Examples with NodeTypeDirection org.eol.globi.util.NodeTypeDirection used on opensource projects

Example 26 with NodeTypeDirection

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

the class ExporterOccurrences method doExportStudy.

@Override
public void doExportStudy(StudyNode study, ExportUtil.Appender writer, boolean includeHeader) throws IOException {
    final List<IOException> first10Exceptions = new ArrayList<>();
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), collectedRel -> {
        Node specimenNode = collectedRel.getEndNode();
        if (isSpecimenClassified(specimenNode)) {
            try {
                handleSpecimen(study, writer, collectedRel, specimenNode);
            } catch (IOException e) {
                if (first10Exceptions.size() < 10) {
                    first10Exceptions.add(e);
                }
            }
        }
    });
    if (first10Exceptions.size() > 0) {
        throw first10Exceptions.get(0);
    }
}

Example 27 with NodeTypeDirection

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

the class ExporterRDF method exportStudy.

@Override
public void exportStudy(StudyNode study, ExportUtil.Appender appender, boolean includeHeader) throws IOException {
    AtomicReference<IOException> lastException = new AtomicReference<>();
    RelationshipListener handler = relationship -> {
        try {
            Node agentNode = relationship.getEndNode();
            for (Relationship ixnR : agentNode.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j())) {
                writeStatement(appender, Arrays.asList(blankNode(ixnR), iriNode(HAS_TYPE), iriNode(INTERACTION)));
                writeParticipantStatements(appender, ixnR, ixnR.getEndNode());
                writeParticipantStatements(appender, ixnR, agentNode);
                writeStatement(appender, Arrays.asList(blankNode(agentNode), iriNode(InteractType.valueOf(ixnR.getType().name()).getIRI()), blankNode(ixnR.getEndNode())));
            }
        } catch (IOException ex) {
            lastException.set(ex);
        }
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), handler);
    if (lastException.get() != null) {
        throw lastException.get();
    }
}

Example 28 with NodeTypeDirection

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

the class ExporterAssociations method doExportStudy.

@Override
public void doExportStudy(StudyNode study, ExportUtil.Appender writer, boolean includeHeader) throws IOException {
    Map<String, String> properties = new TreeMap<String, String>();
    AtomicReference<IOException> lastException = new AtomicReference<>();
    RelationshipListener handler = collectedRel -> {
        Node specimenNode = collectedRel.getEndNode();
        if (isSpecimenClassified(specimenNode)) {
            try {
                handleSpecimen(study, writer, properties, specimenNode);
            } catch (IOException ex) {
                lastException.set(ex);
            }
        }
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), handler);
    if (lastException.get() != null) {
        throw lastException.get();
    }
}

Example 29 with NodeTypeDirection

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

the class ExporterSiteMapForNames method export.

@Override
public void export(GraphDatabaseService graphDatabase, File baseDir) throws StudyImporterException {
    Set<String> names = new HashSet<String>();
    names.add("Homo sapiens");
    NodeUtil.findStudies(graphDatabase, node -> NodeUtil.handleCollectedRelationships(new NodeTypeDirection(new StudyNode(node).getUnderlyingNode()), specimen -> {
        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);
}