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Example 1 with SOURCE_TAXON_FAMILY

use of org.eol.globi.service.TaxonUtil.SOURCE_TAXON_FAMILY 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));
}
Also used : TaxonUtil(org.eol.globi.service.TaxonUtil) Arrays(java.util.Arrays) INTERACTION_TYPE_NAME(org.eol.globi.data.DatasetImporterForTSV.INTERACTION_TYPE_NAME) URL(java.net.URL) URISyntaxException(java.net.URISyntaxException) INTERACTION_TYPE_ID(org.eol.globi.data.DatasetImporterForTSV.INTERACTION_TYPE_ID) InteractionListener(org.eol.globi.process.InteractionListener) StringUtils(org.apache.commons.lang3.StringUtils) NullImportLogger(org.eol.globi.tool.NullImportLogger) InteractType(org.eol.globi.domain.InteractType) Is(org.hamcrest.core.Is) REFERENCE_URL(org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL) CoreMatchers.notNullValue(org.hamcrest.CoreMatchers.notNullValue) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) Map(java.util.Map) Is.is(org.hamcrest.core.Is.is) SOURCE_LIFE_STAGE_NAME(org.eol.globi.data.DatasetImporterForTSV.SOURCE_LIFE_STAGE_NAME) JsonNode(com.fasterxml.jackson.databind.JsonNode) URI(java.net.URI) DatasetImporterForDwCA.parseAssociatedSequences(org.eol.globi.data.DatasetImporterForDwCA.parseAssociatedSequences) DatasetImporterForDwCA.importAssociatedTaxaExtension(org.eol.globi.data.DatasetImporterForDwCA.importAssociatedTaxaExtension) DatasetImporterForDwCA.mapReferenceInfo(org.eol.globi.data.DatasetImporterForDwCA.mapReferenceInfo) TARGET_OCCURRENCE_ID(org.eol.globi.data.DatasetImporterForTSV.TARGET_OCCURRENCE_ID) EXTENSION_RESOURCE_RELATIONSHIP(org.eol.globi.data.DatasetImporterForDwCA.EXTENSION_RESOURCE_RELATIONSHIP) SOURCE_TAXON_NAME(org.eol.globi.service.TaxonUtil.SOURCE_TAXON_NAME) DwcTerm(org.gbif.dwc.terms.DwcTerm) IsNot.not(org.hamcrest.core.IsNot.not) TARGET_FIELD_NUMBER(org.eol.globi.data.DatasetImporterForTSV.TARGET_FIELD_NUMBER) DatasetImporterForDwCA.importResourceRelationshipExtension(org.eol.globi.data.DatasetImporterForDwCA.importResourceRelationshipExtension) CoreMatchers.containsString(org.hamcrest.CoreMatchers.containsString) REFERENCE_ID(org.eol.globi.data.DatasetImporterForTSV.REFERENCE_ID) Record(org.gbif.dwc.record.Record) Set(java.util.Set) TestCase.assertNull(junit.framework.TestCase.assertNull) Matchers.startsWith(org.hamcrest.Matchers.startsWith) DatasetImporterForDwCA.parseDynamicPropertiesForInteractionsOnly(org.eol.globi.data.DatasetImporterForDwCA.parseDynamicPropertiesForInteractionsOnly) List(java.util.List) Matchers.containsInAnyOrder(org.hamcrest.Matchers.containsInAnyOrder) EXTENSION_ASSOCIATED_TAXA(org.eol.globi.data.DatasetImporterForDwCA.EXTENSION_ASSOCIATED_TAXA) Matchers.greaterThan(org.hamcrest.Matchers.greaterThan) TARGET_BODY_PART_NAME(org.eol.globi.data.DatasetImporterForTSV.TARGET_BODY_PART_NAME) DATASET_CITATION(org.eol.globi.data.DatasetImporterForTSV.DATASET_CITATION) CoreMatchers.anyOf(org.hamcrest.CoreMatchers.anyOf) LogContext(org.eol.globi.domain.LogContext) DatasetImpl(org.globalbioticinteractions.dataset.DatasetImpl) TARGET_CATALOG_NUMBER(org.eol.globi.data.DatasetImporterForTSV.TARGET_CATALOG_NUMBER) DwcTerm.relatedResourceID(org.gbif.dwc.terms.DwcTerm.relatedResourceID) AtomicBoolean(java.util.concurrent.atomic.AtomicBoolean) SOURCE_TAXON_FAMILY(org.eol.globi.service.TaxonUtil.SOURCE_TAXON_FAMILY) HashMap(java.util.HashMap) TreeSet(java.util.TreeSet) ArrayList(java.util.ArrayList) RESOURCE_TYPES(org.eol.globi.data.DatasetImporterForTSV.RESOURCE_TYPES) MatcherAssert.assertThat(org.hamcrest.MatcherAssert.assertThat) SOURCE_OCCURRENCE_ID(org.eol.globi.data.DatasetImporterForTSV.SOURCE_OCCURRENCE_ID) CoreMatchers.nullValue(org.hamcrest.CoreMatchers.nullValue) Term(org.gbif.dwc.terms.Term) MapUtils(org.apache.commons.collections4.MapUtils) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Assert.assertTrue(org.junit.Assert.assertTrue) Archive(org.gbif.dwc.Archive) DwCAUtil(org.globalbioticinteractions.dataset.DwCAUtil) Test(org.junit.Test) IOException(java.io.IOException) TARGET_TAXON_NAME(org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME) File(java.io.File) DatasetImporterForDwCA.parseAssociatedOccurrences(org.eol.globi.data.DatasetImporterForDwCA.parseAssociatedOccurrences) TARGET_SEX_NAME(org.eol.globi.data.DatasetImporterForTSV.TARGET_SEX_NAME) TreeMap(java.util.TreeMap) DcTerm(org.gbif.dwc.terms.DcTerm) REFERENCE_CITATION(org.eol.globi.data.DatasetImporterForTSV.REFERENCE_CITATION) AtomicBoolean(java.util.concurrent.atomic.AtomicBoolean) InteractionListener(org.eol.globi.process.InteractionListener) ArrayList(java.util.ArrayList) DatasetImpl(org.globalbioticinteractions.dataset.DatasetImpl) CoreMatchers.containsString(org.hamcrest.CoreMatchers.containsString) URL(java.net.URL) REFERENCE_URL(org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL) Test(org.junit.Test)

Aggregations

JsonNode (com.fasterxml.jackson.databind.JsonNode)1 ObjectMapper (com.fasterxml.jackson.databind.ObjectMapper)1 File (java.io.File)1 IOException (java.io.IOException)1 URI (java.net.URI)1 URISyntaxException (java.net.URISyntaxException)1 URL (java.net.URL)1 ArrayList (java.util.ArrayList)1 Arrays (java.util.Arrays)1 HashMap (java.util.HashMap)1 List (java.util.List)1 Map (java.util.Map)1 Set (java.util.Set)1 TreeMap (java.util.TreeMap)1 TreeSet (java.util.TreeSet)1 AtomicBoolean (java.util.concurrent.atomic.AtomicBoolean)1 AtomicInteger (java.util.concurrent.atomic.AtomicInteger)1 TestCase.assertNull (junit.framework.TestCase.assertNull)1 MapUtils (org.apache.commons.collections4.MapUtils)1 StringUtils (org.apache.commons.lang3.StringUtils)1