@Override
public void render(Parameters blockParameters, Writer w, RenderHints hints)
throws FrameworkException {
log.debug("Error rendering " + blockParameters);
switch (getType()) {
case BODY:
try {
decorateIntro(hints, w, "error");
w.write("<h1>" + error.status);
w.write(": ");
CharTransformer escape = new Xml(Xml.ESCAPE);
w.write(escape.transform(error.exception.getMessage()));
w.write(" ");
w.write(escape.transform(url));
w.write("</h1>");
w.write("<pre>");
HttpServletRequest request = blockParameters.get(Parameter.REQUEST);
error.getErrorReport(w, request, escape);
w.write("</pre>");
decorateOutro(hints, w);
} catch (IOException eio) {
throw new FrameworkException(eio.getMessage(), eio);
}
break;
default:
}
}
public String fetchCleanupReviewDirLinkGenXml() {
String s = null;
try {
s = // Organize and Clean Up Section
"<ReviewDirGenerator class='operator.ReviewDirGenerator' destination.dir='"
+ outputDirectory.getCanonicalPath()
+ "' sample='"
+ outputDirectory.getName()
+ "' submitter='"
+ submitter
+ "' analysis.type='"
+ analysisType
+ "'> \n"
+ " <finalVariants /> \n"
+ " <ViewerCSV /> \n"
+ " <InstanceLog class='buffer.InstanceLogFile' /> \n"
+ " <finalBAM /> \n"
+ " <QCOutputFile /> \n"
+ " <bedForVars /> \n"
+ "</ReviewDirGenerator> \n\n";
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nError fetching clean up and review dir links.\n");
}
return s;
}
/**
* Performs an XPATH lookup in an xml document whose filename is specified by the first parameter
* (assumed to be in the auxiliary subdirectory) The XPATH expression is supplied as the second
* string parameter The return value is of type string e.g. this is currently used primarily for
* looking up the Company Prefix Index for encoding a GS1 Company Prefix into a 64-bit EPC tag
*/
private String xpathlookup(String xml, String expression) {
try {
// Parse the XML as a W3C document.
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document document =
builder.parse(new File(xmldir + File.separator + "auxiliary" + File.separator + xml));
XPath xpath = XPathFactory.newInstance().newXPath();
String rv = (String) xpath.evaluate(expression, document, XPathConstants.STRING);
return rv;
} catch (ParserConfigurationException e) {
System.err.println("ParserConfigurationException caught...");
e.printStackTrace();
return null;
} catch (XPathExpressionException e) {
System.err.println("XPathExpressionException caught...");
e.printStackTrace();
return null;
} catch (SAXException e) {
System.err.println("SAXException caught...");
e.printStackTrace();
return null;
} catch (IOException e) {
System.err.println("IOException caught...");
e.printStackTrace();
return null;
}
}
/**
* Get the noun and verb <roots> (i.e. 'the highest' synsets in WordNet) from the particular
* 'icfile' (Information Content) that you are applying. Store a noun <root>: a synset offset
* number of type Integer in nounroots: an ArrayList<Integer> defined in the constructor of this
* class. Store a verb <root>: a synset offset number of type Integer in verbroots: an
* ArrayList<Integer> defined in the constructor of this class.
*
* <p>An example line in an 'icfile', showing a noun <root>: 1740n 128767 ROOT
*/
private void getRoots() {
Pattern pn = Pattern.compile("[0-9]+n [0-9]+ ROOT"); // find noun <root>
Pattern pv = Pattern.compile("[0-9]+v [0-9]+ ROOT"); // find verb <root>
Matcher m = null;
String root = "";
try {
BufferedReader in = new BufferedReader(new FileReader(icfile));
String line;
while ((line = in.readLine()) != null) {
// nouns
m = pn.matcher(line);
if (m.matches()) {
root = (line.split("\\s")[0]).split("n")[0]; // !!! double split !!!
nounroots.add(Integer.parseInt(root));
}
// verbs
m = pv.matcher(line);
if (m.matches()) {
root = (line.split("\\s")[0]).split("v")[0]; // !!! double split !!!
verbroots.add(Integer.parseInt(root));
}
}
in.close();
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Checks if a given file exists and, if not, create it by copying a default template from
* resources; used to create default conf files.
