ucar.nc2.ncml.NcMLReader java code examples

/**
 * Read an NcML file from a URL location, and construct a NetcdfDataset.
 *
 * @param ncmlLocation the URL location string of the NcML document
 * @param cancelTask   allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
static public NetcdfDataset readNcML(String ncmlLocation, CancelTask cancelTask) throws IOException {
 return readNcML(ncmlLocation, (String) null, cancelTask);
}

public void augmentDataset(NetcdfDataset ncDataset, CancelTask cancelTask) throws IOException {
 NcMLReader.wrapNcMLresource(ncDataset, CoordSysBuilder.resourcesDir + "ATDRadar.ncml", cancelTask);
}

/**
 * Use NCML to directly modify the dataset
 *
 * @param targetDS   referenced dataset
 * @param parentElem parent element - usually the aggregation element of the ncml
 * @return new dataset with the merged info
 * @throws IOException on read error
 */
static public NetcdfDataset mergeNcMLdirect(NetcdfDataset targetDS, Element parentElem) throws IOException {
 NcMLReader reader = new NcMLReader();
 reader.readGroup(targetDS, targetDS, null, null, parentElem);
 targetDS.finish();
 return targetDS;
}

/**
 * Read NcML from a JDOM Document, and pass in the name of the dataset. Used to augment datasetScan with NcML
 *
 * @param ncmlLocation the URL location string of the NcML document, used as a unique name for caching purposes.
 * @param netcdfElem   the JDOM Document's root (netcdf) element
 * @param referencedDatasetUri the URL location string of the underlying dataset, which overrides anything in netcdfElem.
 *                             prepend with "file:" to eliminate reletive resolving against ncmlLocation
 * @param cancelTask   allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
static public NetcdfDataset readNcML(String ncmlLocation, Element netcdfElem, String referencedDatasetUri, CancelTask cancelTask) throws IOException {
 NcMLReader reader = new NcMLReader();
 return reader._readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
}

/**
 * Read NcML from a JDOM Document, and construct a NetcdfDataset.
 *
 * @param ncmlLocation the URL location string of the NcML document, used to resolve reletive path of the referenced dataset,
 *                     or may be just a unique name for caching purposes.
 * @param netcdfElem   the JDOM Document's root (netcdf) element
 * @param cancelTask   allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
static public NetcdfDataset readNcML(String ncmlLocation, Element netcdfElem, CancelTask cancelTask) throws IOException {
 // the ncml probably refers to another dataset, but doesnt have to
 String referencedDatasetUri = netcdfElem.getAttributeValue("location");
 if (referencedDatasetUri == null)
  referencedDatasetUri = netcdfElem.getAttributeValue("url");
 NcMLReader reader = new NcMLReader();
 return reader.readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
}

if (refv == null) { // new
 if (debugConstruct) System.out.println(" add new var = " + name);
 Variable nested = readVariableNew(ds, parentS.getParentGroup(), parentS, varElem);
 parentS.addMemberVariable(nested);
 return;
 readAtt(v, refv, attElem);
 cmdRemove(v, remElem.getAttributeValue("type"), remElem.getAttributeValue("name"));
 java.util.List<Element> varList = varElem.getChildren("variable", ncNS);
 for (Element vElem : varList) {
  readVariableNested(ds, s, refS, vElem);
  readValues(ds, v, varElem, valueElem);

readAtt(g, refg, attElem);
readEnumTypedef(g, refg, elem);
readDim(g, refg, dimElem);
readVariable(newds, g, refg, varElem);
cmdRemove(g, e.getAttributeValue("type"), e.getAttributeValue("name"));
readGroup(newds, refds, g, refg, gElem);
if (debugConstruct) System.out.println(" add group = " + g.getFullName());

if (nameInFile == null)
 nameInFile = name;
else if (null == findAttribute(refParent, nameInFile)) { // has to exists
 errlog.format("NcML attribute orgName '%s' doesnt exist. att=%s in=%s%n", nameInFile, name, parent);
 return;
ucar.nc2.Attribute att = findAttribute(refParent, nameInFile);
if (att == null) { // new
 if (debugConstruct) System.out.println(" add new att = " + name);
 try {
  ucar.ma2.Array values = readAttributeValues(attElem);
  addAttribute(parent, new ucar.nc2.Attribute(name, values));
 } catch (RuntimeException e) {
  errlog.format("NcML new Attribute Exception: %s att=%s in=%s%n", e.getMessage(), name, parent);
 if (hasValue) {
  try {
   ucar.ma2.Array values = readAttributeValues(attElem);
   addAttribute(parent, new ucar.nc2.Attribute(name, values));
  } catch (RuntimeException e) {
   errlog.format("NcML existing Attribute Exception: %s att=%s in=%s%n", e.getMessage(), name, parent);
  addAttribute(parent, new ucar.nc2.Attribute(name, att.getValues()));
  removeAttribute(parent, att);
  if (debugConstruct) System.out.println(" remove old att = " + nameInFile);

