/**
* This constructor is used when running this for QC. Analysis_level, annotation_level, and
* normalize_method are all hard-coded for this call.
*/
public AsyncAffyPowerTools(Dataset selectedDataset, HttpSession session) {
log = Logger.getRootLogger();
this.selectedDataset = selectedDataset;
this.newDatasetVersion = selectedDataset.new DatasetVersion();
this.newDatasetVersion.setVersion_path(selectedDataset.getPath());
this.session = session;
this.analysis_level = "transcript";
this.annotation_level = "core";
this.normalize_method = "rma-sketch";
this.userLoggedIn = (User) session.getAttribute("userLoggedIn");
}
public void run() throws RuntimeException {
Thread thisThread = Thread.currentThread();
log.debug("Starting run method of AsyncAffyPowerTools. thisThread = " + thisThread.getName());
String fileName = "";
try {
//
// If this thread is interrupted, throw an Exception
//
ThreadReturn.ifInterruptedStop();
fileName = newDatasetVersion.getVersion_path() + "AffyPowerTools";
String aptDir = (String) session.getAttribute("aptDir");
log.debug("aptDir = " + aptDir + ", fileName = " + fileName);
boolean mouse = (selectedDataset.getOrganism().equals("Mm") ? true : false);
String mousePrefix = "Mo";
String ratPrefix = "Ra";
String filePrefix = (mouse ? mousePrefix : ratPrefix) + "Ex-1_0-st-v1.r2.";
String version = (mouse ? "mm8." : "rn5.");
String masked = (probeMask.equals("T") ? "MASKED." : "");
String probeSetFile = aptDir + filePrefix + masked + "pgf";
String clfFile = aptDir + filePrefix + "clf";
String gcBackgroundFile = aptDir + filePrefix + "antigenomic.bgp";
String transcriptsFile =
aptDir + filePrefix + "dt1." + version + annotation_level + "." + masked + "mps";
String probesetsFile =
aptDir + filePrefix + "dt1." + version + annotation_level + "." + masked + "ps";
String qcProbesetsFile = aptDir + filePrefix + "qcc";
String analysisPathway = "dabg";
String outputDir = newDatasetVersion.getVersion_path();
String celFileListing = selectedDataset.getPath() + selectedDataset.getFileListingName();
log.debug("outputDir = " + outputDir + ", celFileListing = " + celFileListing);
// Create parameter value records?
String function = aptDir + "apt-probeset-summarize";
List<String> functionArgsList =
new ArrayList<String>(
Arrays.asList(
function,
"-p",
probeSetFile,
"-c",
clfFile,
"-a",
normalize_method,
"-b",
gcBackgroundFile,
"--qc-probesets",
qcProbesetsFile,
"-a",
analysisPathway,
"-o",
outputDir,
"--cel-files",
celFileListing));
if (analysis_level.equals("probeset")) {
functionArgsList.add("-s");
functionArgsList.add(probesetsFile);
} else {
functionArgsList.add("-m");
functionArgsList.add(transcriptsFile);
}
String[] functionArgs =
(String[]) functionArgsList.toArray(new String[functionArgsList.size()]);
log.debug("functionArgs = ");
myDebugger.print(functionArgs);
String[] envVariables = new String[] {"PATH=$PATH:" + aptDir};
log.debug("envVariables = ");
new Debugger().print(envVariables);
ExecHandler myExecHandler = new ExecHandler(aptDir, functionArgs, envVariables, fileName);
log.debug("starting APT exec process");
myExecHandler.runExec();
log.debug("just finished APT exec process");
//
// If this thread is interrupted, throw an Exception
//
ThreadReturn.ifInterruptedStop();
} catch (Throwable t) {
log.error("in exception of AsyncAffyPowerTools", t);
if (t instanceof ThreadException) {
log.error("throwable exception is a ThreadException. cause = " + t.getCause().getMessage());
//
// This saves the Throwable object so an Exception can be detected
// by the calling program
//
ThreadReturn.save(t);
} else if (t instanceof ThreadInterruptedException) {
log.error("throwable exception is a ThreadInterruptedException");
ThreadReturn.save(new Throwable("ThreadInterruptedException in AsyncAffyPowerTools", t));
} else if (t instanceof RException) {
log.error("throwable exception is an RException");
ThreadReturn.save(
new Throwable("RException in AsyncAffyPowerTools is " + t.getMessage(), t));
} else {
log.error("exception caused AsyncAffyPowerTools");
ThreadReturn.save(t);
}
Email myEmail = new Email();
myEmail.setTo(userLoggedIn.getEmail());
myEmail.setSubject("Affymetrix Power Tools process had errors");
String mainContent =
userLoggedIn.getFormal_name()
+ ",\n\n"
+ "Thank you for using the PhenoGen Informatics website. "
+ "The Affymetrix Power Tools process that you initiated ";
String errorContent =
mainContent
+ "was not completed successfully. "
+ "The system administrator has been notified of the error. "
+ "\n"
+ "You will be contacted via email once the problem is resolved.";
String adminErrorContent =
"The following email was sent to "
+ userLoggedIn.getEmail()
+ ":\n"
+ errorContent
+ "\n"
+ "The file is "
+ fileName
+ "\n"
+ "The error cause was "
+ t.getCause()
+ (t.getCause() != null ? t.getCause().getMessage() : t.getMessage())
+ "\n and the Message = "
+ t.getMessage();
try {
myEmail.setContent(errorContent);
myEmail.sendEmail();
myEmail.setContent(adminErrorContent);
myEmail.sendEmailToAdministrator("");
log.debug("just sent email to administrator notifying of Affymetrix Power Tools errors");
} catch (MessagingException e2) {
log.error("in exception of AsyncAffyPowerTools while sending email", e2);
throw new RuntimeException();
}
// throw new RuntimeException(e.getMessage());
} finally {
log.debug("executing finally clause in AsyncAffyPowerTools");
}
log.debug("done with AsyncAffyPowerTools run method");
}