@Override
protected String getDocumentText(String absolutePath, String encoding) throws IOException {
String text;
try {
SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setValidating(false);
spf.setNamespaceAware(true);
spf.setFeature("http://xml.org/sax/features/namespaces", true);
spf.setFeature("http://xml.org/sax/features/validation", false);
spf.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
SAXParser saxParser = spf.newSAXParser();
XMLReader xmlReader = saxParser.getXMLReader();
TeiToTxtSaxHandler handler = new TeiToTxtSaxHandler();
xmlReader.setContentHandler(handler);
xmlReader.parse(new InputSource(absolutePath));
text = handler.getText();
} catch (ParserConfigurationException | SAXException e) {
logger.error("Could not read TEI document: {}", absolutePath);
logger.warn("Ignoring TEI document " + absolutePath);
text = "";
this.failedFileCounter++;
}
return text;
}
/**
* @see MessageBodyReader#readFrom(Class, Type, MediaType, Annotation[], MultivaluedMap,
* InputStream)
*/
@Override
public Object readFrom(
Class<Object> type,
Type genericType,
Annotation[] annotations,
MediaType mediaType,
MultivaluedMap<String, String> httpHeaders,
InputStream entityStream)
throws IOException {
try {
SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setXIncludeAware(isXIncludeAware());
spf.setNamespaceAware(true);
spf.setValidating(isValidatingDtd());
spf.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, isSecureProcessing());
spf.setFeature(
"http://xml.org/sax/features/external-general-entities", isExpandingEntityRefs());
spf.setFeature(
"http://xml.org/sax/features/external-parameter-entities", isExpandingEntityRefs());
XMLReader reader = spf.newSAXParser().getXMLReader();
JAXBContext jaxbContext = getJaxbContext(type);
Unmarshaller um = jaxbContext.createUnmarshaller();
return um.unmarshal(new SAXSource(reader, new InputSource(entityStream)));
} catch (Exception e) {
throw new IOException("Could not unmarshal to " + type.getName());
}
}
/**
* constructor, sets up SAX parser, turns off validation, turns on namespaces, sets up content
* handler and error handler as this object. sax exceptions go to System.err
*/
public XBASEXMLParser() {
try {
SAXParserFactory factory = SAXParserFactory.newInstance();
factory.setFeature("http://xml.org/sax/features/namespaces", false);
factory.setFeature("http://xml.org/sax/features/validation", true);
parser = factory.newSAXParser();
} catch (Exception e1) {
e1.printStackTrace();
}
}
public void init() throws LagoonException {
try {
spf = SAXParserFactory.newInstance();
spf.setNamespaceAware(true);
spf.setValidating(false);
spf.setFeature("http://xml.org/sax/features/namespaces", true);
spf.setFeature("http://xml.org/sax/features/namespace-prefixes", false);
spf.setFeature("http://xml.org/sax/features/validation", false);
} catch (ParserConfigurationException e) {
throw new Error("Unable to configure XML parser");
} catch (SAXException e) {
throw new Error("Unable to configure XML parser");
}
target = null;
}
private static Service parseServicePayload(String payload) throws ResponseParseException {
JAXBContext jaxbContext;
Service service = null;
try {
jaxbContext = JAXBContext.newInstance(Service.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
InputStream inputStream =
new ByteArrayInputStream(payload.getBytes(Charset.forName("UTF-8")));
SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
SAXParser sp = spf.newSAXParser();
XMLReader xmlReader = sp.getXMLReader();
InputSource inputSource = new InputSource(inputStream);
SAXSource saxSource = new SAXSource(xmlReader, inputSource);
service = (Service) jaxbUnmarshaller.unmarshal(saxSource);
} catch (JAXBException
| FactoryConfigurationError
| ParserConfigurationException
| SAXException e) {
throw new ResponseParseException(e);
}
return service;
}
private static synchronized SAXParserFactory getSAXParserFactory()
throws FactoryConfigurationError {
if (ourSAXParserFactory == null) {
ourSAXParserFactory = SAXParserFactory.newInstance();
Map supportedFeatures = new SVNHashMap();
try {
ourSAXParserFactory.setFeature("http://xml.org/sax/features/namespaces", true);
supportedFeatures.put("http://xml.org/sax/features/namespaces", Boolean.TRUE);
} catch (SAXNotRecognizedException e) {
} catch (SAXNotSupportedException e) {
} catch (ParserConfigurationException e) {
}
try {
ourSAXParserFactory.setFeature("http://xml.org/sax/features/validation", false);
supportedFeatures.put("http://xml.org/sax/features/validation", Boolean.FALSE);
} catch (SAXNotRecognizedException e) {
} catch (SAXNotSupportedException e) {
} catch (ParserConfigurationException e) {
}
try {
ourSAXParserFactory.setFeature(
"http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
supportedFeatures.put(
"http://apache.org/xml/features/nonvalidating/load-external-dtd", Boolean.FALSE);
} catch (SAXNotRecognizedException e) {
} catch (SAXNotSupportedException e) {
} catch (ParserConfigurationException e) {
}
if (supportedFeatures.size() < 3) {
ourSAXParserFactory = SAXParserFactory.newInstance();
for (Iterator names = supportedFeatures.keySet().iterator(); names.hasNext(); ) {
String name = (String) names.next();
try {
ourSAXParserFactory.setFeature(name, supportedFeatures.get(name) == Boolean.TRUE);
} catch (SAXNotRecognizedException e) {
} catch (SAXNotSupportedException e) {
} catch (ParserConfigurationException e) {
}
}
}
ourSAXParserFactory.setNamespaceAware(true);
ourSAXParserFactory.setValidating(false);
}
return ourSAXParserFactory;
}
/**
* Parse the xml in the main index to read fields for this object
*
* @param is InputStream for main index file
* @throws org.xml.sax.SAXException
* @throws java.io.IOException
*/
private void parse(InputStream is) throws SAXException, IOException {
SAXParserFactory factory = SAXParserFactory.newInstance();
// Logger.normal(this, "Parsing main index");
try {
factory.setNamespaceAware(true);
factory.setFeature("http://xml.org/sax/features/namespaces", true);
factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
SAXParser saxParser = factory.newSAXParser();
MainIndexParser parser = new MainIndexParser();
saxParser.parse(is, parser);
version = parser.getVersion();
if (version == 1) {
indexMeta.put("title", parser.getHeader("title"));
indexMeta.put("ownerName", parser.getHeader("owner"));
indexMeta.put("ownerEmail", parser.getHeader("email"));
subIndiceList = new ArrayList<String>();
subIndice = new TreeMap<String, SubIndex>();
for (String key : parser.getSubIndice()) {
subIndiceList.add(key);
String stillbase;
try {
FreenetURI furi = new FreenetURI(indexuri);
stillbase = (furi.isUSK() ? furi.sskForUSK() : furi).toString();
} catch (MalformedURLException e) {
stillbase = indexuri;
}
subIndice.put(key, new SubIndex(stillbase, "index_" + key + ".xml"));
}
Collections.sort(subIndiceList);
}
} catch (ParserConfigurationException e) {
Logger.error(this, "SAX ParserConfigurationException", e);
throw new SAXException(e);
}
}
/**
* Returns a Capabilities object created from parsing the XML document
*
* @param document
*/
public SosCapabilities parseCapabilities(String document) {
// check if there is a valid XML declaration
// TODO: needs to be case insensitive
if (!document.trim().startsWith("<?xml")) {
log.warn("The Capabilities document is not a valid XML document");
return null;
}
// get a factory
SAXParserFactory spf = SAXParserFactory.newInstance();
try {
spf.setFeature("http://xml.org/sax/features/namespaces", true);
// get a new instance of parser
SAXParser sp = spf.newSAXParser();
ByteArrayInputStream bs = new ByteArrayInputStream(document.getBytes());
log.info("Starting to parse Capabilities document...");
// parse the document and also register this class for call backs
sp.parse(bs, this);
log.info("Done parsing Capabilities document.");
// return the capabilities object
return capabilities;
} catch (SAXException e) {
log.error("Error parsing Capabilities document: " + e.getMessage());
} catch (ParserConfigurationException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
log.error("Something went wrong when parsing Capabilities document");
// default in case of errors
return null;
}
public Document parseDocument(String fileName) {
SAXParserFactory factory = SAXParserFactory.newInstance();
SAXParser parser;
try {
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
parser = factory.newSAXParser();
parser.parse(new File(fileName), this);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ParserConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (SAXException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return document;
}
public void importXML(
String path,
InputStream inputStream,
int uuidBehavior,
int rootBehavior,
Map<String, String> replacements)
throws IOException, InvalidSerializedDataException, RepositoryException {
JCRNodeWrapper node = getNode(path);
try {
if (!node.isCheckedOut()) {
checkout(node);
}
} catch (UnsupportedRepositoryOperationException ex) {
// versioning not supported
}
DocumentViewImportHandler documentViewImportHandler = new DocumentViewImportHandler(this, path);
documentViewImportHandler.setRootBehavior(rootBehavior);
documentViewImportHandler.setUuidBehavior(uuidBehavior);
documentViewImportHandler.setReplacements(replacements);
try {
SAXParserFactory factory;
factory = new SAXParserFactoryImpl();
factory.setNamespaceAware(true);
factory.setValidating(false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
SAXParser parser = factory.newSAXParser();
parser.parse(inputStream, documentViewImportHandler);
} catch (SAXParseException e) {
logger.error("Cannot import - File is not a valid XML", e);
} catch (Exception e) {
logger.error("Cannot import", e);
}
}
/**
* Create the set of training and evaluation sets from the annotated examples with extraction of
* citations in the patent description body.
