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

Example 1 with RelTypes

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

the class InteractionImporter method createSpecimen.

private Specimen createSpecimen(Map<String, String> link, Study study, String taxonNameLabel, String taxonIdLabel, String bodyPartName, String bodyPartId, String lifeStageName, String lifeStageId, String taxonPathLabel, String taxonPathNamesLabel, String sexLabel, String sexId, String taxonRankLabel, String taxonPathIdsLabel) throws StudyImporterException {
    String argumentTypeId = link.get(ARGUMENT_TYPE_ID);
    RelTypes[] argumentType = refutes(argumentTypeId) ? new RelTypes[] { RelTypes.REFUTES } : new RelTypes[] { RelTypes.COLLECTED, RelTypes.SUPPORTS };
    String sourceTaxonName = link.get(taxonNameLabel);
    String sourceTaxonId = link.get(taxonIdLabel);
    TaxonImpl taxon = new TaxonImpl(sourceTaxonName, sourceTaxonId);
    String taxonRank = link.get(taxonRankLabel);
    if (StringUtils.isNotBlank(taxonRank)) {
        taxon.setRank(taxonRank);
    }
    String taxonPath = link.get(taxonPathLabel);
    if (StringUtils.isNotBlank(taxonPath)) {
        taxon.setPath(taxonPath);
    }
    String taxonPathIds = link.get(taxonPathIdsLabel);
    if (StringUtils.isNotBlank(taxonPathIds)) {
        taxon.setPathIds(taxonPathIds);
    }
    String taxonPathNames = link.get(taxonPathNamesLabel);
    if (StringUtils.isNotBlank(taxonPathNames)) {
        taxon.setPathNames(taxonPathNames);
    }
    Specimen source = nodeFactory.createSpecimen(study, taxon, argumentType);
    setBasisOfRecordIfAvailable(link, source);
    setDateTimeIfAvailable(link, source);
    setBodyPartIfAvailable(link, source, bodyPartName, bodyPartId);
    setLifeStageIfAvailable(link, source, lifeStageName, lifeStageId);
    setSexIfAvailable(link, source, sexLabel, sexId);
    return source;
}

Example 2 with RelTypes

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

the class NodeFactoryNeo4j method createSpecimen.

@Override
public SpecimenNode createSpecimen(Study study, Taxon taxon, RelTypes... types) throws NodeFactoryException {
    if (null == study) {
        throw new NodeFactoryException("specimen needs study, but none is specified");
    }
    if (null == types || types.length == 0) {
        throw new NodeFactoryException("specimen needs at least one study relationship type, but none is specified");
    }
    SpecimenNode specimen = createSpecimen();
    for (RelTypes type : types) {
        ((StudyNode) study).createRelationshipTo(specimen, type);
    }
    specimen.setOriginalTaxonDescription(taxon);
    if (StringUtils.isNotBlank(taxon.getName())) {
        extractTerms(taxon.getName(), specimen);
    }
    return specimen;
}

Example 3 with RelTypes

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

the class NodeFactoryFactoryTransactingOnDatasetNeo4j2 method create.

@Override
public NodeFactory create(GraphDatabaseService service) {
    GraphDatabaseService graphService = graphServiceFactory.getGraphService();
    try (Transaction tx = graphService.beginTx()) {
        NodeFactory nodeFactory = new NodeFactoryNeo4j2(graphService) {

            final AtomicReference<Transaction> tx = new AtomicReference<>();

            final AtomicBoolean closing = new AtomicBoolean(false);

            final AtomicLong counter = new AtomicLong(0);

            @Override
            public Dataset getOrCreateDataset(Dataset dataset) {
                if (closing.get()) {
                    throw new IllegalStateException("cannot create a dataset on closing node factory");
                } else {
                    startBatchTransactionIfNeeded();
                }
                return super.getOrCreateDataset(dataset);
            }

            void startBatchTransactionIfNeeded() {
                tx.getAndUpdate(transaction -> {
                    if (counter.getAndIncrement() % TRANSACTION_BATCH_SIZE_DEFAULT == 0) {
                        if (transaction != null) {
                            transaction.success();
                            transaction.close();
                            transaction = null;
                        }
                    }
                    return transaction == null ? beginTx() : transaction;
                });
            }

            private Transaction beginTx() {
                return graphServiceFactory.getGraphService().beginTx();
            }

            @Override
            public SpecimenNode createSpecimen(Study study, Taxon taxon, RelTypes... types) throws NodeFactoryException {
                startBatchTransactionIfNeeded();
                return super.createSpecimen(study, taxon, types);
            }

            @Override
            public void close() {
                tx.getAndUpdate(tx -> {
                    closing.set(true);
                    if (tx != null) {
                        tx.success();
                        tx.close();
                    }
                    return null;
                });
            }
        };
        tx.success();
        return nodeFactory;
    }
}