Java Occurrence.setTaxonKey方法代码示例

import org.gbif.api.model.occurrence.Occurrence; //导入方法依赖的package包/类
private Occurrence occurrenceOf(
  Integer key, Integer kingdom, Integer phylum, Integer classs, Integer order, Integer family, Integer genus,
  Integer species, Integer nub,
  UUID dataset, BasisOfRecord bor, Country country, Integer year, Double latitude, Double longitude,
  EndpointType protocol) {
  Occurrence occ = new Occurrence();
  occ.setKey(key);
  occ.setKingdomKey(kingdom);
  occ.setPhylumKey(phylum);
  occ.setClassKey(classs);
  occ.setOrderKey(order);
  occ.setFamilyKey(family);
  occ.setGenusKey(genus);
  occ.setSpeciesKey(species);
  occ.setTaxonKey(nub);
  occ.setDatasetKey(dataset);
  occ.setBasisOfRecord(bor);
  occ.setCountry(country);
  occ.setYear(year);
  occ.setDecimalLatitude(latitude);
  occ.setDecimalLongitude(longitude);
  occ.setProtocol(protocol);

  return occ;
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入方法依赖的package包/类
private static void applyMatch(Occurrence occ, NameUsageMatch match, Collection<OccurrenceIssue> issues) {
  occ.setTaxonKey(match.getUsageKey());
  occ.setScientificName(match.getScientificName());
  occ.setTaxonRank(match.getRank());

  // copy issues
  occ.getIssues().addAll(issues);

  // parse name into pieces - we dont get them from the nub lookup
  try {
    ParsedName pn = PARSER.parse(match.getScientificName(), match.getRank());
    occ.setGenericName(pn.getGenusOrAbove());
    occ.setSpecificEpithet(pn.getSpecificEpithet());
    occ.setInfraspecificEpithet(pn.getInfraSpecificEpithet());
  } catch (UnparsableException e) {
    if (e.type.isParsable()) {
      LOG.warn("Fail to parse backbone {} name for occurrence {}: {}", e.type, occ.getKey(), e.name);
    }
  }

  for (Rank r : Rank.DWC_RANKS) {
    org.gbif.api.util.ClassificationUtils.setHigherRank(occ, r, match.getHigherRank(r));
    org.gbif.api.util.ClassificationUtils.setHigherRankKey(occ, r, match.getHigherRankKey(r));
  }
  LOG.debug("Occurrence {} matched to nub {} [{}]", occ.getKey(), occ.getScientificName(), occ.getTaxonKey());
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入方法依赖的package包/类
@Test
public void testCubeMutation() throws Exception {
  final UUID datasetKey = UUID.randomUUID();
  Occurrence occ = new Occurrence();
  occ.setTypeStatus(TypeStatus.HOLOTYPE);
  occ.setDatasetKey(datasetKey);
  occ.setKey(1);
  occ.setElevation(110d);
  occ.setDepth(10d);
  occ.setBasisOfRecord(BasisOfRecord.PRESERVED_SPECIMEN);
  occ.setTaxonKey(1000);
  occ.setKingdomKey(6);
  occ.setPhylumKey(66);
  occ.setClassKey(666);
  occ.setOrderKey(6666);
  occ.setFamilyKey(66666);
  occ.setGenusKey(666666);
  occ.setSubgenusKey(6666666);
  occ.setSpeciesKey(66666666);
  occ.setContinent(Continent.EUROPE);
  occ.setCountry(Country.ALBANIA);
  occ.setProtocol(EndpointType.DWC_ARCHIVE);
  occ.setPublishingCountry(Country.ITALY);
  occ.setYear(1992);
  occ.setMonth(1);
  occ.setDay(31);
  occ.getIssues().add(OccurrenceIssue.TYPE_STATUS_INVALID);
  occ.getIssues().add(OccurrenceIssue.ELEVATION_NON_NUMERIC);

  Batch<LongOp> updates = OccurrenceAddressUtil.cubeMutation(occ, new LongOp(1));

  // make sure we have a single dimension rollup for each dimension
  Set<Dimension<?>> addressed = Sets.newHashSet();
  int nubCounter = 0;
  for (Address a : updates.getMap().keySet()) {
    Dimension<?> singleDim = singleDimensionAddress(a);
    if (singleDim != null) {
      if (OccurrenceCube.TAXON_KEY.equals(singleDim)) {
        nubCounter++;
      } else if (addressed.contains(singleDim)) {
        System.out.println("Warning, single dimension " + singleDim + " used multiple times");
        System.out.println(a);
      }
      addressed.add(singleDim);
    }
  }

