Java Code Examples for ucar.nc2.NetcdfFile#close()

@Test
public void testUpdateLastModified() throws IOException, InvalidRangeException, InterruptedException {
  // make sure that the extra file is not in the agg
  move(extraFile);

  // open the agg
  NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), location, null);
  long start = ncfile.getLastModified();

  // now make sure that the extra file is in the agg
  moveBack(extraFile);

  // reread
  long end = ncfile.getLastModified();
  assert (end > start);

  // again
  long end2 = ncfile.getLastModified();
  assert (end == end2);

  ncfile.close();
}
 

@Test(expected = IOException.class)
public void testNcmlDatasetNoProtocolInNcmlAbsPath() throws IOException, InvalidRangeException {
  // if using an absolute path in the NcML file location attr of the element netcdf, then
  // you must prepend file:
  // this should fail with an IOException
  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggExisting6.xml";

  NetcdfFile ncfile = NetcdfDatasets.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
@Ignore("file in use - testing artifact")
public void testRemove() throws IOException, InterruptedException {
  NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(aggExistingSync), "aggExistingSync", null);
  testAggCoordVar(ncfile, ntimes);
  System.out.println("");
  ncfile.close();

  String fname = dataDir + "WEST-CONUS_4km_3.9_20050912_2130.gini";
  boolean ok = TestOffAggUpdating.move(fname);
  int nfiles = ok ? ntimes - 1 : ntimes; // sometimes fails

  ncfile = NcMLReader.readNcML(new StringReader(aggExistingSync), "aggExistingSync", null);
  testAggCoordVar(ncfile, nfiles);
  ncfile.close();

  TestOffAggUpdating.moveBack(fname);
  System.out.printf("ok testRemove%n");
}
 

@Ignore("Cant use Fmrc on GRIB")
@Test
public void testOpen() throws Exception {
  String dataDir = TestDir.cdmUnitTestDir + "ft/fmrc/rtmodels/";
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2'>\n"
      + "  <aggregation dimName='run' type='forecastModelRunSingleCollection' timeUnitsChange='true' >\n"
      + "    <scanFmrc location='" + dataDir + "' regExp='.*_nmm\\.GrbF[0-9]{5}$'\n"
      + "           runDateMatcher='yyMMddHH#_nmm.GrbF#'\n" + "           forecastOffsetMatcher='#_nmm.GrbF#HHH'/>\n"
      + "  </aggregation>\n" + "</netcdf>";

  String filename = "fake:TestOffAggFmrcScan2/aggFmrcScan2.xml";
  NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), filename, null);
  System.out.println(" TestAggForecastModel.open " + filename);
  System.out.println("file=" + ncfile);

  TestDir.readAllData(ncfile);

  ncfile.close();
}
 

@Test
public void testRename() throws IOException, InvalidRangeException {
  String xml = "<?xml version='1.0' encoding='UTF-8'?>\n" // leavit
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2'>\n" // leavit
      + "  <variable name='Temperature' orgName='T' />\n" // leavit
      + "  <aggregation  dimName='time' type='joinNew'>\n" // leavit
      + "    <variableAgg name='T'/>\n" // leavit
      + "    <scan location='src/test/data/ncml/nc/' suffix='Dir.nc' subdirs='false'/>\n" // leavit
      + "  </aggregation>\n" // leavit
      + "</netcdf>"; // leavit

  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggSynRename.xml";
  NetcdfFile ncfile = NcMLReaderNew.readNcML(new StringReader(xml), null, null).build();

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVarNoCoordsDir(ncfile);
  testReadData(ncfile, "Temperature");
  testReadSlice(ncfile, "Temperature");
  ncfile.close();
}
 

@Test
public void testNcmlDatasetWcoords() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingWcoords.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" testNcmlDatasetWcoords.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
  logger.debug(" testNcmlDatasetWcoords.closed ");
}
 

