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

Example 6 with TaxonNode

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

the class NodeUtil method connectTaxa.

public static void connectTaxa(Taxon taxon, TaxonNode taxonNode, GraphDatabaseService graphDb, RelTypes relType) {
    Transaction tx = graphDb.beginTx();
    try {
        TaxonNode sameAsTaxon = new TaxonNode(graphDb.createNode());
        TaxonUtil.copy(taxon, sameAsTaxon);
        taxonNode.getUnderlyingNode().createRelationshipTo(sameAsTaxon.getUnderlyingNode(), asNeo4j(relType));
        tx.success();
    } finally {
        tx.finish();
    }
}

Example 7 with TaxonNode

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

the class ExporterSiteMapForNames method export.

@Override
public void export(GraphDatabaseService graphDatabase, String baseDir) throws StudyImporterException {
    Set<String> names = new HashSet<String>();
    names.add("Homo sapiens");
    // just do it once
    final List<Study> allStudies = NodeUtil.findAllStudies(graphDatabase);
    for (Study allStudy : allStudies) {
        final Iterable<Relationship> specimens = NodeUtil.getSpecimens(allStudy);
        for (Relationship specimen : specimens) {
            final Iterable<Relationship> relationships = specimen.getEndNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
            if (relationships.iterator().hasNext()) {
                final Node endNode = relationships.iterator().next().getEndNode();
                final TaxonNode taxonNode = new TaxonNode(endNode);
                names.add(taxonNode.getName());
            }
        }
    }
    final String queryParamName = "interactionType=interactsWith&sourceTaxon=";
    final String siteMapLocation = "https://depot.globalbioticinteractions.org/snapshot/target/data/sitemap/names/";
    SiteMapUtils.generateSiteMap(names, baseDir, queryParamName, siteMapLocation);
}

Example 8 with TaxonNode

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

the class StudyImporterForGeminaTest method importFewLines.

@Test
public void importFewLines() throws StudyImporterException {
    StudyImporterForGemina importer = new StudyImporterForGemina(new TestParserFactory(firstFewLines), nodeFactory);
    importStudy(importer);
    assertHuman();
    Taxon taxon = taxonIndex.findTaxonByName("Bacillus anthracis");
    assertThat(taxon, is(notNullValue()));
    assertThat(taxon.getExternalId(), is("NCBI:1392"));
    List<String> antraxHosts = new ArrayList<String>();
    Iterable<Relationship> relationships = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.INCOMING);
    for (Relationship rel : relationships) {
        Node specimen = rel.getStartNode();
        Iterable<Relationship> pathogenRels = specimen.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.PATHOGEN_OF));
        for (Relationship pathogenRel : pathogenRels) {
            Relationship singleRelationship = pathogenRel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
            antraxHosts.add(new TaxonNode(singleRelationship.getEndNode()).getName());
        }
    }
    assertThat(antraxHosts, hasItem("Equus caballus"));
}

Example 9 with TaxonNode

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

the class LinkerTaxonIndexTest method assertSingleHit.

protected void assertSingleHit(String query) {
    IndexHits<Node> hits;
    Node next;
    hits = getGraphDb().index().forNodes(LinkerTaxonIndex.INDEX_TAXON_NAMES_AND_IDS).query(query);
    next = hits.next();
    assertThat(new TaxonNode(next).getName(), is("Homo sapiens"));
    assertThat(hits.hasNext(), is(false));
    hits.close();
}

Example 10 with TaxonNode

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

the class LinkerTestUtil method assertHasOther.

public static Collection<String> assertHasOther(String name, int expectedCount, TaxonIndex taxonIndex, RelTypes relType) throws NodeFactoryException {
    Set<String> externalIds = new HashSet<>();
    Taxon taxon1 = taxonIndex.findTaxonByName(name);
    assertThat(taxon1, is(notNullValue()));
    assertThat(taxon1.getName(), is(name));
    Iterable<Relationship> rels = ((NodeBacked) taxon1).getUnderlyingNode().getRelationships(NodeUtil.asNeo4j(relType), Direction.OUTGOING);
    for (Relationship rel : rels) {
        externalIds.add(new TaxonNode(rel.getEndNode()).getExternalId());
    }
    assertThat("expected [" + expectedCount + "] relationships for [" + name + "]: [" + externalIds.toString() + "]", externalIds.size(), is(expectedCount));
    return externalIds;
}