  System.out.println(OccurrenceCube.API_MAPPING.values());
  System.out.println(addressed);
  assertEquals("Not all higher taxa are mutated", 9, nubCounter);
  assertEquals("Not all cube dimensions are mutated", OccurrenceCube.API_MAPPING.size(), addressed.size());

}
 

import org.gbif.api.model.occurrence.Occurrence; //导入方法依赖的package包/类
private static void applyKingdom(Occurrence occ, Kingdom k){
  occ.setTaxonKey(k.nubUsageKey());
  occ.setScientificName(k.scientificName());
  occ.setTaxonRank(Rank.KINGDOM);
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入方法依赖的package包/类
private Occurrence buildTestOccurrence(){
  Date now = new Date();
  Occurrence occurrence = new Occurrence();
  occurrence.setKey(1227769253);
  occurrence.setDatasetKey(UUID.fromString("50c9509d-22c7-4a22-a47d-8c48425ef4a7"));

  occurrence.setPublishingOrgKey(UUID.fromString("28eb1a3f-1c15-4a95-931a-4af90ecb574d"));
  occurrence.setPublishingCountry(Country.UNITED_STATES);
  occurrence.setProtocol(EndpointType.DWC_ARCHIVE);
  occurrence.setLastCrawled(now);
  occurrence.setLastParsed(now);
  occurrence.setBasisOfRecord(BasisOfRecord.HUMAN_OBSERVATION);
  occurrence.setTaxonKey(6505602);
  occurrence.setKingdomKey(1);
  occurrence.setPhylumKey(52);
  occurrence.setClassKey(225);
  occurrence.setOrderKey(982);
  occurrence.setFamilyKey(2693);
  occurrence.setGenusKey(2305748);
  occurrence.setSpeciesKey(6505602);
  occurrence.setScientificName("Columbella fuscata G.B. Sowerby I, 1832");
  occurrence.setKingdom("Animalia");
  occurrence.setPhylum("Mollusca");
  occurrence.setOrder("Neogastropoda");
  occurrence.setFamily("Columbellidae");
  occurrence.setGenus("Columbella");
  occurrence.setSpecies("Columbella fuscata");
  occurrence.setGenericName("Columbella");
  occurrence.setSpecificEpithet("fuscata");
  occurrence.setTaxonRank(Rank.SPECIES);
  occurrence.setDateIdentified(now);
  occurrence.setDecimalLongitude(-110.32959d);
  occurrence.setDecimalLatitude(24.32329d);
  occurrence.setYear(2016);
  occurrence.setMonth(1);
  occurrence.setDay(2);
  Map<Term,String> verbatimFields = new HashMap<>();
  verbatimFields.put(DwcTerm.geodeticDatum,"WGS84");
  verbatimFields.put(DwcTerm.class_,"Gastropoda");
  verbatimFields.put(DwcTerm.countryCode,"MX");
  verbatimFields.put(DwcTerm.country, "Mexico");
  verbatimFields.put(DcTerm.rightsHolder, "Alison Young");
  verbatimFields.put(DcTerm.identifier, "2544088");
  verbatimFields.put(DwcTerm.verbatimEventDate, "2016-01-01 15:28:43");
  verbatimFields.put(DwcTerm.datasetName, "iNaturalist research-grade observations");
  verbatimFields.put(GbifTerm.gbifID, "1227769253");
  verbatimFields.put(DwcTerm.verbatimLocality, "La Paz, Baja California Sur, México");
  verbatimFields.put(DwcTerm.collectionCode, "Observations");
  verbatimFields.put(DwcTerm.occurrenceID, "http://www.inaturalist.org/observations/2544088");
  verbatimFields.put(DwcTerm.taxonID, "328630");
  verbatimFields.put(DwcTerm.recordedBy, "Alison Young");
  verbatimFields.put(DwcTerm.catalogNumber, "2544088");
  verbatimFields.put(DwcTerm.institutionCode, "iNaturalist");
  verbatimFields.put(DcTerm.rights, "Copyright Alison Young, licensed under a Creative Commons cc_by_nc_sa_name license: http://creativecommons.org/licenses/by-nc-sa/3.0/");
  verbatimFields.put(DwcTerm.eventTime, "23:28:43Z");
  verbatimFields.put(DwcTerm.identificationID, "4737209");
  occurrence.setVerbatimFields(verbatimFields);
  return occurrence;
}