/**
 * Use NCML to modify the dataset, getting NcML from a URL
 *
 * @param ncDataset    modify this dataset
 * @param ncmlLocation URL location of NcML
 * @param cancelTask   allow user to cancel task; may be null
 * @throws IOException on read error
 */
static public void wrapNcML(NetcdfDataset ncDataset, String ncmlLocation, CancelTask cancelTask) throws IOException {
 org.jdom2.Document doc;
 try {
  SAXBuilder builder = new SAXBuilder();
  if (debugURL) System.out.println(" NetcdfDataset URL = <" + ncmlLocation + ">");
  doc = builder.build(ncmlLocation);
 } catch (JDOMException e) {
  throw new IOException(e.getMessage());
 }
 if (debugXML) System.out.println(" SAXBuilder done");
 if (showParsedXML) {
  XMLOutputter xmlOut = new XMLOutputter();
  System.out.println("*** NetcdfDataset/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
 }
 Element netcdfElem = doc.getRootElement();
 NcMLReader reader = new NcMLReader();
 reader.readNetcdf(ncmlLocation, ncDataset, ncDataset, netcdfElem, cancelTask);
 if (debugOpen) System.out.println("***NcMLReader.wrapNcML result= \n" + ncDataset);
}

 Aggregation agg = readAgg(aggElem, ncmlLocation, targetDS, cancelTask);
 targetDS.setAggregation(agg);
 agg.finish(cancelTask);
readGroup(targetDS, refds, null, null, netcdfElem);
String errors = errlog.toString();
if (errors.length() > 0)

if (convNcML != null) {
 CoordSysBuilder csb = new CoordSysBuilder();
 NcMLReader.wrapNcML(ds, convNcML, cancelTask);
 return csb;

public NetcdfFile acquireFile(CancelTask cancelTask) throws IOException {
 if (debugOpenFile) System.out.println(" try to acquire " + cacheLocation);
 long start = System.currentTimeMillis();
 NetcdfFile ncfile = NetcdfDataset.acquireFile(reader, null, cacheLocation, -1, cancelTask, spiObject);
 // must merge NcML before enhancing
 if (mergeNcml != null)
  ncfile = NcMLReader.mergeNcML(ncfile, mergeNcml); // create new dataset
 if (enhance == null || enhance.isEmpty()) {
  if (debugOpenFile) System.out.println(" acquire (no enhance) " + cacheLocation + " took " + (System.currentTimeMillis() - start));
  return ncfile;
 }
 // must enhance
 NetcdfDataset ds;
 if (ncfile instanceof NetcdfDataset) {
  ds = (NetcdfDataset) ncfile;
  ds.enhance(enhance); // enhance "in place", ie modify the NetcdfDataset
 } else {
  ds = new NetcdfDataset(ncfile, enhance); // enhance when wrapping
 }
 if (debugOpenFile) System.out.println(" acquire (enhance) " + cacheLocation + " took " + (System.currentTimeMillis() - start));
 return ds;
}

NcMLReader.mergeNcMLdirect(result, protoConfig.outerNcml);

if (refv == null) { // new
 if (debugConstruct) System.out.println(" add new var = " + name);
 Variable nested = readVariableNew(ds, parentS.getParentGroup(), parentS, varElem);
 if (nested != null) parentS.addMemberVariable(nested);
 return;
 readAtt(v, refv, attElem);
 cmdRemove(v, remElem.getAttributeValue("type"), remElem.getAttributeValue("name"));
 java.util.List<Element> varList = varElem.getChildren("variable", ncNS);
 for (Element vElem : varList) {
  readVariableNested(ds, s, refS, vElem);
  readValues(ds, v, varElem, valueElem);

readAtt(g, refg, attElem);
readEnumTypedef(g, refg, elem);
readDim(g, refg, dimElem);
readVariable(newds, g, refg, varElem);
cmdRemove(g, e.getAttributeValue("type"), e.getAttributeValue("name"));
readGroup(newds, refds, g, refg, gElem);
if (debugConstruct) System.out.println(" add group = " + g.getFullName());

