Java NameUsage.setOrigin方法代碼示例

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
private NameUsage convert(NubUsage nub) {
  NameUsage u = new NameUsage();
  u.setKey(nub.usageKey);
  u.setConstituentKey(nub.datasetKey);
  //TODO: add a scientificNameID property to NameUsage
  //nub.scientificNameID
  u.setTaxonID("gbif:" + nub.usageKey);
  u.setScientificName(nub.parsedName.getScientificName());
  u.setCanonicalName(canonicalOrScientificName(nub.parsedName));
  u.setRank(nub.rank);
  u.setTaxonomicStatus(nub.status);
  u.setNomenclaturalStatus(nub.nomStatus);
  u.setPublishedIn(nub.publishedIn);
  u.setOrigin(nub.origin);
  if (!nub.sourceIds.isEmpty()) {
    u.setSourceTaxonKey(nub.sourceIds.getInt(0));
  } else if (nub.origin.equals(Origin.SOURCE)) {
    LOG.warn("Source usage without source id found {} {}", u.getKey(), u.getScientificName());
  }
  u.setRemarks(remarkJoiner.join(nub.remarks));
  u.setIssues(nub.issues);
  return u;
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
/**
 * Creates a new taxon in neo and the name usage kvp using the source usages as a template for the classification properties.
 * Only copies the classification above genus and ignores genus and below!
 * A verbatim usage is created with just the parentNameUsage(ID) values so they can get resolved into proper neo relations later.
 *
 * @param taxonID the optional taxonID to apply to the new node
 */
private Node createTaxonWithClassification(Origin origin, String sciname, Rank rank, TaxonomicStatus status, NameUsageNode source,
                                           @Nullable String taxonID, @Nullable String remarks, VerbatimNameUsage sourceVerbatim) {
  NameUsage u = new NameUsage();
  u.setScientificName(sciname);
  u.setCanonicalName(sciname);
  u.setRank(rank);
  u.setOrigin(origin);
  u.setTaxonomicStatus(status);
  u.setTaxonID(taxonID);
  u.setRemarks(remarks);
  // copy verbatim classification from source
  ClassificationUtils.copyLinneanClassification(source.usage, u);
  removeGenusAndBelow(u);
  Node n = create(u, false).node;
  // copy parent props from source
  VerbatimNameUsage v = new VerbatimNameUsage();
  v.setCoreField(DwcTerm.parentNameUsageID, sourceVerbatim.getCoreField(DwcTerm.parentNameUsageID));
  v.setCoreField(DwcTerm.parentNameUsage, sourceVerbatim.getCoreField(DwcTerm.parentNameUsage));
  dao.store(n.getId(), v);
  return n;
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
protected NameUsageNode create(Origin origin, String sciname, Rank rank, TaxonomicStatus status, boolean isRoot, @Nullable String taxonID, @Nullable String remark) {
  NameUsage u = new NameUsage();
  u.setScientificName(sciname);
  // or generate via parsed name below???
  u.setCanonicalName(sciname);
  u.setRank(rank);
  u.setOrigin(origin);
  u.setTaxonomicStatus(status);
  u.setTaxonID(taxonID);
  u.setRemarks(remark);
  return create(u, isRoot);
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
private void syncProParte() {
  if (!proParteNodes.isEmpty()) {
    LOG.info("Syncing {} pro parte usages", proParteNodes.size());
    for (List<Long> ids : Iterables.partition(proParteNodes, cfg.chunkSize)) {
      List<NameUsage> usages = Lists.newArrayList();
      List<ParsedName> names = Lists.newArrayList();
      try (Transaction tx = dao.getNeo().beginTx()) {
        for (Long id : ids) {
          Node n = dao.getNeo().getNodeById(id);
          NameUsage primary = readUsage(n);
          ParsedName pn = readName(id);
          // modify as a template for all cloned pro parte usages
