Java Code Examples for ucar.nc2.dataset.NetcdfDataset#close()

/**
 * Try to open Access as a NetcdfDataset.
 *
 * @param access open this Access
 * @param acquire if true, aquire the dataset, else open it
 * @param task may be null
 * @param log error message, may be null
 * @return NetcdfDataset or null if failure
 * @throws IOException on read error
 */
public NetcdfDataset openDataset(Access access, boolean acquire, ucar.nc2.util.CancelTask task, Formatter log)
    throws IOException {
  try (Result result = new Result()) {
    NetcdfDataset ncd = openDataset(access, acquire, task, result);
    if (log != null)
      log.format("%s", result.errLog);
    if (result.fatalError && ncd != null)
      ncd.close();
    return (result.fatalError) ? null : ncd;

    // result.close() will be called at the end of this block, which will close the Result's FeatureDataset, if it
    // exists. That data member won't have been set by any of the code above, so the close() will essentially be a
    // no-op.
  }
}
 

public void testNoCoords() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggExistingNoCoords.xml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    Variable time = ncd.getRootGroup().findVariableLocal("time");
    Array data = time.read();
    // all missing
    // assert data.getInt(0) ==
  } finally {
    if (ncd != null)
      ncd.close();
  }
  // logger.debug("{}", ncd);
  // assert false;
}
 

public void testNoCoords() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggExistingNoCoords.xml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    Variable time = ncd.getRootGroup().findVariableLocal("time");
    Array data = time.read();
    // all missing
    // assert data.getInt(0) ==
  } finally {
    if (ncd != null)
      ncd.close();
  }
  // logger.debug("{}", ncd);
  // assert false;
}
 

public void testNoCoords() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggExistingNoCoords.xml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    Variable time = ncd.getRootGroup().findVariableLocal("time");
    Array data = time.read();
    // all missing
    // assert data.getInt(0) ==
  } finally {
    if (ncd != null)
      ncd.close();
  }
  // logger.debug("{}", ncd);
  // assert false;
}
 

/**
 * Try to open as a NetcdfDataset.
 *
 * @param Dataset open this
 * @param acquire if true, aquire the dataset, else open it
 * @param task may be null
 * @param log error message, may be null
 * @return NetcdfDataset or null if failure
 * @throws IOException on read error
 */
public NetcdfDataset openDataset(Dataset Dataset, boolean acquire, ucar.nc2.util.CancelTask task, Formatter log)
    throws IOException {
  Result result = new Result();
  NetcdfDataset ncd = openDataset(Dataset, acquire, task, result);
  if (log != null)
    log.format("%s", result.errLog);
  if (result.fatalError) {
    result.close();
    if (ncd != null)
      ncd.close();
  }
  return (result.fatalError) ? null : ncd;
}
 

@Test
public void testCoordsAdded() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingAddCoord.ncml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDataset.openDataset(filename, true, null);
    logger.debug("{}", ncd);
  } finally {
    if (ncd != null)
      ncd.close();
  }
}
 

@Test
public void testCoordsAdded() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingAddCoord.ncml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    logger.debug("{}", ncd);
  } finally {
    if (ncd != null)
      ncd.close();
  }
}
 

static void testNcd() throws IOException {
  String filename = "C:/data/test2.nc";
  NetcdfDataset ncfile = NetcdfDataset.openDataset(filename);
  measureSize("C:/data/test2.nc", ncfile, null, true);

  NetcdfDatasetInfo info = new NetcdfDatasetInfo(filename);
  measureSize("info", info, null, true);
  String pifo = info.getParseInfo();
  System.out.println("info= " + pifo);
  ncfile.close();
}
 

@Test
public void testPolygon() throws IOException {

  String failMessage, found, expected;
  boolean testCond;

  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/SimpleGeos/outflow_3seg_5timesteps_vlen.nc";

  // open the test file
  NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile);

  // make sure this dataset used the cfConvention
  expected = cfConvention;
  found = ncd.getConventionUsed();
  testCond = found.equals(expected);
  failMessage =
      format("This dataset used the %s convention, but should have used the %s convention.", found, expected);
  Assert.assertTrue(failMessage, testCond);

  // check that attributes were filled in correctly
  List<Variable> vars = ncd.getVariables();
  for (Variable v : vars) {
    if (v.findAttribute(CF.GEOMETRY) != null) {
      Assert.assertNotNull(v.findAttribute(CF.NODE_COORDINATES));
      Assert.assertNotNull(v.findAttribute(_Coordinate.Axes));
    }
  }
  ncd.close();
}
 

@Test
public void testTryWithWrap() throws IOException {
  String location = TestDir.cdmLocalFromTestDataDir + "testWrite.nc";
  NetcdfDataset ncd = NetcdfDataset.openDataset(location);
  Formatter errlog = new Formatter();
  try (FeatureDataset fdataset = FeatureDatasetFactoryManager.wrap(null, ncd, null, errlog)) {
    assert (fdataset == null);
  }
  ncd.close();
}
 

