Java Code Examples for org.jdom2.JDOMException#getMessage()

/**
 * Read an NcML file from a URL location, and construct a NcmlCollectionReader from its scan or scanFmrc element.
 *
 * @param ncmlLocation the URL location string of the NcML document
 * @param errlog put error messages here
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NcmlCollectionReader open(String ncmlLocation, Formatter errlog) throws IOException {
  if (!ncmlLocation.startsWith("http:") && !ncmlLocation.startsWith("file:"))
    ncmlLocation = "file:" + ncmlLocation;

  URL url = new URL(ncmlLocation);

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    if (debugURL)
      System.out.println(" NetcdfDataset URL = <" + url + ">");
    doc = builder.build(url);
  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
  if (debugXML)
    System.out.println(" SAXBuilder done");

  return readXML(doc, errlog, ncmlLocation);
}
 

/**
 * Read an NcML file from a String, and construct a NcmlCollectionReader from its scan or scanFmrc element.
 *
 * @param ncmlString the NcML to construct the reader from
 * @param errlog put error messages here
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NcmlCollectionReader readNcML(String ncmlString, Formatter errlog) throws IOException {
  StringReader reader = new StringReader(ncmlString);

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    if (debugURL)
      System.out.println(" NetcdfDataset NcML String = <" + ncmlString + ">");
    doc = builder.build(new StringReader(ncmlString));
  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
  if (debugXML)
    System.out.println(" SAXBuilder done");

  return readXML(doc, errlog, null);
}
 

/**
 * 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
 */
public static 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 doc from an InputStream, and construct a NetcdfDataset.
 *
 * @param ins the InputStream containing 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
 */
public static NetcdfDataset readNcML(InputStream ins, CancelTask cancelTask) throws IOException {

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(ins);
  } 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();
  NetcdfDataset ncd = readNcML(null, netcdfElem, cancelTask);
  if (debugOpen)
    System.out.println("***NcMLReader.readNcML (stream) result= \n" + ncd);
  return ncd;
}
 

/**
 * Read NcML doc from a Reader, and construct a NetcdfDataset.
 * eg: NcMLReader.readNcML(new StringReader(ncml), location, null);
 *
 * @param r the Reader containing the NcML document
 * @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 cancelTask allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NetcdfDataset readNcML(Reader r, String ncmlLocation, CancelTask cancelTask) throws IOException {

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(r);
  } 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();
  NetcdfDataset ncd = readNcML(ncmlLocation, netcdfElem, cancelTask);
  if (debugOpen)
    System.out.println("***NcMLReader.readNcML (stream) result= \n" + ncd);
  return ncd;
}
 

public boolean populate(InputStream ncml, NetcdfFile target) throws IOException {
  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(ncml);
  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
  if (showParsedXML) {
    XMLOutputter xmlOut = new XMLOutputter();
    System.out.println("*** NetcdfDataset/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
  }

  Element netcdfElem = doc.getRootElement();
  readGroup(target, target.getRootGroup(), netcdfElem);
  return errlog.toString().isEmpty();
}
 

public void readBmt() throws IOException {
  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(bmt);
    Element root = doc.getRootElement();
    int count = makeBmtTable(root.getChildren("featureCatalogue"));
    System.out.println(" bmt count= " + count);

    /*
     * Format pretty = Format.getPrettyFormat();
     * 
     * // wierd - cant pretty print ??!!
     * XMLOutputter fmt = new XMLOutputter(pretty);
     * //Writer pw = new FileWriter("C:/docs/bufr/wmo/wordNice.txt");
     * fmt.output(doc, new PrintWriter(System.out));
     */

  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
}
 

public void readBmt() throws IOException {
  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(bmt);
    Element root = doc.getRootElement();
    int count = makeBmtTable(root.getChildren("featureCatalogue"));
    System.out.println(" bmt count= " + count);

    /*
     * Format pretty = Format.getPrettyFormat();
     * 
     * // wierd - cant pretty print ??!!
     * XMLOutputter fmt = new XMLOutputter(pretty);
     * //Writer pw = new FileWriter("C:/docs/bufr/wmo/wordNice.txt");
     * fmt.output(doc, new PrintWriter(System.out));
     */

  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
}
 

RoleDatabase(String filename) throws IOException {

    InputStream is = new BufferedInputStream(new FileInputStream(filename));
    org.jdom2.Document doc;
    try {
      SAXBuilder builder = new SAXBuilder();
      doc = builder.build(is);
    } catch (JDOMException e) {
      throw new IOException(e.getMessage());
    }

    // <user username="ccsmData" roles="ccsmData, restrictedDatasetUser"/>

    Element rootElem = doc.getRootElement();
    List<Element> elems = rootElem.getChildren("user");
    for (Element elem : elems) {
      String username = elem.getAttributeValue("username");
      User user = new User(username);
      String roles = elem.getAttributeValue("roles");
      StringTokenizer stoke = new StringTokenizer(roles, ", ");
      while (stoke.hasMoreTokens()) {
        String role = stoke.nextToken();
        user.add(role);
      }
      users.put(username, user);
    }

