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

Example 1 with StudyNode

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

the class LinkerDOI method link.

@Override
public void link() {
    Index<Node> taxons = this.graphDb.index().forNodes("studies");
    IndexHits<Node> hits = taxons.query("*:*");
    int counter = 0;
    int counterResolved = 0;
    String msg = "linking study citations to DOIs";
    LOG.info(msg + " started...");
    StopWatch stopWatch = new StopWatch();
    stopWatch.start();
    Map<String, StudyNode> batch = new HashMap<>();
    for (Node hit : hits) {
        counter++;
        StudyNode study = new StudyNode(hit);
        if (shouldResolve(study)) {
            counterResolved++;
            batch.put(study.getCitation(), study);
        }
        if (batch.size() >= BATCH_SIZE) {
            LOG.info(logProgress(counterResolved, stopWatch));
            resolveBatch(doiResolver, batch);
            batch.clear();
        }
    }
    resolveBatch(doiResolver, batch);
    LOG.info(msg + " complete. Out of [" + counter + "] references, [" + counterResolved + "] needed resolving.");
    if (counter % 100 != 0) {
        LOG.info(logProgress(counterResolved, stopWatch));
    }
    stopWatch.stop();
}

Example 2 with StudyNode

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

the class ExporterAggregateUtil method collectDistinctInteractions.

public static void collectDistinctInteractions(StudyNode aStudy, Map<Fun.Tuple3<Long, String, String>, List<String>> studyOccAggregate) {
    final Iterable<Relationship> specimens = NodeUtil.getSpecimens(aStudy);
    for (Relationship specimen : specimens) {
        final Iterable<Relationship> interactions = specimen.getEndNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j());
        for (Relationship interaction : interactions) {
            if (!interaction.hasProperty(PropertyAndValueDictionary.INVERTED)) {
                final Node targetSpecimen = interaction.getEndNode();
                final Node sourceSpecimen = interaction.getStartNode();
                final String sourceTaxonExternalId = getExternalIdForTaxonOf(sourceSpecimen);
                final String targetTaxonExternalId = getExternalIdForTaxonOf(targetSpecimen);
                if (sourceTaxonExternalId != null && targetTaxonExternalId != null) {
                    final Fun.Tuple3<Long, String, String> key = new Fun.Tuple3<Long, String, String>(aStudy.getNodeID(), sourceTaxonExternalId, interaction.getType().name());
                    List<String> targetTaxonExternalIds = studyOccAggregate.get(key);
                    if (targetTaxonExternalIds == null) {
                        targetTaxonExternalIds = new ArrayList<String>();
                    }
                    if (!targetTaxonExternalIds.contains(targetTaxonExternalId)) {
                        targetTaxonExternalIds.add(targetTaxonExternalId);
                    }
                    studyOccAggregate.put(key, targetTaxonExternalIds);
                }
            }
        }
    }
}

Example 3 with StudyNode

use of org.eol.globi.domain.StudyNode 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 4 with StudyNode

use of org.eol.globi.domain.StudyNode 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", "some source", null, "some citation"));
    new LinkerDOI(getGraphDb()).link();
    Study studyResolved = nodeFactory.getOrCreateStudy(study);
    assertThat(studyResolved.getDOI(), is(nullValue()));
    assertThat(study.getDOI(), is(nullValue()));
}

Example 5 with StudyNode

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

the class LinkerDOITest method addDOIToStudy.

@Test
public void addDOIToStudy() throws NodeFactoryException {
    DOIResolver doiResolver = new DOIResolver() {

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

        @Override
        public String resolveDoiFor(String reference) throws IOException {
            return "doi:1234";
        }
    };
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("my title", "some source", null, ExternalIdUtil.toCitation("my contr", "some description", null)));
    new LinkerDOI(getGraphDb()).linkStudy(doiResolver, study);
    assertThat(study.getDOI(), is("doi:1234"));
    assertThat(study.getExternalId(), is("http://dx.doi.org/1234"));
    assertThat(study.getCitation(), is("my contr. some description"));
    study = getNodeFactory().getOrCreateStudy(new StudyImpl("my other title", "some source", null, ExternalIdUtil.toCitation("my contr", "some description", null)));
    new LinkerDOI(getGraphDb()).linkStudy(new DOIResolverThatExplodes(), study);
    assertThat(study.getDOI(), nullValue());
    assertThat(study.getExternalId(), nullValue());
    assertThat(study.getCitation(), is("my contr. some description"));
}