*
* @param file The path of the file that needs to exist
* @param template The path of the template for the file
*/
public static void ensureFileExists(final String file, final String template) {
if (LAUNCHED_FROM_JAR && !Files.exists(Paths.get(file))) {
if (Debug.on) printDebug("[Meta] " + file + " does not exist: creating a default one.");
InputStream stream = Meta.class.getResourceAsStream(template);
if (stream == null) {
printDebug(
"[ WARNING ] template for "
+ template
+ " not found. Won't create a default "
+ file
+ ".");
} else {
int readBytes;
byte[] buffer = new byte[4096];
try (OutputStream outStream = new FileOutputStream(new File(file))) {
while ((readBytes = stream.read(buffer)) > 0) {
outStream.write(buffer, 0, readBytes);
}
if (Debug.on)
printDebug("[Meta] created default file " + file + " from " + template + ".");
} catch (IOException e) {
e.printStackTrace();
} finally {
try {
stream.close();
} catch (IOException ignore) {
}
}
}
} else {
if (Meta.LAUNCHED_FROM_JAR && Debug.on) printDebug("[Meta] file exists: " + file + ".");
}
}
/** Returns true if this VM has acquired the right to run this TestTask */
private static DUnitRun getDUnitRun() {
if (dunitRun != null) {
System.out.println("BBB dunitRun not null returning");
return dunitRun;
}
try {
SwarmBB.getBB().getSharedLock().lock();
Integer runId = (Integer) SwarmBB.getBB().getSharedMap().get(SwarmBB.RUN_ID);
System.out.println("BBB runID=" + runId);
if (runId != null) {
dunitRun = Swarm.getDUnitRun(runId);
System.out.println("BBB lookedUp RUN:" + dunitRun);
} else {
dunitRun = Swarm.generateNewDUnitRun();
System.out.println(
"BBB GENNED UP A RUN:" + dunitRun + " mapping to id:" + dunitRun.getId());
SwarmBB.getBB().getSharedMap().put(SwarmBB.RUN_ID, dunitRun.getId());
}
} catch (SQLException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} finally {
SwarmBB.getBB().getSharedLock().unlock();
}
return dunitRun;
}
private void dumpFailedLaunchInfo(Process process) {
try {
dumpStream(process.getErrorStream());
dumpStream(process.getInputStream());
} catch (IOException e) {
MessageOutput.println("Unable to display process output:", e.getMessage());
}
}
static void searchFiles() {
try {
for (int i = 0; i < options.filenames.length; i++) {
Scanner input = new Scanner(new File(options.filenames[i]));
scanfile(input, options.filenames[i], options.pattern);
input.close();
}
} catch (IOException e) {
messages.warn(e.getMessage());
messages.exit_status = messages.EXIT_NOMATCH;
}
}
/** The main program for ReTrace. */
public static void main(String[] args) {
if (args.length < 1) {
System.err.println(
"Usage: java proguard.ReTrace [-verbose] <mapping_file> [<stacktrace_file>]");
System.exit(-1);
}
String regularExpresssion = STACK_TRACE_EXPRESSION;
boolean verbose = false;
int argumentIndex = 0;
while (argumentIndex < args.length) {
String arg = args[argumentIndex];
if (arg.equals(REGEX_OPTION)) {
regularExpresssion = args[++argumentIndex];
} else if (arg.equals(VERBOSE_OPTION)) {
verbose = true;
} else {
break;
}
argumentIndex++;
}
if (argumentIndex >= args.length) {
System.err.println(
"Usage: java proguard.ReTrace [-regex <regex>] [-verbose] <mapping_file> [<stacktrace_file>]");
System.exit(-1);
}
File mappingFile = new File(args[argumentIndex++]);
File stackTraceFile = argumentIndex < args.length ? new File(args[argumentIndex]) : null;
ReTrace reTrace = new ReTrace(regularExpresssion, verbose, mappingFile, stackTraceFile);
try {
// Execute ReTrace with its given settings.
reTrace.execute();
} catch (IOException ex) {
if (verbose) {
// Print a verbose stack trace.
ex.printStackTrace();
} else {
// Print just the stack trace message.
