Java DwcTerm.taxonID方法代码示例

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
private void writeHeader(TabWriter writer, Term rowType, List<Term> columns) throws IOException {
  int idx = 0;
  String[] row = new String[columns.size() + 1];
  Term idTerm;
  if (DwcTerm.Taxon == coreRowType){
    idTerm = DwcTerm.taxonID;
  } else if (DwcTerm.Occurrence == coreRowType){
    idTerm = DwcTerm.occurrenceID;
  } else if (DwcTerm.Identification == coreRowType){
    idTerm = DwcTerm.identificationID;
  } else if (DwcTerm.Event == coreRowType){
    idTerm = DwcTerm.eventID;
  } else {
    // default to generic dc identifier for id column
    idTerm = DcTerm.identifier;
  }
  row[idx] = idTerm.simpleName();

  for (Term term : columns) {
    idx ++;
    row[idx] = term.simpleName();
  }
  writer.write(row);

  headersOut.add(rowType);
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test
public void testDefaultValue() {
  final String DATASET = "ITIS";
  ArchiveField id = new ArchiveField(0, DwcTerm.taxonID, null, null);
  Set<ArchiveField> fields = new HashSet<ArchiveField>();
  fields.add(new ArchiveField(1, DwcTerm.datasetName, DATASET, null));
  RecordImpl rec = new RecordImpl(id, fields, DwcTerm.Taxon, true, true);

  String[] row = {"5432", "IPNI"};
  rec.setRow(row);
  assertEquals(row[1], rec.value(DwcTerm.datasetName));

  row = new String[] {"5432", null};
  rec.setRow(row);
  assertEquals(DATASET, rec.value(DwcTerm.datasetName));

  row = new String[] {"5432", ""};
  rec.setRow(row);
  assertEquals(DATASET, rec.value(DwcTerm.datasetName));
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test
public void testWriterUsingCoreIdTerm() throws Exception {
  File dwcaDir = FileUtils.createTempDir();
  dwcaDir.deleteOnExit();
  LOG.info("Test archive writer in {}", dwcaDir.getAbsolutePath());

  DwcaWriter writer = new DwcaWriter(DwcTerm.Taxon, DwcTerm.taxonID, dwcaDir, true);

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

  Archive arch = ArchiveFactory.openArchive(dwcaDir);
  Iterator<Record> recIt = arch.getCore().iterator();
  Record firstRecord = recIt.next();
  assertEquals("dummy1", firstRecord.id());
  assertEquals("dummy1", firstRecord.value(DwcTerm.taxonID));
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test
public void write() throws Exception {
    File dwca = FileUtils.createTempDir();
    Map<Term, Integer> mapping = ImmutableMap.of(
            DwcTerm.taxonID, 0,
            DwcTerm.scientificName, 1,
            DwcTerm.taxonRank, 2);
    try (DwcaStreamWriter dwcaWriter = new DwcaStreamWriter(dwca, DwcTerm.Taxon, DwcTerm.taxonID, true)){
        Dataset d = new Dataset();
        d.setTitle("Abies of the Alps");
        d.setDescription("Abies of the Alps excl Switzerland.");
        dwcaWriter.setMetadata(d);
        dwcaWriter.write(DwcTerm.Taxon, 0, mapping, ImmutableList.<String[]>builder()
                .add(new String[] { "tax-1", "Abies Mill.", "genus" })
                .add(new String[] { "tax-2", "Abies alba Mill.", "species" })
                .add(new String[] { "tax-3", "Piceae abies L.", "species" })
                .add(new String[] { "tax-4", "Piceae abies subsp. helvetica L.", "subspecies" })
                .build()
        );

    } finally {
        org.apache.commons.io.FileUtils.deleteQuietly(dwca);
    }
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test
public void testGetFullScientificName() {
  ArchiveField id = new ArchiveField(0, DwcTerm.taxonID, null, null);
  Set<ArchiveField> fields = new HashSet<ArchiveField>();
  fields.add(new ArchiveField(1, DwcTerm.scientificName, null, null));
  fields.add(new ArchiveField(2, DwcTerm.scientificNameAuthorship, null, null));
  fields.add(new ArchiveField(null, DwcTerm.kingdom, "Plantae", null));
  fields.add(new ArchiveField(4, DwcTerm.phylum, null, null));
  fields.add(new ArchiveField(6, DwcTerm.class_, null, null));
  fields.add(new ArchiveField(7, DwcTerm.acceptedNameUsage, null, null));
  RecordImpl rec = new RecordImpl(id, fields, DwcTerm.Taxon, true, true);

