Examples with NodeTypeDirection org.eol.globi.util.NodeTypeDirection used on opensource projects

Example 11 with NodeTypeDirection

use of org.eol.globi.util.NodeTypeDirection in project eol-globi-data by jhpoelen.

the class DatasetImporterForRaymondTest method assertThatAllStudiesHaveAtLeastOneInteraction.

protected void assertThatAllStudiesHaveAtLeastOneInteraction() {
    AtomicBoolean foundAtLeastOne = new AtomicBoolean(false);
    List<StudyNode> studies = NodeUtil.findAllStudies(getGraphDb());
    for (StudyNode study : studies) {
        NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), next -> {
            Specimen specimen = new SpecimenNode(next.getEndNode());
            assertThat(specimen.getSampleLocation().getLongitude(), is(-61.66666667d));
            assertThat(next.getProperty(SpecimenConstant.EVENT_DATE), is(not(nullValue())));
            foundAtLeastOne.set(true);
        });
    }
    assertTrue(foundAtLeastOne.get());
}

Example 12 with NodeTypeDirection

use of org.eol.globi.util.NodeTypeDirection in project eol-globi-data by jhpoelen.

the class DatasetImporterForRoopnarineTest method validateSpecimen.

private int validateSpecimen() {
    AtomicInteger totalRels = new AtomicInteger(0);
    RelationshipListener handler = rel -> {
        Node specimen = rel.getEndNode();
        assertNotNull(specimen);
        Relationship collectedAtRelationship = specimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED_AT), Direction.OUTGOING);
        assertNotNull("missing location information", collectedAtRelationship);
        Node locationNode = collectedAtRelationship.getEndNode();
        assertNotNull(locationNode);
        assertTrue(locationNode.hasProperty(LocationConstant.LATITUDE));
        assertTrue(locationNode.hasProperty(LocationConstant.LONGITUDE));
        totalRels.incrementAndGet();
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(getStudySingleton(getGraphDb()).getUnderlyingNode()), handler);
    return totalRels.get();
}

Example 13 with NodeTypeDirection

use of org.eol.globi.util.NodeTypeDirection in project eol-globi-data by jhpoelen.

the class DatasetImporterForSeltmannIT method importArchive.

private void importArchive(String archiveName) throws StudyImporterException {
    DatasetImporterForSeltmann importer = new DatasetImporterForSeltmann(null, nodeFactory);
    URI archiveURI = URI.create(ARCHIVE_URI_PREFIX + archiveName);
    DatasetImpl dataset = new DatasetImpl("some/namespace", archiveURI, inStream -> inStream);
    createAndSetConfig(archiveURI, dataset);
    importer.setDataset(dataset);
    importStudy(importer);
    List<StudyNode> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (StudyNode allStudy : allStudies) {
        assertThat(allStudy.getCitation(), is("Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388"));
        NodeUtil.handleCollectedRelationships(new NodeTypeDirection(allStudy.getUnderlyingNode()), relationship -> {
            Specimen spec = new SpecimenNode(relationship.getEndNode());
            Term basisOfRecord = spec.getBasisOfRecord();
            assertThat(basisOfRecord.getId(), either(is("TEST:PreservedSpecimen")).or(is("TEST:LabelObservation")));
            assertThat(basisOfRecord.getName(), either(is("PreservedSpecimen")).or(is("LabelObservation")));
        });
    }
    assertThat(taxonIndex.findTaxonByName("Megandrena mentzeliae"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Mentzelia tricuspis"), is(notNullValue()));
}

Example 14 with NodeTypeDirection

use of org.eol.globi.util.NodeTypeDirection in project eol-globi-data by jhpoelen.

the class DatasetImporterForSimonsTest method createAndPopulateStudy.

