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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
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/*
* Copyright 1998-2009 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package thredds.catalog.crawl;
import ucar.nc2.dataset.*;
import ucar.nc2.time.CalendarDateRange;
import ucar.nc2.units.TimeUnit;
import ucar.nc2.util.CancelTask;
import ucar.nc2.util.IO;
import ucar.nc2.util.NamedObject;
import ucar.nc2.thredds.ThreddsDataFactory;
import ucar.nc2.Attribute;
import ucar.nc2.constants.FeatureType;
import ucar.nc2.dt.GridDataset;
import ucar.nc2.dt.GridCoordSystem;
import ucar.nc2.dt.GridDatatype;
import ucar.unidata.geoloc.*;
import java.io.*;
import java.util.List;
import java.util.Formatter;
import thredds.catalog.*;
import ucar.unidata.util.Format;
import ucar.unidata.util.Parameter;
import ucar.unidata.util.StringUtil2;
/**
* Utilities for extracting info from a catalog.
*
* @author John Caron
*/
public class CatalogExtractor implements CatalogCrawler.Listener {
private boolean verbose = true;
private InvCatalogFactory catFactory = InvCatalogFactory.getDefaultFactory(true);
private ThreddsDataFactory tdataFactory = new ThreddsDataFactory();
private int countDatasets, countNoAccess, countNoOpen;
private PrintStream out;
private String transferDir = "C:/data/bad/";
private String copyDir = null;
/**
* Constuctor
* @param verbose output status messages
*/
public CatalogExtractor(boolean verbose) {
this.verbose = verbose;
}
public void copy(String catUrl, String copyToDir, CancelTask task) throws IOException {
this.copyDir = copyToDir;
InvCatalogImpl cat = catFactory.readXML(catUrl);
StringBuilder buff = new StringBuilder();
if (!cat.check(buff, false))
return;
countDatasets = 0;
countNoAccess = 0;
countNoOpen = 0;
int countCatRefs = 0;
CatalogCrawler crawler = new CatalogCrawler(CatalogCrawler.USE_ALL_DIRECT, false, new CatalogCrawler.Listener() {
public void getDataset(InvDataset dd, Object context) {
InvAccess access = tdataFactory.chooseDatasetAccess(dd.getAccess());
if (null != access) transfer(access.getStandardUrlName(), copyDir);
}
public boolean getCatalogRef(InvCatalogRef dd, Object context) { return true; }
});
long start = System.currentTimeMillis();
try {
countCatRefs = crawler.crawl(cat, task, out, null);
} finally {
int took = (int) (System.currentTimeMillis() - start) / 1000;
out.println("***Done " + catUrl + " took = " + took + " secs\n" +
" datasets=" + countDatasets + " no access=" + countNoAccess + " open failed=" + countNoOpen + " total catalogs=" + countCatRefs);
if (verbose) System.out.println("***Done " + catUrl + " took = " + took + " secs\n" +
" datasets=" + countDatasets + " no access=" + countNoAccess + " open failed=" + countNoOpen + " total catalogs=" + countCatRefs);
}
}
public void extractLoop(PrintStream out, String catUrl, int type, boolean skipDatasetScan, CancelTask task) throws IOException {
while (true) {
extract(out, catUrl, type, skipDatasetScan, task);
if ((task != null) && task.isCancel())
break;
}
}
public void extract(PrintStream out, String catUrl, int type, boolean skipDatasetScan, CancelTask task) throws IOException {
this.out = out;
out.println("***read " + catUrl);
InvCatalogImpl cat = catFactory.readXML(catUrl);
StringBuilder buff = new StringBuilder();
boolean isValid = cat.check(buff, false);
if (!isValid) {
System.out.println("***Catalog invalid= " + catUrl + " validation output=\n" + buff);
out.println("***Catalog invalid= " + catUrl + " validation output=\n" + buff);
return;
}
out.println("catalog <" + cat.getName() + "> is valid");
out.println(" validation output=\n" + buff);
countDatasets = 0;
countNoAccess = 0;
countNoOpen = 0;
int countCatRefs = 0;
CatalogCrawler crawler = new CatalogCrawler(type, skipDatasetScan, this);
long start = System.currentTimeMillis();
try {
countCatRefs = crawler.crawl(cat, task, out, null);
} finally {
int took = (int) (System.currentTimeMillis() - start) / 1000;
out.println("***Done " + catUrl + " took = " + took + " secs\n" +
" datasets=" + countDatasets + " no access=" + countNoAccess + " open failed=" + countNoOpen + " total catalogs=" + countCatRefs);
if (verbose) {
