private void create_default_ini(string execPath, string ini_path)
{
var timer = Stopwatch.StartNew();
var ini_loc = String.Format("\"{0}\"", ini_path);
//SendAndLogMessage(execPath + NodeScratchDirectory + ini_loc);
var process = new Process
{
StartInfo =
{
FileName = execPath,
WorkingDirectory = NodeScratchDirectory,
Arguments = " -write_ini " + String.Format("\"{0}\"", ini_path),
UseShellExecute = false,
RedirectStandardOutput = false,
CreateNoWindow = false
}
};
try
{
var openMS_shared_dir = Path.Combine(ServerConfiguration.ToolsDirectory, "OpenMS-2.0/share/OpenMS");
process.StartInfo.EnvironmentVariables["OPENMS_DATA_PATH"] = openMS_shared_dir;
process.Start();
try
{
process.Refresh();
//process.PriorityClass = ProcessPriorityClass.BelowNormal;//Do not use, causes exception!
process.WaitForExit();
}
catch (InvalidOperationException ex)
{
NodeLogger.ErrorFormat(ex, "The following exception is raised during the execution of \"{0}\":", execPath);
throw;
}
if (process.ExitCode != 0)
{
throw new MagellanProcessingException(
String.Format(
"The exit code of {0} was {1}. (The expected exit code is 0)",
Path.GetFileName(process.StartInfo.FileName), process.ExitCode));
}
}
catch (System.Threading.ThreadAbortException)
{
throw;
}
catch (Exception ex)
{
NodeLogger.ErrorFormat(ex, "The following exception is raised during the execution of \"{0}\":", execPath);
throw;
}
finally
{
if (!process.HasExited)
{
NodeLogger.WarnFormat(
"The process [{0}] isn't finished correctly -> force the process to exit now", process.StartInfo.FileName);
process.Kill();
}
}
}
//execute specific OpenMS Tool (execPath) with specified Ini (ParamPath)
private void RunTool(string execPath, string ParamPath, bool mute = false)
{
var timer = Stopwatch.StartNew();
var process = new Process
{
StartInfo =
{
FileName = execPath,
WorkingDirectory = NodeScratchDirectory,
//WorkingDirectory = FileHelper.GetShortFileName(NodeScratchDirectory),
Arguments = " -ini " + String.Format("\"{0}\"", ParamPath),
UseShellExecute = false,
RedirectStandardOutput = true,
CreateNoWindow = false,
//WindowStyle = ProcessWindowStyle.Hidden
}
};
var openMS_shared_dir = Path.Combine(ServerConfiguration.ToolsDirectory, "OpenMS-2.0/share/OpenMS");
process.StartInfo.EnvironmentVariables["OPENMS_DATA_PATH"] = openMS_shared_dir;
SendAndLogTemporaryMessage("Starting process [{0}] in working directory [{1}] with arguments [{2}]",
process.StartInfo.FileName, process.StartInfo.WorkingDirectory, process.StartInfo.Arguments);
WriteLogMessage(MessageLevel.Debug,
"Starting process [{0}] in working directory [{1}] with arguments [{2}]",
process.StartInfo.FileName, process.StartInfo.WorkingDirectory, process.StartInfo.Arguments);
try
{
process.Start();
try
{
//process.PriorityClass = ProcessPriorityClass.BelowNormal;
string current_work = "";
while (process.HasExited == false)
{
var output = process.StandardOutput.ReadLine();
if (mute)
{
continue;
}
// move on if no new announcement.
if (String.IsNullOrEmpty(output))
{
continue;
}
//store all results (for now?) of OpenMS Tool output
WriteLogMessage(MessageLevel.Debug, output);
// Parse the output and report progress using the method SendAndLogTemporaryMessage
if (output.Contains(@"Progress of 'loading mzML file':"))
{
current_work = "Progress of 'loading mzML file':";
}
else if (output.Contains("Progress of 'loading chromatograms':"))
{
current_work = "Progress of 'loading chromatograms':";
}
else if (output.Contains("Progress of 'mass trace detection':"))
{
current_work = "Progress of 'mass trace detection':";
}
else if (output.Contains("Progress of 'elution peak detection':"))
{
current_work = "Progress of 'elution peak detection':";
}
else if (output.Contains("Progress of 'assembling mass traces to features':"))
{
current_work = "Progress of 'assembling mass traces to features':";
}
else if (output.Contains("Progress of 'Aligning input maps':"))
{
current_work = "Progress of 'Aligning input maps':";
}
else if (output.Contains("Progress of 'linking features':"))
{
current_work = "Progress of 'linking features':";
}
else if (output.Contains("%"))
{
SendAndLogTemporaryMessage("{0} {1}", current_work, output);
}
}
// Note: The child process waits until everything is read from the standard output -> A Deadlock could arise here
using (var reader = new StringReader(process.StandardOutput.ReadToEnd()))
{
string output;
if (!mute)
{
while ((output = reader.ReadLine()) != null)
{
WriteLogMessage(MessageLevel.Debug, output);
if (String.IsNullOrEmpty(output) == false)
{
SendAndLogMessage(output, false);
}
}
}
}
process.WaitForExit();
}
catch (InvalidOperationException ex)
{
NodeLogger.ErrorFormat(ex, "The following exception is raised during the execution of \"{0}\":", execPath);
throw;
}
if (process.ExitCode != 0)
{
throw new MagellanProcessingException(
String.Format(
"The exit code of {0} was {1}. (The expected exit code is 0)",
Path.GetFileName(process.StartInfo.FileName), process.ExitCode));
}
}
catch (System.Threading.ThreadAbortException)
{
throw;
}
catch (Exception ex)
{
NodeLogger.ErrorFormat(ex, "The following exception is raised during the execution of \"{0}\":", execPath);
throw;
}
finally
{
if (!process.HasExited)
{
NodeLogger.WarnFormat(
"The process [{0}] isn't finished correctly -> force the process to exit now", process.StartInfo.FileName);
process.Kill();
}
}
SendAndLogMessage("{0} tool processing took {1}.", execPath, StringHelper.GetDisplayString(timer.Elapsed));
}