  }
 

public void readTable() throws IOException {
  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(robbxml);
    Element root = doc.getRootElement();
    int count = makeTable(root.getChildren("sequence"));
    System.out.println(" robb count= " + count);

  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
}
 

public static void read(InputStream is, StringBuilder errlog) throws IOException {

    Document doc;
    SAXBuilder saxBuilder = new SAXBuilder();
    try {
      doc = saxBuilder.build(is);
    } catch (JDOMException e) {
      throw new IOException(e.getMessage());
    }

    read(doc.getRootElement(), errlog);
  }
 

/**
 * Read an XML Document from a URL and return the root element.
 *
 * @param location the URL location
 * @return the root element of the Document
 * @throws java.io.IOException on read error
 */
public static Element readRootElement(String location) throws IOException {
  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(location);
  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }

  return doc.getRootElement();
}
 

public TableConfig readConfigXML(String fileLocation, FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog)
    throws IOException {

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    if (debugURL)
      System.out.println(" PointConfig URL = <" + fileLocation + ">");
    doc = builder.build(fileLocation);
  } catch (JDOMException e) {
    throw new IOException(e.getMessage());
  }
  if (debugXML)
    System.out.println(" SAXBuilder done");

  if (showParsedXML) {
    XMLOutputter xmlOut = new XMLOutputter();
    System.out.println("*** PointConfig/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
  }

  Element configElem = doc.getRootElement();
  String featureType = configElem.getAttributeValue("featureType");
  Element tableElem = configElem.getChild("table");
  TableConfig tc = parseTableConfig(ds, tableElem, null);
  tc.featureType = FeatureType.valueOf(featureType);

  return tc;
}
 

/**
 * Read NcML doc from a Reader, and construct a NetcdfDataset.
 * eg: NcMLReader.readNcML(new StringReader(ncml), location, null);
 *
 * @param r the Reader containing the NcML document
 * @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 cancelTask allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NetcdfDataset.Builder readNcML(Reader r, String ncmlLocation, CancelTask cancelTask)
    throws IOException {

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    doc = builder.build(r);
  } 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();

  // the ncml probably refers to another dataset, but doesnt have to
  String referencedDatasetUri = netcdfElem.getAttributeValue("location");
  if (referencedDatasetUri == null)
    referencedDatasetUri = netcdfElem.getAttributeValue("url");
  if (referencedDatasetUri != null)
    referencedDatasetUri = AliasTranslator.translateAlias(referencedDatasetUri);

  NcMLReaderNew reader = new NcMLReaderNew();
  return reader.readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
}
 

/**
 * Use NCML to modify the dataset, getting NcML from a URL. Used by CoordSysFactory.
 *
 * @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
 */
public static void wrapNcML(NetcdfDataset.Builder 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();

  NcMLReaderNew reader = new NcMLReaderNew();
  reader.readNetcdf(ncmlLocation, ncDataset, netcdfElem, cancelTask);
  if (debugOpen) {
    System.out.println("***NcMLReader.wrapNcML result= \n" + ncDataset);
  }
}
 

/**
 * Use NCML to modify a dataset, getting the NcML document as a resource stream.
 * Uses ClassLoader.getResourceAsStream(ncmlResourceLocation), so the NcML can be inside of a jar file, for example.
 *
 * @param ncDataset modify this dataset
 * @param ncmlResourceLocation resource location of NcML
 * @param cancelTask allow user to cancel task; may be null
 * @throws IOException on read error
 */
public static void wrapNcMLresource(NetcdfDataset ncDataset, String ncmlResourceLocation, CancelTask cancelTask)
    throws IOException {
  ClassLoader cl = ncDataset.getClass().getClassLoader();
  try (InputStream is = cl.getResourceAsStream(ncmlResourceLocation)) {
    if (is == null)
      throw new FileNotFoundException(ncmlResourceLocation);

    if (debugXML) {
      System.out.println(" NetcdfDataset URL = <" + ncmlResourceLocation + ">");
      try (InputStream is2 = cl.getResourceAsStream(ncmlResourceLocation)) {
        System.out.println(" contents=\n" + IO.readContents(is2));
      }
    }

    org.jdom2.Document doc;
    try {
      SAXBuilder builder = new SAXBuilder();
      if (debugURL)
        System.out.println(" NetcdfDataset URL = <" + ncmlResourceLocation + ">");
      doc = builder.build(is);
    } 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(ncDataset.getLocation(), ncDataset, ncDataset, netcdfElem, cancelTask);
    if (debugOpen)
      System.out.println("***NcMLReader.wrapNcML result= \n" + ncDataset);
  }
}
 

