/** monitors the run. */
public boolean monitorAndCleanUpShell() {
lastModified = null;
boolean stillGoing = true;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
if (!StringUtil.blank(
runningFilePath)) // is file at runningFilePath; watch for its disappearance
while (MesquiteFile.fileExists(runningFilePath) && stillGoing) {
processOutputFiles();
try {
Thread.sleep(sleepTime);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer(
"InterruptedException in shell script executed by " + name);
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(proc);
}
if (outputFileProcessor != null)
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
return true;
}
/*.................................................................................................................*/
boolean checkUsernamePassword(boolean tellUserAboutCipres) {
if (StringUtil.blank(username) || StringUtil.blank(password)) {
MesquiteBoolean answer = new MesquiteBoolean(false);
MesquiteString usernameString = new MesquiteString();
if (username != null) usernameString.setValue(username);
MesquiteString passwordString = new MesquiteString();
if (password != null) passwordString.setValue(password);
String help =
"You will need an account on the CIPRes REST system to use this service. To register, go to https://www.phylo.org/restusers/register.action";
new UserNamePasswordDialog(
ownerModule.containerOfModule(),
"Sign in to CIPRes",
help,
"",
"Username",
"Password",
answer,
usernameString,
passwordString);
if (answer.getValue()) {
username = usernameString.getValue();
password = passwordString.getValue();
}
ownerModule.storePreferences();
}
boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
if (!success && tellUserAboutCipres) {
MesquiteMessage.discreetNotifyUser(
"Use of the CIPRes service requires an account with CIPRes's REST service. Go to https://www.phylo.org/restusers/register.action to register for an account");
}
return success;
}
/*.................................................................................................................*/
public boolean monitorAndCleanUpShell(String jobURL) {
boolean stillGoing = true;
if (!checkUsernamePassword(true)) {
return false;
}
lastModified = null;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
String status = "";
while (!jobCompleted(jobURL) && stillGoing) {
if (StringUtil.blank(status))
ownerModule.logln(
"CIPRes Job Status: " + getJobStatus(jobURL) + " (" + StringUtil.getDateTime() + ")");
// if (jobSubmitted(jobURL))
// processOutputFiles();
try {
Thread.sleep(minPollIntervalSeconds * 1000);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(null);
String newStatus = getJobStatus(jobURL);
if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
ownerModule.logln(
"CIPRes Job Status: " + newStatus + " (" + StringUtil.getDateTime() + ")");
status = newStatus;
} else ownerModule.log(".");
if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
processOutputFiles(jobURL);
}
}
ownerModule.logln("CIPRes job completed.");
if (outputFileProcessor != null) {
if (rootDir != null) {
ownerModule.logln("About to download results from CIPRes.");
if (downloadResults(jobURL, rootDir, false))
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
else return false;
}
}
return true;
}
/**
* executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then
* Mesquite will create a file there that will serve as a flag to Mesquite that the script is
* running.
*/
public boolean executeInShell() {
proc = null;
try {
ShellScriptUtil.setScriptFileToBeExecutable(scriptPath);
if (!StringUtil.blank(runningFilePath)) {
if (StringUtil.blank(runningFileMessage))
MesquiteFile.putFileContents(runningFilePath, "Script running...", true);
else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true);
if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath))
MesquiteFile.appendFileContents(
scriptPath,
StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath),
true); // append remove command to guarantee that the runningFile is deleted
// +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand()
}
proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal);
} catch (IOException e) {
MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name);
return false;
}
return true;
}