System.out.println("***Done " + catUrl + " took = " + took + " secs\n" +
" datasets=" + countDatasets + " no access=" + countNoAccess + " open failed=" + countNoOpen + " total catalogs=" + countCatRefs);
}
}
}
public void getDataset(InvDataset ds, Object context) {
countDatasets++;
openDataset(out, ds);
//return extractTypedDatasetInfo( out, ds);
}
public boolean getCatalogRef(InvCatalogRef dd, Object context) { return true; }
public boolean openDataset(PrintStream out, InvDataset ds) {
InvAccess access = tdataFactory.chooseDatasetAccess(ds.getAccess());
if (access == null) {
countNoAccess++;
out.println(" **FAILED to find access " + ds.getName());
System.out.println(" **FAILED to find access " + ds.getName());
return false;
}
NetcdfDataset ncd = null;
long start = System.currentTimeMillis();
try {
// ncd = NetcdfDataset.openDataset( access.getStandardUrlName());
Formatter log = new Formatter();
ncd = tdataFactory.openDataset(access, true, null, log);
if (ncd == null) {
countNoOpen++;
out.println(" **FAILED to open " + access.getStandardUrlName() + " " + log);
System.out.println(" **FAILED to open " + access.getStandardUrlName() + " " + log);
transfer(access.getStandardUrlName(), transferDir);
return false;
}
int took = (int) (System.currentTimeMillis() - start);
boolean ok = true; // ucar.nc2.iosp.nexrad2.TestNexrad2.testCoordSystem( ncd);
out.println(" **Open " + ds.getDataType() + " " + ncd.getLocation() + " (" + ds.getName() + ") " + took + " msecs");
if (verbose)
System.out.println(" **Open " + ds.getDataType() + " " + ncd.getLocation() + " (" + ds.getName() + ") " + took + " msecs");
} catch (Throwable e) {
countNoOpen++;
out.println(" **FAILED to open " + access.getStandardUrlName());
System.out.println(" **FAILED to open " + access.getStandardUrlName());
transfer(access.getStandardUrlName(), transferDir);
return false;
} finally {
if (ncd != null) try {
ncd.close();
out.println(" Close " + ncd.getLocation());
} catch (IOException e) {
e.printStackTrace();
}
}
return true;
}
private void transfer(String url, String copyToDir) {
String new_url = StringUtil2.substitute(url, "dodsC", "fileServer");
int pos = url.lastIndexOf('/');
String filename = url.substring(pos + 1);
File file = new File(copyToDir, filename);
IO.readURLtoFile(new_url, file);
System.out.println(" **copied to " + file.getPath() + " size=" + file.length());
}
public boolean extractTypedDatasetInfo(PrintStream out, InvDataset ds) {
boolean ok = true;
long start = System.currentTimeMillis();
ThreddsDataFactory.Result result = null;
try {
result = tdataFactory.openFeatureDataset(ds, null);
int took = (int) (System.currentTimeMillis() - start);
if (verbose)
System.out.println(" **Open " + result.featureType + " " + result.location + " (" + ds.getName() + ") " + took + " msecs");
out.println(" **Open " + result.featureType + " " + result.location + " (" + ds.getName() + ") " + took + " msecs");
if (result.location == null)
ok = false;
else if (result.featureType == FeatureType.GRID)
extractGridDataset(out, (GridDataset) result.featureDataset);
} catch (Throwable e) {
out.println(" **FAILED " + ds.getName());
e.printStackTrace(out);
e.printStackTrace();
return false;
} finally {
if ((result != null) && (result.featureDataset != null)) try {
result.featureDataset.close();
out.println(" Close " + result.featureType + " " + result.location);
} catch (IOException e) {
e.printStackTrace();
}
}
return ok;
}
private void extractGridDataset(PrintStream out, GridDataset gridDs) {
if (!verbose) {
out.println(" ngrids = " + gridDs.getGrids().size());
return;
}
if (gridDs == null) return;
out.println("Global Attributes");
NetcdfDataset ds = (NetcdfDataset) gridDs.getNetcdfFile();
showAtts(out, ds.getGlobalAttributes());
out.println();
GridCoordSystem gcsMax = null;
LatLonRect llbbMax = null;
LatLonRect llbb = null;
CalendarDateRange dateRange = null;
long nx = 0, ny = 0;
for (GridDataset.Gridset gset : gridDs.getGridsets()) {
GridCoordSystem gcs = gset.getGeoCoordSystem();
CoordinateAxis1D xaxis = (CoordinateAxis1D) gcs.getXHorizAxis();
CoordinateAxis1D yaxis = (CoordinateAxis1D) gcs.getYHorizAxis();
long nx2 = xaxis.getSize();
long ny2 = yaxis.getSize();
if ((nx != nx2) || (ny != ny2)) {
