/** {@inheritDoc} */
@Override
public void cancel() {
this.canceled = true;
if (parser != null) {
parser.cancel();
}
}
/** {@inheritDoc} */
@SuppressWarnings("null")
@Override
public RawDataFile execute() throws MSDKException {
String osName = System.getProperty("os.name").toUpperCase();
if (!osName.contains("WINDOWS")) {
throw new MSDKException("Native data format import only works on MS Windows");
}
logger.info("Started parsing file " + sourceFile);
try {
// Decompress the thermo raw dump executable to a temporary folder
File tempFolder = Files.createTempDirectory("msdk").toFile();
tempFolder.deleteOnExit();
InputStream dumpArchive =
this.getClass().getClassLoader().getResourceAsStream("thermorawdump.zip");
if (dumpArchive == null)
throw new MSDKException("Failed to load the thermorawdump.zip archive from the MSDK jar");
ZipUtils.extractStreamToFolder(dumpArchive, tempFolder);
// Path to the rawdump executable
File rawDumpPath = new File(tempFolder, "ThermoRawDump.exe");
if (!rawDumpPath.canExecute())
throw new MSDKException("Cannot execute program " + rawDumpPath);
// Create a separate process and execute RAWdump.exe
final String cmdLine[] = new String[] {rawDumpPath.getPath(), sourceFile.getPath()};
dumperProcess = Runtime.getRuntime().exec(cmdLine);
// Get the stdout of RAWdump process as InputStream
InputStream dumpStream = dumperProcess.getInputStream();
// Create the new RawDataFile
String fileName = sourceFile.getName();
newRawFile = MSDKObjectBuilder.getRawDataFile(fileName, sourceFile, fileType, dataStore);
// Read the dump data
parser = new RawDumpParser(newRawFile, dataStore);
parser.readRAWDump(dumpStream);
// Cleanup
dumpStream.close();
dumperProcess.destroy();
try {
FileUtils.deleteDirectory(tempFolder);
} catch (IOException e) {
// Ignore errors while deleting the tmp folder
}
if (canceled) return null;
} catch (Throwable e) {
if (dumperProcess != null) dumperProcess.destroy();
throw new MSDKException(e);
}
logger.info("Finished parsing " + sourceFile);
return newRawFile;
}
/** {@inheritDoc} */
@Override
public Float getFinishedPercentage() {
if (parser == null) return 0f;
else return parser.getFinishedPercentage();
}