System.err.println("Error: " + ex.getMessage());
}
System.exit(1);
}
System.exit(0);
}
/* attach to running target vm */
private VirtualMachine attachTarget() {
AttachingConnector attacher = (AttachingConnector) connector;
try {
return attacher.attach(connectorArgs);
} catch (IOException ioe) {
ioe.printStackTrace();
MessageOutput.fatalError("Unable to attach to target VM.");
} catch (IllegalConnectorArgumentsException icae) {
icae.printStackTrace();
MessageOutput.fatalError("Internal debugger error.");
}
return null; // Shuts up the compiler
}
public static void main(String[] args) {
File f = new File(args[0]);
try {
Parser<GeneOrthologyEntry> entries =
new Parser<GeneOrthologyEntry>(f, new GeneOrthologyEntry.ParsingMapper());
while (entries.hasNext()) {
GeneOrthologyEntry entry = entries.next();
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public Class<?> findClass(String s) {
try {
byte[] bytes = loadClassData(s);
return defineClass(s, bytes, 0, bytes.length);
} catch (IOException ioe) {
try {
return super.loadClass(s);
} catch (ClassNotFoundException ignore) {
}
ioe.printStackTrace(System.out);
return null;
}
}
// Writes the program to a source file, compiles it, and runs it.
private void compileAndRun(String fileName, String code) {
// Exceptions here can pick and choose what font to use, as needed.
// Exceptions thrown by the program, that cause the Playground to be unstable, should be in
// blue.
println("Deleting old temp files...", progErr);
new File(fileName + ".java").delete();
new File(fileName + ".class").delete();
println("Creating source file...", progErr);
file = new File(fileName + ".java");
println("Writing code to source file...", progErr);
try {
new FileWriter(file).append(code).close();
} catch (IOException i) {
println("Had an IO Exception when trying to write the code. Stack trace:", error);
i.printStackTrace();
return; // Exit on error
}
println("Compiling code...", progErr);
// This should only ever be called if the JDK isn't installed. How you'd get here, I don't
// know.
if (compiler == null) {
println("Fatal Error: JDK not installed. Go to java.sun.com and install.", error);
return;
}
// Tries to compile. Success code is 0, so if something goes wrong, do stuff.
int result =
compiler.run(
null,
null,
null,
file
.getAbsolutePath()); // Possibly add a new outputstream to parse through the
// compiler errors
if (result != 0) {
displayLog();
println("Failed to compile.", error);
return; // Return on error
}
println("Code compiled with 0 errors.", progErr);
println("Attempting to run code...", progErr);
run(fileName);
}
public static void main(String[] args) {
try {
BufferedReader br = new BufferedReader(new FileReader(args[0]));
int tIndex = 0;
int pIndex = 0;
// This will probably change soon (name and implementation)
NgramParser tnp = new NgramParser(args[1]);
ArrayList<String> triplet = tnp.getTriplet();
ArrayList<String> polarity = tnp.getPolarity();
FileWriter sw = new FileWriter(args[2]);
String line = null;
while (((line = br.readLine()) != null)
&& (tIndex < triplet.size())
&& (pIndex < polarity.size())) {
if (line.matches("^[\\d]*:")) {
// System.out.println(line);
sw.write(line + "\n");
} else {
Scanner sc = new Scanner(line);
String trip = sc.findInLine(Pattern.compile("[a-zA-Z]+#[a-z]+[#]?[0-9]*"));
// if (trip != null && trip.equals(triplet.get(tIndex))) {
System.out.println(trip);
if (trip != null && !trip.toLowerCase().contains("no#cl")) {
// System.out.println(triplet.get(tIndex) + ":" +polarity.get(pIndex));
String pol = polarity.get(pIndex);
sw.write(line + " " + pol + "\n");
sc.close();
tIndex++;
pIndex++;
} else {
String pol = "neg";
sw.write("no#a#1" + " " + pol + "\n");
sc.close();
}
}
// sw.flush();
}
sw.close();
} catch (IOException e) {
e.printStackTrace();
}
}
public void run() {
for (; ; ) {
try {
int n = sel.select();
if (n > 0) processSelectedKeys();
processPendingTargets();
if (shutdown) {
sel.close();
return;
}
} catch (IOException x) {
x.printStackTrace();
}
}
}
public BackupHdfs() {
try {
m_wrMkdirs = new PrintWriter(new BufferedWriter(new FileWriter("hdfs-mkdirs.sh")));
m_wrMkdirs.println("hadoop fs -mkdir /mapred");
m_wrMkdirs.println("hadoop fs -mkdir /mapred/system");
m_wrChmods = new PrintWriter(new BufferedWriter(new FileWriter("hdfs-chmods.sh")));
m_wrChmods.println("hadoop fs -chmod 775 /");
m_wrChmods.println("hadoop fs -chown hdfs:hadoop /");
m_wrChmods.println("hadoop fs -chown mapred:hadoop /mapred/system");
m_wrChmods.println("hadoop fs -chmod 700 /mapred/system");
} catch (IOException e) {
System.err.println("ERROR: failed to open files for writing: " + e.toString());
}
}
public static void lookingCode() {
int procura = 0;
boolean entrou = false;
do {
procura = Entrada.leiaInt("Digite o código da carta: ");
} while (procura < 0 || procura > 32);
try {
FileReader arq = new FileReader(FileManenger.fileName);
BufferedReader lerArq = new BufferedReader(arq);
String linha = lerArq.readLine();
while (linha != null) {
// procura na string '.'
