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

Example 61 with Dataset

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

the class DatasetTest method unknownResourceURL.

@Test(expected = IOException.class)
public void unknownResourceURL() throws IOException, URISyntaxException {
    URL resource = getClass().getResource("archive.zip");
    File archive = new File(resource.toURI());
    assertThat(archive.exists(), is(true));
    URI parentDir = archive.getParentFile().toURI();
    Dataset dataset = new DatasetImpl("some/namespace", parentDir, inStream -> inStream);
    assertThat(dataset.retrieve(URI.create("archivezz.zip")), is(notNullValue()));
}

Example 62 with Dataset

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

the class NodeFactoryNeo4j method createInteraction.

@Override
public Interaction createInteraction(Study study) throws NodeFactoryException {
    InteractionNode interactionNode;
    Node node = graphDb.createNode();
    StudyNode studyNode = getOrCreateStudy(study);
    interactionNode = new InteractionNode(node);
    interactionNode.createRelationshipTo(studyNode, RelTypes.DERIVED_FROM);
    Dataset dataset = getOrCreateDatasetNoTx(study.getOriginatingDataset());
    if (dataset instanceof DatasetNode) {
        interactionNode.createRelationshipTo(dataset, RelTypes.ACCESSED_AT);
    }
    return interactionNode;
}

Example 63 with Dataset

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

the class NodeFactoryNeo4j method createStudyNode.

private StudyNode createStudyNode(Study study, Node node) {
    StudyNode studyNode;
    studyNode = new StudyNode(node, study.getTitle());
    studyNode.setCitation(study.getCitation());
    studyNode.setDOI(study.getDOI());
    if (study.getDOI() != null) {
        String doiString = study.getDOI().toString();
        createExternalIdRelationIfExists(node, doiString, RelTypes.HAS_DOI);
    }
    String externalId = getExternalIdOrDOI(study);
    studyNode.setExternalId(externalId);
    createExternalIdRelationIfExists(node, externalId, RelTypes.HAS_EXTERNAL_ID);
    Dataset dataset = getOrCreateDatasetNoTx(study.getOriginatingDataset());
    if (dataset instanceof DatasetNode) {
        studyNode.createRelationshipTo(dataset, RelTypes.IN_DATASET);
    }
    studyNode.getUnderlyingNode().setProperty(StudyConstant.TITLE_IN_NAMESPACE, getIdInNamespace(study));
    return studyNode;
}

Example 64 with Dataset

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

the class NodeFactoryNeo4j3 method getOrCreateDatasetNoTx.

@Override
protected Dataset getOrCreateDatasetNoTx(Dataset originatingDataset) {
    Dataset datasetCreated = null;
    if (originatingDataset != null && StringUtils.isNotBlank(originatingDataset.getNamespace())) {
        Node node = getGraphDb().findNode(NodeLabel.Dataset, DatasetConstant.NAMESPACE, originatingDataset.getNamespace());
        Node datasetNode = node == null ? createDatasetNode(originatingDataset) : node;
        datasetCreated = new DatasetNode(datasetNode);
    }
    return datasetCreated;
}

Example 65 with Dataset

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

the class ExporterAssociationsBase method addStudyInfo.

protected void addStudyInfo(StudyNode study, Map<String, String> properties) {
    final Dataset originatingDataset = study.getOriginatingDataset();
    properties.put(EOLDictionary.SOURCE, originatingDataset == null ? study.getCitation() : originatingDataset.getCitation());
    properties.put(EOLDictionary.REFERENCE_ID, "globi:ref:" + study.getNodeID());
}