Java GbifTerm类代码示例

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
public static Map<Term, String> getPropertyMap(Term conceptTerm) {
	if(conceptTerm.equals(DwcTerm.Taxon)) {
		return taxonTerms;
	} else if(conceptTerm.equals(GbifTerm.Description)) {
		return descriptionTerms;
	} else if(conceptTerm.equals(GbifTerm.Distribution)) {
		return distributionTerms;
	} else if(conceptTerm.equals(GbifTerm.Identifier)) {
		return identifierTerms;
	} else if(conceptTerm.equals(DwcTerm.MeasurementOrFact)) {
		return measurementOrFactTerms;
	} else if(conceptTerm.equals(GbifTerm.VernacularName)) {
		return vernacularNameTerms;
	} else if(conceptTerm.equals(GbifTerm.Image)) {
		return imageTerms;
	} else if(conceptTerm.equals(GbifTerm.TypesAndSpecimen)) {
		return typeAndSpecimenTerms;
	} else if(conceptTerm.equals(GbifTerm.Reference)) {
		return referenceTerms;
	} else if(conceptTerm.equals(SkosTerm.Concept)) {
		return skosTerms;
	} else {
		throw new IllegalArgumentException(conceptTerm.qualifiedName() + " is not a supported term");
	}
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
public static Map<Term, String> getPropertyMap(Term conceptTerm) {
	if(conceptTerm.equals(DwcTerm.Taxon)) {
		return taxonTerms;
	} else if(conceptTerm.equals(GbifTerm.Description)) {
		return descriptionTerms;
	} else if(conceptTerm.equals(GbifTerm.Distribution)) {
		return distributionTerms;
	} else if(conceptTerm.equals(GbifTerm.Identifier)) {
		return identifierTerms;
	} else if(conceptTerm.equals(DwcTerm.MeasurementOrFact)) {
		return measurementOrFactTerms;
	} else if(conceptTerm.equals(GbifTerm.VernacularName)) {
		return vernacularNameTerms;
	} else if(conceptTerm.equals(ExtendedAcTerm.Multimedia)) {
		return imageTerms;
	} else if(conceptTerm.equals(GbifTerm.TypesAndSpecimen)) {
		return typeAndSpecimenTerms;
	} else if(conceptTerm.equals(GbifTerm.Reference)) {
		return referenceTerms;
	} else if(conceptTerm.equals(SkosTerm.Concept)) {
		return skosTerms;
	} else {
		throw new IllegalArgumentException(conceptTerm.qualifiedName() + " is not a supported term");
	}
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
@Test(expected = IllegalStateException.class)
public void testHeaders3() throws Exception {
  File dwcaDir = FileUtils.createTempDir();
  dwcaDir.deleteOnExit();
  DwcaWriter writer = new DwcaWriter(DwcTerm.Taxon, dwcaDir, true);

  writer.newRecord("dummy1");
  writer.addCoreColumn(DwcTerm.parentNameUsageID);
  writer.addCoreColumn(DwcTerm.acceptedNameUsageID);

  // define extension columns
  Map<Term, String> eData = Maps.newHashMap();
  eData.put(DwcTerm.locality, "locality1");
  eData.put(DwcTerm.occurrenceStatus, "present");
  writer.addExtensionRecord(GbifTerm.Distribution, eData);