*
* @param rank rank associated to the set for n-fold data generation
* @param type type of data to be created, 0 is training data, 1 is evaluation data
*/
public void createDataSet(
String setName, String rank, String corpusPath, String outputPath, int type) {
int nbFiles = 0;
int nbNPLRef = 0;
int nbPatentRef = 0;
int maxRef = 0;
try {
// PATENT REF. textual data
// we use a SAX parser on the patent XML files
MarecSaxParser sax = new MarecSaxParser();
sax.patentReferences = true;
sax.nplReferences = false;
int srCitations = 0;
int previousSrCitations = 0;
int withSR = 0;
List<OffsetPosition> journalsPositions = null;
List<OffsetPosition> abbrevJournalsPositions = null;
List<OffsetPosition> conferencesPositions = null;
List<OffsetPosition> publishersPositions = null;
if (type == 0) {
// training set
sax.setN(trainWindow);
} else {
// for the test set we enlarge the focus window to include all the document.
sax.setN(-1);
}
// get a factory
/*SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setValidating(false);
spf.setFeature("http://xml.org/sax/features/namespaces", false);
spf.setFeature("http://xml.org/sax/features/validation", false);
LinkedList<File> fileList = new LinkedList<File>();
if (setName == null) {
fileList.add(new File(corpusPath));
} else if (rank == null) {
fileList.add(new File(corpusPath));
} else {
// n-fold evaluation
fileList.add(new File(corpusPath + File.separator + setName + "ing" + rank + File.separator));
}
Writer writer = null;
if ((setName == null) || (setName.length() == 0)) {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + "/patent.train"), false), "UTF-8");
} else if (rank == null) {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + "/patent." + setName), false), "UTF-8");
} else {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + setName + "ing" + rank + "/patent." + setName), false), "UTF-8");
}
while (fileList.size() > 0) {
File file = fileList.removeFirst();
if (file.isDirectory()) {
for (File subFile : file.listFiles())
fileList.addLast(subFile);
} else {
if (file.getName().endsWith(".xml")) {
nbFiles++;
System.out.println(file.getAbsolutePath());
try {
//get a new instance of parser
SAXParser p = spf.newSAXParser();
FileInputStream in = new FileInputStream(file);
sax.setFileName(file.getName());
p.parse(in, sax);
//writer1.write("\n");
nbPatentRef += sax.getNbPatentRef();
if (sax.citations != null) {
if (sax.citations.size() > previousSrCitations) {
previousSrCitations = sax.citations.size();
withSR++;
}
}
journalsPositions = sax.journalsPositions;
abbrevJournalsPositions = sax.abbrevJournalsPositions;
conferencesPositions = sax.conferencesPositions;
publishersPositions = sax.publishersPositions;
if (sax.accumulatedText != null) {
String text = sax.accumulatedText.toString();
if (text.trim().length() > 0) {
// add features for the patent tokens
addFeatures(text,
writer,
journalsPositions,
abbrevJournalsPositions,
conferencesPositions,
publishersPositions);
writer.write("\n \n");
}
}
} catch (Exception e) {
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
}
}*/
// NPL REF. textual data
/*sax = new MarecSaxParser();
sax.patentReferences = false;
sax.nplReferences = true;
if (type == 0) {
// training set
sax.setN(trainWindow);
}
else {
// for the test set we enlarge the focus window to include all the document.
sax.setN(-1);
}
// get a factory
spf = SAXParserFactory.newInstance();
spf.setValidating(false);
spf.setFeature("http://xml.org/sax/features/namespaces", false);
spf.setFeature("http://xml.org/sax/features/validation", false);
fileList = new LinkedList<File>();
if (setName == null) {
fileList.add(new File(corpusPath));
} else if (rank == null) {
fileList.add(new File(corpusPath));
} else {
fileList.add(new File(corpusPath + File.separator + setName + "ing" + rank + File.separator));
}
if ((setName == null) || (setName.length() == 0)) {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + "/npl.train"), false), "UTF-8");
} else if (rank == null) {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + "/npl." + setName), false), "UTF-8");
} else {
writer = new OutputStreamWriter(new FileOutputStream(
new File(outputPath + File.separator + setName + "ing" + rank + File.separator +
"npl." + setName), false), "UTF-8");
}
while (fileList.size() > 0) {
File file = fileList.removeFirst();
if (file.isDirectory()) {
for (File subFile : file.listFiles())
fileList.addLast(subFile);
} else {
if (file.getName().endsWith(".xml")) {
//nbFiles++;
//String text = Files.readFromFile(file,"UTF-8");
try {
//get a new instance of parser
SAXParser p = spf.newSAXParser();
FileInputStream in = new FileInputStream(file);
sax.setFileName(file.toString());
p.parse(in, sax);
//writer2.write("\n");
nbNPLRef += sax.getNbNPLRef();
if (sax.nbAllRef > maxRef) {
maxRef = sax.nbAllRef;
}
if (sax.citations != null) {
if (sax.citations.size() > previousSrCitations) {
previousSrCitations = sax.citations.size();
withSR++;
}
}
journalsPositions = sax.journalsPositions;
abbrevJournalsPositions = sax.abbrevJournalsPositions;
conferencesPositions = sax.conferencesPositions;
publishersPositions = sax.publishersPositions;
//totalLength += sax.totalLength;
if (sax.accumulatedText != null) {
String text = sax.accumulatedText.toString();
// add features for NPL
addFeatures(text,
writer,
journalsPositions,
abbrevJournalsPositions,
conferencesPositions,
publishersPositions);
writer.write("\n");
}
} catch (Exception e) {
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
}
}
if (sax.citations != null)
srCitations += sax.citations.size();*/
// Patent + NPL REF. textual data (the "all" model)
sax = new MarecSaxParser();
sax.patentReferences = true;
sax.nplReferences = true;
if (type == 0) {
// training set
sax.setN(trainWindow);
} else {
// for the test set we enlarge the focus window to include all the document.
sax.setN(-1);
}
// get a factory
SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setValidating(false);
spf.setFeature("http://xml.org/sax/features/namespaces", false);
spf.setFeature("http://xml.org/sax/features/validation", false);
LinkedList<File> fileList = new LinkedList<File>();
if (setName == null) {
fileList.add(new File(corpusPath));
} else if (rank == null) {
fileList.add(new File(corpusPath));
} else {
fileList.add(
new File(corpusPath + File.separator + setName + "ing" + rank + File.separator));
}
Writer writer = null;
if ((setName == null) || (setName.length() == 0)) {
writer =
new OutputStreamWriter(
new FileOutputStream(new File(outputPath + File.separator + "all.train"), false),
"UTF-8");
} else if (rank == null) {
writer =
new OutputStreamWriter(
new FileOutputStream(
new File(outputPath + File.separator + "all." + setName), false),
"UTF-8");
} else {
writer =
new OutputStreamWriter(
new FileOutputStream(
new File(
outputPath
+ File.separator
+ setName
+ "ing"
+ rank
+ File.separator
+ "all."