@Test
public void test2() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggSynthetic2.xml";
  NetcdfFile ncfile = NcMLReaderNew.readNcML(filename, null, null).build();

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar2(ncfile);
  testReadData(ncfile, "T");
  testReadSlice(ncfile, "T");

  ncfile.close();
}
 

@Test
public void testNcmlDatasetNoProtocolInNcmlRelPath() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExisting7.xml";

  NetcdfFile ncfile = NetcdfDatasets.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

static void openFile(String filename, Average avg, boolean enhance) throws IOException, InvalidRangeException {
  try {
    long start = System.nanoTime();
    NetcdfFile ncfile = enhance ? NetcdfDataset.openDataset(filename) : NetcdfDataset.openFile(filename, null);
    long end = System.nanoTime();
    double took = (double) ((end - start)) / 1000 / 1000 / 1000;
    ncfile.close();
    if (avg != null)
      avg.add(took);
  } catch (Exception e) {
    System.out.println("BAD " + filename);
    e.printStackTrace();
  }
}
 

public void testNcmlDataset() throws IOException {
  String filename = "file:" + TestDir.cdmUnitTestDir + "ncml/nc/seawifs/aggDirectory.ncml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.openDataset {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData2(ncfile);

  ncfile.close();
}
 

@Test
public void testNcmlDirect() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExisting.xml";

  NetcdfFile ncfile = NcMLReaderNew.readNcML(filename, null, null).build();
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
public void testNcmlDatasetNoProtocolInFilenameOrNcmlRelPath() throws IOException, InvalidRangeException {
  String filename = "./" + TestNcMLRead.topDir + "aggExisting7.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
public void test3() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggSynthetic3.xml";
  NetcdfFile ncfile = NcMLReaderNew.readNcML(filename, null, null).build();

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar3(ncfile);
  testReadData(ncfile, "T");
  testReadSlice(ncfile, "T");

  ncfile.close();
}
 

@Test
public void testNcmlDatasetNoProtocolInFilenameOrNcmlRelPath() throws IOException, InvalidRangeException {
  String filename = "./" + TestNcMLRead.topDir + "aggExisting7.xml";

  NetcdfFile ncfile = NetcdfDatasets.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
public void testNcmlDatasetNoProtocolInFilename() throws IOException, InvalidRangeException {
  String filename = "./" + TestNcMLRead.topDir + "aggExisting.xml";

  NetcdfFile ncfile = NetcdfDatasets.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
public void testProblem() throws IOException {
  String filename = TestDir.cdmUnitTestDir + "formats/grib1/testproj2.grb";
  System.out.println("read file= " + filename);
  NetcdfFile ncfile = NetcdfDatasets.openFile(filename, null);
  ncfile.close();
}
 

@Test
public void testNcmlDataset() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExisting.xml";

  NetcdfFile ncfile = NetcdfDatasets.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.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());
  }
}
 

protected void close(NetcdfFile ncfile) throws IOException {
  if (ncfile == null)
    return;
  cacheVariables(ncfile);
  ncfile.close();
}
 

/**
 * Read an NcML and write an equivilent NetcdfFile to a physical file, using Netcdf-3 file format.
 * The NcML may have a referenced dataset in the location URL, in which case the underlying data
 * (modified by the NcML) is written to the new file. If the NcML does not have a referenced dataset,
 * then the new file is filled with fill values, like ncgen.
 *
 * @param ncml read NcML from this input stream
 * @param fileOutName write to this local file
 * @param version kind of netcdf file
 * @param chunker optional chunking (netcdf4 only)
 */
public static void writeNcMLToFile(InputStream ncml, String fileOutName, NetcdfFileWriter.Version version,
    Nc4Chunking chunker) throws IOException {
  NetcdfDataset ncd = NcMLReader.readNcML(ncml, null);
  FileWriter2 writer = new FileWriter2(ncd, fileOutName, version, chunker);
  NetcdfFile result = writer.write();
  result.close();
  ncd.close();
}