  eData.put(DwcTerm.establishmentMeans, "alien");
  writer.addExtensionRecord(GbifTerm.Distribution, eData);
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
private void interpretVernacularNames(NameUsage u, UsageExtensions e, VerbatimNameUsage v) {
  if (v.hasExtension(Extension.VERNACULAR_NAME)) {
    for (Map<Term, String> rec : v.getExtensions().get(Extension.VERNACULAR_NAME)) {
      VernacularName vn = new VernacularName();
      vn.setVernacularName(value(rec, DwcTerm.vernacularName));
      if (vn.getVernacularName() == null) {
        u.addIssue(NameUsageIssue.VERNACULAR_NAME_INVALID);
        continue;
      }
      // locationID > locality
      vn.setArea(value(rec, DwcTerm.locationID, DwcTerm.locality));
      vn.setCountry(enumify(rec, null, countryParser, u,
                            DwcTerm.countryCode, DwcTerm.country, DwcTerm.locationID, DwcTerm.locality));
      vn.setLanguage(enumify(rec, NameUsageIssue.VERNACULAR_NAME_INVALID, languageParser, u, DcTerm.language));
      vn.setLifeStage(enumify(rec, NameUsageIssue.VERNACULAR_NAME_INVALID, lifeStageParser, u, DwcTerm.lifeStage));
      vn.setPlural(bool(rec, NameUsageIssue.VERNACULAR_NAME_INVALID, u, GbifTerm.isPlural));
      vn.setPreferred(bool(rec, NameUsageIssue.VERNACULAR_NAME_INVALID, u, GbifTerm.isPreferredName));
      vn.setSex(enumify(rec, NameUsageIssue.VERNACULAR_NAME_INVALID, sexParser, u, DwcTerm.sex));
      vn.setSource(value(rec, DcTerm.source));
      // interpret rec
      e.vernacularNames.add(vn);
    }
  }
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * We only keep type names and ignore specimens...
 */
private void interpretTypes(NameUsage u, UsageExtensions e, VerbatimNameUsage v) {
  if (v.hasExtension(Extension.TYPES_AND_SPECIMEN)) {
    for (Map<Term, String> rec : v.getExtensions().get(Extension.TYPES_AND_SPECIMEN)) {
      TypeSpecimen t = new TypeSpecimen();
      // interpret
      t.setScientificName(expandGenus(value(rec, DwcTerm.scientificName), u.getScientificName()));

      if (t.getScientificName() == null || t.getScientificName().equalsIgnoreCase(u.getScientificName())) {
        LOG.debug("Ignore type name for {} as the name is the same as the taxon", u.getScientificName());
        continue;
      }
      t.setTypeDesignatedBy(value(rec, GbifTerm.typeDesignatedBy));
      t.setTypeStatus(enumify(rec, null, typeStatusParser, u, DwcTerm.typeStatus));
      t.setSource(value(rec, DcTerm.source));
      //t.setCitation(value(rec, DcTerm.bibliographicCitation));
      //t.setTypeDesignationType(value(rec, GbifTerm.typeDesignatedType));
      e.typeSpecimens.add(t);
    }
  }
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
private void interpretSpeciesProfiles(NameUsage u, UsageExtensions e, VerbatimNameUsage v) {
  if (v.hasExtension(Extension.SPECIES_PROFILE)) {
    for (Map<Term, String> rec : v.getExtensions().get(Extension.SPECIES_PROFILE)) {
      SpeciesProfile s = new SpeciesProfile();
      // interpret rec
      s.setSource(value(rec, DcTerm.source));
      s.setAgeInDays(integer(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.ageInDays));
      s.setMassInGram(integer(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.massInGram));
      s.setSizeInMillimeter(integer(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.sizeInMillimeter));
      s.setHybrid(bool(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.isHybrid));
      s.setMarine(bool(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.isMarine));
      s.setFreshwater(bool(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.isFreshwater));
      s.setTerrestrial(bool(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.isTerrestrial));
      s.setExtinct(bool(rec, NameUsageIssue.SPECIES_PROFILE_INVALID, u, GbifTerm.isExtinct));
      s.setLivingPeriod(value(rec, GbifTerm.livingPeriod));
      s.setLifeForm(value(rec, GbifTerm.lifeForm));
      s.setHabitat(value(rec, DwcTerm.habitat));
      e.speciesProfiles.add(s);
    }
  }
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
@Test
public void testRoundTripping() throws Exception {
  VerbatimNameUsage v = new VerbatimNameUsage();
  v.setCoreField(DwcTerm.scientificName, "Abies alba");
  v.setCoreField(DwcTerm.taxonRank, "Gattung");
  v.setCoreField(DwcTerm.taxonID, "dqwd23");
  v.setCoreField(GbifTerm.depth, "1200");
  v.setCoreField(new UnknownTerm(qname1), "1200");
  v.setCoreField(new UnknownTerm(qname2), null);

  List<Map<Term, String>> vernaculars = Lists.newArrayList();
  vernaculars.add(map(DwcTerm.vernacularName, "Tanne", DcTerm.language, "de"));
  vernaculars.add(map(DwcTerm.vernacularName, "Fir", DcTerm.language, "en", new UnknownTerm(qname2), ""));
  v.getExtensions().put(Extension.VERNACULAR_NAME, vernaculars);