/**
 * Read an NcML file from a URL location, and construct a NetcdfDataset.
 *
 * @param ncmlLocation the URL location string of the NcML document
 * @param referencedDatasetUri if null (usual case) get this from NcML, otherwise use URI as the location of the
 *        referenced dataset.
 * @param cancelTask allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NetcdfDataset.Builder readNcML(String ncmlLocation, String referencedDatasetUri, CancelTask cancelTask)
    throws IOException {
  URL url = new URL(ncmlLocation);

  if (debugURL) {
    System.out.println(" NcMLReader open " + ncmlLocation);
    System.out.println("   URL = " + url);
    System.out.println("   external form = " + url.toExternalForm());
    System.out.println("   protocol = " + url.getProtocol());
    System.out.println("   host = " + url.getHost());
    System.out.println("   path = " + url.getPath());
    System.out.println("  file = " + url.getFile());
  }

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    if (debugURL) {
      System.out.println(" NetcdfDataset URL = <" + url + ">");
    }
    doc = builder.build(url);
  } 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();

  if (referencedDatasetUri == null) {
    // the ncml probably refers to another dataset, but doesnt have to
    referencedDatasetUri = netcdfElem.getAttributeValue("location");
    if (referencedDatasetUri == null) {
      referencedDatasetUri = netcdfElem.getAttributeValue("url");
    }
  }
  if (referencedDatasetUri != null) {
    referencedDatasetUri = AliasTranslator.translateAlias(referencedDatasetUri);
  }

  NcMLReaderNew reader = new NcMLReaderNew();
  return reader.readNcML(ncmlLocation, referencedDatasetUri, netcdfElem, cancelTask);
}
 

/**
 * Use NCML to modify a dataset, getting the NcML document as a resource stream. Uses
 * ClassLoader.getResourceAsStream(ncmlResourceLocation),
 * so the NcML can be inside of a jar file, for example.
 *
 * @param ncDataset modify this dataset
 * @param ncmlResourceLocation resource location of NcML
 * @param cancelTask allow user to cancel task; may be null
 * @throws IOException on read error
 */
public static void wrapNcMLresource(NetcdfDataset.Builder ncDataset, String ncmlResourceLocation,
    CancelTask cancelTask) throws IOException {
  ClassLoader cl = ncDataset.getClass().getClassLoader();
  try (InputStream is = cl.getResourceAsStream(ncmlResourceLocation)) {
    if (is == null) {
      throw new FileNotFoundException(ncmlResourceLocation);
    }

    if (debugXML) {
      System.out.println(" NetcdfDataset URL = <" + ncmlResourceLocation + ">");
      try (InputStream is2 = cl.getResourceAsStream(ncmlResourceLocation)) {
        System.out.println(" contents=\n" + IO.readContents(is2));
      }
    }

    org.jdom2.Document doc;
    try {
      SAXBuilder builder = new SAXBuilder();
      if (debugURL) {
        System.out.println(" NetcdfDataset URL = <" + ncmlResourceLocation + ">");
      }
      doc = builder.build(is);
    } 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();

    NcMLReaderNew reader = new NcMLReaderNew();
    reader.readNetcdf(ncDataset.location, ncDataset, netcdfElem, cancelTask);
    if (debugOpen) {
      System.out.println("***NcMLReader.wrapNcML result= \n" + ncDataset);
    }
  }
}
 

/**
 * Read an NcML file from a URL location, and construct a NetcdfDataset.
 *
 * @param ncmlLocation the URL location string of the NcML document
 * @param referencedDatasetUri if null (usual case) get this from NcML, otherwise use URI as the location of the
 *        referenced dataset.
 * @param cancelTask allow user to cancel the task; may be null
 * @return the resulting NetcdfDataset
 * @throws IOException on read error, or bad referencedDatasetUri URI
 */
public static NetcdfDataset readNcML(String ncmlLocation, String referencedDatasetUri, CancelTask cancelTask)
    throws IOException {
  URL url = new URL(ncmlLocation);

  if (debugURL) {
    System.out.println(" NcMLReader open " + ncmlLocation);
    System.out.println("   URL = " + url);
    System.out.println("   external form = " + url.toExternalForm());
    System.out.println("   protocol = " + url.getProtocol());
    System.out.println("   host = " + url.getHost());
    System.out.println("   path = " + url.getPath());
    System.out.println("  file = " + url.getFile());
  }

  org.jdom2.Document doc;
  try {
    SAXBuilder builder = new SAXBuilder();
    if (debugURL)
      System.out.println(" NetcdfDataset URL = <" + url + ">");
    doc = builder.build(url);
  } 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();

  if (referencedDatasetUri == null) {
    // the ncml probably refers to another dataset, but doesnt have to
    referencedDatasetUri = netcdfElem.getAttributeValue("location");
    if (referencedDatasetUri == null)
      referencedDatasetUri = netcdfElem.getAttributeValue("url");
  }
  if (referencedDatasetUri != null)
    referencedDatasetUri = AliasTranslator.translateAlias(referencedDatasetUri);

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