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

Example 1 with SOURCE_OCCURRENCE_ID

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

the class DatasetImporterForDwCATest method importRecordsFromArctosArchive.

@Test
public void importRecordsFromArctosArchive() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/arctos_mvz_bird_small.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream));
    List<String> families = new ArrayList<>();
    AtomicBoolean someRecords = new AtomicBoolean(false);
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(REFERENCE_URL), startsWith("http://arctos.database.museum/guid/"));
            assertThat(interaction.get(SOURCE_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Bird:180448?seid=587053"), is("http://arctos.database.museum/guid/MVZ:Bird:183644?seid=158590"), is("http://arctos.database.museum/guid/MVZ:Bird:58090?seid=657121")));
            if (interaction.containsKey(DatasetImporterForTSV.TARGET_OCCURRENCE_ID)) {
                assertThat(interaction.get(DatasetImporterForTSV.TARGET_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Herp:241200"), is("http://arctos.database.museum/guid/MVZ:Bird:183643"), is("http://arctos.database.museum/guid/MVZ:Bird:58093")));
            }
            assertThat(interaction.get(SOURCE_TAXON_FAMILY), anyOf(is("Accipitridae"), is("Strigidae")));
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/associatedOccurrences | http://rs.tdwg.org/dwc/terms/Occurrence"));
            someRecords.set(true);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(someRecords.get(), is(true));
}

Example 2 with SOURCE_OCCURRENCE_ID

use of org.eol.globi.data.DatasetImporterForTSV.SOURCE_OCCURRENCE_ID 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_OCCURRENCE_ID

use of org.eol.globi.data.DatasetImporterForTSV.SOURCE_OCCURRENCE_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));
}