if (linha.toLowerCase().contains(".".toLowerCase())) {
// separ em um array a linha que tem o nome do personagem ex: 1.CARLOS
String columnArray[] = linha.split(Pattern.quote("."));
// testa se o codigo é o que ele procura
if (procura == Integer.parseInt(columnArray[0])) {
// achou o codigo que ele procura
entrou = true;
}
}
// testa se a linha é igual a * se for ele já não é mais o personagem que procuramos
if (linha.equals("*")) {
entrou = false;
}
// mostra as inforamações do personagem
if (entrou) {
System.out.println(linha);
}
linha = lerArq.readLine();
}
arq.close();
} catch (IOException e) {
System.err.printf("Erro na abertura do arquivo: %s.\n", e.getMessage());
}
}
/* listen for connection from target vm */
private VirtualMachine listenTarget() {
ListeningConnector listener = (ListeningConnector) connector;
try {
String retAddress = listener.startListening(connectorArgs);
MessageOutput.println("Listening at address:", retAddress);
vm = listener.accept(connectorArgs);
listener.stopListening(connectorArgs);
return vm;
} catch (IOException ioe) {
ioe.printStackTrace();
MessageOutput.fatalError("Unable to attach to target VM.");
} catch (IllegalConnectorArgumentsException icae) {
icae.printStackTrace();
MessageOutput.fatalError("Internal debugger error.");
}
return null; // Shuts up the compiler
}
private void dumpStream(InputStream stream) throws IOException {
BufferedReader in = new BufferedReader(new InputStreamReader(stream));
int i;
try {
while ((i = in.read()) != -1) {
MessageOutput.printDirect((char) i); // Special case: use
// printDirect()
}
} catch (IOException ex) {
String s = ex.getMessage();
if (!s.startsWith("Bad file number")) {
throw ex;
}
// else we got a Bad file number IOException which just means
// that the debuggee has gone away. We'll just treat it the
// same as if we got an EOF.
}
}
public static void readFile() {
try {
FileReader arq = new FileReader(FileManenger.fileName);
BufferedReader lerArq = new BufferedReader(arq);
String linha =
lerArq
.readLine(); // lê a primeira linha a variável "linha" recebe o valor "null" quando o
// processo de repetição atingir o final do arquivo texto
while (linha != null) {
System.out.println(linha);
linha = lerArq.readLine(); // lê da segunda até a última linha
}
arq.close();
} catch (IOException e) {
System.err.printf("Erro na abertura do arquivo: %s.\n", e.getMessage());
}
}
public static void main(String[] args) {
try {
Genome g = Organism.findGenome(args[0]);
File blasttab = new File(args[1]);
ProbesFromPrimers pfp = new ProbesFromPrimers(g, blasttab);
Collection<NamedRegion> probes = pfp.parseProbes();
for (NamedRegion probe : probes) {
String probeName = probe.getName();
System.out.println(
String.format(
"%s\t%s\t%d\t%d", probeName, probe.getChrom(), probe.getStart(), probe.getEnd()));
}
} catch (NotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
/* launch child target vm */
private VirtualMachine launchTarget() {
LaunchingConnector launcher = (LaunchingConnector) connector;
try {
VirtualMachine vm = launcher.launch(connectorArgs);
process = vm.process();
displayRemoteOutput(process.getErrorStream());
displayRemoteOutput(process.getInputStream());
return vm;
} catch (IOException ioe) {
ioe.printStackTrace();
MessageOutput.fatalError("Unable to launch target VM.");
} catch (IllegalConnectorArgumentsException icae) {
icae.printStackTrace();
MessageOutput.fatalError("Internal debugger error.");
} catch (VMStartException vmse) {
MessageOutput.println("vmstartexception", vmse.getMessage());
MessageOutput.println();
dumpFailedLaunchInfo(vmse.process());
MessageOutput.fatalError("Target VM failed to initialize.");
}
return null; // Shuts up the compiler
}
protected void getDimensionsFromLogFile(BufferedReader reader, PicText text) {
if (reader == null) {
return;
}
String line = ""; // il rale si j'initialise pas ...