  List<Map<Term, String>> infos = Lists.newArrayList();
  infos.add(map(GbifTerm.ageInDays, "750", IucnTerm.threatStatus, "extinct", GbifTerm.isExtinct, "true"));
  v.getExtensions().put(Extension.SPECIES_PROFILE, infos);

  String json = mapper.write(v);

  VerbatimNameUsage v2 = mapper.read(json);
  assertEquals(v, v2);
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
@Test
public void testOcc() throws IOException {
  ObjectMapper mapper = new ObjectMapper();

  final Term custom = UnknownTerm.build("http://me.com/mum", "mum");
  Occ o = new Occ();
  o.setTerm(custom);
  o.getData().put(custom, "custom");
  o.getData().put(GbifTerm.ageInDays, "21");

  for (Term t : DwcTerm.values()) {
    o.getData().put(t, t.simpleName());
  }

  String json = mapper.writeValueAsString(o);
  Occ o2 = mapper.readValue(json, Occ.class);
  System.out.println(o.equals(o2));

  assertEquals(o, mapper.readValue(json, Occ.class));
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * @return the select fields for the verbatim table in the simple download
 */
static List<InitializableField> selectVerbatimFields() {
  ImmutableList.Builder<InitializableField> builder = ImmutableList.builder();
  // always add the GBIF ID
  builder.add(new InitializableField(GbifTerm.gbifID,
                                     HiveColumns.columnFor(GbifTerm.gbifID),
                                     HiveDataTypes.typeForTerm(GbifTerm.gbifID, true)));

  for (Term term : DownloadTerms.DOWNLOAD_VERBATIM_TERMS) {
    if (GbifTerm.gbifID == term) {
      continue; // for safety, we code defensively as it may be added
    }

    builder.add(new InitializableField(term,
                                       HiveColumns.VERBATIM_COL_PREFIX + term.simpleName().toLowerCase(),
                                       // no escape needed due to prefix
                                       HiveDataTypes.TYPE_STRING));
  }
  return builder.build();
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * @return the select fields for the interpreted table in the simple download
 */
private static List<InitializableField> selectDownloadFields(Set<Term> terms, boolean useInitializers) {
  ImmutableList.Builder<InitializableField> builder = ImmutableList.builder();
  // always add the GBIF ID
  builder.add(new InitializableField(GbifTerm.gbifID,
                                     HiveColumns.columnFor(GbifTerm.gbifID),
                                     HiveDataTypes.typeForTerm(GbifTerm.gbifID, true)));

  for (Term term : terms) {
    if (GbifTerm.gbifID == term) {
      continue; // for safety, we code defensively as it may be added
    }
    if (useInitializers && TermUtils.isInterpretedDate(term)) {
      builder.add(new InitializableField(term, toISO8601Initializer(term), HiveDataTypes.TYPE_STRING));
    } else if (useInitializers && HiveColumnsUtils.isHiveArray(term)){
      builder.add(new InitializableField(term, String.format(JOIN_ARRAY_FMT,HiveColumns.columnFor(term)), HiveDataTypes.TYPE_STRING));
    } else {
      builder.add(new InitializableField(term, HiveColumns.columnFor(term), HiveDataTypes.TYPE_STRING));
    }
  }
  return builder.build();
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * Creates a new archive file description for a dwc archive and sets the id field to the column of gbifID.
 * Used to generate the meta.xml with the help of the dwca-writer
 */
public static ArchiveFile createArchiveFile(String filename, Term rowType, Iterable<? extends Term> columns) {
  ArchiveFile af = buildBaseArchive(filename, rowType);
  int index = 0;
  for (Term term : columns) {
    ArchiveField field = new ArchiveField();
    field.setIndex(index);
    field.setTerm(term);
    if (HiveColumnsUtils.isHiveArray(term)) {
      field.setDelimitedBy(DEFAULT_DELIMITER);
    }
    af.addField(field);
    index++;
  }
  ArchiveField coreId = af.getField(GbifTerm.gbifID);
  if (coreId == null) {
    throw new IllegalArgumentException("Archive columns MUST include the gbif:gbifID term");
  }
  af.setId(coreId);
  return af;
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * Creates an meta.xml descriptor file in the directory parameter.
 */
public static void createArchiveDescriptor(File directory) {
  LOG.info("Creating archive meta.xml descriptor");

  Archive downloadArchive = new Archive();
  downloadArchive.setMetadataLocation(METADATA_FILENAME);

