Java Occurrence类代码示例

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
private static Occurrence buildOccurrence(UUID datasetKey, UUID ook) {
  Occurrence occ1 = new Occurrence();
  occ1.setKey(1);
  occ1.setDatasetKey(datasetKey);
  occ1.setPublishingOrgKey(ook);
  occ1.setBasisOfRecord(BasisOfRecord.FOSSIL_SPECIMEN);
  occ1.setKingdomKey(1);
  occ1.setPhylumKey(1);
  occ1.setClassKey(1);
  occ1.setOrderKey(1);
  occ1.setFamilyKey(1);
  occ1.setGenusKey(1);
  occ1.setSpeciesKey(1);
  occ1.setScientificName("Ursus horribilis");
  occ1.addIssue(OccurrenceIssue.COUNTRY_COORDINATE_MISMATCH);
  occ1.setDecimalLatitude(1.234);
  occ1.setDecimalLongitude(4.567);
  occ1.setCountry(Country.AFGHANISTAN);
  occ1.setPublishingCountry(Country.CANADA);
  occ1.setProtocol(EndpointType.BIOCASE);

  return occ1;
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的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; //导入依赖的package包/类
@Test
public void testSingleOccurrence() {
  Occurrence occ = occurrenceService.get(3);
  assertNotNull(occ);
  occurrenceDeletionService.deleteOccurrence(3, null);
  occ = occurrenceService.get(3);
  assertNull(occ);

  occ = occurrenceService.get(4);
  assertNotNull(occ);
  occurrenceDeletionService.deleteOccurrence(4, null);
  occ = occurrenceService.get(4);
  assertNull(occ);

  occ = occurrenceService.get(5);
  assertNotNull(occ);
  //test deletion of a record with a target crawl of 1
  occurrenceDeletionService.deleteOccurrence(5, 1);
  occ = occurrenceService.get(5);
  assertNotNull(occ);

  occurrenceDeletionService.deleteOccurrence(5, 2);
  occ = occurrenceService.get(5);
  assertNull(occ);
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
<T extends VerbatimOccurrence> RowUpdate buildRowUpdate(T occ) {
  checkNotNull(occ, "occurrence can't be null");
  checkNotNull(occ.getKey(), "occurrence's key can't be null");

  RowUpdate upd = new RowUpdate(occ.getKey());
  try (Table table = connection.getTable(TableName.valueOf(occurrenceTableName))) {
    if (occ instanceof Occurrence) {
      populateVerbatimPutDelete(table, upd, occ, false);
      populateInterpretedPutDelete(upd, (Occurrence) occ);
    } else {
      populateVerbatimPutDelete(table, upd, occ, true);
    }
  } catch (IOException e) {
    throw new ServiceUnavailableException("Could not access HBase", e);
  }

  return upd;
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
@Test
public void testOccRowMutations() {
  // identical shouldn't do anything
  Occurrence occ = occurrenceService.get(KEY);
  RowMutations mutations = occurrenceService.buildRowUpdate(occ).getRowMutations();
  assertEquals(0, mutations.getMutations().size());

  // one put and three deletes
  occ = occurrenceService.get(KEY);
  occ.setLastInterpreted(new Date());
  occ.setVerbatimField(DwcTerm.acceptedNameUsage, null);
  occ.setVerbatimField(DcTerm.accessRights, null);
  occ.setVerbatimField(GbifTerm.ageInDays, null);
  mutations = occurrenceService.buildRowUpdate(occ).getRowMutations();
  assertEquals(4, mutations.getMutations().size());
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
@Test
public void testOccurrenceXML() throws IOException {
  MessageBodyWriter<Occurrence> occurrenceDwcXMLBodyWriter = new OccurrenceDwcXMLBodyWriter();
  ByteArrayOutputStream baos = new ByteArrayOutputStream();
  Occurrence occ = new Occurrence();

  occ.setCountry(Country.MADAGASCAR);
  occ.setVerbatimField(DwcTerm.verbatimLocality, "mad");
  occ.setReferences(URI.create("http://www.gbif.org"));

  Term customTerm = TermFactory.instance().findTerm("MyTerm");
  occ.setVerbatimField(customTerm, "MyTerm value");

  occurrenceDwcXMLBodyWriter.writeTo(occ, null, null, null, null, null, baos);

  String expectedContent = IOUtils.toString(new FileInputStream(FileUtils.getClasspathFile("dwc_xml/occurrence.xml")));
  assertEquals(CharMatcher.WHITESPACE.removeFrom(expectedContent), CharMatcher.WHITESPACE.removeFrom(baos.toString()));
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
/**
 * Performs a search by MediaType.
 */
@Test
public void testSearchByMediaType() {
  // There are 3 occurrences with media objects: 1 still image, 1 video and 1 sound
  OccurrenceSearchRequest occurrenceSearchRequest = new OccurrenceSearchRequest();
  occurrenceSearchRequest.addMediaTypeFilter(MediaType.StillImage);
  SearchResponse<Occurrence, OccurrenceSearchParameter> response =
    occurrenceSearchService.search(occurrenceSearchRequest);
  Assert.assertTrue(response.getCount() == 1);
  occurrenceSearchRequest.addMediaTypeFilter(MediaType.MovingImage);
  response = occurrenceSearchService.search(occurrenceSearchRequest);
  Assert.assertTrue(response.getCount() == 2);
  occurrenceSearchRequest.addMediaTypeFilter(MediaType.Sound);
  response = occurrenceSearchService.search(occurrenceSearchRequest);
  Assert.assertTrue(response.getCount() == 3);
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的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; //导入依赖的package包/类
@Test
public void testInterpretMediaCore() throws Exception {
  VerbatimOccurrence v = new VerbatimOccurrence();
  Occurrence o = new Occurrence();