boolean finished = false;
while (!finished) {
try {
line = reader.readLine();
} catch (IOException ioex) {
ioex.printStackTrace();
return;
}
if (line == null) {
System.out.println("Size of text not found in log file...");
return;
}
System.out.println(line);
Matcher matcher = LogFilePattern.matcher(line);
if (line != null && matcher.find()) {
System.out.println("FOUND :" + line);
finished = true;
try {
text.setDimensions(
0.3515 * Double.parseDouble(matcher.group(1)), // height, pt->mm (1pt=0.3515 mm)
0.3515 * Double.parseDouble(matcher.group(2)), // width
0.3515 * Double.parseDouble(matcher.group(3))); // depth
areDimensionsComputed = true;
} catch (NumberFormatException e) {
System.out.println("Logfile number format problem: $line" + e.getMessage());
} catch (IndexOutOfBoundsException e) {
System.out.println("Logfile regexp problem: $line" + e.getMessage());
}
}
}
return;
}
/**
* Searches for the directory 'dirPath'; if not found, tries to create it, then returns a File
* object for that directory.
*/
public static File ensureDirExists(final String dirPath) {
File dirpath = new File(dirPath);
if (!dirpath.isDirectory()) {
if (!dirpath.exists()) {
printDebug("[Meta] " + dirpath + " does not exist: creating it...");
try {
Files.createDirectories(Paths.get(dirpath.getPath()));
return dirpath;
} catch (IOException e) {
printDebug("[Meta] Exception while creating directory:");
e.printStackTrace();
return null;
}
} else {
printDebug(
"[Meta] Error: path `"
+ dirpath
+ "' is not a valid directory path, and could not create it.");
return null;
}
} else return dirpath;
}
// Takes a PImage and compresses it into a JPEG byte stream
// Adapted from Dan Shiffman's UDP Sender code
public byte[] compressImage(PImage img) {
// We need a buffered image to do the JPG encoding
BufferedImage bimg = new BufferedImage(img.width, img.height, BufferedImage.TYPE_INT_RGB);
img.loadPixels();
bimg.setRGB(0, 0, img.width, img.height, img.pixels, 0, img.width);
// Need these output streams to get image as bytes for UDP communication
ByteArrayOutputStream baStream = new ByteArrayOutputStream();
BufferedOutputStream bos = new BufferedOutputStream(baStream);
// Turn the BufferedImage into a JPG and put it in the BufferedOutputStream
// Requires try/catch
try {
ImageIO.write(bimg, "jpg", bos);
} catch (IOException e) {
e.printStackTrace();
}
// Get the byte array, which we will send out via UDP!
return baStream.toByteArray();
}
// Creates a new thread, runs the program in that thread, and reports any errors as needed.
private void run(String clazz) {
try {
// Makes sure the JVM resets if it's already running.
if (JVMrunning) kill();
// Some String constants for java path and OS-specific separators.
String separator = System.getProperty("file.separator");
String path = System.getProperty("java.home") + separator + "bin" + separator + "java";
// Tries to run compiled code.
ProcessBuilder builder = new ProcessBuilder(path, clazz);
// Should be good now! Everything past this is on you. Don't mess it up.
println(
"Build succeeded on " + java.util.Calendar.getInstance().getTime().toString(), progErr);
println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~", progErr);
JVM = builder.start();
// Note that as of right now, there is no support for input. Only output.
Reader errorReader = new InputStreamReader(JVM.getErrorStream());
Reader outReader = new InputStreamReader(JVM.getInputStream());
// Writer inReader = new OutputStreamWriter(JVM.getOutputStream());
redirectErr = redirectIOStream(errorReader, err);
redirectOut = redirectIOStream(outReader, out);
// redirectIn = redirectIOStream(null, inReader);
} catch (IOException e) {
// JVM = builder.start() can throw this.