  ArchiveFile occurrence = createArchiveFile(INTERPRETED_FILENAME, DwcTerm.Occurrence, TermUtils.interpretedTerms());
  downloadArchive.setCore(occurrence);

  ArchiveFile verbatim = createArchiveFile(VERBATIM_FILENAME, DwcTerm.Occurrence, TermUtils.verbatimTerms());
  downloadArchive.addExtension(verbatim);

  ArchiveFile multimedia = createArchiveFile(MULTIMEDIA_FILENAME, GbifTerm.Multimedia, TermUtils.multimediaTerms());
  downloadArchive.addExtension(multimedia);

  try {
    File metaFile = new File(directory, DESCRIPTOR_FILENAME);
    MetaDescriptorWriter.writeMetaFile(metaFile, downloadArchive);
  } catch (IOException e) {
    LOG.error("Error creating meta.xml file", e);
  }
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
@Test
public void testTermsConsistency(){
  Set<Term> interpretedFromTermUtils = Sets.newHashSet(TermUtils.interpretedTerms());
  Set<Term> interpretedFromTerms = Sets.newHashSet(Terms.interpretedTerms());

  Set<Term> diff = Sets.symmetricDifference(interpretedFromTermUtils, interpretedFromTerms);
  assertEquals("TermUtils.interpretedTerms() and Terms.interpretedTerms() must use the same terms. Difference(s): " +
                  diff, 0, diff.size());

  Set<Term> hdfsTerms = DownloadTerms.DOWNLOAD_INTERPRETED_TERMS_HDFS;
  diff = Sets.newHashSet(Sets.symmetricDifference(interpretedFromTermUtils, hdfsTerms));
  diff.remove(GbifTerm.gbifID);
  diff.remove(GbifTerm.mediaType);
  assertEquals("TermUtils.interpretedTerms() and DownloadTerms.DOWNLOAD_INTERPRETED_TERMS_HDFS must use the same terms. Difference(s): " +
          diff, 0, diff.size());

}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
/**
 * Deletes both the secondary indexes ("lookups") as well as the occurrence proper for the scan that matches the
 * given column and value. Note any exceptions thrown during the deletions will cause this method to fail, leaving
 * deletions in an incomplete state.
 *
 * @param columnValue value to match
 * @param column interpreted column on which to match values
 */
private void deleteByColumn(byte[] columnValue, GbifTerm column) {
  LOG.debug("Starting delete by column for [{}]", column);
  int deleteCount = 0;
  Iterator<Integer> keyIterator = occurrenceService.getKeysByColumn(columnValue, Columns.column(column));
  List<Integer> keys = Lists.newArrayListWithCapacity(KEYS_BATCH_SIZE);
  while (keyIterator.hasNext()) {
    int key = keyIterator.next();
    // TODO: this is critical, but causes extreme performance problems (full scan of lookups per deleted key)
    occurrenceKeyService.deleteKey(key, null);
    keys.add(key);
    if ((keys.size() % KEYS_BATCH_SIZE) == 0) {
      LOG.debug("Writing batch of [{}] deletes", keys.size());
      occurrenceService.delete(keys);
      deleteCount += keys.size();
      keys = Lists.newArrayListWithCapacity(KEYS_BATCH_SIZE);
    }
  }
  LOG.debug("Writing batch of [{}] deletes", keys.size());
  occurrenceService.delete(keys);
  deleteCount += keys.size();
  LOG.debug("Finished delete by column for [{}] giving [{}] total rows deleted", column, deleteCount);
}
 

import org.gbif.dwc.terms.GbifTerm; //导入依赖的package包/类
@Test
public void testVerbRowMutations() {
  // identical shouldn't do anything
  VerbatimOccurrence occ = occurrenceService.getVerbatim(KEY);
  RowMutations mutations = occurrenceService.buildRowUpdate(occ).getRowMutations();
  assertEquals(0, mutations.getMutations().size());

  // one put and three deletes
  occ = occurrenceService.getVerbatim(KEY);
  occ.setLastParsed(new Date());
  occ.setVerbatimField(DwcTerm.acceptedNameUsage, null);
  occ.setVerbatimField(DcTerm.accessRights, null);
  occ.setVerbatimField(GbifTerm.distanceAboveSurface, null);

  mutations = occurrenceService.buildRowUpdate(occ).getRowMutations();
  assertEquals(4, mutations.getMutations().size());
}