  String[] row =
    {"5432", "Abies alba Mill.", "Mill.", "Harry", "Monocotyledonae", "Bertram", "Pincodiae", "Picea picaea L."};
  rec.setRow(row);

  assertEquals(row[1], rec.value(DwcTerm.scientificName));
  assertEquals(row[2], rec.value(DwcTerm.scientificNameAuthorship));
  assertEquals("Plantae", rec.value(DwcTerm.kingdom));
  assertEquals(row[4], rec.value(DwcTerm.phylum));
  assertEquals(row[6], rec.value(DwcTerm.class_));
  assertEquals(row[6], rec.value(DwcTerm.class_));
  assertNull(rec.value(DwcTerm.order));
  assertEquals(row[7], rec.value(DwcTerm.acceptedNameUsage));

  assertEquals(row[0], rec.id());
  assertEquals(DwcTerm.Taxon, rec.rowType());
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test(expected = IllegalStateException.class)
public void testAddingCoreIdTermTwice() throws Exception {
  File dwcaDir = FileUtils.createTempDir();
  dwcaDir.deleteOnExit();
  DwcaWriter writer = new DwcaWriter(DwcTerm.Taxon, DwcTerm.taxonID, dwcaDir, true);
  writer.newRecord("dummy1");
  writer.addCoreColumn(DwcTerm.taxonID, "dummy1");
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test(expected = IllegalStateException.class)
public void writeEmpty() throws Exception {
    File dwca = FileUtils.createTempDir();
    try (DwcaStreamWriter dwcaWriter = new DwcaStreamWriter(dwca, DwcTerm.Taxon, DwcTerm.taxonID, true)){

    } finally {
        org.apache.commons.io.FileUtils.deleteQuietly(dwca);
    }
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
/**
 * Test the writing of an archive that includes some default values in the core and in one extension.
 * 
 * @throws Exception
 */
@Test
public void testWriterUsingDefaultValues() throws Exception {
  File dwcaDir = FileUtils.createTempDir();
  dwcaDir.deleteOnExit();
  LOG.info("Test archive writer in {}", dwcaDir.getAbsolutePath());

  DwcaWriter writer = new DwcaWriter(DwcTerm.Taxon, DwcTerm.taxonID, dwcaDir, true);

  writer.newRecord("dummy1");
  writer.addCoreColumn(DwcTerm.parentNameUsageID, "1");
  writer.addCoreColumn(DwcTerm.acceptedNameUsageID, "2");
  writer.addCoreColumn(DwcTerm.countryCode);
  
  // add a VernacularName extension record
  Map<Term,String> extensionRecord = new HashMap<Term, String>();
  extensionRecord.put(DwcTerm.vernacularName, "Komodo Dragon");
  extensionRecord.put(DcTerm.language, null);
  writer.addExtensionRecord(GbifTerm.VernacularName, extensionRecord);
  
  writer.addCoreDefaultValue(DwcTerm.collectionCode, "A2Z");
  writer.addCoreDefaultValue(DwcTerm.countryCode, "CA");
  writer.addDefaultValue(GbifTerm.VernacularName, DcTerm.language, "en");
  
  // add a second records and overwrite the default value
  writer.newRecord("dummy2");
  writer.addCoreColumn(DwcTerm.parentNameUsageID, "1");
  writer.addCoreColumn(DwcTerm.acceptedNameUsageID, "2");
  writer.addCoreColumn(DwcTerm.countryCode, "ID");
  
  // add a VernacularName extension record
  extensionRecord = new HashMap<Term, String>();
  extensionRecord.put(DwcTerm.vernacularName, "Varano De Komodo");
  extensionRecord.put(DcTerm.language, "es");
  writer.addExtensionRecord(GbifTerm.VernacularName, extensionRecord);
  
  writer.close();

  // validate core content
  Archive arch = ArchiveFactory.openArchive(dwcaDir);
  Iterator<Record> recIt = arch.getCore().iterator();
  Record firstRecord = recIt.next();
  assertEquals("dummy1", firstRecord.id());
  assertEquals("dummy1", firstRecord.value(DwcTerm.taxonID));
  assertEquals("A2Z", firstRecord.value(DwcTerm.collectionCode));
  assertEquals("CA", firstRecord.value(DwcTerm.countryCode));
  assertEquals("A2Z", arch.getCore().getField(DwcTerm.collectionCode).getDefaultValue());
  assertEquals("CA", arch.getCore().getField(DwcTerm.countryCode).getDefaultValue());
  
  Record secondRecord = recIt.next();
  assertEquals("dummy2", secondRecord.id());
  assertEquals("dummy2", secondRecord.value(DwcTerm.taxonID));
  assertEquals("A2Z", secondRecord.value(DwcTerm.collectionCode));
  assertEquals("ID", secondRecord.value(DwcTerm.countryCode));
  
  // validate extension content
  Iterator<Record> extRecIt = arch.getExtension(GbifTerm.VernacularName).iterator();
  assertEquals("en", arch.getExtension(GbifTerm.VernacularName).getField(DcTerm.language).getDefaultValue());
  firstRecord = extRecIt.next();
  assertEquals("dummy1", firstRecord.id());
  assertEquals("en", firstRecord.value(DcTerm.language));
  
  secondRecord = extRecIt.next();
  assertEquals("dummy2", secondRecord.id());
  assertEquals("es", secondRecord.value(DcTerm.language));
}