private static String getAbsoluteExecutablePath(final Config config) {
if (Strings.isNullOrEmpty(config.getWrapperScript())) {
return "";
}
return FileUtilities.getAbsoluteFileForExecutables(new File(config.getWrapperScript()))
.getPath();
}
@Override
public Worker create(final Config config, final DependencyResolver dependencies) {
final MSMSEvalWorker worker = new MSMSEvalWorker();
worker.setMsmsEvalExecutable(
FileUtilities.getAbsoluteFileForExecutables(new File(config.get(MSMS_EVAL_EXECUTABLE))));
worker.setConverter(getConverter());
return worker;
}
@Override
public ExitCode run(final SwiftEnvironment environment) {
if (environment.getParameters().size() < 1) {
throw new MprcException(
"Missing path to configuration file.\nUsage: reformat-config <config> [<result>]");
}
final File file = new File(environment.getParameters().get(0));
final PrintWriter printWriter;
if (environment.getParameters().size() >= 2) {
String pathname = environment.getParameters().get(1);
try {
printWriter = new PrintWriter(new File(pathname));
} catch (FileNotFoundException e) {
environment.logCommandError(
"Could not open file for writing: "
+ pathname
+ "\n"
+ MprcException.getDetailedMessage(e));
return ExitCode.Error;
}
} else {
printWriter = new PrintWriter(System.out);
}
final AppConfigReader reader = new AppConfigReader(file, getFactory());
try {
reader.load(environment.getApplicationConfig());
} finally {
FileUtilities.closeQuietly(reader);
}
AppConfigWriter writer = null;
try {
writer = new AppConfigWriter(printWriter, getFactory());
writer.save(environment.getApplicationConfig());
} finally {
FileUtilities.closeQuietly(writer);
FileUtilities.closeQuietly(printWriter);
}
return ExitCode.Ok;
}
/**
* goes to the first sequence in the sequence database file so that the next call to getHeader()
* will return the first header in the file.
*/
public void beforeFirst() {
try {
FileUtilities.closeQuietly(this.reader);
reopenReader();
this.nextHeader = this.reader.readLine();
} catch (Exception e) {
throw new MprcException(
"Cannot open FASTA file [" + this.fastaFile.getAbsolutePath() + "]", e);
}
}
private static void writeWorkerAllocatorInputObject(final File file, final SgePacket object)
throws IOException {
BufferedWriter bufferedWriter = null;
try {
final XStream xStream = new XStream(new DomDriver());
bufferedWriter = new BufferedWriter(new FileWriter(file));
bufferedWriter.write(xStream.toXML(object));
} finally {
FileUtilities.closeQuietly(bufferedWriter);
}
}
/** Start reading from the beginning */
public void resetCurrentRowPointer() throws IOException {
currentRowValue = null;
FileUtilities.closeQuietly(reader);
reader = new BufferedReader(new FileReader(file), BUFFER_SIZE);
// Initialize by reading the first row
nextRow();
// Next call to nextRow will return the line we just read
previousRow();
}
/**
* @param mgf .mgf file
* @return List of all spectra titles.
*/
public static List<String> getTitles(final File mgf) {
PeakListReader sourceMgfReader = new MgfPeakListReader(mgf, false);
List<String> titles = new ArrayList<String>(1000);
try {
MascotGenericFormatPeakList peakList;
while ((peakList = sourceMgfReader.nextPeakList()) != null) {
titles.add(peakList.getTitle());
}
} finally {
FileUtilities.closeQuietly(sourceMgfReader);
}
return titles;
}
private GridWorkPacket getBaseGridWorkPacket(final String command) {
final GridWorkPacket gridWorkPacket = new GridWorkPacket(command, null);
gridWorkPacket.setNativeSpecification(nativeSpecification);
gridWorkPacket.setQueueName(queueName);
gridWorkPacket.setMemoryRequirement(memoryRequirement);
gridWorkPacket.setWorkingFolder(new File(".").getAbsolutePath());
gridWorkPacket.setLogFolder(
FileUtilities.getDateBasedDirectory(getDaemonLoggerFactory().getLogFolder(), new Date())
.getAbsolutePath());
return gridWorkPacket;
}
/**
* Process message from the grid engine itself. In case the process failed, we keep the work
* packet around so the developer can reproduce the error.
