Examples with TARGET_BODY_PART_ID org.eol.globi.data.DatasetImporterForTSV.TARGET_BODY_PART_ID used on opensource projects

Example 1 with TARGET_BODY_PART_ID

use of org.eol.globi.data.DatasetImporterForTSV.TARGET_BODY_PART_ID in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importBlankCitation.

@Test
public void importBlankCitation() throws StudyImporterException {
    final InteractionListener listener = new InteractionImporter(nodeFactory, (GeoNamesService) null, null);
    final TreeMap<String, String> link = new TreeMap<String, String>();
    link.put(SOURCE_OCCURRENCE_ID, "123");
    link.put(SOURCE_CATALOG_NUMBER, "catalogNumber123");
    link.put(SOURCE_COLLECTION_CODE, "collectionCode123");
    link.put(SOURCE_COLLECTION_ID, "collectionId123");
    link.put(SOURCE_INSTITUTION_CODE, "institutionCode123");
    link.put(TARGET_OCCURRENCE_ID, "456");
    link.put(TARGET_CATALOG_NUMBER, "targetCatalogNumber123");
    link.put(TARGET_COLLECTION_CODE, "targetCollectionCode123");
    link.put(TARGET_COLLECTION_ID, "targetCollectionId123");
    link.put(TARGET_INSTITUTION_CODE, "targetInstitutionCode123");
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(SOURCE_BODY_PART_ID, "bla:123");
    link.put(SOURCE_BODY_PART_NAME, "snout");
    link.put(SOURCE_LIFE_STAGE_ID, "some:stage");
    link.put(SOURCE_LIFE_STAGE_NAME, "stage");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(TARGET_BODY_PART_ID, "bla:345");
    link.put(TARGET_BODY_PART_NAME, "tail");
    link.put(DatasetImporterForMetaTable.EVENT_DATE, "20160404T21:31:40Z");
    link.put(DatasetImporterForMetaTable.LATITUDE, "12.1");
    link.put(DatasetImporterForMetaTable.LONGITUDE, "13.2");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:1234");
    listener.on(link);
    final AtomicBoolean foundPair = new AtomicBoolean(false);
    RelationshipListener relationshipListener = relationship -> {
        final SpecimenNode predator = new SpecimenNode(relationship.getEndNode());
        for (Relationship stomachRel : NodeUtil.getStomachContents(predator)) {
            final SpecimenNode prey = new SpecimenNode(stomachRel.getEndNode());
            final TaxonNode preyTaxon = getOrigTaxon(prey);
            final TaxonNode predTaxon = getOrigTaxon(predator);
            assertThat(preyTaxon.getName(), is("mini"));
            assertThat(preyTaxon.getExternalId(), is("mouse"));
            assertThat(predTaxon.getName(), is("donald"));
            assertThat(predTaxon.getExternalId(), is("duck"));
            assertLocation(predator.getSampleLocation());
            assertLocation(prey.getSampleLocation());
            assertThat(predator.getExternalId(), is("123"));
            assertThat(prey.getExternalId(), is("456"));
            assertThat(predator.getLifeStage().getId(), is("some:stage"));
            assertThat(predator.getLifeStage().getName(), is("stage"));
            assertThat(predator.getProperty(OCCURRENCE_ID), is("123"));
            assertThat(predator.getProperty(CATALOG_NUMBER), is("catalogNumber123"));
            assertThat(predator.getProperty(COLLECTION_CODE), is("collectionCode123"));
            assertThat(predator.getProperty(COLLECTION_ID), is("collectionId123"));
            assertThat(predator.getProperty(INSTITUTION_CODE), is("institutionCode123"));
            assertThat(prey.getProperty(OCCURRENCE_ID), is("456"));
            assertThat(prey.getProperty(CATALOG_NUMBER), is("targetCatalogNumber123"));
            assertThat(prey.getProperty(COLLECTION_CODE), is("targetCollectionCode123"));
            assertThat(prey.getProperty(COLLECTION_ID), is("targetCollectionId123"));
            assertThat(prey.getProperty(INSTITUTION_CODE), is("targetInstitutionCode123"));
            foundPair.set(true);
            assertThat(relationship.getProperty(SpecimenConstant.EVENT_DATE), is(notNullValue()));
            List<SpecimenNode> specimens = Arrays.asList(predator, prey);
            for (SpecimenNode specimen : specimens) {
                assertThat(specimen.getBodyPart().getId(), is(notNullValue()));
                assertThat(specimen.getBodyPart().getName(), is(notNullValue()));
            }
        }
    };
    handleRelations(relationshipListener, RelTypes.COLLECTED);
    assertThat(foundPair.get(), is(true));
}