println("IOException when running the JVM.", progErr);
e.printStackTrace();
displayLog();
return;
}
}
/** * Compare the checksums of the hdfs file as well as the local copied file. * * @author [email protected] * @date Fri Jan 27 06:06:00 2012 */ boolean compareChecksums(FileSystem fs, Path p, String sFsPath) { try { // get hdfs file info FileStatus stat = fs.getFileStatus(p); // get HDFS checksum FileChecksum ck = fs.getFileChecksum(p); String sCk, sCkShort; if (ck == null) { sCk = sCkShort = "<null>"; } else { sCk = ck.toString(); sCkShort = sCk.replaceAll("^.*:", ""); } // System.out.println(p.toUri().getPath() + " len=" + stat.getLen() // + " " + stat.getOwner() + "/" + stat.getGroup() // + " checksum=" + sCk); // find the local file File fLocal = new File(sFsPath); if (!fLocal.exists()) { System.out.println("CHECKSUM-ERROR: file does not exist: " + sFsPath); return false; } if (!fLocal.isFile()) { System.out.println("CHECKSUM-ERROR: path is not a file: " + sFsPath); return false; } if (stat.getLen() != fLocal.length()) { System.out.println( "CHECKSUM-ERROR: length mismatch: " + sFsPath + " hdfslen=" + stat.getLen() + " fslen=" + fLocal.length()); return false; } // get local fs checksum FileChecksum ckLocal = getLocalFileChecksum(sFsPath); if (ckLocal == null) { System.out.println("ERROR Failed to get checksum for local file " + sFsPath); return false; } // compare checksums as a string, after stripping the // algorithm name from the beginning String sCkLocal = ckLocal.toString(); String sCkLocalShort = sCkLocal.replaceAll("^.*:", ""); if (false == sCkShort.equals(sCkLocalShort)) { System.out.println( "CHECKSUM-ERROR: checksum mismatch: " + sFsPath + "\nhdfs = " + sCk + "\nlocal= " + sCkLocal); return false; } return true; } catch (IOException e) { System.out.println("CHECKSUM-ERROR: " + sFsPath + " exception " + e.toString()); } return false; }
public void init() throws ServletException {
final String CONFIG_PATH = getServletContext().getRealPath("/") + "config.ini";
final String APPLICATION_NAME = getServletContext().getServletContextName();
BasicConfigurator.configure();
FileInputStream config_file = null;
File config = new File(CONFIG_PATH);
if (config.canRead()) {
log.debug("Parsing " + CONFIG_PATH);
try {
config_file = new FileInputStream(CONFIG_PATH);
} catch (java.io.FileNotFoundException e) {
throw new ServletException(e);
}
Properties config_prop = new Properties();
try {
config_prop.load(config_file);
} catch (java.io.IOException e) {
throw new ServletException(e);
}
this.config = config_prop;
log.debug("Parsing finished");
} else {
log.fatal("Error, cannot read " + CONFIG_PATH);
}
log.debug("maximumRecords : " + this.config.getProperty("default_maximumRecords"));
log.debug("srw_header_file: " + this.config.getProperty("srw_header_file"));
log.debug("srw_diag: " + this.config.getProperty("srw_diag_file"));
// log.debug("server_list: " + this.config.getProperty("server_list"));
try {
FileReader fis =
new FileReader(
getServletContext().getRealPath("/") + this.config.getProperty("srw_header_file"));
BufferedReader in1 = new BufferedReader(fis);
fis =
new FileReader(
getServletContext().getRealPath("/") + this.config.getProperty("srw_footer_file"));
BufferedReader in2 = new BufferedReader(fis);
fis =
new FileReader(
getServletContext().getRealPath("/") + this.config.getProperty("srw_diag_file"));
BufferedReader in3 = new BufferedReader(fis);
try {
String line = null;
while ((line = in1.readLine()) != null) {
this.SRW_HEADER = this.SRW_HEADER + line;
}
while ((line = in2.readLine()) != null) {
this.SRW_FOOTER = this.SRW_FOOTER + line;
}
while ((line = in3.readLine()) != null) {
this.SRW_DIAG = this.SRW_DIAG + line;
}
} finally {
in1.close();
in2.close();
in3.close();
}
} catch (IOException ex) {
ex.printStackTrace();
}
}
/** Performs the subsequent ReTrace operations. */
public void execute() throws IOException {
// Read the mapping file.
