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();
}
/** 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();
}
}
/**
* 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;
}
}
