Examples with SOURCE_TAXON_NAME org.eol.globi.service.TaxonUtil.SOURCE_TAXON_NAME used on opensource projects

Example 1 with SOURCE_TAXON_NAME

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

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDir.

@Test
public void importTaxonDescriptionsFromDir() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size() > 0, is(true));
    assertThat(links.get(0).get(DATASET_CITATION), containsString("org/globalbioticinteractions/dataset/coetzer/"));
    assertThat(links.get(0).get(REFERENCE_CITATION), is("Cockerell, T.D.A. 1937. African bees of the genera Ceratina, Halictus and Megachile. 254 pp. William Clowes and Sons, London"));
    assertThat(links.get(0).get(TARGET_TAXON_NAME), is("Chaetodactylus leleupi"));
    assertThat(links.get(0).get(SOURCE_TAXON_NAME), is("Ceratina ruwenzorica Cockerell, 1937"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is("Parasite"));
    assertThat(links.get(0).get(RESOURCE_TYPES), is("http://rs.gbif.org/terms/1.0/Reference"));
}

Example 2 with SOURCE_TAXON_NAME

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

the class DatasetImporterForDwCATest method importRecordsFromResourceRelationshipArchiveRemarksOnly.

@Test
public void importRecordsFromResourceRelationshipArchiveRemarksOnly() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("fmnh-rr-8278596f-4d3f-4f82-8cd1-b5070fe1bc7c.zip");
    AtomicInteger recordCounter = new AtomicInteger(0);
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(interaction -> {
        assertThat(interaction.get(TARGET_TAXON_NAME), is("Glaucomys volans"));
        assertThat(interaction.get(TARGET_OCCURRENCE_ID), is(nullValue()));
        assertThat(interaction.get(SOURCE_TAXON_NAME), is("Orchopeas fulleri Traub, 1950"));
        assertThat(interaction.get(SOURCE_OCCURRENCE_ID), is("8278596f-4d3f-4f82-8cd1-b5070fe1bc7c"));
        recordCounter.incrementAndGet();
        assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), greaterThan(0));
}

Example 3 with SOURCE_TAXON_NAME

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

the class InteractionImporterTest method importWithLocalityAndLatLng.

@Test
public void importWithLocalityAndLatLng() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(LOCALITY_ID, "back:yard");
    link.put(LOCALITY_NAME, "my back yard");
    link.put(DECIMAL_LATITUDE, "12.2");
    link.put(DECIMAL_LONGITUDE, "13.2");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:10.12/34");
    listener.on(link);
    AtomicBoolean foundSpecimen = new AtomicBoolean(false);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        LocationNode sampleLocation = someSpecimen.getSampleLocation();
        assertThat(sampleLocation.getLatitude(), is(12.2d));
        assertThat(sampleLocation.getLongitude(), is(13.2d));
        assertThat(sampleLocation.getLocality(), is("my back yard"));
        assertThat(sampleLocation.getLocalityId(), is("back:yard"));
        foundSpecimen.set(true);
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(true));
}

Example 4 with SOURCE_TAXON_NAME

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

the class InteractionImporterTest method importRefutingClaim.

@Test
public void importRefutingClaim() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(ARGUMENT_TYPE_ID, "https://en.wiktionary.org/wiki/refute");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:10.12/34");
    listener.on(link);
    AtomicBoolean foundSpecimen = new AtomicBoolean(false);
    RelationshipListener relHandler = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.REFUTES)));
        assertFalse(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        foundSpecimen.set(true);
    };
    handleRelations(relHandler, RelTypes.REFUTES);
    assertThat(foundSpecimen.get(), is(true));
}

Example 5 with SOURCE_TAXON_NAME

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

the class InteractionImporterTest method importWithSex.

@Test
public void importWithSex() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_SEX_NAME, "female");
    link.put(SOURCE_SEX_ID, "some:female");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, InteractType.ATE.getIRI());
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_SEX_NAME, "male");
    link.put(TARGET_SEX_ID, "some:male");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_ID, "123");
    link.put(REFERENCE_CITATION, "");
    listener.on(link);
    AtomicInteger foundSpecimen = new AtomicInteger(0);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(NodeUtil.asNeo4j(InteractType.ATE)));
        if (someSpecimen.getUnderlyingNode().hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE))) {
            assertThat(someSpecimen.getSex().getName(), is("female"));
            assertThat(someSpecimen.getSex().getId(), is("some:female"));
        } else {
            assertThat(someSpecimen.getSex().getName(), is("male"));
            assertThat(someSpecimen.getSex().getId(), is("some:male"));
        }
        foundSpecimen.incrementAndGet();
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(2));
}