/** 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 execute() throws Exception {
getNewCount();
File executable = new File(getEXEPath());
if (!executable.exists())
throw new FileNotFoundException("executable file does not exist! " + executable);
workingDir = getWorkingDirectory(executable);
initExecution();
instruction = getInstructionFileName(workingDir);
output = getOutputFileName(workingDir);
createInstructionFile(instruction);
// Profiler pofiler = new Profiler();
// profiler.start("exec-ilink-search " + xmlFileName, "exec-ilink-search " + xmlFileName);
ExecShell shell = new ExecShell();
shell.setExecutable(executable.getAbsolutePath());
shell.setWorkingDirectory(workingDir);
setArguments(shell);
shell.addCommandLineArgument(executable.getParent());
shell.execute();
// profiler.start("exec-ilink-search " + xmlFileName, "shell-wait-for");
exitCode = shell.timeout(timeout);
// profiler.stop("exec-ilink-search " + xmlFileName, "shell-wait-for");
// instructionFile.delete();
handleResponse(output);
finishExecution();
if (zws.Server.debugMode()) return;
// cleanup
File[] contents = workingDir.listFiles();
for (int idx = 0; idx < contents.length; contents[idx++].delete()) ;
workingDir.delete();
}
public boolean accept(File pathname) {
if (pathname.isDirectory()) return true;
else {
if (pathname.getName().indexOf(".scl") != -1) return true;
else return false;
}
}
private void tidyUnicode(String filename) {
FileInputStream in = null;
FileOutputStream out = null;
InputStreamReader reader = null;
OutputStreamWriter writer = null;
File f0 = new File(filename + "0");
File f1 = new File(filename);
f1.renameTo(f0);
try {
in = new FileInputStream(f0);
reader = new InputStreamReader(in);
out = new FileOutputStream(f1);
writer = new OutputStreamWriter(out);
UTF8Tidy u = new UTF8Tidy(reader, writer);
u.execute();
} catch (Exception e) {
{
} // System.out.println("e: " + e ); }
} finally {
try {
reader.close();
writer.close();
} catch (Exception ex) {
ex.printStackTrace();
}
f0.delete();
}
}
public void load(File xml, File mapping)
throws SAXException, ParserConfigurationException, IOException {
System.out.println("Loading " + xml.getPath() + " with " + mapping.getPath());
XMLValidator.validate(xml, false);
TagMap loader = new TagMap();
loader.load(mapping, actionMap, targetMap, attributeMaps);
getParser(false).parse(xml, new Parser(actionMap, targetMap, attributeMaps));
{
} // System.out.println("---------------------------------------------------------------------------------------");
}
/**
* Write the component descriptors to the file.
*
* @param components
* @param file
* @throws SCRDescriptorException
*/
public static void write(Components components, File file, boolean isScrPrivateFile)
throws SCRDescriptorException {
try {
generateXML(components, IOUtils.getSerializer(file), isScrPrivateFile);
} catch (TransformerException e) {
throw new SCRDescriptorException("Unable to write xml", file.toString(), 0, e);
} catch (SAXException e) {
throw new SCRDescriptorException("Unable to generate xml", file.toString(), 0, e);
} catch (IOException e) {
throw new SCRDescriptorException("Unable to write xml", file.toString(), 0, e);
}
}
/**
* EPML2PNML
*
* @param args String[]
*/
private static void EPML2PNML(String[] args) {
if (args.length != 2) {
System.out.println("���ṩEPML�ļ�·����PNML���Ŀ¼!");
System.exit(-1);
}
epmlImport epml = new epmlImport();
// load the single epml file
String filename = args[0];
try {
EPCResult epcRes = (EPCResult) epml.importFile(new FileInputStream(filename));
// convert all epc models to pnml files
ArrayList<ConfigurableEPC> alEPCs = epcRes.getAllEPCs();
PnmlExport export = new PnmlExport();
for (ConfigurableEPC epc : alEPCs) {
String id = epc.getIdentifier();
if (id.equals("1An_klol")
|| id.equals("1An_l1y8")
|| id.equals("1Ex_dzq9")
|| id.equals("1Ex_e6dx")
|| id.equals("1Ku_9soy")
|| id.equals("1Ku_a4cg")