@Test
public void testCoordsAdded() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingAddCoord.ncml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    logger.debug("{}", ncd);
  } finally {
    if (ncd != null)
      ncd.close();
  }
}
 

@Test
public void testCoordsAdded() throws IOException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingAddCoord.ncml";
  logger.debug("{}", filename);
  NetcdfDataset ncd = null;

  try {
    ncd = NetcdfDatasets.openDataset(filename, true, null);
    logger.debug("{}", ncd);
  } finally {
    if (ncd != null)
      ncd.close();
  }
}
 

/**
 * Open a file as a GridDataset, using getNetcdfFile(), so that it gets wrapped in NcML if needed.
 */
// return null means request has been handled, and calling routine should exit without further processing
public GridDataset openGridDataset(HttpServletRequest req, HttpServletResponse res, String reqPath)
    throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    GridDataset gds = fc.getGridDataset(match.remaining);
    if (gds == null)
      throw new FileNotFoundException(reqPath);
    return gds;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  NetcdfDataset ncd = null;
  try {
    // Convert to NetcdfDataset
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return new ucar.nc2.dt.grid.GridDataset(ncd);


  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset"
        : "Problem creating GridDataset from NetcdfDataset";
    log.error("openGridDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}
 

public static PointObsDataset open(String location, ucar.nc2.util.CancelTask task, StringBuffer log)
    throws java.io.IOException {

  // otherwise open as netcdf and have a look. use NetcdfDataset in order to deal with scale/enhance, etc.
  DatasetUrl durl = DatasetUrl.findDatasetUrl(location);
  NetcdfDataset ncfile = NetcdfDataset.acquireDataset(durl, true, task);

  // add record variable if there is one.
  ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);

  if (UnidataStationObsDataset.isValidFile(ncfile))
    return new UnidataStationObsDataset(ncfile);

  if (UnidataPointObsDataset.isValidFile(ncfile))
    return new UnidataPointObsDataset(ncfile);

  /*
   * if (DapperDataset.isValidFile( ncfile))
   * return DapperDataset.factory( ncfile);
   * 
   * if (SequenceObsDataset.isValidFile( ncfile))
   * return new SequenceObsDataset( ncfile, task);
   */

  if (UnidataStationObsDataset2.isValidFile(ncfile))
    return new UnidataStationObsDataset2(ncfile);

  if (NdbcDataset.isValidFile(ncfile))
    return new NdbcDataset(ncfile);

  if (MadisStationObsDataset.isValidFile(ncfile))
    return new MadisStationObsDataset(ncfile);

  if (OldUnidataStationObsDataset.isValidFile(ncfile))
    return new OldUnidataStationObsDataset(ncfile);

  // put at end to minimize false positive
  if (OldUnidataPointObsDataset.isValidFile(ncfile))
    return new OldUnidataPointObsDataset(ncfile);

  if (null != log)
    log.append("Cant find a Point/Station adapter for ").append(location);
  ncfile.close();
  return null;
}
 

static void testNcml() throws IOException {
  String filename = "C:/dev/tds/thredds/cdm/src/test/data/ncml/aggUnionSimple.xml";
  NetcdfDataset ncfile = NetcdfDataset.openDataset(filename, false, null);
  measureSize("aggUnionSimple", ncfile, null, true);
  ncfile.close();
}
 

@Test
public void testCoardsDefaultCalendar() throws IOException {
  String failMessage, found, expected;
  boolean testCond;

  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/coardsMissingCalendarAttr.nc";

  // open the test file
  NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile);

  // make sure this dataset used the coardsConvention
  found = ncd.getConventionUsed();
  expected = coardsConvention;
  testCond = found.equals(expected);
  failMessage =
      format("This dataset used the %s convention, but should have used the %s convention.", found, expected);
  Assert.assertTrue(failMessage, testCond);

  // get the Time Coordinate Axis and read the values
  CoordinateAxis tca = ncd.findCoordinateAxis(AxisType.Time);
  Array times = tca.read();
  ncd.close();

  // first date in this file is 1.766292E7 [hours since 0001-01-01T00:00:00],
  // which is 2008-06-27 00:00:00
  found = Integer.toString(times.getInt(0));
  expected = "17662920";
  testCond = found.equals(expected);
  failMessage = format("The first value in the times array should be %s. I got %s instead.", expected, found);
  Assert.assertTrue(failMessage, testCond);

  // look for the calendar attached to the time variable...if there isn't one,
  // then a default was not set and the assert will fail.
  Calendar cal = Calendar.get(tca.findAttributeIgnoreCase(CF.CALENDAR).getStringValue());
  found = cal.toString();
  expected = defaultCoardsCalendar.toString();
  testCond = found.equals(expected);
  failMessage =
      format("The calendar should equal %s, but got %s instead. Failed to add a default calendar.", expected, found);
  Assert.assertTrue(failMessage, testCond);

