public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref IProgressStatus status, TextWriter writer)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
_messageLog.Clear();
var proc = Process.Start(psi);
if (proc == null)
{
throw new IOException(string.Format(@"Failure starting {0} command.", psi.FileName));
}
if (stdin != null)
{
try
{
proc.StandardInput.Write(stdin);
}
finally
{
proc.StandardInput.Close();
}
}
var reader = new ProcessStreamReader(proc);
StringBuilder sbError = new StringBuilder();
int percentLast = 0;
string line;
while ((line = reader.ReadLine(progress)) != null)
{
if (writer != null && !line.StartsWith(HideLinePrefix))
{
writer.WriteLine(line);
}
if (progress == null || line.ToLowerInvariant().StartsWith(@"error"))
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(MessagePrefix) && line.StartsWith(MessagePrefix))
{
_messageLog.Add(line.Substring(MessagePrefix.Length));
}
else if (line.EndsWith(@"%"))
{
double percent;
string[] parts = line.Split(' ');
string percentPart = parts[parts.Length - 1];
if (double.TryParse(percentPart.Substring(0, percentPart.Length - 1), out percent))
{
percentLast = (int)percent;
status = status.ChangePercentComplete(percentLast);
if (percent >= 100 && status.SegmentCount > 0)
{
status = status.NextSegment();
}
progress.UpdateProgress(status);
}
}
else if (StatusPrefix == null || line.StartsWith(StatusPrefix))
{
// Remove prefix, if there is one.
if (StatusPrefix != null)
{
line = line.Substring(StatusPrefix.Length);
}
status = status.ChangeMessage(line);
progress.UpdateProgress(status);
}
}
}
proc.WaitForExit();
int exit = proc.ExitCode;
if (exit != 0)
{
line = proc.StandardError.ReadLine();
if (line != null)
{
sbError.AppendLine(line);
}
if (sbError.Length == 0)
{
sbError.AppendLine(@"Error occurred running process.");
}
string processPath = Path.GetDirectoryName(psi.FileName)?.Length == 0
? Path.Combine(Environment.CurrentDirectory, psi.FileName)
: psi.FileName;
// ReSharper disable LocalizableElement
sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath,
// ReSharper restore LocalizableElement
string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory,
stdin != null ? "\r\nStandard input:\r\n" + stdin : "");
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
{
status = status.NextSegment();
}
if (progress != null)
{
progress.UpdateProgress(status);
}
}
}
private bool BuildLibraryOrThrow(IProgressMonitor progress, ref IProgressStatus progressStatus)
{
progressStatus = progressStatus.ChangeSegments(0, 5);
var standardSpectra = new List <SpectrumMzInfo>();
// First get predictions for iRT standards specified by the user which may or may not be in the document
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY) && !ReferenceEquals(IrtStandard, IrtStandard.AUTO))
{
var standardPeptidesToAdd = ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
progressStatus = progressStatus.NextSegment();
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, IsotopeLabelType.light, _nce)).ToArray(),
CancellationToken.None);
progressStatus = progressStatus.NextSegment();
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctModifiedSequences = new HashSet <string>();
var distinctPeps = new List <PrositRetentionTimeModel.PeptideDocNodeWrapper>();
foreach (var p in _peptides)
{
if (distinctModifiedSequences.Add(p.ModifiedSequence))
{
distinctPeps.Add(new PrositRetentionTimeModel.PeptideDocNodeWrapper(p));
}
}
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
distinctPeps, CancellationToken.None);
progressStatus = progressStatus.NextSegment();
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
progressStatus = progressStatus.NextSegment().ChangeMessage(Resources.SkylineWindow_SaveDocument_Saving___);
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress, ref progressStatus);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