          primary.setProParteKey(primary.getKey());
          primary.setOrigin(Origin.PROPARTE);
          primary.setTaxonID(null); // if we keep the original id we will do an update, not an insert
          primary.setParentKey(null);
          for (Relationship rel : n.getRelationships(RelType.PROPARTE_SYNONYM_OF, Direction.OUTGOING)) {
            // pro parte synonyms keep their id in the relation, read it
            // http://dev.gbif.org/issues/browse/POR-2872
            NameUsage u = clone(primary);
            u.setKey( (Integer) rel.getProperty(NeoProperties.USAGE_KEY, null));
            Node accN = rel.getEndNode();
            // all nodes should be synced by now, so clb keys must be known
            u.setAcceptedKey(clbKeys.get((int) accN.getId()));
            // use accepted taxon classification for this synonym record
            applyClbClassification(u, accN.getId());
            usages.add(u);
            names.add(pn);
          }
        }
      }
      // submit sync job
      syncCounterProParte = syncCounterProParte + usages.size();
      proParteFuture = sqlService.sync(datasetKey, this, usages, names);
    }
  }
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
private void usage(Node n, String name, Rank rank, TaxonomicStatus status) {
  NameUsage u = new NameUsage();
  u.setScientificName(name);
  u.setRank(rank);
  u.setTaxonomicStatus(status);
  u.setOrigin(Origin.SOURCE);
  dao.store(n.getId(), u, true);
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
private NameUsage createNameUsage5231190(Locale locale) {
NameUsage nameUsage = new NameUsage();
nameUsage.setKey(5231190);
nameUsage.setKingdom("Animalia");
nameUsage.setPhylum("Chordata");
nameUsage.setClazz("Aves");
nameUsage.setOrder("Passeriformes");
nameUsage.setFamily("Passeridae");
nameUsage.setGenus("Passer");
nameUsage.setSpecies("Passer domesticus");
nameUsage.setKingdomKey(1);
nameUsage.setPhylumKey(44);
nameUsage.setClassKey(212);
nameUsage.setOrderKey(729);
nameUsage.setFamilyKey(5264);
nameUsage.setGenusKey(2492321);
nameUsage.setSpeciesKey(5231190);
nameUsage.setDatasetKey(UUID.fromString("d7dddbf4-2cf0-4f39-9b2a-bb099caae36c"));
nameUsage.setNubKey(5231190);
nameUsage.setParentKey(2492321);
nameUsage.setParent("Passer");
nameUsage.setScientificName("Passer domesticus (Linnaeus, 1758)");
nameUsage.setCanonicalName("Passer domesticus");
if(locale != null) {
    if(locale.equals(Locale.ENGLISH))
       nameUsage.setVernacularName("House Sparrow");
}
nameUsage.setAuthorship(" (Linnaeus, 1758)");
nameUsage.setNameType(NameType.SCIENTIFIC);
nameUsage.setRank(Rank.SPECIES);
nameUsage.setOrigin(Origin.SOURCE);
nameUsage.setTaxonomicStatus(TaxonomicStatus.ACCEPTED);
//nameUsage.setNomenclaturalStatus();
nameUsage.setAccordingTo("The Catalogue of Life, 3rd January 2011");
nameUsage.setNumDescendants(12);
// nameUsage.setSourceId("119127243");
nameUsage.setTaxonID("119127243");
/*
nameUsage.setSynonym(false);
Identifier identifier = new Identifier();
identifier.setKey(3191745);
identifier.setUsageKey(5231190);
identifier.setDatasetKey(UUID.fromString("d7dddbf4-2cf0-4f39-9b2a-bb099caae36c"));
identifier.setIdentifier("119127243");
// identifier.setType(IdentifierType.SOURCE_ID);
List<Identifier> identifiers = newArrayList();
identifiers.add(identifier);
nameUsage.setIdentifiers(identifiers);
*/
nameUsage.setModified(parseDateTime("2013-02-08T03:15:41.847+0000"));
nameUsage.setLastInterpreted(parseDateTime("2014-11-03T15:22:26.302+0000"));

