/** Writes the data provenance into xml formatted file */
public void writeXML() throws IOException {
FileWriter fw;
if (file.exists() == true) {
file.delete();
file = new File(fileDir + File.separator + fileName);
}
try {
fw = new FileWriter(file);
bw = new BufferedWriter(fw);
Vector<XMLAttributes> atVector = new Vector<XMLAttributes>();
bw.write(XML_HEADER);
bw.newLine();
bw.write(DATA_PROVENANCE);
bw.newLine();
openTag("provenance", true);
int numEntries = pHolder.size();
ProvenanceEntry entry;
for (int i = 0; i < numEntries; i++) {
entry = pHolder.elementAt(i);
openTag("processStep", true);
atVector.add(new XMLAttributes("version", entry.getMipavVersion()));
this.closedTag("program", entry.getProgramName(), atVector);
atVector.add(new XMLAttributes("inputs", entry.getProgramInputs()));
closedTag("programArguments", entry.getAction(), atVector);
closedTag("timeStamp", entry.getTimeStamp());
closedTag("user", entry.getUser());
closedTag("hostName", entry.getHostName());
closedTag("architecture", entry.getArchitecture());
atVector.add(new XMLAttributes("version", entry.getPlatformVersion()));
closedTag("platform", entry.getPlatform(), atVector);
atVector.add(new XMLAttributes("version", entry.getJavaVersion()));
closedTag("compiler", "java", atVector);
openTag("processStep", false);
}
openTag("provenance", false);
bw.close();
} catch (Exception e) {
System.err.println("CAUGHT EXCEPTION WITHIN writeXML() of FileDataProvenance");
e.printStackTrace();
}
}
public void parse() {
try {
// Create SAX Parser factory
SAXParserFactory spfactory = SAXParserFactory.newInstance();
// Create SAX Parser
SAXParser parser = spfactory.newSAXParser();
// Process XML file by given default handler
parser.parse(new ByteArrayInputStream(data.getBytes()), new XMLParseContent(result, data));
// parser.parse(new File("tmp.xml"), new XMLParseRevId(userName,result,data));
} catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] argv) {
try {
// SAXパーサーファクトリを生成
SAXParserFactory spfactory = SAXParserFactory.newInstance();
// SAXパーサーを生成
SAXParser parser = spfactory.newSAXParser();
// XMLファイルを指定されたデフォルトハンドラーで処理します
String fileName = "dos2unix.mm";
// parser.parse(new File("helloworld.xml"), new HelloWorldSax());
parser.parse(new File(fileName), new HelloWorldSax());
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Main program.
*
* <p>\u0040param args Program parameters.
*/
public static void main(String[] args) {
// Initialize.
try {
if (!initialize(args)) {
System.exit(1);
}
// Process all files.
long startTime = System.currentTimeMillis();
int filesProcessed = processFiles(args);
long processingTime = (System.currentTimeMillis() - startTime + 999) / 1000;
// Terminate.
terminate(filesProcessed, processingTime);
} catch (Exception e) {
System.out.println(e.getMessage());
}
}
/** The main entry point */
public static void main(String[] args) throws FileNotFoundException, IOException {
String xmlfile = null;
int debug = 0;
int maxErrs = 10;
boolean nsAware = true;
boolean validating = true;
boolean showWarnings = (debug > 2);
boolean showErrors = true;
Vector catalogFiles = new Vector();
for (int i = 0; i < args.length; i++) {
if (args[i].equals("-c")) {
++i;
catalogFiles.add(args[i]);
continue;
}
if (args[i].equals("-w")) {
validating = false;
continue;
}
if (args[i].equals("-v")) {
validating = true;
continue;
}
if (args[i].equals("-n")) {
nsAware = false;
continue;
}
if (args[i].equals("-N")) {
nsAware = true;
continue;
}
if (args[i].equals("-d")) {
++i;
String debugstr = args[i];
try {
debug = Integer.parseInt(debugstr);
if (debug >= 0) {
Debug.setDebug(debug);
showWarnings = (debug > 2);
}
} catch (Exception e) {
// nop
}
continue;
}
if (args[i].equals("-E")) {
++i;
String errstr = args[i];
try {
int errs = Integer.parseInt(errstr);
if (errs >= 0) {
maxErrs = errs;
}
} catch (Exception e) {
// nop
}
continue;
}
xmlfile = args[i];
}
if (xmlfile == null) {
