public void ExecuteArbitraryPythonDirect()
{
PythonProcessManager.Verbose = true;
PythonProcessManager proc = new PythonProcessManager("python", " -c print('Hello')");
Console.WriteLine("PYTHONPATH = {0}", proc.PythonPath);
proc.Start();
Console.WriteLine("Running");
proc.WaitForExit();
}
public String RunReclassifyWithModelTask(String targetFilePath, String modelFilePath, String method)
{
String argumentStringTemplate = " reclassify-with-model --target-file {0} --model-file {1} --method {2}";
String arguments = String.Format(argumentStringTemplate, targetFilePath.QuoteWrap(), modelFilePath.QuoteWrap(), method.QuoteWrap());
PythonProcessManager proc = new PythonProcessManager(PythonEntryPoint, arguments);
proc.Start();
proc.WaitForExit();
if (!proc.CheckExitSuccessfully())
{
throw new PythonScriptErrorException(
proc.GenerateDumpMessage()
);
}
//Sniff the StdOut stream of the pipeline ProcessManager to pull out
//the output file path. It should be the last line emitted.
String outputFile = null;
try
{
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException)
{
try
{
Thread.Sleep(100);
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException ex)
{
throw new PythonScriptErrorException("Could not find output file in " + proc.Out);
}
}
//Store this ProcessManager instance for inspection later
this.LastCall = proc;
return outputFile;
}
public String RunModelBuildingPythonPipeline(String ms1MatchFilePath,
String glycosylationSitesFilePath, String ms2DeconvolutionFilePath,
double ms1MatchingTolerance, double ms2MatchingTolerance,
String proteinProspectorXMLFilePath, String method, int numProcesses=2)
{
String argumentStringTemplate = " --n {7} build-model --ms1-results-file {0} --glycosylation-sites-file {1} --deconvoluted-spectra-file {2} --ms1-match-tolerance {3} --ms2-match-tolerance {4}" +
" --protein_prospector_xml {5} --method {6}";
String arguments = String.Format(argumentStringTemplate, new object[]{
ms1MatchFilePath.QuoteWrap(),
glycosylationSitesFilePath.QuoteWrap(),
ms2DeconvolutionFilePath.QuoteWrap(), ms1MatchingTolerance,
ms2MatchingTolerance, proteinProspectorXMLFilePath.QuoteWrap(),
method.QuoteWrap(), numProcesses
});
Console.WriteLine(arguments);
PythonProcessManager proc = new PythonProcessManager(PythonEntryPoint, arguments);
proc.Start();
proc.WaitForExit();
if (!proc.CheckExitSuccessfully())
{
throw new PythonScriptErrorException(
proc.GenerateDumpMessage()
);
}
//Sniff the StdOut stream of the pipeline ProcessManager to pull out
//the output file path. It should be the last line emitted.
String outputFile = null;
try
{
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException)
{
try
{
Thread.Sleep(100);
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException ex)
{
throw new PythonScriptErrorException("Could not find output file in " + proc.Out, new PythonScriptErrorException(
proc.GenerateDumpMessage()));
}
}
//Store this ProcessManager instance for inspection later
this.LastCall = proc;
return outputFile;
}
//public void CheckPythonDependencies()
//{
//}
/// <summary>
/// Executes the Python script pipeline stored at @ScriptRoot, with the
/// entry_point.py entry-point. The pipeline emits intermediary file names,
/// and the last line printed on a successful run is the final output
/// file name.
///
/// Will check the exit code of the pipeline, and throw a PythonScriptErrorException
/// if it is not 0.
/// </summary>
/// <returns>String path to the output file generated by the pipeline</returns>
public String RunClassificationPythonPipeline(String ms1MatchFilePath,
String glycosylationSitesFilePath, String ms2DeconvolutionFilePath,
String modelDataFilePath,
double ms1MatchingTolerance, double ms2MatchingTolerance,
String proteinProspectorXMLFilePath,
String method, String outputFilePath = null,
int numProcesses = 2,
int decoyToRealRatio = 20,
bool randomOnly = false
)
{
String argumentStringTemplate = " --n {9} classify-with-model --ms1-results-file {0} --glycosylation-sites-file {1} --deconvoluted-spectra-file {2} --model-file {3} --ms1-match-tolerance {4} --ms2-match-tolerance {5} --method {6} --protein_prospector_xml {7} {8} --decoy-to-real-ratio {10} {11}";
String arguments = String.Format(argumentStringTemplate, new object[]{
ms1MatchFilePath.QuoteWrap(),
glycosylationSitesFilePath.QuoteWrap(),
ms2DeconvolutionFilePath.QuoteWrap(),
modelDataFilePath.QuoteWrap(),
ms1MatchingTolerance,
ms2MatchingTolerance,
method.QuoteWrap(),
proteinProspectorXMLFilePath.QuoteWrap(),
outputFilePath == null ? "" : "--out " + outputFilePath.QuoteWrap(),
numProcesses,
decoyToRealRatio,
randomOnly ? " --random-only " : ""
});
PythonProcessManager proc = new PythonProcessManager(PythonEntryPoint, arguments);
proc.Start();
proc.WaitForExit();
if (!proc.CheckExitSuccessfully())
{
throw new PythonScriptErrorException(
proc.GenerateDumpMessage()
);
}
//Sniff the StdOut stream of the pipeline ProcessManager to pull out
//the output file path. It should be the last line emitted.
String outputFile = null;
try
{
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException)
{
try
{
Thread.Sleep(100);
outputFile = proc.Out.Split(new String[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries).Last();
}
catch (InvalidOperationException ex)
{
throw new PythonScriptErrorException("Could not find output file in " + proc.Out);
}
}
this.PythonPipelineOutFile = outputFile;
//Store this ProcessManager instance for inspection later
this.LastCall = proc;
return outputFile;
}
public void InstallPythonDependencies()
{
PythonProcessManager proc = new PythonProcessManager(this.PythonExecutablePath, "-m pip -h");
proc.Start();
proc.WaitForExit();
if (!proc.CheckExitSuccessfully())
{
throw new PythonDependencyInstallerException("The Python Package Manager pip wasn't found. Is it installed? If not, go to https://pip.readthedocs.org/en/latest/installing.html for more information on how to get it. " + proc.GenerateDumpMessage());
}
proc = new PythonProcessManager(PythonEntryPoint, " -h");
proc.Start();
proc.WaitForExit();
Console.WriteLine(proc.ExitCode);
if (!proc.CheckExitSuccessfully())
{
throw new PythonScriptErrorException(proc.GenerateDumpMessage());
}
}
public String ConvertToCSV(String targetFilePath, String resultFile=null)
{
resultFile = resultFile == null ?
Path.Combine(Path.GetDirectoryName(targetFilePath), Path.GetFileNameWithoutExtension(targetFilePath) + ".csv") : resultFile;
String arguments = String.Format(
" -c \"from glycresoft_ms2_classification import prediction_tools;data=prediction_tools.prepare_model_file(r'{0}');data.to_csv(r'{1}')\"",
targetFilePath, resultFile);
Console.WriteLine(arguments);
PythonProcessManager proc = new PythonProcessManager(PythonExecutablePath, arguments);
proc.Start();
proc.WaitForExit();
if (!proc.CheckExitSuccessfully())
{
throw new PythonScriptErrorException(
proc.GenerateDumpMessage()
);
}
return resultFile;
}