*
* @param w Work packet whose state changed
*/
@Override
public void stateChanged(final GridWorkPacket w) {
if (w == null) {
return;
}
// We report state change just once.
if (!reported) {
try {
if (w.getPassed()) {
// This is the last response we will send - request is completed.
// There might have been an error from RMI, check that
if (allocatorListener.getLastThrowable() == null) {
sendResponse(
request, new DaemonProgressMessage(DaemonProgress.RequestCompleted), true);
} else {
sendResponse(
request, new DaemonException(allocatorListener.getLastThrowable()), true);
}
} else if (w.getFailed()) {
// This is the last response we will send - request failed
if (allocatorListener.getLastThrowable() == null) {
sendResponse(request, new DaemonException(w.getErrorMessage()), true);
} else {
sendResponse(
request,
new DaemonException(w.getErrorMessage(), allocatorListener.getLastThrowable()),
true);
}
}
reported = true;
} finally {
if (!w.getFailed()) {
// Delete workPacket file
LOGGER.debug("Deleting sge packet file: " + sgePacketFile.getAbsolutePath());
FileUtilities.quietDelete(sgePacketFile);
} else {
LOGGER.warn("Retaining sge packet file: " + sgePacketFile.getAbsolutePath());
}
}
}
}
/** Process failure, return more descriptive exception */
private DaemonException processFailedJob(
final GridWorkPacket gridWorkPacket, final File packageFile, final Exception exception) {
final DaemonException daemonException;
final File storedFile = failedJobManager.storeFile(packageFile);
if (storedFile != null) {
daemonException =
new DaemonException(
MessageFormat.format(
"Failed passing work packet to grid engine:\n{0}\nUse {1} for the --sge parameter",
gridWorkPacket.toString(), storedFile.getAbsolutePath()),
exception);
} else {
daemonException =
new DaemonException(
"Failed passing work packet to grid engine:\n" + gridWorkPacket.toString(),
exception);
}
FileUtilities.quietDelete(packageFile);
LOGGER.error(MprcException.getDetailedMessage(daemonException), daemonException);
return daemonException;
}
@Override
protected void doGet(final HttpServletRequest req, final HttpServletResponse resp)
throws ServletException {
PrintWriter out = null;
try {
swiftDao.begin(); // Transaction-per-request
final SearchRunFilter searchRunFilter = new SearchRunFilter();
searchRunFilter.setStart("0");
searchRunFilter.setCount("50");
out = resp.getWriter();
final StringBuilder response = new StringBuilder(TYPICAL_RESPONSE_SIZE);
response.append("[");
final List<SearchRun> searchRuns = swiftDao.getSearchRunList(searchRunFilter);
for (int i = 0; i < searchRuns.size(); i++) {
final SearchRun searchRun = searchRuns.get(i);
final int runningTasks = swiftDao.getNumberRunningTasksForSearchRun(searchRun);
JsonWriter.appendSearchRunJson(response, i, searchRun, runningTasks, null, false);
if (i + 1 < searchRuns.size()) {
response.append(",\n");
}
}
response.append("]");
out.print(response.toString());
swiftDao.commit();
} catch (Exception e) {
swiftDao.rollback();
throw new MprcException("Could not obtain list of search runs", e);
} finally {
FileUtilities.closeQuietly(out);
}
}
/**
* goes through each header in a fasta file and checks to make sure it is a valid fasta header. If
* any problems are encountered or a header does not check out then false is returned
*
* @param toCheck the file you want to see is a valid FASTA file
* @return true if the file is a valid fasta file else false
*/
public static boolean isFASTAFileValid(final File toCheck) {
DBInputStream in = null;
try {
in = new FASTAInputStream(toCheck);
int sequenceCount = 0;
in.beforeFirst();