+ setName),
false),
"UTF-8");
}
// int totalLength = 0;
while (fileList.size() > 0) {
File file = fileList.removeFirst();
if (file.isDirectory()) {
for (File subFile : file.listFiles()) {
fileList.addLast(subFile);
}
} else {
if (file.getName().endsWith(".xml")) {
nbFiles++;
try {
// get a new instance of parser
SAXParser p = spf.newSAXParser();
FileInputStream in = new FileInputStream(file);
sax.setFileName(file.toString());
p.parse(in, sax);
// writer3.write("\n");
nbNPLRef += sax.getNbNPLRef();
nbPatentRef += sax.getNbPatentRef();
if (sax.nbAllRef > maxRef) {
maxRef = sax.nbAllRef;
}
if (sax.citations != null) {
if (sax.citations.size() > previousSrCitations) {
previousSrCitations = sax.citations.size();
withSR++;
}
}
journalsPositions = sax.journalsPositions;
abbrevJournalsPositions = sax.abbrevJournalsPositions;
conferencesPositions = sax.conferencesPositions;
publishersPositions = sax.publishersPositions;
// totalLength += sax.totalLength;
if (sax.accumulatedText != null) {
String text = sax.accumulatedText.toString();
// add features for patent+NPL
addFeatures(
text,
writer,
journalsPositions,
abbrevJournalsPositions,
conferencesPositions,
publishersPositions);
writer.write("\n");
}
} catch (Exception e) {
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
}
}
if (sax.citations != null) {
srCitations += sax.citations.size();
}
if (setName != null) {
System.out.println(setName + "ing on " + nbFiles + " files");
} else {
System.out.println("training on " + nbFiles + " files");
}
// System.out.println("Number of file with search report: " + withSR);
System.out.println("Number of references: " + (nbNPLRef + nbPatentRef));
System.out.println("Number of patent references: " + nbPatentRef);
System.out.println("Number of NPL references: " + nbNPLRef);
// System.out.println("Number of search report citations: " + srCitations);
System.out.println(
"Average number of references: "
+ TextUtilities.formatTwoDecimals((double) (nbNPLRef + nbPatentRef) / nbFiles));
System.out.println("Max number of references in file: " + maxRef);
/*if ((setName == null) || (setName.length() == 0)) {
System.out.println("patent data set under: " + outputPath + "/patent.train");
} else {
System.out.println("patent data set under: " + outputPath + "/patent." + setName);
}
if ((setName == null) || (setName.length() == 0)) {
System.out.println("npl data set under: " + outputPath + "/npl.train");
} else {
System.out.println("npl data set under: " + outputPath + "/npl." + setName);
}*/
if ((setName == null) || (setName.length() == 0)) {
System.out.println("common data set under: " + outputPath + "/all.train");
} else {
System.out.println("common data set under: " + outputPath + "/all." + setName);
}
} catch (Exception e) {
throw new GrobidException("An exception occurred while running Grobid.", e);
}
}
public void parseSubIndex() throws TaskAbortException {
synchronized (parsingSubindex) {
// Transfer all requests waiting on this subindex to the parsing list
synchronized (waitingOnSubindex) {
parsingSubindex.addAll(waitingOnSubindex);
waitingOnSubindex.removeAll(parsingSubindex);
}
// Set status of all those about to be parsed to PARSE
for (FindRequest r : parsingSubindex) r.setStage(FindRequest.Stages.PARSE);
// Multi-stage parse to minimise memory usage.
// Stage 1: Extract the declaration (first tag), copy everything before "<files " to one
// bucket, plus everything after "</files>".
// Copy the declaration, plus everything between the two (inclusive) to another bucket.
Bucket mainBucket, filesBucket;
try {
InputStream is = bucket.getInputStream();
mainBucket = pr.getNode().clientCore.tempBucketFactory.makeBucket(-1);
filesBucket = pr.getNode().clientCore.tempBucketFactory.makeBucket(-1);
OutputStream mainOS = new BufferedOutputStream(mainBucket.getOutputStream());
OutputStream filesOS = new BufferedOutputStream(filesBucket.getOutputStream());
// OutputStream mainOS = new BufferedOutputStream(new FileOutputStream("main.tmp"));
// OutputStream filesOS = new BufferedOutputStream(new FileOutputStream("files.tmp"));
BufferedInputStream bis = new BufferedInputStream(is);
byte greaterThan = ">".getBytes("UTF-8")[0];
byte[] filesPrefix = "<files ".getBytes("UTF-8");
byte[] filesPrefixAlt = "<files>".getBytes("UTF-8");
assert (filesPrefix.length == filesPrefixAlt.length);
byte[] filesEnd = "</files>".getBytes("UTF-8");
final int MODE_SEEKING_DECLARATION = 1;
final int MODE_SEEKING_FILES = 2;
final int MODE_COPYING_FILES = 3;
final int MODE_COPYING_REST = 4;
int mode = MODE_SEEKING_DECLARATION;
int b;
byte[] declarationBuf = new byte[100];
int declarationPtr = 0;
byte[] prefixBuffer = new byte[filesPrefix.length];
int prefixPtr = 0;
byte[] endBuffer = new byte[filesEnd.length];
int endPtr = 0;
while ((b = bis.read()) != -1) {
if (mode == MODE_SEEKING_DECLARATION) {
if (declarationPtr == declarationBuf.length)
throw new TaskAbortException("Could not split up XML: declaration too long", null);
declarationBuf[declarationPtr++] = (byte) b;
mainOS.write(b);
filesOS.write(b);
if (b == greaterThan) {
mode = MODE_SEEKING_FILES;
}
} else if (mode == MODE_SEEKING_FILES) {
if (prefixPtr != prefixBuffer.length) {
prefixBuffer[prefixPtr++] = (byte) b;
} else {
if (Fields.byteArrayEqual(filesPrefix, prefixBuffer)
|| Fields.byteArrayEqual(filesPrefixAlt, prefixBuffer)) {
mode = MODE_COPYING_FILES;
filesOS.write(prefixBuffer);
filesOS.write(b);
} else {
mainOS.write(prefixBuffer[0]);
System.arraycopy(prefixBuffer, 1, prefixBuffer, 0, prefixBuffer.length - 1);
prefixBuffer[prefixBuffer.length - 1] = (byte) b;
}
}
} else if (mode == MODE_COPYING_FILES) {
if (endPtr != endBuffer.length) {
endBuffer[endPtr++] = (byte) b;
} else {
if (Fields.byteArrayEqual(filesEnd, endBuffer)) {
mode = MODE_COPYING_REST;
filesOS.write(endBuffer);
mainOS.write(b);
} else {
filesOS.write(endBuffer[0]);
System.arraycopy(endBuffer, 1, endBuffer, 0, endBuffer.length - 1);
endBuffer[endBuffer.length - 1] = (byte) b;
}
}
} else if (mode == MODE_COPYING_REST) {
mainOS.write(b);
}
}
if (mode != MODE_COPYING_REST)
throw new TaskAbortException("Could not split up XML: Last mode was " + mode, null);
mainOS.close();
filesOS.close();
} catch (IOException e) {
throw new TaskAbortException("Could not split XML: ", e);
}
if (logMINOR) Logger.minor(this, "Finished splitting XML");
try {
SAXParserFactory factory = SAXParserFactory.newInstance();
factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
SAXParser saxParser = factory.newSAXParser();
// Stage 2: Parse the first bucket, find the keyword we want, find the file id's.
