Examples with NodeFactoryWithDatasetContext org.eol.globi.data.NodeFactoryWithDatasetContext used on opensource projects

Example 1 with NodeFactoryWithDatasetContext

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

the class LinkerTrustyNanoPubsTest method writingNanopub.

@Test
public void writingNanopub() throws NodeFactoryException, OpenRDFException, IOException, MalformedNanopubException, TrustyUriException {
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com/dataset"));
    NodeFactoryWithDatasetContext factory = populateDataset(dataset);
    LinkerTrustyNanoPubs linker = new LinkerTrustyNanoPubs(getGraphDb());
    linker.link();
    DatasetNode datasetNode = (DatasetNode) factory.getOrCreateDataset(dataset);
    Iterable<Relationship> rels = datasetNode.getUnderlyingNode().getRelationships(NodeUtil.asNeo4j(RelTypes.ACCESSED_AT), Direction.INCOMING);
    InteractionNode interactionNode = new InteractionNode(rels.iterator().next().getStartNode());
    String nanoPubText = LinkerTrustyNanoPubs.writeNanoPub(datasetNode, interactionNode);
    InputStream rdfIn = IOUtils.toInputStream(nanoPubText);
    String rdfActual = toTrigString(rdfIn);
    String rdfExpected = toTrigString(getClass().getResourceAsStream("nanopub.trig"));
    assertThat(rdfActual, is(rdfExpected));
}

Example 2 with NodeFactoryWithDatasetContext

use of org.eol.globi.data.NodeFactoryWithDatasetContext 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 3 with NodeFactoryWithDatasetContext

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

the class LinkerTrustyNanoPubsTest method populateDataset.

public NodeFactoryWithDatasetContext populateDataset(DatasetImpl dataset) 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, dataset);
    Interaction interaction = factory.createInteraction(factory.createStudy(study));
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    Taxon mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonEOL = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonEOL, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxonEOL);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxonEOL));
    donald.ate(mickey);
    return factory;
}

Example 4 with NodeFactoryWithDatasetContext

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

the class GitHubImporterFactory method createImporter.

public StudyImporter createImporter(Dataset dataset, final NodeFactory nodeFactory) throws StudyImporterException {
    Class<? extends StudyImporter> anImporter = findImporterFor(dataset);
    try {
        Constructor<? extends StudyImporter> constructor = anImporter.getConstructor(ParserFactory.class, NodeFactory.class);
        ParserFactoryForDataset parserFactory = new ParserFactoryForDataset(dataset);
        StudyImporter studyImporter = constructor.newInstance(parserFactory, new NodeFactoryWithDatasetContext(nodeFactory, dataset));
        studyImporter.setDataset(dataset);
        return studyImporter;
    } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException | InstantiationException e) {
        throw new StudyImporterException("failed to instantiate importer for [" + dataset.getNamespace() + "]", e);
    }
}

Example 5 with NodeFactoryWithDatasetContext

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

the class ExportFlatInteractionsTest method init.

@Before
public void init() throws IOException {
    super.startGraphDb();
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"));
    factory = new NodeFactoryWithDatasetContext(nodeFactory, dataset);
}