System.out.println("Usage: org.apache.xml.resolver.apps.xread [opts] xmlfile");
System.exit(1);
}
ResolvingXMLReader reader = new ResolvingXMLReader();
try {
reader.setFeature("http://xml.org/sax/features/namespaces", nsAware);
reader.setFeature("http://xml.org/sax/features/validation", validating);
} catch (SAXException e) {
// nop;
}
Catalog catalog = reader.getCatalog();
for (int count = 0; count < catalogFiles.size(); count++) {
String file = (String) catalogFiles.elementAt(count);
catalog.parseCatalog(file);
}
XParseError xpe = new XParseError(showErrors, showWarnings);
xpe.setMaxMessages(maxErrs);
reader.setErrorHandler(xpe);
String parseType = validating ? "validating" : "well-formed";
String nsType = nsAware ? "namespace-aware" : "namespace-ignorant";
if (maxErrs > 0) {
System.out.println("Attempting " + parseType + ", " + nsType + " parse");
}
Date startTime = new Date();
try {
reader.parse(xmlfile);
} catch (SAXException sx) {
System.out.println("SAX Exception: " + sx);
} catch (Exception e) {
e.printStackTrace();
}
Date endTime = new Date();
long millisec = endTime.getTime() - startTime.getTime();
long secs = 0;
long mins = 0;
long hours = 0;
if (millisec > 1000) {
secs = millisec / 1000;
millisec = millisec % 1000;
}
if (secs > 60) {
mins = secs / 60;
secs = secs % 60;
}
if (mins > 60) {
hours = mins / 60;
mins = mins % 60;
}
if (maxErrs > 0) {
System.out.print("Parse ");
if (xpe.getFatalCount() > 0) {
System.out.print("failed ");
} else {
System.out.print("succeeded ");
System.out.print("(");
if (hours > 0) {
System.out.print(hours + ":");
}
if (hours > 0 || mins > 0) {
System.out.print(mins + ":");
}
System.out.print(secs + "." + millisec);
System.out.print(") ");
}
System.out.print("with ");
int errCount = xpe.getErrorCount();
int warnCount = xpe.getWarningCount();
if (errCount > 0) {
System.out.print(errCount + " error");
System.out.print(errCount > 1 ? "s" : "");
System.out.print(" and ");
} else {
System.out.print("no errors and ");
}
if (warnCount > 0) {
System.out.print(warnCount + " warning");
System.out.print(warnCount > 1 ? "s" : "");
System.out.print(".");
} else {
System.out.print("no warnings.");
}
System.out.println("");
}
if (xpe.getErrorCount() > 0) {
System.exit(1);
}
}
/**
* Process one file.
*
* <p>\u0040param xmlFileName Input file name to check for part of speech/lemma mismatches..
*/
protected static void processOneFile(String xmlFileName) {
try {
// Report document being processed.
System.out.println(
"(" + ++currentDocNumber + "/" + docsToProcess + ") " + "processing " + xmlFileName);
// Create filter to strip <w> and <c>
// elements.
XMLFilter filter = new StripAllWordElementsFilter(XMLReaderFactory.createXMLReader());
// Strip path from input file name.
String strippedFileName = FileNameUtils.stripPathName(xmlFileName);
strippedFileName = FileNameUtils.changeFileExtension(strippedFileName, "");
// Generate output file name.
String xmlOutputFileName =
new File(outputDirectoryName, strippedFileName + ".xml").getAbsolutePath();
// Make sure output directory exists.
FileUtils.createPathForFile(xmlOutputFileName);
// Copy input xml to output xml,
// stripping <w> and <c> elements.
new FilterAdornedFile(xmlFileName, xmlOutputFileName, filter);
// Read it back and fix spacing.
String fixedXML = FileUtils.readTextFile(xmlOutputFileName, "utf-8");
fixedXML = fixedXML.replaceAll("(\\s+)", " ");
fixedXML = fixedXML.replaceAll(" ([\\.?!,;:\\)])", "\u00241");
fixedXML = fixedXML.replaceAll("\\( ", "(");
fixedXML = fixedXML.replaceAll("\u00b6 ", "\u00b6");
fixedXML = fixedXML.replaceAll("__NS1:", "");
fixedXML = fixedXML.replaceAll("__NS1", "");
/*
fixedXML =
fixedXML.replaceAll
(
"</__NS1:" ,
""
);
*/
// Emit unadorned XML.
SAXBuilder builder = new SAXBuilder();
Document document = builder.build(new StringReader(fixedXML));
new AdornedXMLWriter(document, xmlOutputFileName);
} catch (Exception e) {
System.out.println(" Error: " + e.getMessage());
e.printStackTrace();
}
}