MappingReader mappingReader = new MappingReader(mappingFile);
mappingReader.pump(this);
StringBuffer expressionBuffer = new StringBuffer(regularExpression.length() + 32);
char[] expressionTypes = new char[32];
int expressionTypeCount = 0;
int index = 0;
while (true) {
int nextIndex = regularExpression.indexOf('%', index);
if (nextIndex < 0
|| nextIndex == regularExpression.length() - 1
|| expressionTypeCount == expressionTypes.length) {
break;
}
expressionBuffer.append(regularExpression.substring(index, nextIndex));
expressionBuffer.append('(');
char expressionType = regularExpression.charAt(nextIndex + 1);
switch (expressionType) {
case 'c':
expressionBuffer.append(REGEX_CLASS);
break;
case 'C':
expressionBuffer.append(REGEX_CLASS_SLASH);
break;
case 'l':
expressionBuffer.append(REGEX_LINE_NUMBER);
break;
case 't':
expressionBuffer.append(REGEX_TYPE);
break;
case 'f':
expressionBuffer.append(REGEX_MEMBER);
break;
case 'm':
expressionBuffer.append(REGEX_MEMBER);
break;
case 'a':
expressionBuffer.append(REGEX_ARGUMENTS);
break;
}
expressionBuffer.append(')');
expressionTypes[expressionTypeCount++] = expressionType;
index = nextIndex + 2;
}
expressionBuffer.append(regularExpression.substring(index));
Pattern pattern = Pattern.compile(expressionBuffer.toString());
// Read the stack trace file.
LineNumberReader reader =
new LineNumberReader(
stackTraceFile == null
? (Reader) new InputStreamReader(System.in)
: (Reader) new BufferedReader(new FileReader(stackTraceFile)));
try {
StringBuffer outLine = new StringBuffer(256);
List extraOutLines = new ArrayList();
String className = null;
// Read the line in the stack trace.
while (true) {
String line = reader.readLine();
if (line == null) {
break;
}
Matcher matcher = pattern.matcher(line);
if (matcher.matches()) {
int lineNumber = 0;
String type = null;
String arguments = null;
// Figure out a class name, line number, type, and
// arguments beforehand.
for (int expressionTypeIndex = 0;
expressionTypeIndex < expressionTypeCount;
expressionTypeIndex++) {
int startIndex = matcher.start(expressionTypeIndex + 1);
if (startIndex >= 0) {
String match = matcher.group(expressionTypeIndex + 1);
char expressionType = expressionTypes[expressionTypeIndex];
switch (expressionType) {
case 'c':
className = originalClassName(match);
break;
case 'C':
className = originalClassName(ClassUtil.externalClassName(match));
break;
case 'l':
lineNumber = Integer.parseInt(match);
break;
case 't':
type = originalType(match);
break;
case 'a':
arguments = originalArguments(match);
break;
}
}
}
// Actually construct the output line.
int lineIndex = 0;
outLine.setLength(0);
extraOutLines.clear();
for (int expressionTypeIndex = 0;
expressionTypeIndex < expressionTypeCount;
expressionTypeIndex++) {
int startIndex = matcher.start(expressionTypeIndex + 1);
if (startIndex >= 0) {
int endIndex = matcher.end(expressionTypeIndex + 1);
String match = matcher.group(expressionTypeIndex + 1);
// Copy a literal piece of input line.
outLine.append(line.substring(lineIndex, startIndex));
char expressionType = expressionTypes[expressionTypeIndex];
switch (expressionType) {
case 'c':
className = originalClassName(match);
outLine.append(className);
break;
case 'C':
className = originalClassName(ClassUtil.externalClassName(match));
outLine.append(ClassUtil.internalClassName(className));
break;
case 'l':
lineNumber = Integer.parseInt(match);
outLine.append(match);
break;
case 't':
type = originalType(match);
outLine.append(type);
break;
case 'f':
originalFieldName(className, match, type, outLine, extraOutLines);
break;
case 'm':
originalMethodName(
className, match, lineNumber, type, arguments, outLine, extraOutLines);
break;
case 'a':
arguments = originalArguments(match);
outLine.append(arguments);
break;
}
// Skip the original element whose processed version
// has just been appended.
lineIndex = endIndex;
}
}
// Copy the last literal piece of input line.
outLine.append(line.substring(lineIndex));
// Print out the main line.
System.out.println(outLine);
// Print out any additional lines.
for (int extraLineIndex = 0; extraLineIndex < extraOutLines.size(); extraLineIndex++) {
System.out.println(extraOutLines.get(extraLineIndex));
}
} else {
// Print out the original line.
System.out.println(line);
}
}
} catch (IOException ex) {
throw new IOException("Can't read stack trace (" + ex.getMessage() + ")");
} finally {
if (stackTraceFile != null) {
try {
reader.close();
} catch (IOException ex) {
// This shouldn't happen.