InputStream is = mainBucket.getInputStream();
StageTwoHandler stageTwoHandler = new StageTwoHandler();
saxParser.parse(is, stageTwoHandler);
if (logMINOR) Logger.minor(this, "Finished stage two XML parse");
is.close();
// Stage 3: Parse the second bucket, extract the <file>'s for the specific ID's.
is = filesBucket.getInputStream();
StageThreeHandler stageThreeHandler = new StageThreeHandler();
saxParser.parse(is, stageThreeHandler);
if (logMINOR) Logger.minor(this, "Finished stage three XML parse");
is.close();
Logger.minor(this, "parsing finished " + parsingSubindex.toString());
for (FindRequest findRequest : parsingSubindex) {
findRequest.setFinished();
}
parsingSubindex.clear();
} catch (Exception err) {
Logger.error(this, "Error parsing " + filename, err);
throw new TaskAbortException("Could not parse XML: ", err);
}
}
}
/* */ private void doTransform() {
/* */ try {
/* 101 */ Class clazz = ObjectFactory.findProviderClass(this._className, true);
/* 102 */ AbstractTranslet translet = (AbstractTranslet) clazz.newInstance();
/* 103 */ translet.postInitialization();
/* */
/* 106 */ SAXParserFactory factory = SAXParserFactory.newInstance();
/* */ try {
/* 108 */ factory.setFeature("http://xml.org/sax/features/namespaces", true);
/* */ }
/* */ catch (Exception e) {
/* 111 */ factory.setNamespaceAware(true);
/* */ }
/* 113 */ SAXParser parser = factory.newSAXParser();
/* 114 */ XMLReader reader = parser.getXMLReader();
/* */
/* 117 */ XSLTCDTMManager dtmManager =
(XSLTCDTMManager) XSLTCDTMManager.getDTMManagerClass().newInstance();
/* */ DTMWSFilter wsfilter;
/* */ DTMWSFilter wsfilter;
/* 122 */ if ((translet != null) && ((translet instanceof StripFilter)))
/* 123 */ wsfilter = new DOMWSFilter(translet);
/* */ else {
/* 125 */ wsfilter = null;
/* */ }
/* */
/* 128 */ DOMEnhancedForDTM dom =
(DOMEnhancedForDTM)
dtmManager.getDTM(
new SAXSource(reader, new InputSource(this._fileName)),
false,
wsfilter,
true,
false,
translet.hasIdCall());
/* */
/* 133 */ dom.setDocumentURI(this._fileName);
/* 134 */ translet.prepassDocument(dom);
/* */
/* 137 */ int n = this._params.size();
/* 138 */ for (int i = 0; i < n; i++) {
/* 139 */ Parameter param = (Parameter) this._params.elementAt(i);
/* 140 */ translet.addParameter(param._name, param._value);
/* */ }
/* */
/* 144 */ TransletOutputHandlerFactory tohFactory =
TransletOutputHandlerFactory.newInstance();
/* */
/* 146 */ tohFactory.setOutputType(0);
/* 147 */ tohFactory.setEncoding(translet._encoding);
/* 148 */ tohFactory.setOutputMethod(translet._method);
/* */
/* 150 */ if (this._iterations == -1) {
/* 151 */ translet.transform(dom, tohFactory.getSerializationHandler());
/* */ }
/* 153 */ else if (this._iterations > 0) {
/* 154 */ long mm = System.currentTimeMillis();
/* 155 */ for (int i = 0; i < this._iterations; i++) {
/* 156 */ translet.transform(dom, tohFactory.getSerializationHandler());
/* */ }
/* */
/* 159 */ mm = System.currentTimeMillis() - mm;
/* */
/* 161 */ System.err.println("\n<!--");
/* 162 */ System.err.println(" transform = " + mm / this._iterations + " ms");
/* */
/* 165 */ System.err.println(
" throughput = " + 1000.0D / (mm / this._iterations) + " tps");
/* */
/* 169 */ System.err.println("-->");
/* */ }
/* */ }
/* */ catch (TransletException e) {
/* 173 */ if (this._debug) e.printStackTrace();
/* 174 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + e.getMessage());
/* */ }
/* */ catch (RuntimeException e)
/* */ {
/* 178 */ if (this._debug) e.printStackTrace();
/* 179 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + e.getMessage());
/* */ }
/* */ catch (FileNotFoundException e)
/* */ {
/* 183 */ if (this._debug) e.printStackTrace();
/* 184 */ ErrorMsg err = new ErrorMsg("FILE_NOT_FOUND_ERR", this._fileName);
/* 185 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + err.toString());
/* */ }
/* */ catch (MalformedURLException e)
/* */ {
/* 189 */ if (this._debug) e.printStackTrace();
/* 190 */ ErrorMsg err = new ErrorMsg("INVALID_URI_ERR", this._fileName);
/* 191 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + err.toString());
/* */ }
/* */ catch (ClassNotFoundException e)
/* */ {
/* 195 */ if (this._debug) e.printStackTrace();
/* 196 */ ErrorMsg err = new ErrorMsg("CLASS_NOT_FOUND_ERR", this._className);
/* 197 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + err.toString());
/* */ }
/* */ catch (UnknownHostException e)
/* */ {
/* 201 */ if (this._debug) e.printStackTrace();
/* 202 */ ErrorMsg err = new ErrorMsg("INVALID_URI_ERR", this._fileName);
/* 203 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + err.toString());
/* */ }
/* */ catch (SAXException e)
/* */ {
/* 207 */ Exception ex = e.getException();
/* 208 */ if (this._debug) {
/* 209 */ if (ex != null) ex.printStackTrace();
/* 210 */ e.printStackTrace();
/* */ }
/* 212 */ System.err.print(new ErrorMsg("RUNTIME_ERROR_KEY"));
/* 213 */ if (ex != null) /* 214 */ System.err.println(ex.getMessage());
/* */ else /* 216 */ System.err.println(e.getMessage());
/* */ }
/* */ catch (Exception e) {
/* 219 */ if (this._debug) e.printStackTrace();
/* 220 */ System.err.println(new ErrorMsg("RUNTIME_ERROR_KEY") + e.getMessage());
/* */ }
/* */ }
public Phylogeny[] parse() throws IOException, PhylogenyParserException {
reset();
final TolXmlHandler handler = new TolXmlHandler();
final SAXParserFactory factory = SAXParserFactory.newInstance();
factory.setNamespaceAware(true);
try {
if (!ForesterUtil.isEmpty(getSchemaLocation())) {
factory.setFeature(SAX_FEATURES_VALIDATION, true);
factory.setFeature(APACHE_FEATURES_VALIDATION_SCHEMA, true);
factory.setFeature(APACHE_FEATURES_VALIDATION_SCHEMA_FULL, true);
}
} catch (final SAXNotRecognizedException e) {
e.printStackTrace();
throw new PhylogenyParserException("sax not recognized exception: " + e.getMessage());
} catch (final SAXNotSupportedException e) {
e.printStackTrace();
throw new PhylogenyParserException("sax not supported exception: " + e.getMessage());
} catch (final ParserConfigurationException e) {
e.printStackTrace();
throw new PhylogenyParserException("parser _configuration exception: " + e.getMessage());
} catch (final Exception e) {
e.printStackTrace();
throw new PhylogenyParserException("error while configuring sax parser: " + e.getMessage());
}
try {
final SAXParser parser = factory.newSAXParser();
if (!ForesterUtil.isEmpty(getSchemaLocation())) {
parser.setProperty(JAXP_SCHEMA_LANGUAGE, W3C_XML_SCHEMA);
parser.setProperty(JAXP_SCHEMA_SOURCE, getSchemaLocation());
parser.setProperty(APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION, getSchemaLocation());
}
final XMLReader xml_reader = parser.getXMLReader();
xml_reader.setContentHandler(handler);
xml_reader.setErrorHandler(new TolParserErrorHandler());
if (getSource() instanceof File) {
if (!getSource().toString().toLowerCase().endsWith(".zip")) {
xml_reader.parse(new InputSource(new FileReader((File) getSource())));
} else {
final Reader reader = getReaderFromZipFile();
if (reader == null) {
throw new PhylogenyParserException(
"Zip file \"" + getSource() + "\" appears not to contain any entries");
}
xml_reader.parse(new InputSource(reader));
}
} else if (getSource() instanceof InputSource) {
xml_reader.parse((InputSource) getSource());
} else if (getSource() instanceof InputStream) {
if (!isZippedInputstream()) {
final InputStream is = (InputStream) getSource();
final Reader reader = new InputStreamReader(is);
xml_reader.parse(new InputSource(reader));
} else {
final ZipInputStream zip_is = new ZipInputStream((InputStream) getSource());
zip_is.getNextEntry();
final Reader reader = new InputStreamReader(zip_is);
if (reader == null) {
throw new PhylogenyParserException(
"Zip input stream \"" + getSource() + "\" appears not to contain any data");
}
xml_reader.parse(new InputSource(reader));
}
} else if (getSource() instanceof String) {
final File file = new File(getSource().toString());
final Reader reader = new FileReader(file);
xml_reader.parse(new InputSource(reader));
} else if (getSource() instanceof StringBuffer) {
final StringReader string_reader = new StringReader(getSource().toString());
xml_reader.parse(new InputSource(string_reader));
} else {
throw new PhylogenyParserException(
"attempt to parse object of unsupported type: \"" + getSource().getClass() + "\"");
}
} catch (final SAXException sax_exception) {
throw new PhylogenyParserException(
"Failed to parse [" + getSource() + "]: " + sax_exception.getMessage());