|| id.equals("1Or_lojl")
|| id.equals("1Pr_d1ur")
|| id.equals("1Pr_djki")
|| id.equals("1Pr_dkfa")
|| id.equals("1Pr_dl73")
|| id.equals("1Ve_musj")
|| id.equals("1Ve_mvwz")) continue;
// save pnml files to the same folder
File outFile = new File(args[1] + "/" + id + ".pnml");
if (outFile.exists()) continue;
FileOutputStream fos = new FileOutputStream(outFile);
PetriNet petri = AMLtoPNML.convert(epc);
try {
export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
} catch (Exception ex1) {
ex1.printStackTrace(System.out);
}
}
} catch (IOException ex) {
ex.printStackTrace(System.out);
}
System.out.println("EPML Conversion Done");
}
private static InputSource getConfigSource(Class pAppClass) throws DataNotFoundException {
URL resource = pAppClass.getResource(CONFIG_FILE_NAME);
String resourceFileName = resource.toExternalForm();
File resourceFile = new File(resourceFileName);
InputStream configResourceStream = pAppClass.getResourceAsStream(CONFIG_FILE_NAME);
if (null == configResourceStream) {
throw new DataNotFoundException(
"unable to find XML configuration file resource: "
+ CONFIG_FILE_NAME
+ " for class: "
+ pAppClass.getName());
}
InputSource inputSource = new InputSource(configResourceStream);
if (!resourceFile.exists()) {
inputSource.setSystemId(resourceFileName);
}
return (inputSource);
}
public static AppConfig get(Class pAppClass, String pAppDir)
throws DataNotFoundException, InvalidInputException, FileNotFoundException {
AppConfig appConfig = null;
if (null == pAppDir) {
// we don't know where we are installed, so punt and look for
// the config file as a class resource:
appConfig = new AppConfig(pAppClass);
} else {
File appDirFile = new File(pAppDir);
if (!appDirFile.exists()) {
throw new DataNotFoundException("could not find application directory: " + pAppDir);
}
String configFileName =
appDirFile.getAbsolutePath() + "/config/" + AppConfig.CONFIG_FILE_NAME;
appConfig = new AppConfig(new File(configFileName));
}
return appConfig;
}
private void execExtractor() throws Exception {
ExecShell shell = new ExecShell();
File f = new File(Config.getProperty(Config.EXE_ILINK_SEARCH));
if (!f.exists())
throw new Exception(
"executable file does not exist! " + Config.getProperty(Config.EXE_ILINK_SEARCH));
shell.setExecutable(f.getAbsolutePath());
shell.setWorkingDirectory(f.getParent());
shell.addCommandLineArgument(criteria);
shell.addCommandLineArgument(String.valueOf(maxCount));
shell.addCommandLineArgument(releaseLevel);
shell.addCommandLineArgument(metadataSpec);
shell.addCommandLineArgument(username);
shell.addCommandLineArgument(password);
shell.addCommandLineArgument(outputFile);
shell.addCommandLineArgument(proiTkEnv);
shell.execute();
exitCode = shell.waitFor();
}
private File getWorkingDirectory(File f) {
try {
File workingDir =
new File(
Properties.get(Names.WORKING_DIR)
+ Names.PATH_SEPARATOR
+ getOpType()
+ Names.PATH_SEPARATOR
+ "work"
+ getNewCount());
if (!workingDir.exists()) workingDir.mkdirs();
FileUtil.deleteContents(workingDir);
return workingDir;
} catch (Exception ignore) {
// ++ notify of error - maybe out of disk space
ignore.printStackTrace();
return null;
}
}
private static void AML2PNML(String[] args) {
if (args.length != 3) {
System.out.println("���ṩAML����Ŀ¼��PNML���Ŀ¼�Լ��ֵ��ļ�!");
System.exit(-1);
}
System.out.println("����Ŀ¼��" + args[0]);
System.out.println("���Ŀ¼��" + args[1]);
System.out.println("�ֵ��ļ���" + args[2]);
// load the dict
AMLtoPNML.loadDict(args[2]);
File srcDir = new File(args[0]);
File[] lstAML = srcDir.listFiles();
PnmlExport export = new PnmlExport();
for (int i = 0; i < lstAML.length; i++) {
if (lstAML[i].isDirectory()) {
continue;
}
System.out.print(lstAML[i].getName() + "==>");
try {
FileInputStream fis = new FileInputStream(lstAML[i]);
int idx = lstAML[i].getName().indexOf(".xml");
File outFile = new File(args[1] + "/" + lstAML[i].getName().substring(0, idx) + ".pnml");