return nameUsage;
   }
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
@Test
   public void list_wo_page() {
PagingResponse<NameUsage> expected = new PagingResponse<NameUsage>(0,20);
expected.setEndOfRecords(true);
List<NameUsage> results = newArrayList();
expected.setResults(results);

NameUsage result = new NameUsage();
results.add(result);
result.setKey(113490264);
result.setKingdom("Plantae");
result.setPhylum("Magnoliophyta");
result.setClazz("Magnoliopsida");
result.setOrder("Sapindales");
result.setFamily("Sapindaceae");
result.setGenus("Acer");
result.setSpecies("Acer sterculiaceum");
result.setKingdomKey(127971322);
result.setPhylumKey(127971328);
result.setClassKey(127971374);
result.setOrderKey(127971477);
result.setFamilyKey(127971478);
result.setGenusKey(127971479);
result.setSpeciesKey(113490264);
result.setDatasetKey(UUID.fromString("00a0607f-fd7e-4268-9707-0f53aa265f1f"));
result.setNubKey(7262989);
result.setParentKey(127971479);
result.setParent("Acer");
result.setScientificName("Acer sterculiaceum");
result.setCanonicalName("Acer sterculiaceum");
result.setAuthorship("");
result.setNameType(NameType.SCIENTIFIC);
result.setRank(Rank.SPECIES);
result.setOrigin(Origin.SOURCE);
result.setNumDescendants(0);
/*
Identifier identifier = new Identifier();
result.addIdentifier(identifier);
identifier.setKey(12524207);
identifier.setUsageKey(113490264);
identifier.setDatasetKey(UUID.fromString("00a0607f-fd7e-4268-9707-0f53aa265f1f"));
identifier.setIdentifier("ICIMOD_Barsey_Plants_001");
// identifier.setType(IdentifierType.SOURCE_ID);
*/
result.setTaxonID("ICIMOD_Barsey_Plants_001");
result.setModified(parseDateTime("2013-12-12T13:56:13.204+0000"));
result.setLastInterpreted(parseDateTime("2014-11-03T15:22:26.302+0000"));
// result.setSynonym(false);

SpeciesAPIClient sut = new SpeciesAPIClient();
PagingResponse<NameUsage> actual = sut.list(Locale.ENGLISH, UUID.fromString("00a0607f-fd7e-4268-9707-0f53aa265f1f"),"ICIMOD_Barsey_Plants_001",null);

printCollections("list_wo_page", actual.getResults(), results);

assertThat(actual, is(expected));
   }
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
/**
    * Creates response to http://api.gbif.org/v1/species/100710497/synonyms
    */
   private PagingResponse<NameUsage> createSynonyms100710497 ()
   {
PagingResponse<NameUsage> expected = new PagingResponse<NameUsage>(0,20);
expected.setEndOfRecords(true);
List<NameUsage> results = newArrayList();
expected.setResults(results);
NameUsage result = new NameUsage();
results.add(result);
result.setKey(102382983);
result.setNubKey(3204909);
result.setTaxonID("1290714");
result.setKingdom("Protista");
result.setPhylum("Ciliophora");
result.setClazz("Oligohymenophora");
result.setOrder("Scuticociliatida");
result.setFamily("Cohnilembidae");
result.setGenus("Cohnilembus");
result.setKingdomKey(102545060);
result.setPhylumKey(102545140);
result.setClassKey(102514394);
result.setOrderKey(102143947);
result.setFamilyKey(102238321);
result.setGenusKey(100710497);
result.setDatasetKey(UUID.fromString("0938172b-2086-439c-a1dd-c21cb0109ed5"));
result.setParentKey(102238321);
result.setParent("Cohnilembidae");
result.setAcceptedKey(100710497);
result.setAccepted("Cohnilembus Kahl, 1933");
result.setScientificName("Lembus Cohn, 1866");
result.setCanonicalName("Lembus");
result.setAuthorship("Cohn, 1866");
result.setNameType(NameType.SCIENTIFIC);
result.setRank(Rank.GENUS);
result.setOrigin(Origin.SOURCE);
result.setTaxonomicStatus(TaxonomicStatus.SYNONYM);
result.setRemarks("See Cohnilembus Kahl 1933. (Nomen. Zool.).");
result.setPublishedIn("Z. wiss. Zool. , 16, 270.");
result.setAccordingTo("SN2000 unverified; Nomenclator Zoologicus");
result.setNumDescendants(0);
result.setModified(parseDateTime("2014-06-15T15:45:33.692+0000"));
result.setLastInterpreted(parseDateTime("2014-11-03T15:22:26.302+0000"));
result.setSynonym(true);
return expected;
   }
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
/**
    * Creates response to http://api.gbif.org/v1/species/126926284/synonyms
    */
   private PagingResponse<NameUsage> createSynonyms126926284 () {
PagingResponse<NameUsage> expected = new PagingResponse<NameUsage>(0,20);
expected.setEndOfRecords(true);
List<NameUsage> results = newArrayList();
expected.setResults(results);
NameUsage result = new NameUsage();
results.add(result);

