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

Example 16 with SpecimenNode

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

the class StudyImporterForGoMexSI2IT method assertSpecimenProperties.

private static void assertSpecimenProperties(GraphDatabaseService service) {
    Index<Node> taxa = service.index().forNodes("taxons");
    boolean detectedAtLeastOneLifeState = false;
    boolean detectedAtLeastOnePhysiologicalState = false;
    boolean detectedAtLeastOnePreyBodyPart = false;
    boolean detectedAtLeastOneBodyLength = false;
    boolean detectedAtLeastOneLocation = false;
    boolean detectedAtLeastOneFrequencyOfOccurrence = false;
    boolean detectedAtLeastOneTotalNumberConsumed = false;
    boolean detectedAtLeastOneTotalVolume = false;
    boolean detectedAtLeastOneGoMexSIProperty = false;
    assertThat(taxa, is(notNullValue()));
    for (Node taxonNode : taxa.query("name", "*")) {
        Iterable<Relationship> classifiedAs = taxonNode.getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
        for (Relationship classifiedA : classifiedAs) {
            Node specimenNode = classifiedA.getStartNode();
            detectedAtLeastOneLifeState |= specimenNode.hasProperty(SpecimenConstant.LIFE_STAGE_LABEL);
            detectedAtLeastOnePhysiologicalState |= specimenNode.hasProperty(SpecimenConstant.PHYSIOLOGICAL_STATE_LABEL);
            detectedAtLeastOnePreyBodyPart |= specimenNode.hasProperty(SpecimenConstant.BODY_PART_LABEL);
            detectedAtLeastOneBodyLength |= specimenNode.hasProperty(SpecimenConstant.LENGTH_IN_MM);
            detectedAtLeastOneFrequencyOfOccurrence |= specimenNode.hasProperty(SpecimenConstant.FREQUENCY_OF_OCCURRENCE);
            detectedAtLeastOneTotalNumberConsumed |= specimenNode.hasProperty(SpecimenConstant.TOTAL_COUNT);
            detectedAtLeastOneTotalVolume |= specimenNode.hasProperty(SpecimenConstant.TOTAL_VOLUME_IN_ML);
            detectedAtLeastOneGoMexSIProperty |= specimenNode.hasProperty(StudyImporterForGoMexSI2.GOMEXSI_NAMESPACE + "PRED_DATABASE_NAME");
            detectedAtLeastOneGoMexSIProperty |= specimenNode.hasProperty(StudyImporterForGoMexSI2.GOMEXSI_NAMESPACE + "PREY_DATABASE_NAME");
            if (specimenNode.hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED))) {
                detectedAtLeastOneLocation = true;
            }
        }
    }
    assertThat(detectedAtLeastOneLifeState, is(true));
    assertThat(detectedAtLeastOnePhysiologicalState, is(true));
    assertThat(detectedAtLeastOnePreyBodyPart, is(true));
    assertThat(detectedAtLeastOneLocation, is(true));
    assertThat(detectedAtLeastOneBodyLength, is(true));
    assertThat(detectedAtLeastOneFrequencyOfOccurrence, is(true));
    assertThat(detectedAtLeastOneTotalNumberConsumed, is(true));
    assertThat(detectedAtLeastOneTotalVolume, is(true));
    assertThat(detectedAtLeastOneGoMexSIProperty, is(true));
}

Example 17 with SpecimenNode

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

the class StudyImporterForINaturalistTest method importTestResponse.

@Test
public void importTestResponse() throws IOException, StudyImporterException {
    importer.parseJSON(getClass().getResourceAsStream("inaturalist/sample_inaturalist_response.json"), new ArrayList<Integer>() {

        {
            add(47);
        }
    }, new HashMap<Integer, InteractType>() {

        {
            put(13, InteractType.ATE);
        }
    });
    resolveNames();
    assertThat(NodeUtil.findAllStudies(getGraphDb()).size(), is(22));
    Study anotherStudy = nodeFactory.findStudy("INAT:831");
    assertThat(anotherStudy, is(notNullValue()));
    assertThat(anotherStudy.getCitation(), containsString("Ken-ichi Ueda. 2008. Argiope eating Orthoptera. iNaturalist.org. Accessed at <https://www.inaturalist.org/observations/831> on "));
    assertThat(anotherStudy.getExternalId(), is("https://www.inaturalist.org/observations/831"));
    anotherStudy = nodeFactory.findStudy("INAT:97380");
    assertThat(anotherStudy, is(notNullValue()));
    assertThat(anotherStudy.getCitation(), containsString("annetanne. 2012. Misumena vatia eating Eristalis nemorum."));
    assertThat(anotherStudy.getExternalId(), is("https://www.inaturalist.org/observations/97380"));
    Taxon sourceTaxonNode = taxonIndex.findTaxonByName("Arenaria interpres");
    assertThat(sourceTaxonNode, is(not(nullValue())));
    Iterable<Relationship> relationships = ((NodeBacked) sourceTaxonNode).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    for (Relationship relationship : relationships) {
        Node sourceSpecimen = relationship.getStartNode();
        assertThat(new SpecimenNode(sourceSpecimen).getBasisOfRecord().getName(), is("HumanObservation"));
        assertThat(new SpecimenNode(sourceSpecimen).getBasisOfRecord().getId(), is("TEST:HumanObservation"));
        assertThat(new SpecimenNode(sourceSpecimen).getExternalId(), containsString(TaxonomyProvider.ID_PREFIX_INATURALIST));
        Relationship ateRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(InteractType.ATE), Direction.OUTGOING);
        Node preySpecimen = ateRel.getEndNode();
        assertThat(preySpecimen, is(not(nullValue())));
        Relationship preyClassification = preySpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
        String actualPreyName = (String) preyClassification.getEndNode().getProperty("name");
        assertThat(actualPreyName, is("Crepidula fornicata"));
        Relationship locationRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED_AT), Direction.OUTGOING);
        assertThat((Double) locationRel.getEndNode().getProperty("latitude"), is(41.249813));
        assertThat((Double) locationRel.getEndNode().getProperty("longitude"), is(-72.542556));
        Relationship collectedRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat((Long) collectedRel.getProperty(SpecimenConstant.DATE_IN_UNIX_EPOCH), is(any(Long.class)));
    }
}

Example 18 with SpecimenNode

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

the class StudyImporterForRobledoTest method createAndPopulateStudy.

@Test
public void createAndPopulateStudy() throws StudyImporterException, NodeFactoryException {
    StudyImporterForRobledo importer = new StudyImporterForRobledo(new ParserFactoryLocal(), nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    assertNotNull(taxonIndex.findTaxonByName("Heliconia imbricata"));
    assertNotNull(taxonIndex.findTaxonByName("Renealmia alpinia"));
    assertNotNull(nodeFactory.findStudy(study.getTitle()));
    int count = 0;
    Iterable<Relationship> specimenRels = NodeUtil.getSpecimens(study);
    for (Relationship specimenRel : specimenRels) {
        Specimen specimen1 = new SpecimenNode(specimenRel.getEndNode());
        Location sampleLocation = specimen1.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getAltitude(), is(35.0));
        assertThat(Math.round(sampleLocation.getLongitude()), is(-84L));
        assertThat(Math.round(sampleLocation.getLatitude()), is(10L));
        count++;
    }
    assertThat(count, is(93));
}