Examples with Dataset org.eol.globi.service.Dataset used on opensource projects

Example 21 with Dataset

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

the class NodeFactoryNeo4j method createStudy.

@Override
public StudyNode createStudy(Study study) {
    Transaction transaction = graphDb.beginTx();
    StudyNode studyNode;
    try {
        Node node = graphDb.createNode();
        studyNode = new StudyNode(node, study.getTitle());
        studyNode.setSource(study.getSource());
        studyNode.setCitation(study.getCitation());
        studyNode.setDOI(study.getDOI());
        if (StringUtils.isBlank(study.getExternalId()) && StringUtils.isNotBlank(study.getDOI())) {
            studyNode.setExternalId(ExternalIdUtil.urlForExternalId(study.getDOI()));
        } else {
            studyNode.setExternalId(study.getExternalId());
        }
        studyNode.setSourceId(study.getSourceId());
        Dataset dataset = getOrCreateDatasetNoTx(study.getOriginatingDataset());
        if (dataset != null && dataset instanceof DatasetNode) {
            studyNode.createRelationshipTo(dataset, RelTypes.IN_DATASET);
        }
        studies.add(node, StudyConstant.TITLE, study.getTitle());
        studies.add(node, StudyConstant.TITLE_IN_NAMESPACE, getTitleInNamespace(study));
        transaction.success();
    } finally {
        transaction.finish();
    }
    return studyNode;
}

Example 22 with Dataset

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

the class NodeFactoryNeo4j method getOrCreateDatasetNoTx.

private Dataset getOrCreateDatasetNoTx(Dataset originatingDataset) {
    Dataset datasetCreated = null;
    if (originatingDataset != null && StringUtils.isNotBlank(originatingDataset.getNamespace())) {
        IndexHits<Node> datasetHits = datasets.get(DatasetConstant.NAMESPACE, originatingDataset.getNamespace());
        Node datasetNode = datasetHits.hasNext() ? datasetHits.next() : createDatasetNode(originatingDataset);
        datasetCreated = new DatasetNode(datasetNode);
    }
    return datasetCreated;
}

Example 23 with Dataset

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

the class NodeFactoryNeo4j method createInteraction.

@Override
public Interaction createInteraction(Study study) throws NodeFactoryException {
    Transaction transaction = graphDb.beginTx();
    InteractionNode interactionNode;
    try {
        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 != null && dataset instanceof DatasetNode) {
            interactionNode.createRelationshipTo(dataset, RelTypes.ACCESSED_AT);
        }
        transaction.success();
    } finally {
        transaction.finish();
    }
    return interactionNode;
}

Example 24 with Dataset

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

the class DatasetFinderLocalTest method init.

@Before
public void init() throws URISyntaxException {
    URL accessFile = getClass().getResource("/test-cache/globalbioticinteractions/template-dataset/access.tsv");
    assertNotNull(accessFile);
    File cacheDir = new File(accessFile.toURI()).getParentFile().getParentFile().getParentFile();
    datasetFinderLocal = new DatasetFinderLocal(cacheDir.getAbsolutePath(), dataset -> CacheUtil.cacheFor(dataset.getNamespace(), cacheDir.getAbsolutePath()));
}

Example 25 with Dataset

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

the class DatasetFinderLocalTest method dataset.

@Test
public void dataset() throws DatasetFinderException, URISyntaxException {
    Dataset actual = datasetFinderLocal.datasetFor("globalbioticinteractions/template-dataset");
    assertThat(actual, is(notNullValue()));
    assertThat(actual.getConfigURI().toString(), endsWith("/test-cache/globalbioticinteractions/template-dataset/6bfc17b8717e6e8e478552f12404bc8887d691a155ffd9cd9bfc80cb6747c5d2!/template-dataset-8abd2ba18457288f33527193299504015fae6def/globi.json"));
    assertThat(actual.getArchiveURI().toString(), is("https://github.com/globalbioticinteractions/template-dataset/archive/8abd2ba18457288f33527193299504015fae6def.zip"));
    assertThat(actual.getCitation(), is("Jorrit H. Poelen. 2014. Species associations manually extracted from literature. Accessed on 2017-09-14T16:45:38Z via <https://github.com/globalbioticinteractions/template-dataset/archive/8abd2ba18457288f33527193299504015fae6def.zip>."));
}