result.setKey(100496585);
result.setKingdom("Protista");
result.setPhylum("Ciliophora");
result.setClazz("Oligohymenophora");
result.setOrder("Scuticociliatida");
result.setFamily("Cohnilembidae");
result.setKingdomKey(126940483);
result.setPhylumKey(100533110);
result.setClassKey(126940663);
result.setOrderKey(126940683);
result.setFamilyKey(126940686);
result.setDatasetKey(UUID.fromString("714c64e3-2dc1-4bb7-91e4-54be5af4da12"));
result.setNubKey(3204909);
result.setParentKey(126940686);
result.setParent("Cohnilembidae");
result.setAcceptedKey(126926284);
result.setAccepted("Cohnilembus");
result.setScientificName("Lembus Cohn, 1866");
result.setCanonicalName("Lembus");
result.setAuthorship("Cohn, 1866");
result.setNameType(NameType.SCIENTIFIC);
result.setRank(Rank.GENUS);
result.setOrigin(Origin.SOURCE);
result.setTaxonomicStatus(TaxonomicStatus.SYNONYM);
result.setRemarks("See Cohnilembus Kahl 1933. (Nomen. Zool.).");
result.setPublishedIn("Z. wiss. Zool. , 16, 270.");
result.setAccordingTo("SN2000 unverified; Nomenclator Zoologicus");
result.setNumDescendants(0);
/*
Identifier identifier = new Identifier();
result.addIdentifier(identifier);
identifier.setKey(4467557);
identifier.setUsageKey(100496585);
identifier.setDatasetKey(UUID.fromString("714c64e3-2dc1-4bb7-91e4-54be5af4da12"));
identifier.setIdentifier("1290714");
// identifier.setType(IdentifierType.SOURCE_ID);
*/
// result.setTaxonID("1290714");
result.setSynonym(true);

return expected;
   }
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
@Test
public void testToObject() throws Exception {
    NameUsageDocConverter conv = new NameUsageDocConverter();

    NameUsage u = new NameUsage();
    u.setKey(12);
    u.setDatasetKey(UUID.randomUUID());
    u.setScientificName("Abies alba Mill.");
    u.setCanonicalName("Abies alba");
    u.setRank(Rank.SPECIES);
    u.setOrigin(Origin.SOURCE);
    u.setTaxonomicStatus(TaxonomicStatus.ACCEPTED);
    u.setParentKey(1);
    u.setFamilyKey(1024);
    u.setFamily("Pinaceae");
    u.getIssues().add(NameUsageIssue.RANK_INVALID);
    u.getIssues().add(NameUsageIssue.CLASSIFICATION_NOT_APPLIED);

    UsageExtensions ext = new UsageExtensions();
    SpeciesProfile sp = new SpeciesProfile();
    sp.setTerrestrial(true);
    sp.setHabitat("brackish");
    ext.speciesProfiles.add(sp);

    VernacularName v1 = new VernacularName();
    v1.setLanguage(Language.GERMAN);
    v1.setVernacularName("Weißtanne");
    VernacularName v2 = new VernacularName();
    v2.setLanguage(Language.GERMAN);
    v2.setVernacularName("Kohl Tanne");
    ext.vernacularNames.add(v1);
    ext.vernacularNames.add(v2);