}
}
}
}
// Thread's run method aimed at creating a bitmap asynchronously
public void run() {
Drawing drawing = new Drawing();
PicText rawPicText = new PicText();
String s = ((PicText) element).getText();
rawPicText.setText(s);
drawing.add(
rawPicText); // bug fix: we must add a CLONE of the PicText, otherwise it loses it former
// parent... (then pb with the view )
drawing.setNotparsedCommands(
"\\newlength{\\jpicwidth}\\settowidth{\\jpicwidth}{"
+ s
+ "}"
+ CR_LF
+ "\\newlength{\\jpicheight}\\settoheight{\\jpicheight}{"
+ s
+ "}"
+ CR_LF
+ "\\newlength{\\jpicdepth}\\settodepth{\\jpicdepth}{"
+ s
+ "}"
+ CR_LF
+ "\\typeout{JPICEDT INFO: \\the\\jpicwidth, \\the\\jpicheight, \\the\\jpicdepth }"
+ CR_LF);
RunExternalCommand.Command commandToRun = RunExternalCommand.Command.BITMAP_CREATION;
// RunExternalCommand command = new RunExternalCommand(drawing, contentType,commandToRun);
boolean isWriteTmpTeXfile = true;
String bitmapExt = "png"; // [pending] preferences
String cmdLine =
"{i}/unix/tetex/create_bitmap.sh {p} {f} "
+ bitmapExt
+ " "
+ fileDPI; // [pending] preferences
ContentType contentType = getContainer().getContentType();
RunExternalCommand.isGUI = false; // System.out, no dialog box // [pending] debug
RunExternalCommand command =
new RunExternalCommand(drawing, contentType, cmdLine, isWriteTmpTeXfile);
command
.run(); // synchronous in an async. thread => it's ok (anyway, we must way until the LaTeX
// process has completed)
if (wantToComputeLatexDimensions) {
// load size of text:
try {
File logFile = new File(command.getTmpPath(), command.getTmpFilePrefix() + ".log");
BufferedReader reader = null;
try {
reader = new BufferedReader(new FileReader(logFile));
} catch (FileNotFoundException fnfe) {
System.out.println("Cannot find log file! " + fnfe.getMessage());
System.out.println(logFile);
} catch (IOException ioex) {
System.out.println("Log file IO exception");
ioex.printStackTrace();
} // utile ?
System.out.println("Log file created! file=" + logFile);
getDimensionsFromLogFile(reader, (PicText) element);
syncStringLocation(); // update dimensions
syncBounds();
syncFrame();
SwingUtilities.invokeLater(
new Thread() {
public void run() {
repaint(null);
}
});
// repaint(null); // now that dimensions are available, we force a repaint() [pending]
// smart-repaint ?
} catch (Exception e) {
e.printStackTrace();
}
}
if (wantToGetBitMap) {
// load image:
try {
File bitmapFile =
new File(command.getTmpPath(), command.getTmpFilePrefix() + "." + bitmapExt);
this.image = ImageIO.read(bitmapFile);
System.out.println(
"Bitmap created! file="
+ bitmapFile
+ ", width="
+ image.getWidth()
+ "pixels, height="
+ image.getHeight()
+ "pixels");
if (image == null) return;
syncStringLocation(); // sets strx, stry, and dimensions of text
syncBounds();
// update the AffineTransform that will be applied to the bitmap before displaying on screen
PicText te = (PicText) element;
text2ModelTr.setToIdentity(); // reset
PicPoint anchor = te.getCtrlPt(TextEditable.P_ANCHOR, ptBuf);
text2ModelTr.rotate(getRotation(), anchor.x, anchor.y); // rotate along P_ANCHOR !
text2ModelTr.translate(te.getLeftX(), te.getTopY());
text2ModelTr.scale(
te.getWidth() / image.getWidth(),
-(te.getHeight() + te.getDepth()) / image.getHeight());
// [pending] should do something special to avoid dividing by 0 or setting a rescaling
// factor to 0 [non invertible matrix] (java will throw an exception)
syncFrame();
SwingUtilities.invokeLater(
new Thread() {
public void run() {
repaint(null);
}
});
// repaint(null); // now that bitmap is available, we force a repaint() [pending]
// smart-repaint ?
} catch (Exception e) {
e.printStackTrace();
}
}
}