} catch (final ParserConfigurationException parser_config_exception) {
throw new PhylogenyParserException(
"Failed to parse ["
+ getSource()
+ "] Problem with xml parser _configuration: "
+ parser_config_exception.getMessage());
} catch (final IOException e) {
throw new PhylogenyParserException(
"Problem with input source [" + getSource() + "]: \n" + e.getMessage());
} catch (final Exception e) {
e.printStackTrace();
throw new PhylogenyParserException(
"Failed to parse [" + getSource() + "]: " + e.getMessage());
} catch (final Error err) {
err.printStackTrace();
throw new PhylogenyParserException("Severe error: " + err.getMessage());
}
final Phylogeny[] ps = new Phylogeny[handler.getPhylogenies().size()];
int i = 0;
for (final Phylogeny phylogeny : handler.getPhylogenies()) {
ps[i++] = phylogeny;
}
return ps;
}
/** Creates a SAX2 InputSource object from a TrAX Source object */
public static InputSource getInputSource(XSLTC xsltc, Source source)
throws TransformerConfigurationException {
InputSource input = null;
String systemId = source.getSystemId();
try {
// Try to get InputSource from SAXSource input
if (source instanceof SAXSource) {
final SAXSource sax = (SAXSource) source;
input = sax.getInputSource();
// Pass the SAX parser to the compiler
try {
XMLReader reader = sax.getXMLReader();
/*
* Fix for bug 24695
* According to JAXP 1.2 specification if a SAXSource
* is created using a SAX InputSource the Transformer or
* TransformerFactory creates a reader via the
* XMLReaderFactory if setXMLReader is not used
*/
if (reader == null) {
try {
reader = XMLReaderFactory.createXMLReader();
} catch (Exception e) {
try {
// Incase there is an exception thrown
// resort to JAXP
SAXParserFactory parserFactory = SAXParserFactory.newInstance();
parserFactory.setNamespaceAware(true);
if (xsltc.isSecureProcessing()) {
try {
parserFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (org.xml.sax.SAXException se) {
}
}
reader = parserFactory.newSAXParser().getXMLReader();
} catch (ParserConfigurationException pce) {
throw new TransformerConfigurationException("ParserConfigurationException", pce);
}
}
}
reader.setFeature("http://xml.org/sax/features/namespaces", true);
reader.setFeature("http://xml.org/sax/features/namespace-prefixes", false);
xsltc.setXMLReader(reader);
} catch (SAXNotRecognizedException snre) {
throw new TransformerConfigurationException("SAXNotRecognizedException ", snre);
} catch (SAXNotSupportedException snse) {
throw new TransformerConfigurationException("SAXNotSupportedException ", snse);
} catch (SAXException se) {
throw new TransformerConfigurationException("SAXException ", se);
}
}
// handle DOMSource
else if (source instanceof DOMSource) {
final DOMSource domsrc = (DOMSource) source;
final Document dom = (Document) domsrc.getNode();
final DOM2SAX dom2sax = new DOM2SAX(dom);
xsltc.setXMLReader(dom2sax);
// Try to get SAX InputSource from DOM Source.
input = SAXSource.sourceToInputSource(source);
if (input == null) {
input = new InputSource(domsrc.getSystemId());
}
}
// Try to get InputStream or Reader from StreamSource
else if (source instanceof StreamSource) {
final StreamSource stream = (StreamSource) source;
final InputStream istream = stream.getInputStream();
final Reader reader = stream.getReader();
xsltc.setXMLReader(null); // Clear old XML reader
// Create InputSource from Reader or InputStream in Source
if (istream != null) {
input = new InputSource(istream);
} else if (reader != null) {
input = new InputSource(reader);
} else {
input = new InputSource(systemId);
}
} else {
ErrorMsg err = new ErrorMsg(ErrorMsg.JAXP_UNKNOWN_SOURCE_ERR);
throw new TransformerConfigurationException(err.toString());
}
input.setSystemId(systemId);
} catch (NullPointerException e) {
ErrorMsg err = new ErrorMsg(ErrorMsg.JAXP_NO_SOURCE_ERR, "TransformerFactory.newTemplates()");
throw new TransformerConfigurationException(err.toString());
} catch (SecurityException e) {
ErrorMsg err = new ErrorMsg(ErrorMsg.FILE_ACCESS_ERR, systemId);
throw new TransformerConfigurationException(err.toString());
}
return input;
}
public void parse(
InputStream stream, ContentHandler handler, Metadata metadata, ParseContext context)
throws IOException, SAXException, TikaException {
final XHTMLContentHandler xhtml = new XHTMLContentHandler(handler, metadata);
DefaultHandler dh =
new ElementMappingContentHandler(xhtml, MAPPINGS) {
private final BitSet textNodeStack = new BitSet();
private int nodeDepth = 0;
private int completelyFiltered = 0;
private Stack<String> headingStack = new Stack<String>();
@Override
public void characters(char[] ch, int start, int length) throws SAXException {
// only forward content of tags from text:-namespace
if (completelyFiltered == 0 && nodeDepth > 0 && textNodeStack.get(nodeDepth - 1)) {
super.characters(ch, start, length);
}
}
// helper for checking tags which need complete filtering
// (with sub-tags)
private boolean needsCompleteFiltering(String namespaceURI, String localName) {
if (TEXT_NS.equals(namespaceURI)) {
return localName.endsWith("-template") || localName.endsWith("-style");
} else if (TABLE_NS.equals(namespaceURI)) {
return "covered-table-cell".equals(localName);
} else {
return false;
}
}
// map the heading level to <hX> HTML tags
private String getXHTMLHeaderTagName(Attributes atts) {
String depthStr = atts.getValue(TEXT_NS, "outline-level");
if (depthStr == null) {
return "h1";
}
int depth = Integer.parseInt(depthStr);
if (depth >= 6) {
return "h6";
} else if (depth <= 1) {
return "h1";
} else {
return "h" + depth;
}
}
/** Check if a node is a text node */
private boolean isTextNode(String namespaceURI, String localName) {
if (TEXT_NS.equals(namespaceURI)) {
return true;
}
if (SVG_NS.equals(namespaceURI)) {
return "title".equals(localName) || "desc".equals(localName);
}
return false;
}
@Override
public void startElement(
String namespaceURI, String localName, String qName, Attributes atts)
throws SAXException {
// keep track of current node type. If it is a text node,
// a bit at the current depth ist set in textNodeStack.
// characters() checks the top bit to determine, if the
// actual node is a text node to print out nodeDepth contains
// the depth of the current node and also marks top of stack.
assert nodeDepth >= 0;
textNodeStack.set(nodeDepth++, isTextNode(namespaceURI, localName));
// filter *all* content of some tags
assert completelyFiltered >= 0;
if (needsCompleteFiltering(namespaceURI, localName)) {
completelyFiltered++;
}
// call next handler if no filtering
if (completelyFiltered == 0) {
// special handling of text:h, that are directly passed
// to xhtml handler
if (TEXT_NS.equals(namespaceURI) && "h".equals(localName)) {
xhtml.startElement(headingStack.push(getXHTMLHeaderTagName(atts)));
} else {
super.startElement(namespaceURI, localName, qName, atts);
}
}
}
@Override
public void endElement(String namespaceURI, String localName, String qName)
throws SAXException {
// call next handler if no filtering
if (completelyFiltered == 0) {
// special handling of text:h, that are directly passed
// to xhtml handler
if (TEXT_NS.equals(namespaceURI) && "h".equals(localName)) {
xhtml.endElement(headingStack.pop());
} else {
super.endElement(namespaceURI, localName, qName);
}
// special handling of tabulators
if (TEXT_NS.equals(namespaceURI)
&& ("tab-stop".equals(localName) || "tab".equals(localName))) {
this.characters(TAB, 0, TAB.length);
}
}
// revert filter for *all* content of some tags
if (needsCompleteFiltering(namespaceURI, localName)) {
completelyFiltered--;
}
assert completelyFiltered >= 0;
// reduce current node depth
nodeDepth--;
assert nodeDepth >= 0;
}
@Override
public void startPrefixMapping(String prefix, String uri) {
// remove prefix mappings as they should not occur in XHTML
}
@Override
public void endPrefixMapping(String prefix) {
// remove prefix mappings as they should not occur in XHTML
}
};
try {
SAXParserFactory factory = SAXParserFactory.newInstance();
factory.setValidating(false);
factory.setNamespaceAware(true);
try {
factory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (SAXNotRecognizedException e) {
// TIKA-329: Some XML parsers do not support the secure-processing
// feature, even though it's required by JAXP in Java 5. Ignoring
// the exception is fine here, deployments without this feature
// are inherently vulnerable to XML denial-of-service attacks.