nx = nx2;
ny = ny2;
double dx = xaxis.getIncrement();
double dy = yaxis.getIncrement();
out.println(" horizontal = " + nx + " by " + ny + " points, resolution " + Format.d(dx, 4) + " " + Format.d(dy, 4)
+ " " + xaxis.getUnitsString());
}
ProjectionImpl proj = gcs.getProjection();
if (proj != null) {
out.println(", " + proj.getClassName() + " projection;");
List params = proj.getProjectionParameters();
for (Parameter p : params)
out.println(" " + p.getName() + " " + p.getStringValue());
} else
out.println();
LatLonRect llbb2 = gcs.getLatLonBoundingBox();
if ((llbb == null) || !llbb2.equals(llbb)) {
llbb = llbb2;
if (llbbMax == null)
llbbMax = llbb;
else
llbbMax.extend(llbb);
if (llbb.getWidth() >= 360.0) {
out.println(" BoundingBox == GLOBAL");
} else {
StringBuilder buff = new StringBuilder();
LatLonPointImpl ll = llbb.getLowerLeftPoint();
LatLonPointImpl ur = llbb.getUpperRightPoint();
buff.append(Double.toString(ll.getLongitude()));
buff.append(" ");
buff.append(Double.toString(ll.getLatitude()));
buff.append(" ");
buff.append(Double.toString(ur.getLongitude()));
buff.append(" ");
buff.append(Double.toString(ur.getLatitude()));
buff.append(" ");
out.println(" BoundingBox == " + buff + " width= " + llbb.getWidth() + " " + (llbb.getWidth() >= 360.0 ? "global" : ""));
}
}
CoordinateAxis1DTime taxis = gcs.getTimeAxis1D();
CalendarDateRange dateRange2 = gcs.getCalendarDateRange();
if ((taxis != null) && ((dateRange == null) || !dateRange2.equals(dateRange))) {
long ntimes = taxis.getSize();
try {
TimeUnit tUnit = taxis.getTimeResolution();
if (dateRange != null)
out.printf(" DateRange == %s duration = %d secs; ntimes = %d data resolution = %s%n", dateRange, dateRange.getDurationInSecs(), ntimes, tUnit);
} catch (Exception e) {
e.printStackTrace();
}
}
CoordinateAxis1D vaxis = gcs.getVerticalAxis();
if (vaxis != null) {
long nvert = vaxis.getSize();
out.print(" Vertical axis= " + vaxis.getFullName() + " units=" + vaxis.getUnitsString() + " size= " + nvert);
VerticalCT vt = gcs.getVerticalCT();
if (vt != null)
out.print(" transform= " + vt.getVerticalTransformType());
List vertNames = vaxis.getNames();
for (NamedObject vertName : vertNames)
out.print(" " + vertName);
out.println();
if ((gcsMax == null) || (gcsMax.getVerticalAxis().getSize() < vaxis.getSize()))
gcsMax = gcs;
}
}
/* ThreddsMetadata.GeospatialCoverage gc = new ThreddsMetadata.GeospatialCoverage();
gc.setBoundingBox(llbbMax);
if (gcsMax != null) {
gc.setVertical(gcsMax.getVerticalAxis());
gc.setZPositiveUp(gcsMax.isZPositive());
}
try {
gc.toXML(out);
} catch (IOException e) {
e.printStackTrace();
} */
/* java.util.List grids = gridDs.getGrids();
String fileFormat = ds.findAttValueIgnoreCase(null, "FileFormat", "");
if (fileFormat.equals("GRIB-1"))
makeGrib1Vocabulary(grids, out); */
}
private void showAtts(PrintStream out, List atts) {
for (Attribute att : atts)
out.println(" " + att);
}
private void makeGrib1Vocabulary(List grids, PrintStream out) {
String stdName;
out.println("\n");
for (GridDatatype grid : grids) {
Attribute att = grid.findAttributeIgnoreCase("GRIB_param_number");
stdName = (att != null) ? att.getNumericValue().toString() : null;
out.print(" ");
}
/* private void showDatasetInfo(InvDataset ds) {
if (ds == null) return;
String bbString = ds.findProperty("BoundingBox");
if (bbString == null) {
displayMap.drawBoundingBox( null);
return;
}
if (Debug.isSet("extract/boundingBox")) System.out.println("showDatasetInfo BoundingBox attribute= "+bbString);
ProjectionRect bb = null;
if (bbString.equals("global")) {
LatLonProjection displayProj = (LatLonProjection) displayMap.getProjectionImpl();
double centerLon = displayProj.getCenterLon();
bb = new ProjectionRect(centerLon-180.0, -90.0, centerLon+180.0, 90.0);
} else {
double[] dval = new double[4];
int count = 0;
StringTokenizer stoke = new StringTokenizer(bbString);
while (stoke.hasMoreTokens() && (count < 4)) {
String token = stoke.nextToken();
try{
dval[count] = Double.parseDouble(token);
count++;
} catch (NumberFormatException e) {}
}
bb = new ProjectionRect(dval[0], dval[1], dval[2], dval[3]);
}
displayMap.drawBoundingBox( bb);
} */
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