while (in.gotoNextSequence()) {
if (isHeader(in.getHeader())) {
sequenceCount++;
} else {
return false;
}
}
return (sequenceCount != 0);
} catch (Exception e) {
// SWALLOWED: We just return false as in "not valid"
LOGGER.warn(e);
return false;
} finally {
FileUtilities.closeQuietly(in);
}
}
/** performs any cleaning up that may be necessary. Always call when you are done. */
public void close() {
FileUtilities.closeQuietly(this.reader);
}
@Override
public void close() throws IOException {
FileUtilities.closeQuietly(reader);
}
@Override
public void process(
final WorkPacket workPacket, final File tempWorkFolder, final UserProgressReporter reporter) {
if (!MSMSEvalWorkPacket.class.isInstance(workPacket)) {
throw new DaemonException(
"Unknown request type ["
+ workPacket.getClass().getName()
+ "] expecting ["
+ MSMSEvalWorkPacket.class.getName()
+ "]");
}
final MSMSEvalWorkPacket msmsEvalWorkPacket = (MSMSEvalWorkPacket) workPacket;
/** MGF source file. */
final File sourceFile = msmsEvalWorkPacket.getSourceFile();
checkFile(sourceFile, false, "The source file");
/** MsmsEval parameter file. */
final File msmsEvalParamFile = msmsEvalWorkPacket.getMsmsEvalParamFile();
checkFile(msmsEvalParamFile, false, "The msmsEval parameter file");
/** Output directory. */
final File outputDirectory = msmsEvalWorkPacket.getOutputFile().getParentFile();
FileUtilities.ensureFolderExists(outputDirectory);
checkFile(outputDirectory, true, "The msmsEval output directory");
/** Temporary files. */
final File outputMzXMLFile =
MSMSEvalWorkPacket.getExpectedMzXMLOutputFileName(sourceFile, tempWorkFolder);
final File msmsEvalOutputFile =
MSMSEvalWorkPacket.getExpectedMsmsEvalOutputFileName(sourceFile, tempWorkFolder);
/** Files to be published. */
final File finalOutputFile = msmsEvalWorkPacket.getOutputFile();
final File outputFile = getTempOutputFile(tempWorkFolder, finalOutputFile);
final File finalEmFile = msmsEvalWorkPacket.getOutputEmFile();
final File emFile = getTempOutputFile(tempWorkFolder, finalEmFile);
// If msmsEval has been executed, skip operation.
if (!msmsEvalWorkPacket.isFromScratch() && hasMSMSEvalFilterWorkerRun(finalOutputFile)) {
skippedExecution = true;
return;
}
MSMSEval msmsEval = null;
try {
LOGGER.info("Converting mgf to mzxml.");
final Map<Integer, String> mzXMLScanToMGFTitle =
getConverter().convert(sourceFile, outputMzXMLFile, true);
LOGGER.info("Convertion mgf to mzxml completed.");
LOGGER.info("Created mzxml file: " + outputMzXMLFile.getAbsolutePath());
LOGGER.info("Running msmsEval on the mzxml file.");
msmsEval = new MSMSEval(outputMzXMLFile, msmsEvalParamFile, msmsEvalExecutable);
msmsEval.execute(reporter);
LOGGER.info("Command msmsEval execution completed.");
LOGGER.info("Formatting msmsEval output file with mgf scan numbers.");
MSMSEvalOutputFileFormatter.replaceMzXMLScanIdsWithMgfNumbers(
msmsEvalOutputFile, outputFile, mzXMLScanToMGFTitle);
LOGGER.info("Formatted msmsEval output file " + outputFile.getAbsolutePath() + " created.");
publish(outputFile, finalOutputFile);
publish(emFile, finalEmFile);
} catch (Exception e) {
throw new DaemonException(e);
} finally {
// Clean up.
LOGGER.info(
"Deleting files: ["
+ msmsEvalOutputFile.getAbsolutePath()
+ ", "
+ outputMzXMLFile.getAbsolutePath()
+ "]");
FileUtilities.deleteNow(msmsEvalOutputFile);
FileUtilities.deleteNow(outputMzXMLFile);
}
}
/** performs any cleaning up that may be necessary. */
public void close() {
FileUtilities.closeQuietly(this.out);
}
@AfterTest
public void teardown() throws IOException {
FileUtilities.cleanupTempFile(logFile);
}