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

Example 36 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 37 with StudyImpl

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

the class LinkerDOITest method createStudyDOIlookupCitationDisabled.

@Test
public void createStudyDOIlookupCitationDisabled() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("title", "some source", null, "some citation");
    study1.setExternalId("some:id");
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, false);
    originatingDataset.setConfig(objectNode);
    study1.setOriginatingDataset(originatingDataset);
    Study study = getNodeFactory().getOrCreateStudy(study1);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getDOI(), is(nullValue()));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
    assertThat(study.getExternalId(), is("some:id"));
}

Example 38 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 39 with StudyImpl

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

the class LinkerDOITest method shouldResolveStudy.

@Test
public void shouldResolveStudy() {
    StudyImpl study = new StudyImpl("some title", "some source", "doi:some/doi", "some citation");
    assertFalse(LinkerDOI.shouldResolve(study));
}

Example 40 with StudyImpl

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