Java DwcTerm.Taxon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(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.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 testTaxonIDUnique() throws Exception {

  addColumn(DwcTerm.taxonID, "1");
  addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
  StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
  RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
  rec.setRow(values.toArray(new String[]{}));
  star.newCoreRecord(rec);
  ins.insertStarRecord(star);

  values = Lists.newArrayList();
  fields = Lists.newArrayList();
  addColumn(DwcTerm.taxonID, "2");
  addColumn(DwcTerm.scientificName, "Picea alba");
  rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
  rec.setRow(values.toArray(new String[]{}));
  star.newCoreRecord(rec);
  ins.insertStarRecord(star);

  ins.close();

  try (Transaction tx = dao.beginTx()) {
    assertNotNull(Iterators.singleOrNull(dao.getNeo().findNodes(Labels.TAXON, NeoProperties.TAXON_ID, "1")));
  }
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test(expected = NotUniqueRuntimeException.class)
public void testTaxonIDNotUnique() throws Exception {

  addColumn(DwcTerm.taxonID, "1");
  addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
  StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
  RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
  rec.setRow(values.toArray(new String[]{}));
  star.newCoreRecord(rec);
  ins.insertStarRecord(star);

  values = Lists.newArrayList();
  fields = Lists.newArrayList();
  addColumn(DwcTerm.taxonID, "1");
  addColumn(DwcTerm.scientificName, "Picea alba");
  rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
  rec.setRow(values.toArray(new String[]{}));
  star.newCoreRecord(rec);
  ins.insertStarRecord(star);

  ins.close();
}
 

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
public void testHeaders1() 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);
  writer.newRecord("dummy2");
  writer.addCoreColumn(DwcTerm.parentNameUsageID);
  writer.addCoreColumn(DwcTerm.acceptedNameUsageID);
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test(expected = IllegalStateException.class)
public void testHeaders2() 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);
  writer.newRecord("dummy2");
  writer.addCoreColumn(DwcTerm.scientificName);
}
 

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
public void testHeaderWriting() throws Exception {
  File dwcaDir = FileUtils.createTempDir();
  dwcaDir.deleteOnExit();
  LOG.info("Test archive writer in {}", dwcaDir.getAbsolutePath());

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

  writer.newRecord("dummy1");
  writer.addCoreColumn(DwcTerm.parentNameUsageID);
  writer.addCoreColumn(DwcTerm.acceptedNameUsageID);
  writer.addCoreColumn(DwcTerm.scientificName);
  writer.addCoreColumn(GbifTerm.canonicalName);
  writer.addCoreColumn(DwcTerm.taxonRank, "species");
  writer.addCoreColumn(DwcTerm.taxonomicStatus);
  writer.addCoreColumn(DwcTerm.kingdom);
  writer.addCoreColumn(DwcTerm.phylum);
  writer.addCoreColumn(DwcTerm.class_);
  writer.addCoreColumn(DwcTerm.order);
  writer.addCoreColumn(DwcTerm.family);
  writer.addCoreColumn(GbifTerm.depth);
  writer.addCoreColumn(GbifTerm.depthAccuracy);

  writer.newRecord("dummy2");
  writer.addCoreColumn(DwcTerm.kingdom, "Plantae");
  writer.addCoreColumn(DwcTerm.phylum);
  writer.addCoreColumn(DwcTerm.class_);
  writer.addCoreColumn(DwcTerm.order);
  writer.addCoreColumn(DwcTerm.family, "Asteraceae");

  writer.newRecord("dummy3");
  writer.addCoreColumn(GbifTerm.depth, "2");
  writer.addCoreColumn(GbifTerm.depthAccuracy, "1");

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

  eData.put(DwcTerm.locality, "locality2");
  writer.addExtensionRecord(GbifTerm.Distribution, eData);

  writer.close();

  File cf = new File(dwcaDir, writer.getDataFiles().get(DwcTerm.Taxon));
  File df = new File(dwcaDir, writer.getDataFiles().get(GbifTerm.Distribution));

  // check if taxon file contains headers
  String[] headers = getFirstRow(cf);
  LOG.debug(Joiner.on("; ").useForNull("NULL").join(headers));
  assertEquals(14, headers.length);
  assertEquals("taxonID", headers[0]);
  assertEquals("parentNameUsageID", headers[1]);
  assertEquals("kingdom", headers[7]);

  // check if extension file contains headers
  headers = getFirstRow(df);
  LOG.debug(Joiner.on("; ").useForNull("NULL").join(headers));
  assertEquals(4, headers.length);
  assertEquals("taxonID", headers[0]);
}
 

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));
}
 

import org.gbif.dwc.terms.DwcTerm; //导入方法依赖的package包/类
@Test
public void testNonDwcProperties() throws Exception {

  addColumn(DwcTerm.taxonID, "1");
  addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
  addColumn(DwcTerm.scientificNameAuthorship, "Mill.");
  addColumn(DwcTerm.namePublishedIn, "Führ. Pilzk. (Zwickau) 136 (1871)");
  addColumn(DwcTerm.namePublishedInID, "12345678");
  addColumn(DwcTerm.namePublishedInYear, "1871");
  addColumn(DwcTerm.nameAccordingTo, "Miller");
  addColumn(DwcTerm.nameAccordingToID, "123456");
  addColumn(DwcTerm.taxonRemarks, "bugger off");
  addColumn(DcTerm.references, "http://gbif.org");

  StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
  RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
  rec.setRow(values.toArray(new String[]{}));
  star.newCoreRecord(rec);
  ins.insertStarRecord(star);
  ins.close();

  try (Transaction tx = dao.beginTx()) {
    Node n = dao.getNeo().getNodeById(0);
    assertEquals("1", n.getProperty(NeoProperties.TAXON_ID));

    VerbatimNameUsage v = dao.readVerbatim(n.getId());
    assertEquals("1", v.getCoreField(DwcTerm.taxonID));
    assertEquals("Abies alba Mill., 1982", v.getCoreField(DwcTerm.scientificName));
    assertEquals("Mill.", v.getCoreField(DwcTerm.scientificNameAuthorship));
    assertEquals("Führ. Pilzk. (Zwickau) 136 (1871)", v.getCoreField(DwcTerm.namePublishedIn));
    assertEquals("12345678", v.getCoreField(DwcTerm.namePublishedInID));
    assertEquals("1871", v.getCoreField(DwcTerm.namePublishedInYear));
    assertEquals("Miller", v.getCoreField(DwcTerm.nameAccordingTo));
    assertEquals("123456", v.getCoreField(DwcTerm.nameAccordingToID));
    assertEquals("bugger off", v.getCoreField(DwcTerm.taxonRemarks));
    assertEquals("http://gbif.org", v.getCoreField(DcTerm.references));

    NameUsage u = dao.readUsage(n, true);
    assertEquals("1", u.getTaxonID());
    assertEquals("Abies alba Mill., 1982", u.getScientificName());
    assertEquals("Mill.", u.getAuthorship());
    assertEquals("Führ. Pilzk. (Zwickau) 136 (1871)", u.getPublishedIn());
    assertEquals("Miller", u.getAccordingTo());
    assertEquals("bugger off", u.getRemarks());
    assertEquals(URI.create("http://gbif.org"), u.getReferences());
  }
}