Examples with DatasetImpl org.globalbioticinteractions.dataset.DatasetImpl used on opensource projects

Example 6 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForZenodoMetadataTest method paginate.

@Test
public void paginate() throws IOException, StudyImporterException {
    AtomicInteger counter = new AtomicInteger(0);
    final DatasetImporterForZenodoMetadata studyImporterForZenodoMetadata = new DatasetImporterForZenodoMetadata(null, null);
    studyImporterForZenodoMetadata.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
        }
    });
    final DatasetImpl dataset = new DatasetImpl("name/space", URI.create("some:uri"), in -> in) {

        @Override
        public InputStream retrieve(URI resourceName) throws IOException {
            if (StringUtils.contains(resourceName.getHost(), "zenodo.org")) {
                counter.incrementAndGet();
            }
            InputStream is;
            if (URI.create("https://sandbox.zenodo.org/api/records/?sort=mostrecent&custom=%5Bobo%3ARO_0002453%5D%3A%5B%3A%5D&page=2&size=10").equals(resourceName)) {
                is = DatasetImporterForZenodoMetadataTest.class.getResourceAsStream("zenodo/search-results-page-2.json");
            } else if (URI.create("https://zenodo.org/api/records/?custom=%5Bobo%3ARO_0002453%5D%3A%5B%3A%5D").equals(resourceName)) {
                is = DatasetImporterForZenodoMetadataTest.class.getResourceAsStream("zenodo/search-results-page-1.json");
            } else {
                throw new IOException("kaboom!");
            }
            return is;
        }
    };
    studyImporterForZenodoMetadata.setDataset(dataset);
    studyImporterForZenodoMetadata.importStudy();
    assertThat(counter.get(), Is.is(2));
}

Example 7 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class NodeFactoryWithDatasetContextTest method getOrCreateStudyEmptyStudySource.

@Test
public void getOrCreateStudyEmptyStudySource() throws NodeFactoryException {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    factoryWithDS.getOrCreateStudy(new StudyImpl("some title"));
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).getOrCreateStudy(argument.capture());
    assertEquals("some title", argument.getValue().getTitle());
}

Example 8 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class NodeFactoryWithDatasetContextTest method getOrCreateStudy.

@Test
public void getOrCreateStudy() throws NodeFactoryException {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    factoryWithDS.getOrCreateStudy(new StudyImpl("some title"));
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).getOrCreateStudy(argument.capture());
    assertEquals("some title", argument.getValue().getTitle());
    String sourceCitation = CitationUtil.sourceCitationLastAccessed(dataset);
    assertThat(StringUtils.contains(sourceCitation, "<some:uri>. Accessed at <some:uri> on"), Is.is(true));
}

Example 9 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class InteractionListenerImplTest method processMessageWithOIgnoredInteractionType.

@Test
public void processMessageWithOIgnoredInteractionType() throws StudyImporterException, IOException {
    ResourceService resourceService = Mockito.mock(ResourceService.class);
    when(resourceService.retrieve(URI.create("interaction_types_ignored.csv"))).thenReturn(IOUtils.toInputStream("provided_interaction_type_id\nshouldBeIgnored", StandardCharsets.UTF_8)).thenReturn(IOUtils.toInputStream("provided_interaction_type_id\nshouldBeIgnored", StandardCharsets.UTF_8));
    when(resourceService.retrieve(URI.create("interaction_types_mapping.csv"))).thenReturn(IOUtils.toInputStream(getTestMap(), StandardCharsets.UTF_8));
    Dataset dataset = new DatasetImpl("bla", resourceService, URI.create("foo:bar"));
    InteractionListenerImpl interactionListener = new InteractionListenerImpl(nodeFactory, null, null, dataset);
    HashMap<String, String> interaction = new HashMap<>();
    interaction.put(SOURCE_TAXON_NAME, "sourceName");
    interaction.put(DatasetImporterForTSV.INTERACTION_TYPE_NAME, "shouldBeIgnored");
    interaction.put(TARGET_TAXON_NAME, "targetName");
    interaction.put(REFERENCE_ID, "citation");
    assertStudyCount(0L);
    interactionListener.on(interaction);
    assertStudyCount(0L);
}

Example 10 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl 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)));
}