@Test
public void createAndPopulateStudy() throws StudyImporterException {
    String csvString = "\"Obs\",\"spcode\", \"sizecl\", \"cruise\", \"stcode\", \"numstom\", \"numfood\", \"pctfull\", \"predator famcode\", \"prey\", \"number\", \"season\", \"depth\", \"transect\", \"alphcode\", \"taxord\", \"station\", \"long\", \"lat\", \"time\", \"sizeclass\", \"predator\"\n";
    csvString += "1, 1, 16, 3, 2, 6, 6, 205.5, 1, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 60, \"Chandeleur Islands\", \"aabd\", 47.11, \"C2\", 348078.84, 3257617.25, 313, \"201-300\", \"Rhynchoconger flavus\"\n";
    csvString += "1, 1, 16, 3, 2, 6, 6, 205.5, 1, \"Ampelisca agassizi\", 1, \"Summer\", 60, \"Chandeleur Islands\", \"aabd\", 47.11, \"C2\", 348078.84, 3257617.25, 313, \"201-300\", \"Rhynchoconger flavus\"\n";
    csvString += "2, 11, 2, 1, 1, 20, 15, 592.5, 6, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 20, \"Chandeleur Islands\", \"aabd\", 47.11, \"C1\", 344445.31, 3323087.25, 144, \"26-50\", \"Halieutichthys aculeatus\"\n";
    DatasetImporterForSimons importer = new DatasetImporterForSimons(new TestParserFactory(csvString), nodeFactory);
    importStudy(importer);
    assertNotNull(taxonIndex.findTaxonByName("Rhynchoconger flavus"));
    assertNotNull(taxonIndex.findTaxonByName("Halieutichthys aculeatus"));
    assertNotNull(taxonIndex.findTaxonByName("Ampelisca sp. (abdita complex)"));
    assertNotNull(nodeFactory.findStudy(new StudyImpl("Simons 1997")));
    assertNotNull(nodeFactory.findLocation(new LocationImpl(LAT_1, LONG_1, -60.0d, null)));
    assertNotNull(nodeFactory.findLocation(new LocationImpl(LAT_2, LONG_2, -20.0d, null)));
    assertNotNull(nodeFactory.findSeason("summer"));
    StudyNode foundStudy = (StudyNode) nodeFactory.findStudy(new StudyImpl("Simons 1997"));
    assertNotNull(foundStudy);
    RelationshipListener handler = rel -> {
        Node specimen = rel.getEndNode();
        Node speciesNode = specimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode();
        String scientificName = (String) speciesNode.getProperty("name");
        if ("Rhynchoconger flavus".equals(scientificName)) {
            String seasonName = "summer";
            String genusName = "Ampelisca sp. (abdita complex)";
            double length = (201.0d + 300.0d) / 2.0d;
            assertSpecimen(specimen, LONG_1, LAT_1, -60.0, seasonName, genusName, length);
            Iterable<Relationship> ateRelationships = specimen.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
            List<String> preyNames = new ArrayList<String>();
            for (Relationship ateRel : ateRelationships) {
                Node preyTaxonNode = ateRel.getEndNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS)).iterator().next().getEndNode();
                preyNames.add(preyTaxonNode.getProperty(PropertyAndValueDictionary.NAME).toString());
            }
            assertThat(preyNames, hasItem("Ampelisca sp. (abdita complex)"));
            assertThat(preyNames.contains("Ampelisca agassizi"), Is.is(true));
            assertThat(preyNames.size(), Is.is(2));
        } else if ("Halieutichthys aculeatus".equals(scientificName)) {
            String genusName = "Ampelisca sp. (abdita complex)";
            String seasonName = "summer";
            double length = (26.0d + 50.0d) / 2.0d;
            assertSpecimen(specimen, LONG_2, LAT_2, -20.0, seasonName, genusName, length);
        } else if ("Ampelisca sp. (abdita complex)".equals(scientificName)) {
            Node locationNode = specimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED_AT), Direction.OUTGOING).getEndNode();
            assertNotNull(locationNode);
            assertTrue(locationNode.hasProperty(LocationConstant.LONGITUDE));
            assertTrue(locationNode.hasProperty(LocationConstant.ALTITUDE));
            assertTrue(locationNode.hasProperty(LocationConstant.LATITUDE));
        } else if ("Ampelisca agassizi".equals(scientificName)) {
            assertPreySpecimen(specimen, LONG_1, LAT_1, -60.0);
        } else {
            fail("found predator with unexpected scientificName [" + scientificName + "]");
        }
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(foundStudy.getUnderlyingNode()), handler);
}

Example 15 with NodeTypeDirection

use of org.eol.globi.util.NodeTypeDirection in project eol-globi-data by jhpoelen.

the class DatasetImporterForBaremoreTest method validateSpecimen.

private int validateSpecimen(StudyNode study) {
    AtomicInteger totalRels = new AtomicInteger(0);
    RelationshipListener handler = rel -> {
        assertTrue(rel.hasProperty(SpecimenConstant.EVENT_DATE));
        Node specimen = rel.getEndNode();
        assertNotNull(specimen);
        Iterable<Relationship> rels = specimen.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
        for (Relationship ignored : rels) {
            assertTrue(specimen.hasProperty(SpecimenConstant.LENGTH_IN_MM));
            assertTrue(specimen.hasProperty(SpecimenConstant.LIFE_STAGE_LABEL));
        }
        Relationship collectedAtRelationship = specimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED_AT), Direction.OUTGOING);
        assertNotNull(collectedAtRelationship);
        Node locationNode = collectedAtRelationship.getEndNode();
        assertNotNull(locationNode);
        assertThat(locationNode.getProperty(LocationConstant.LATITUDE), is(29.219302));
        assertThat(locationNode.getProperty(LocationConstant.LONGITUDE), is(-87.06665));
        totalRels.incrementAndGet();
    };
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(study.getUnderlyingNode()), handler);
    return totalRels.get();
}