if (nameInFile == null)
 nameInFile = name;
else if (null == findAttribute(refParent, nameInFile)) { // has to exists
 errlog.format("NcML attribute orgName '%s' doesnt exist. att=%s in=%s%n", nameInFile, name, parent);
 return;
ucar.nc2.Attribute oldatt = findAttribute(refParent, nameInFile);
if (oldatt == null) { // new
 if (debugConstruct) System.out.println(" add new att = " + name);
 try {
  ucar.ma2.Array values = readAttributeValues(attElem);
  addAttribute(parent, new ucar.nc2.Attribute(name, values));
 } catch (RuntimeException e) {
  errlog.format("NcML new Attribute Exception: %s att=%s in=%s%n", e.getMessage(), name, parent);
 if (hasValue) {  // has a new value
  try {
   ucar.ma2.Array values = readAttributeValues(attElem);
   addAttribute(parent, new ucar.nc2.Attribute(name, values));
  } catch (RuntimeException e) {
   errlog.format("NcML existing Attribute Exception: %s att=%s in=%s%n", e.getMessage(), name, parent);
  Array oldval = oldatt.getValues();
  if (oldval != null)
   addAttribute(parent, new ucar.nc2.Attribute(name, oldatt.getValues()));
  else {  // weird corner case of attribute with no value - must use the type
   String unS = attElem.getAttributeValue("isUnsigned");
   String typeS = attElem.getAttributeValue("type");

/**
 * Use NCML to modify the dataset, getting NcML from a URL
 *
 * @param ncDataset    modify this dataset
 * @param ncmlLocation URL location of NcML
 * @param cancelTask   allow user to cancel task; may be null
 * @throws IOException on read error
 */
static public void wrapNcML(NetcdfDataset ncDataset, String ncmlLocation, CancelTask cancelTask) throws IOException {
 org.jdom2.Document doc;
 try {
  SAXBuilder builder = new SAXBuilder();
  if (debugURL) System.out.println(" NetcdfDataset URL = <" + ncmlLocation + ">");
  doc = builder.build(ncmlLocation);
 } catch (JDOMException e) {
  throw new IOException(e.getMessage());
 }
 if (debugXML) System.out.println(" SAXBuilder done");
 if (showParsedXML) {
  XMLOutputter xmlOut = new XMLOutputter();
  System.out.println("*** NetcdfDataset/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
 }
 Element netcdfElem = doc.getRootElement();
 NcMLReader reader = new NcMLReader();
 reader.readNetcdf(ncmlLocation, ncDataset, ncDataset, netcdfElem, cancelTask);
 if (debugOpen) System.out.println("***NcMLReader.wrapNcML result= \n" + ncDataset);
}

/**
 * Read NcML from a JDOM Document, and pass in the name of the dataset. Used to augment datasetScan with NcML
 *
 * @param ncmlLocation the URL location string of the NcML document, used as a unique name for caching purposes.
 * @param netcdfElem   the JDOM Document's root (netcdf) element
 * @param referencedDatasetUri the URL location string of the underlying dataset, which overrides anything in netcdfElem.
 *                             prepend with "file:" to eliminate reletive resolving against ncmlLocation
 * @param cancelTask   allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
static public NetcdfDataset readNcML(String ncmlLocation, Element netcdfElem, String referencedDatasetUri, CancelTask cancelTask) throws IOException {
 NcMLReader reader = new NcMLReader();
 return reader._readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
}

NcMLReader reader = new NcMLReader();
NetcdfDataset ncd = reader.readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
if (debugOpen) System.out.println("***NcMLReader.readNcML result= \n" + ncd);
return ncd;

 Aggregation agg = readAgg(aggElem, ncmlLocation, targetDS, cancelTask);
 targetDS.setAggregation(agg);
 agg.finish(cancelTask);
readGroup(targetDS, refds, null, null, netcdfElem);
String errors = errlog.toString();
if (errors.length() > 0)

Javadoc

Read NcML and create NetcdfDataset.

Most used methods

readNcML
Read an NcML file from a URL location, and construct a NetcdfDataset.
wrapNcML
Use NCML to modify the dataset, getting NcML from a URL
wrapNcMLresource
Use NCML to modify a dataset, getting the NcML document as a resource stream. Uses ClassLoader.getRe
<init>
addAttribute
cmdRemove
findAttribute
mergeNcML
Use NCML to modify the referenced dataset, create a new dataset with the merged info Used to wrap ea
mergeNcMLdirect
Use NCML to directly modify the dataset
readAgg
readAtt
Read an NcML attribute element.
readAttributeValues
Parse the values element

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How to useNcMLReader in ucar.nc2.ncml

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