\"a kingdom name2\"");
        assertThat(hits.size(), is(1));
        for (Node hit : hits) {
            TaxonNode taxonHit = new TaxonNode(hit);
            assertNotNull(taxonHit);
            assertThat(taxonHit.getNodeID(), is(indexedTaxonNode.getNodeID()));
        }
    }
    TaxonNode someOtherFoundTaxonNodeTake2 = taxonService.findTaxonByName("some name2");
    assertNull(someOtherFoundTaxonNodeTake2);
}

Example 2 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy 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 GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class LinkerDOITest method assertLinkMany.

private void assertLinkMany(long numberOfStudies) throws NodeFactoryException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", null, "HOCKING"));
    getNodeFactory().getOrCreateStudy(new StudyImpl("title1", null, "MEDAN"));
    assertThat(study.getDOI(), is(nullValue()));
    for (int i = 0; i < numberOfStudies; i++) {
        getNodeFactory().getOrCreateStudy(new StudyImpl("id" + i, null, "foo bar this is not a citation" + i));
    }
    new LinkerDOI(new GraphServiceFactoryProxy(getGraphDb()), new DOIResolver() {

        @Override
        public Map<String, DOI> resolveDoiFor(Collection<String> references) throws IOException {
            Map<String, DOI> resolved = new HashMap<>();
            for (String reference : references) {
                resolved.put(reference, resolveDoiFor(reference));
            }
            return resolved;
        }

        @Override
        public DOI resolveDoiFor(String reference) throws IOException {
            return new DOI("123", "456");
        }
    }).index();
    StudyNode studyResolved = getNodeFactory().getOrCreateStudy(study);
    assertThat(studyResolved.getDOI(), is(new DOI("123", "456")));
}

Example 4 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class LinkerDOITest method doLink.

@Test
public void doLink() throws NodeFactoryException, PropertyEnricherException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", null, "some citation"));
    new LinkerDOI(new GraphServiceFactoryProxy(getGraphDb())).index();
    Study studyResolved = nodeFactory.getOrCreateStudy(study);
    assertThat(studyResolved.getDOI(), is(nullValue()));
    assertThat(study.getDOI(), is(nullValue()));
}

Example 5 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class LinkerTaxonIndexTest method linkingWithNameOnly.

@Test
public void linkingWithNameOnly() throws NodeFactoryException {
    Taxon taxonFound = new TaxonImpl("urn:catalog:AMNH:Mammals:M-39582", null);
    taxonIndex.getOrCreateTaxon(taxonFound);
    Taxon foundTaxon = taxonIndex.findTaxonByName("urn:catalog:AMNH:Mammals:M-39582");
    assertThat(foundTaxon, is(not(nullValue())));
    assertThat(foundTaxon.getName(), is("urn:catalog:AMNH:Mammals:M-39582"));
    resolveNames();
    new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb())).index();
    IndexHits<Node> hits = getGraphDb().index().forNodes(LinkerTaxonIndex.INDEX_TAXON_NAMES_AND_IDS).query("path:\"urn:catalog:AMNH:Mammals:M-39582\"");
    Node next = hits.next();
    assertThat(new TaxonNode(next).getName(), is("urn:catalog:AMNH:Mammals:M-39582"));
    assertThat(hits.hasNext(), is(false));
    hits.close();
}