  v.setVerbatimField(
    DwcTerm.associatedMedia,
    "http://farm8.staticflickr.com/7093/7039524065_3ed0382368.jpg, http://www.flickr.com/photos/[email protected]/7039524065.png");
  MultiMediaInterpreter.interpretMedia(v, o);

  assertEquals(2, o.getMedia().size());
  for (MediaObject m : o.getMedia()) {
    assertEquals(MediaType.StillImage, m.getType());
    assertTrue(m.getFormat().startsWith("image/"));
    assertNotNull(m.getIdentifier());
  }
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
@Test
public void testCoordinatesUncertaintyIssues() throws InterruptedException {
  verb = new VerbatimOccurrence();

  verb.setKey(1);
  verb.setDatasetKey(UUID.randomUUID());
  verb.setVerbatimField(DwcTerm.country, "CANADA");
  verb.setVerbatimField(DwcTerm.verbatimLatitude, "45.5088400");
  verb.setVerbatimField(DwcTerm.verbatimLongitude, "-73.5878100");
  verb.setVerbatimField(DwcTerm.coordinateUncertaintyInMeters, "abc");
  verb.setVerbatimField(DwcTerm.geodeticDatum, "WSG84");
  occ = new Occurrence(verb);

  interpreter.interpretLocation(verb, occ);
  assertNotNull(occ);

  assertNull(occ.getCoordinateUncertaintyInMeters());
  assertTrue(occ.getIssues().contains(OccurrenceIssue.COORDINATE_UNCERTAINTY_METERS_INVALID));
  assertEquals(1, occ.getIssues().size());
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
@Test
public void testDeriveFromNotEquivalentMappedCountry() throws InterruptedException {
  verb = new VerbatimOccurrence();
  verb.setKey(1);
  verb.setDatasetKey(UUID.randomUUID());
  verb.setVerbatimField(DwcTerm.country, "France");
  verb.setVerbatimField(DwcTerm.decimalLatitude, "-17.65");
  verb.setVerbatimField(DwcTerm.decimalLongitude, "-149.46");
  verb.setVerbatimField(DwcTerm.geodeticDatum, "EPSG:4326");
  occ = new Occurrence(verb);

  interpreter.interpretLocation(verb, occ);
  assertNotNull(occ);
  assertEquals(-17.65, occ.getDecimalLatitude(), 0.0001);
  assertEquals(-149.46, occ.getDecimalLongitude(), 0.0001);
  assertEquals(Country.FRENCH_POLYNESIA, occ.getCountry());
  assertEquals(1, occ.getIssues().size());
  assertTrue(occ.getIssues().contains(OccurrenceIssue.COUNTRY_DERIVED_FROM_COORDINATES));
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
/**
 * Reads and processes the occurrence object.
 */
@Override
public boolean apply(Occurrence input) {
  try {
    write(input);
    return true;
  } catch (IOException e) {
    return false;
  }
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
/**
 * True if the subset of fields of occurrence, that are interesting to metrics and cube-updating, are the same.
 */
public static boolean equivalent(Occurrence occ1, Occurrence occ2) {
  // TODO: Do we need to compare the holy triple too?
  /*
   * && Objects.equal(occ1.getInstitutionCode(), occ2.getInstitutionCode())
   * && Objects.equal(occ1.getCollectionCode(), occ2.getCollectionCode())
   * && Objects.equal(occ1.getCatalogNumber(), occ2.getCatalogNumber())
   */

  return Objects.equal(occ1.getKey(), occ2.getKey())
    && Objects.equal(occ1.getDatasetKey(), occ2.getDatasetKey())
    && Objects.equal(occ1.getPublishingOrgKey(), occ2.getPublishingOrgKey())
    && Objects.equal(occ1.getBasisOfRecord(), occ2.getBasisOfRecord())
    && Objects.equal(occ1.getKingdomKey(), occ2.getKingdomKey())
    && Objects.equal(occ1.getPhylumKey(), occ2.getPhylumKey())
    && Objects.equal(occ1.getClassKey(), occ2.getClassKey())
    && Objects.equal(occ1.getOrderKey(), occ2.getOrderKey())
    && Objects.equal(occ1.getFamilyKey(), occ2.getFamilyKey())
    && Objects.equal(occ1.getGenusKey(), occ2.getGenusKey())
    && Objects.equal(occ1.getSpeciesKey(), occ2.getSpeciesKey())
    && Objects.equal(occ1.getScientificName(), occ2.getScientificName())
    && Objects.equal(occ1.hasSpatialIssue(), occ2.hasSpatialIssue())
    && Objects.equal(occ1.getDecimalLatitude(), occ2.getDecimalLatitude())
    && Objects.equal(occ1.getDecimalLongitude(), occ2.getDecimalLongitude())
    && Objects.equal(occ1.getCountry(), occ2.getCountry())
    && Objects.equal(occ1.getPublishingCountry(), occ2.getPublishingCountry())
    && Objects.equal(occ1.getProtocol(), occ2.getProtocol());
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
public OccurrenceUuidIntMapCubeUpdaterService(CubeConfiguration configuration, DataCube<UuidIntMap> dataCube,
  Dimension<T> dimension, Function<Occurrence, T> valueGetter) {
  super(configuration);
  this.dataCube = dataCube;
  this.dimension = dimension;
  this.valueGetter = valueGetter;
}
 

import org.gbif.api.model.occurrence.Occurrence; //导入依赖的package包/类
/**
 * Function that return the country value from an occurrence object.
 */
private Function<Occurrence, Country> countryGetter() {
  return new Function<Occurrence, Country>() {

    @Override
    public Country apply(Occurrence occurrence) {
      return occurrence.getCountry();
    }

  };
}