    SolrInputDocument doc = conv.toDoc(u, Lists.newArrayList(12, 15, 20, 100), ext);

    assertEquals(u.getKey(), doc.get("key").getValue());
    assertEquals(u.getDatasetKey().toString(), doc.get("dataset_key").getValue());
    assertEquals(u.getParentKey(), doc.get("parent_key").getValue());
    assertEquals(u.getFamily(), doc.get("family").getValue());
    assertEquals(u.getFamilyKey(), doc.get("family_key").getValue());
    assertEquals(u.getScientificName(), doc.get("scientific_name").getValue());
    assertEquals(u.getCanonicalName(), doc.get("canonical_name").getValue());
    assertEquals(u.getOrigin().ordinal(), doc.get("origin_key").getValue());
    assertEquals(u.getTaxonomicStatus().ordinal(), doc.get("taxonomic_status_key").getValue());
    assertEquals(u.getRank().ordinal(), doc.get("rank_key").getValue());
    assertThat((List<Integer>) doc.get("issues").getValue()).contains(NameUsageIssue.RANK_INVALID.ordinal(),
            NameUsageIssue.CLASSIFICATION_NOT_APPLIED.ordinal());
    assertThat((List<Integer>) doc.get("habitat_key").getValue()).containsOnlyOnce(Habitat.TERRESTRIAL.ordinal(), Habitat.FRESHWATER.ordinal());
    assertThat((List<Integer>) doc.get("higher_taxon_key").getValue()).containsOnlyOnce(12, 15, 20, 100);

    // trip back
    NameUsageSearchResult u2 = conv.toSearchUsage(ClientUtils.toSolrDocument(doc), true);
    assertEquals(ClassificationUtils.getHigherClassificationMap(u2), ClassificationUtils.getHigherClassificationMap(u));
    assertEquals(u2.getKey(), u.getKey());
    assertEquals(u2.getDatasetKey(), u.getDatasetKey());
    assertEquals(u2.getParentKey(), u.getParentKey());
    assertEquals(u2.getScientificName(), u.getScientificName());
    assertEquals(u2.getCanonicalName(), u.getCanonicalName());
    assertEquals(u2.getOrigin(), u.getOrigin());
    assertEquals(u2.getTaxonomicStatus(), u.getTaxonomicStatus());
    assertEquals(u2.getRank(), u.getRank());
}
 

import org.gbif.api.model.checklistbank.NameUsage; //導入方法依賴的package包/類
/**
 * pro parte usages are synced differently and not tested here
 */
@Test
public void testRegularImport() throws ExecutionException, InterruptedException {

  ParsedName pn = new ParsedName();
  pn.setGenusOrAbove("Abies");
  pn.setSpecificEpithet("alba");
  pn.setAuthorship("Mill.");
  pn.setScientificName(pn.fullName());
  pn.setType(NameType.SCIENTIFIC);

  NameUsage u = new NameUsage();
  u.setKey(USAGE_ID);
  u.setScientificName(pn.getScientificName());
  u.setCanonicalName(pn.canonicalName());
  u.setNameType(pn.getType());
  u.setAuthorship(pn.getAuthorship());
  u.setRank(Rank.SPECIES);
  u.setDatasetKey(Constants.NUB_DATASET_KEY);
  u.setOrigin(Origin.SOURCE);
  u.getIssues().add(NameUsageIssue.CONFLICTING_BASIONYM_COMBINATION);
  u.getIssues().add(NameUsageIssue.ACCEPTED_NAME_MISSING);

  UsageExtensions ext = new UsageExtensions();
  VerbatimNameUsage v = new VerbatimNameUsage();
  NameUsageMetrics m = new NameUsageMetrics();

  DummyData data = new DummyData(u, pn, ext, v, m);

  Future<?> f = service.sync(u.getDatasetKey(), data, Lists.newArrayList(1));
  f.get();

  NameUsageService usageService = getInstance(NameUsageService.class);
  NameUsage u2 = usageService.get(USAGE_ID, null);

  u2.setLastInterpreted(null);

  // name key is newly assigned
  u.setNameKey(u2.getNameKey());
  u.setNameKey(u2.getNameKey());
  assertNotNull(u.getNameKey());

  assertFalse(u2.getIssues().isEmpty());

  assertEquals(u, u2);
}