}
SAXParser parser = factory.newSAXParser();
parser.parse(
new CloseShieldInputStream(stream),
new OfflineContentHandler(new NSNormalizerContentHandler(dh)));
} catch (ParserConfigurationException e) {
throw new TikaException("XML parser configuration error", e);
}
}
/**
* Configure schema validation as recommended by the Xerces spec. Both DTD and Schema validation
* will be enabled simultaneously.
*
* @param factory SAXParserFactory to be configured
*/
private static void configureXerces(SAXParserFactory factory)
throws ParserConfigurationException, SAXNotRecognizedException, SAXNotSupportedException {
factory.setFeature(XERCES_DYNAMIC, true);
factory.setFeature(XERCES_SCHEMA, true);
}
@Override
public void setFeature(String name, boolean value)
throws ParserConfigurationException, SAXNotRecognizedException, SAXNotSupportedException {
delegate.setFeature(name, value);
}
// J2SE does not support Xalan interpretive
// main -> _main
public static void _main(String argv[]) {
// Runtime.getRuntime().traceMethodCalls(false); // turns Java tracing off
boolean doStackDumpOnError = false;
boolean setQuietMode = false;
boolean doDiag = false;
String msg = null;
boolean isSecureProcessing = false;
// Runtime.getRuntime().traceMethodCalls(false);
// Runtime.getRuntime().traceInstructions(false);
/** The default diagnostic writer... */
java.io.PrintWriter diagnosticsWriter = new PrintWriter(System.err, true);
java.io.PrintWriter dumpWriter = diagnosticsWriter;
ResourceBundle resbundle =
(SecuritySupport.getResourceBundle(
com.sun.org.apache.xml.internal.utils.res.XResourceBundle.ERROR_RESOURCES));
String flavor = "s2s";
if (argv.length < 1) {
printArgOptions(resbundle);
} else {
// J2SE does not support Xalan interpretive
// false -> true
boolean useXSLTC = true;
for (int i = 0; i < argv.length; i++) {
if ("-XSLTC".equalsIgnoreCase(argv[i])) {
useXSLTC = true;
}
}
TransformerFactory tfactory;
if (useXSLTC) {
String key = "javax.xml.transform.TransformerFactory";
String value = "com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl";
Properties props = System.getProperties();
props.put(key, value);
System.setProperties(props);
}
try {
tfactory = TransformerFactory.newInstance();
tfactory.setErrorListener(new DefaultErrorHandler());
} catch (TransformerFactoryConfigurationError pfe) {
pfe.printStackTrace(dumpWriter);
// "XSL Process was not successful.");
msg = XSLMessages.createMessage(XSLTErrorResources.ER_NOT_SUCCESSFUL, null);
diagnosticsWriter.println(msg);
tfactory = null; // shut up compiler
doExit(msg);
}
boolean formatOutput = false;
boolean useSourceLocation = false;
String inFileName = null;
String outFileName = null;
String dumpFileName = null;
String xslFileName = null;
String treedumpFileName = null;
// J2SE does not support Xalan interpretive
/*
PrintTraceListener tracer = null;
*/
String outputType = null;
String media = null;
Vector params = new Vector();
boolean quietConflictWarnings = false;
URIResolver uriResolver = null;
EntityResolver entityResolver = null;
ContentHandler contentHandler = null;
int recursionLimit = -1;
for (int i = 0; i < argv.length; i++) {
if ("-XSLTC".equalsIgnoreCase(argv[i])) {
// The -XSLTC option has been processed.
}
// J2SE does not support Xalan interpretive
/*
else if ("-TT".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
{
if (null == tracer)
tracer = new PrintTraceListener(diagnosticsWriter);
tracer.m_traceTemplates = true;
}
else
printInvalidXSLTCOption("-TT");
// tfactory.setTraceTemplates(true);
}
else if ("-TG".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
{
if (null == tracer)
tracer = new PrintTraceListener(diagnosticsWriter);
tracer.m_traceGeneration = true;
}
else
printInvalidXSLTCOption("-TG");
// tfactory.setTraceSelect(true);
}
else if ("-TS".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
{
if (null == tracer)
tracer = new PrintTraceListener(diagnosticsWriter);
tracer.m_traceSelection = true;
}
else
printInvalidXSLTCOption("-TS");
// tfactory.setTraceTemplates(true);
}
else if ("-TTC".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
{
if (null == tracer)
tracer = new PrintTraceListener(diagnosticsWriter);
tracer.m_traceElements = true;
}
else
printInvalidXSLTCOption("-TTC");
// tfactory.setTraceTemplateChildren(true);
}
*/
else if ("-INDENT".equalsIgnoreCase(argv[i])) {
int indentAmount;
if (((i + 1) < argv.length) && (argv[i + 1].charAt(0) != '-')) {
indentAmount = Integer.parseInt(argv[++i]);
} else {
indentAmount = 0;
}
// TBD:
// xmlProcessorLiaison.setIndent(indentAmount);
} else if ("-IN".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') inFileName = argv[++i];
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-IN"})); // "Missing argument for);
} else if ("-MEDIA".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length) media = argv[++i];
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-MEDIA"})); // "Missing argument for);
} else if ("-OUT".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') outFileName = argv[++i];
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-OUT"})); // "Missing argument for);
} else if ("-XSL".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') xslFileName = argv[++i];
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-XSL"})); // "Missing argument for);
} else if ("-FLAVOR".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length) {
flavor = argv[++i];
} else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-FLAVOR"})); // "Missing argument for);
} else if ("-PARAM".equalsIgnoreCase(argv[i])) {
if (i + 2 < argv.length) {
String name = argv[++i];
params.addElement(name);
String expression = argv[++i];
params.addElement(expression);
} else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-PARAM"})); // "Missing argument for);
} else if ("-E".equalsIgnoreCase(argv[i])) {
// TBD:
// xmlProcessorLiaison.setShouldExpandEntityRefs(false);
} else if ("-V".equalsIgnoreCase(argv[i])) {
diagnosticsWriter.println(
resbundle.getString("version") // ">>>>>>> Xalan Version "
+ Version.getVersion()
+ ", "
+
/* xmlProcessorLiaison.getParserDescription()+ */
resbundle.getString("version2")); // "<<<<<<<");
}
// J2SE does not support Xalan interpretive
/*
else if ("-QC".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
quietConflictWarnings = true;
else
printInvalidXSLTCOption("-QC");
}
*/
else if ("-Q".equalsIgnoreCase(argv[i])) {
setQuietMode = true;
} else if ("-DIAG".equalsIgnoreCase(argv[i])) {
doDiag = true;
} else if ("-XML".equalsIgnoreCase(argv[i])) {
outputType = "xml";
} else if ("-TEXT".equalsIgnoreCase(argv[i])) {
outputType = "text";
} else if ("-HTML".equalsIgnoreCase(argv[i])) {
outputType = "html";
} else if ("-EDUMP".equalsIgnoreCase(argv[i])) {
doStackDumpOnError = true;
if (((i + 1) < argv.length) && (argv[i + 1].charAt(0) != '-')) {
dumpFileName = argv[++i];
}
} else if ("-URIRESOLVER".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length) {
try {
uriResolver = (URIResolver) ObjectFactory.newInstance(argv[++i], true);
tfactory.setURIResolver(uriResolver);
} catch (ConfigurationError cnfe) {
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_CLASS_NOT_FOUND_FOR_OPTION,
new Object[] {"-URIResolver"});
System.err.println(msg);
doExit(msg);
}
} else {
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-URIResolver"}); // "Missing argument for);
System.err.println(msg);
doExit(msg);
}
} else if ("-ENTITYRESOLVER".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length) {
try {
entityResolver = (EntityResolver) ObjectFactory.newInstance(argv[++i], true);
} catch (ConfigurationError cnfe) {
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_CLASS_NOT_FOUND_FOR_OPTION,
new Object[] {"-EntityResolver"});
System.err.println(msg);
doExit(msg);
}
} else {
// "Missing argument for);
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION, new Object[] {"-EntityResolver"});
System.err.println(msg);
doExit(msg);
}
} else if ("-CONTENTHANDLER".equalsIgnoreCase(argv[i])) {
if (i + 1 < argv.length) {
try {
contentHandler = (ContentHandler) ObjectFactory.newInstance(argv[++i], true);
} catch (ConfigurationError cnfe) {
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_CLASS_NOT_FOUND_FOR_OPTION,
new Object[] {"-ContentHandler"});
System.err.println(msg);
doExit(msg);
}
} else {
// "Missing argument for);
msg =
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION, new Object[] {"-ContentHandler"});
System.err.println(msg);
doExit(msg);
}
}
// J2SE does not support Xalan interpretive
/*
else if ("-L".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
tfactory.setAttribute(XalanProperties.SOURCE_LOCATION, Boolean.TRUE);
else
printInvalidXSLTCOption("-L");
}
else if ("-INCREMENTAL".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
tfactory.setAttribute
("http://xml.apache.org/xalan/features/incremental",
java.lang.Boolean.TRUE);
else
printInvalidXSLTCOption("-INCREMENTAL");
}
else if ("-NOOPTIMIZE".equalsIgnoreCase(argv[i]))
{
// Default is true.