FileOutputStream fos = new FileOutputStream(outFile);
EPCResult epcRes = (EPCResult) AMLtoPNML.importFile(fis);
ConfigurableEPC epc = epcRes.getMainEPC();
PetriNet petri = AMLtoPNML.convert(epc);
export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
System.out.println(outFile.getName());
} catch (FileNotFoundException ex) {
ex.printStackTrace(System.out);
} catch (IOException ioe) {
ioe.printStackTrace(System.out);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
System.out.println("Conversion Done");
}
/**
* opens existing file
*
* @param a_file
*/
public GlyphFile(File a_file) {
super();
m_fileName = a_file;
URL url = null;
try {
url = a_file.toURI().toURL();
} catch (MalformedURLException e) {
e.printStackTrace();
}
init(url);
}
public String getShortFileName() {
return m_fileName.getName();
}
public void saveUnsaved() throws SaveAbortedException {
if (!saved) {
int option = 0;
if (loadedFile == null)
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to UNTITLED?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
else
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to " + loadedFile.getName() + "?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
if (option == JOptionPane.YES_OPTION) {
if (loadedFile == null) // SAVE NEW FILE
{
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
throw new SaveAbortedException();
}
fileChooser.setFileFilter(filter);
int option2 = fileChooser.showSaveDialog(this);
if (option2 == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this,
new JLabel("Error: " + ex.getMessage()),
"Error",
JOptionPane.ERROR_MESSAGE);
}
} else throw new SaveAbortedException();
;
} else // save LOADED FILE
{
try {
PrintStream stream = new PrintStream(new FileOutputStream(loadedFile), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (option == JOptionPane.CANCEL_OPTION) throw new SaveAbortedException();
;
}
}
protected String getInstructionFileName(File f) {
return f.getAbsolutePath() + Names.PATH_SEPARATOR + "instruction.xml";
}
protected String getOutputFileName(File f) {
return f.getAbsolutePath() + Names.PATH_SEPARATOR + "response.xml";
}
/**
* Initializes the <code>TextTransition</code> by the File <code>file</code>.
*
* @param file
* @exception IOException
* @exception SAXException
* @exception ParserConfigurationException
*/
public void setup(File file) throws IOException, SAXException, ParserConfigurationException {
setup(file.toURL());
}
public void actionPerformed(ActionEvent e) {
JButton b = (JButton) e.getSource();
if (b.getText() == "PLAY") {
if (scoreP != null) scoreP.playScale(sp.getScale(), tempoP.getValue());
} else if (b.getText() == "New") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
sp.notes.removeAllElements();
sp.repaint();
nameTF.setText("");
loadedFile = null;
} else if (b.getText() == "Save") {
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showSaveDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
if (target.getName().indexOf(".scl") == -1) target = new File(target.getPath() + ".scl");
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (b.getText() == "Load") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showOpenDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
loadedFile = fileChooser.getSelectedFile();
SAXParserFactory factory = SAXParserFactory.newInstance();
ScaleParser handler = new ScaleParser(false);
try {
SAXParser parser = factory.newSAXParser();
parser.parse(loadedFile, handler);
// System.out.println("success");
} catch (Exception ex) {
// System.out.println("no!!!!!! exception: "+e);
// System.out.println(ex.getMessage());
ex.printStackTrace();
}
// -----now :P:P---------------
System.out.println("name: " + handler.getName());
nameTF.setText(handler.getName());
sp.notes.removeAllElements();
int[] scale = handler.getScale();
for (int i = 0; i < scale.length; i++) {
sp.addNote(scale[i]);
}
sp.repaint();
} else loadedFile = null;
}
}