  // convert the time value to a CalendarDate
  CoordinateAxisTimeHelper coordAxisTimeHelper =
      new CoordinateAxisTimeHelper(cal, tca.findAttributeIgnoreCase("units").getStringValue());
  CalendarDate date = coordAxisTimeHelper.makeCalendarDateFromOffset(times.getInt(0));

  // read the correct date from the time attribute and turn it into a CalendarDate
  String correctIsoDateTimeString = tca.findAttributeIgnoreCase("correct_iso_time_value_str").getStringValue();
  CalendarDate correctDate = CalendarDate.parseISOformat(defaultCoardsCalendar.toString(), correctIsoDateTimeString);

  // If everything is correct, then the date and correct date should be the same
  found = date.toString();
  expected = correctDate.toString();
  testCond = found.equals(expected);
  failMessage = format("The correct date is %s, but I got %s instead.", expected, found);
  Assert.assertTrue(failMessage, testCond);
}
 

@Test
public void testCfDefaultCalendar() throws IOException {
  String failMessage, found, expected;
  boolean testCond;

  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/cfMissingCalendarAttr.nc";

  // open the test file
  NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile);

  // make sure this dataset used the cfConvention
  expected = cfConvention;
  found = ncd.getConventionUsed();
  testCond = found.equals(expected);
  failMessage =
      format("This dataset used the %s convention, but should have used the %s convention.", found, expected);
  Assert.assertTrue(failMessage, testCond);

  // get the Time Coordinate Axis and read the values
  CoordinateAxis tca = ncd.findCoordinateAxis(AxisType.Time);
  Array times = tca.read();
  ncd.close();

  // first date in this file is 90 [hours since 2015-12-18T06:00:00],
  // which is 2015-12-22 00:00:00\
  expected = "90";
  found = Integer.toString(times.getInt(0));
  testCond = found.equals(expected);
  failMessage = format("The first value in the times array should be %s. I got %s instead.", expected, found);
  Assert.assertTrue(failMessage, testCond);

  // look for the calendar attached to the time variable...if there isn't one,
  // then a default was not set and the assert will fail.
  Calendar cal = Calendar.get(tca.findAttributeIgnoreCase(CF.CALENDAR).getStringValue());
  expected = defaultCFCalendar.toString();
  found = cal.toString();
  testCond = found.equals(expected);
  failMessage =
      format("The calendar should equal %s, but got %s instead. Failed to set a default calendar.", expected, found);
  Assert.assertTrue(failMessage, testCond);

  // convert the time value to a CalendarDate
  CoordinateAxisTimeHelper coordAxisTimeHelper =
      new CoordinateAxisTimeHelper(cal, tca.findAttributeIgnoreCase("units").getStringValue());
  CalendarDate date = coordAxisTimeHelper.makeCalendarDateFromOffset(times.getInt(0));

  // create the correct date as requested from NCSS
  String correctIsoDateTimeString = "2015-12-22T00:00:00Z";
  CalendarDate correctDate = CalendarDate.parseISOformat(defaultCFCalendar.toString(), correctIsoDateTimeString);

  // If everything is correct, then the date and correct date should be the same
  expected = correctDate.toString();
  found = date.toString();
  testCond = date.equals(correctDate);
  failMessage = format("The correct date is %s, but I got %s instead.", expected, found);
  Assert.assertTrue(failMessage, testCond);
}
 

public FeatureDatasetPoint openPointDataset(HttpServletRequest req, HttpServletResponse res, String reqPath)
    throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    FeatureDatasetPoint fd = fc.getPointDataset(match.remaining);
    if (fd == null)
      throw new IllegalArgumentException("Not a Point Dataset " + fc.getName());
    return fd;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  Formatter errlog = new Formatter();
  NetcdfDataset ncd = null;
  try {
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return (FeatureDatasetPoint) FeatureDatasetFactoryManager.wrap(FeatureType.ANY_POINT, ncd, null, errlog);

  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset; "
        : "Problem calling FeatureDatasetFactoryManager; ";
    msg += errlog.toString();
    log.error("openGridDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}
 

public SimpleGeometryFeatureDataset openSimpleGeometryDataset(HttpServletRequest req, HttpServletResponse res,
    String reqPath) throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    SimpleGeometryFeatureDataset fd = fc.getSimpleGeometryDataset(match.remaining);
    if (fd == null)
      throw new IllegalArgumentException("Not a Simple Geometry Dataset " + fc.getName());
    return fd;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  Formatter errlog = new Formatter();
  NetcdfDataset ncd = null;
  try {
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return (SimpleGeometryFeatureDataset) FeatureDatasetFactoryManager.wrap(FeatureType.SIMPLE_GEOMETRY, ncd, null,
        errlog);

  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset; "
        : "Problem calling FeatureDatasetFactoryManager; ";
    msg += errlog.toString();
    log.error("openSimpleGeometryDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}
 

private void closeAll(Map<String, NetcdfDataset> openFiles) throws IOException {
  for (NetcdfDataset ncfile : openFiles.values())
    ncfile.close();
  openFiles.clear();
}