//
// %REVIEW% We should have a generalized syntax for negative
// switches... and probably should accept the inverse even
// if it is the default.
if (!useXSLTC)
tfactory.setAttribute
("http://xml.apache.org/xalan/features/optimize",
java.lang.Boolean.FALSE);
else
printInvalidXSLTCOption("-NOOPTIMIZE");
}
else if ("-RL".equalsIgnoreCase(argv[i]))
{
if (!useXSLTC)
{
if (i + 1 < argv.length)
recursionLimit = Integer.parseInt(argv[++i]);
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[]{ "-rl" })); //"Missing argument for);
}
else
{
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-')
i++;
printInvalidXSLTCOption("-RL");
}
}
*/
// Generate the translet class and optionally specify the name
// of the translet class.
else if ("-XO".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') {
tfactory.setAttribute("generate-translet", "true");
tfactory.setAttribute("translet-name", argv[++i]);
} else tfactory.setAttribute("generate-translet", "true");
} else {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') i++;
printInvalidXalanOption("-XO");
}
}
// Specify the destination directory for the translet classes.
else if ("-XD".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-')
tfactory.setAttribute("destination-directory", argv[++i]);
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-XD"})); // "Missing argument for);
} else {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') i++;
printInvalidXalanOption("-XD");
}
}
// Specify the jar file name which the translet classes are packaged into.
else if ("-XJ".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') {
tfactory.setAttribute("generate-translet", "true");
tfactory.setAttribute("jar-name", argv[++i]);
} else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-XJ"})); // "Missing argument for);
} else {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') i++;
printInvalidXalanOption("-XJ");
}
}
// Specify the package name prefix for the generated translet classes.
else if ("-XP".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-')
tfactory.setAttribute("package-name", argv[++i]);
else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_MISSING_ARG_FOR_OPTION,
new Object[] {"-XP"})); // "Missing argument for);
} else {
if (i + 1 < argv.length && argv[i + 1].charAt(0) != '-') i++;
printInvalidXalanOption("-XP");
}
}
// Enable template inlining.
else if ("-XN".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
tfactory.setAttribute("enable-inlining", "true");
} else printInvalidXalanOption("-XN");
}
// Turns on additional debugging message output
else if ("-XX".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
tfactory.setAttribute("debug", "true");
} else printInvalidXalanOption("-XX");
}
// Create the Transformer from the translet if the translet class is newer
// than the stylesheet.
else if ("-XT".equalsIgnoreCase(argv[i])) {
if (useXSLTC) {
tfactory.setAttribute("auto-translet", "true");
} else printInvalidXalanOption("-XT");
} else if ("-SECURE".equalsIgnoreCase(argv[i])) {
isSecureProcessing = true;
try {
tfactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (TransformerConfigurationException e) {
}
} else
System.err.println(
XSLMessages.createMessage(
XSLTErrorResources.ER_INVALID_OPTION,
new Object[] {argv[i]})); // "Invalid argument:);
}
// Print usage instructions if no xml and xsl file is specified in the command line
if (inFileName == null && xslFileName == null) {
msg = resbundle.getString("xslProc_no_input");
System.err.println(msg);
doExit(msg);
}
// Note that there are usage cases for calling us without a -IN arg
// The main XSL transformation occurs here!
try {
long start = System.currentTimeMillis();
if (null != dumpFileName) {
dumpWriter = new PrintWriter(new FileWriter(dumpFileName));
}
Templates stylesheet = null;
if (null != xslFileName) {
if (flavor.equals("d2d")) {
// Parse in the xml data into a DOM
DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
dfactory.setNamespaceAware(true);
if (isSecureProcessing) {
try {
dfactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (ParserConfigurationException pce) {
}
}
DocumentBuilder docBuilder = dfactory.newDocumentBuilder();
Node xslDOM = docBuilder.parse(new InputSource(xslFileName));
stylesheet = tfactory.newTemplates(new DOMSource(xslDOM, xslFileName));
} else {
// System.out.println("Calling newTemplates: "+xslFileName);
stylesheet = tfactory.newTemplates(new StreamSource(xslFileName));
// System.out.println("Done calling newTemplates: "+xslFileName);
}
}
PrintWriter resultWriter;
StreamResult strResult;
if (null != outFileName) {
strResult = new StreamResult(new FileOutputStream(outFileName));
// One possible improvement might be to ensure this is
// a valid URI before setting the systemId, but that
// might have subtle changes that pre-existing users
// might notice; we can think about that later -sc r1.46
strResult.setSystemId(outFileName);
} else {
strResult = new StreamResult(System.out);
// We used to default to incremental mode in this case.
// We've since decided that since the -INCREMENTAL switch is
// available, that default is probably not necessary nor
// necessarily a good idea.
}
SAXTransformerFactory stf = (SAXTransformerFactory) tfactory;
// J2SE does not support Xalan interpretive
/*
// This is currently controlled via TransformerFactoryImpl.
if (!useXSLTC && useSourceLocation)
stf.setAttribute(XalanProperties.SOURCE_LOCATION, Boolean.TRUE);
*/
// Did they pass in a stylesheet, or should we get it from the
// document?
if (null == stylesheet) {
Source source =
stf.getAssociatedStylesheet(new StreamSource(inFileName), media, null, null);
if (null != source) stylesheet = tfactory.newTemplates(source);
else {
if (null != media)
throw new TransformerException(
XSLMessages.createMessage(
XSLTErrorResources.ER_NO_STYLESHEET_IN_MEDIA,
new Object[] {inFileName, media})); // "No stylesheet found in: "
// + inFileName + ", media="
// + media);
else
throw new TransformerException(
XSLMessages.createMessage(
XSLTErrorResources.ER_NO_STYLESHEET_PI,
new Object[] {inFileName})); // "No xml-stylesheet PI found in: "
// + inFileName);
}
}
if (null != stylesheet) {
Transformer transformer = flavor.equals("th") ? null : stylesheet.newTransformer();
transformer.setErrorListener(new DefaultErrorHandler());
// Override the output format?
