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

Example 11 with StudyNode

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

the class NodeUtil method findStudies.

public static void findStudies(GraphDatabaseService graphService, StudyNodeListener listener) {
    Index<Node> studyIndex = graphService.index().forNodes("studies");
    IndexHits<Node> hits = studyIndex.query("title", "*");
    for (Node hit : hits) {
        listener.onStudy(new StudyNode(hit));
    }
    hits.close();
}

Example 12 with StudyNode

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

the class ExporterOccurrences method addOccurrenceProperties.

private void addOccurrenceProperties(Node locationNode, Relationship collectedRelationship, Map<String, String> properties, Node specimenNode, Study study) throws IOException {
    if (specimenNode != null) {
        Iterable<Relationship> relationships = specimenNode.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
        Iterator<Relationship> iterator = relationships.iterator();
        if (iterator.hasNext()) {
            Relationship classifiedAs = iterator.next();
            if (classifiedAs != null) {
                Node taxonNode = classifiedAs.getEndNode();
                if (taxonNode.hasProperty(PropertyAndValueDictionary.EXTERNAL_ID)) {
                    String taxonId = (String) taxonNode.getProperty(PropertyAndValueDictionary.EXTERNAL_ID);
                    if (taxonId != null) {
                        properties.put(EOLDictionary.TAXON_ID, taxonId);
                    }
                }
                if (taxonNode.hasProperty(PropertyAndValueDictionary.NAME)) {
                    String taxonName = (String) taxonNode.getProperty(PropertyAndValueDictionary.NAME);
                    if (taxonName != null) {
                        properties.put(EOLDictionary.SCIENTIFIC_NAME, taxonName);
                    }
                }
            }
        }
    }
    properties.put(EOLDictionary.OCCURRENCE_ID, "globi:occur:" + specimenNode.getId());
    addProperty(properties, specimenNode, SpecimenConstant.BASIS_OF_RECORD_LABEL, EOLDictionary.BASIS_OF_RECORD);
    addProperty(properties, specimenNode, SpecimenConstant.LIFE_STAGE_LABEL, EOLDictionary.LIFE_STAGE);
    addProperty(properties, specimenNode, SpecimenConstant.PHYSIOLOGICAL_STATE_LABEL, EOLDictionary.PHYSIOLOGICAL_STATE);
    addProperty(properties, specimenNode, SpecimenConstant.BODY_PART_LABEL, EOLDictionary.BODY_PART);
    addProperty(properties, locationNode, LocationConstant.LATITUDE, EOLDictionary.DECIMAL_LATITUDE);
    addProperty(properties, locationNode, LocationConstant.LONGITUDE, EOLDictionary.DECIMAL_LONGITUDE);
    if (locationNode != null && locationNode.hasProperty(LocationConstant.ALTITUDE)) {
        properties.put(EOLDictionary.VERBATIM_ELEVATION, locationNode.getProperty(LocationConstant.ALTITUDE).toString() + " m");
    }
    addProperty(properties, ((StudyNode) study).getUnderlyingNode(), StudyConstant.TITLE, EOLDictionary.EVENT_ID);
    addCollectionDate(properties, collectedRelationship, EOLDictionary.EVENT_DATE);
}

Example 13 with StudyNode

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

the class ExporterAggregateUtil method exportDistinctInteractionsByStudy.

public static void exportDistinctInteractionsByStudy(Writer writer, GraphDatabaseService graphDatabase, RowWriter rowWriter) throws IOException {
    DB db = DBMaker.newMemoryDirectDB().compressionEnable().transactionDisable().make();
    final Map<Fun.Tuple3<Long, String, String>, List<String>> studyOccAggregate = db.createTreeMap("studyOccAggregate").make();
    NodeUtil.findStudies(graphDatabase, new StudyNodeListener() {

        @Override
        public void onStudy(StudyNode aStudy) {
            collectDistinctInteractions(aStudy, studyOccAggregate);
        }
    });
    for (Map.Entry<Fun.Tuple3<Long, String, String>, List<String>> distinctInteractions : studyOccAggregate.entrySet()) {
        rowWriter.writeRow(writer, new StudyNode(graphDatabase.getNodeById(distinctInteractions.getKey().a)), distinctInteractions.getKey().b, distinctInteractions.getKey().c, distinctInteractions.getValue());
    }
    db.close();
}

Example 14 with StudyNode

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

the class LinkerDOITest method createStudyDOIlookupCitationWithURL.

@Test
public void createStudyDOIlookupCitationWithURL() throws NodeFactoryException {
    StudyNode study = getNodeFactory().getOrCreateStudy(new StudyImpl("title", "some source", null, "http://bla"));
    new LinkerDOI(getGraphDb()).linkStudy(new DOIResolverThatFails(), study);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getCitation(), is("http://bla"));
    assertThat(study.getTitle(), is("title"));
}

Example 15 with StudyNode

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

the class LinkerDOITest method createStudyDOIlookupCitationEnabled.

@Test
public void createStudyDOIlookupCitationEnabled() throws NodeFactoryException {
    StudyImpl title = new StudyImpl("title", "some source", null, "some citation");
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, true);
    originatingDataset.setConfig(objectNode);
    title.setOriginatingDataset(originatingDataset);
    StudyNode study = getNodeFactory().getOrCreateStudy(title);
    new LinkerDOI(getGraphDb()).linkStudy(new TestDOIResolver(), study);
    assertThat(study.getSource(), is("some source"));
    assertThat(study.getDOI(), is("doi:some citation"));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
}