if (null != outputType) {
transformer.setOutputProperty(OutputKeys.METHOD, outputType);
}
// J2SE does not support Xalan interpretive
/*
if (transformer instanceof com.sun.org.apache.xalan.internal.transformer.TransformerImpl)
{
com.sun.org.apache.xalan.internal.transformer.TransformerImpl impl = (com.sun.org.apache.xalan.internal.transformer.TransformerImpl)transformer;
TraceManager tm = impl.getTraceManager();
if (null != tracer)
tm.addTraceListener(tracer);
impl.setQuietConflictWarnings(quietConflictWarnings);
// This is currently controlled via TransformerFactoryImpl.
if (useSourceLocation)
impl.setProperty(XalanProperties.SOURCE_LOCATION, Boolean.TRUE);
if(recursionLimit>0)
impl.setRecursionLimit(recursionLimit);
// sc 28-Feb-01 if we re-implement this, please uncomment helpmsg in printArgOptions
// impl.setDiagnosticsOutput( setQuietMode ? null : diagnosticsWriter );
}
*/
int nParams = params.size();
for (int i = 0; i < nParams; i += 2) {
transformer.setParameter(
(String) params.elementAt(i), (String) params.elementAt(i + 1));
}
if (uriResolver != null) transformer.setURIResolver(uriResolver);
if (null != inFileName) {
if (flavor.equals("d2d")) {
// Parse in the xml data into a DOM
DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
dfactory.setCoalescing(true);
dfactory.setNamespaceAware(true);
if (isSecureProcessing) {
try {
dfactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (ParserConfigurationException pce) {
}
}
DocumentBuilder docBuilder = dfactory.newDocumentBuilder();
if (entityResolver != null) docBuilder.setEntityResolver(entityResolver);
Node xmlDoc = docBuilder.parse(new InputSource(inFileName));
Document doc = docBuilder.newDocument();
org.w3c.dom.DocumentFragment outNode = doc.createDocumentFragment();
transformer.transform(new DOMSource(xmlDoc, inFileName), new DOMResult(outNode));
// Now serialize output to disk with identity transformer
Transformer serializer = stf.newTransformer();
serializer.setErrorListener(new DefaultErrorHandler());
Properties serializationProps = stylesheet.getOutputProperties();
serializer.setOutputProperties(serializationProps);
if (contentHandler != null) {
SAXResult result = new SAXResult(contentHandler);
serializer.transform(new DOMSource(outNode), result);
} else serializer.transform(new DOMSource(outNode), strResult);
} else if (flavor.equals("th")) {
for (int i = 0; i < 1; i++) // Loop for diagnosing bugs with inconsistent behavior
{
// System.out.println("Testing the TransformerHandler...");
XMLReader reader = null;
// Use JAXP1.1 ( if possible )
try {
javax.xml.parsers.SAXParserFactory factory =
javax.xml.parsers.SAXParserFactory.newInstance();
factory.setNamespaceAware(true);
if (isSecureProcessing) {
try {
factory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (org.xml.sax.SAXException se) {
}
}
javax.xml.parsers.SAXParser jaxpParser = factory.newSAXParser();
reader = jaxpParser.getXMLReader();
} catch (javax.xml.parsers.ParserConfigurationException ex) {
throw new org.xml.sax.SAXException(ex);
} catch (javax.xml.parsers.FactoryConfigurationError ex1) {
throw new org.xml.sax.SAXException(ex1.toString());
} catch (NoSuchMethodError ex2) {
} catch (AbstractMethodError ame) {
}
if (null == reader) {
reader = XMLReaderFactory.createXMLReader();
}
// J2SE does not support Xalan interpretive
/*
if (!useXSLTC)
stf.setAttribute(com.sun.org.apache.xalan.internal.processor.TransformerFactoryImpl.FEATURE_INCREMENTAL,
Boolean.TRUE);
*/
TransformerHandler th = stf.newTransformerHandler(stylesheet);
reader.setContentHandler(th);
reader.setDTDHandler(th);
if (th instanceof org.xml.sax.ErrorHandler)
reader.setErrorHandler((org.xml.sax.ErrorHandler) th);
try {
reader.setProperty("http://xml.org/sax/properties/lexical-handler", th);
} catch (org.xml.sax.SAXNotRecognizedException e) {
} catch (org.xml.sax.SAXNotSupportedException e) {
}
try {
reader.setFeature("http://xml.org/sax/features/namespace-prefixes", true);
} catch (org.xml.sax.SAXException se) {
}
th.setResult(strResult);
reader.parse(new InputSource(inFileName));
}
} else {
if (entityResolver != null) {
XMLReader reader = null;
// Use JAXP1.1 ( if possible )
try {
javax.xml.parsers.SAXParserFactory factory =
javax.xml.parsers.SAXParserFactory.newInstance();
factory.setNamespaceAware(true);
if (isSecureProcessing) {
try {
factory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
} catch (org.xml.sax.SAXException se) {
}
}
javax.xml.parsers.SAXParser jaxpParser = factory.newSAXParser();
reader = jaxpParser.getXMLReader();
} catch (javax.xml.parsers.ParserConfigurationException ex) {
throw new org.xml.sax.SAXException(ex);
} catch (javax.xml.parsers.FactoryConfigurationError ex1) {
throw new org.xml.sax.SAXException(ex1.toString());
} catch (NoSuchMethodError ex2) {
} catch (AbstractMethodError ame) {
}
if (null == reader) {
reader = XMLReaderFactory.createXMLReader();
}
reader.setEntityResolver(entityResolver);
if (contentHandler != null) {
SAXResult result = new SAXResult(contentHandler);
transformer.transform(new SAXSource(reader, new InputSource(inFileName)), result);
} else {
transformer.transform(
new SAXSource(reader, new InputSource(inFileName)), strResult);
}
} else if (contentHandler != null) {
SAXResult result = new SAXResult(contentHandler);
transformer.transform(new StreamSource(inFileName), result);
} else {
// System.out.println("Starting transform");
transformer.transform(new StreamSource(inFileName), strResult);
// System.out.println("Done with transform");
}
}
} else {
StringReader reader = new StringReader("<?xml version=\"1.0\"?> <doc/>");
transformer.transform(new StreamSource(reader), strResult);
}
} else {
// "XSL Process was not successful.");
msg = XSLMessages.createMessage(XSLTErrorResources.ER_NOT_SUCCESSFUL, null);
diagnosticsWriter.println(msg);
doExit(msg);
}
// close output streams
if (null != outFileName && strResult != null) {
java.io.OutputStream out = strResult.getOutputStream();
java.io.Writer writer = strResult.getWriter();
try {
if (out != null) out.close();
if (writer != null) writer.close();
} catch (java.io.IOException ie) {
}
}
long stop = System.currentTimeMillis();
long millisecondsDuration = stop - start;
if (doDiag) {
Object[] msgArgs = new Object[] {inFileName, xslFileName, new Long(millisecondsDuration)};
msg = XSLMessages.createMessage("diagTiming", msgArgs);
diagnosticsWriter.println('\n');
diagnosticsWriter.println(msg);
}
} catch (Throwable throwable) {
while (throwable instanceof com.sun.org.apache.xml.internal.utils.WrappedRuntimeException) {
throwable =
((com.sun.org.apache.xml.internal.utils.WrappedRuntimeException) throwable)
.getException();
}
if ((throwable instanceof NullPointerException)
|| (throwable instanceof ClassCastException)) doStackDumpOnError = true;
diagnosticsWriter.println();
if (doStackDumpOnError) throwable.printStackTrace(dumpWriter);
else {
DefaultErrorHandler.printLocation(diagnosticsWriter, throwable);
diagnosticsWriter.println(
XSLMessages.createMessage(XSLTErrorResources.ER_XSLT_ERROR, null)
+ " ("
+ throwable.getClass().getName()
+ "): "
+ throwable.getMessage());
}
// diagnosticsWriter.println(XSLMessages.createMessage(XSLTErrorResources.ER_NOT_SUCCESSFUL,
// null)); //"XSL Process was not successful.");
if (null != dumpFileName) {
dumpWriter.close();
}
doExit(throwable.getMessage());
}
if (null != dumpFileName) {
dumpWriter.close();
}
if (null != diagnosticsWriter) {
// diagnosticsWriter.close();
}
// if(!setQuietMode)
// diagnosticsWriter.println(resbundle.getString("xsldone")); //"Xalan: done");
// else
// diagnosticsWriter.println(""); //"Xalan: done");
}
}