public static List <SearchResult> ReadSearchResultsViaBiblioSpec(String filename, Func <int, bool> progressMonitor)
{
string tempFile = null;
try
{
tempFile = Path.GetTempFileName();
var blibBuild = new BlibBuild(tempFile, new[] { filename })
{
CompressLevel = 0,
};
var status = new ProgressStatus("");
var progressMonitorImpl = ProgressMonitorImpl.NewProgressMonitorImpl(status, progressMonitor);
string[] ambiguousPeptides;
blibBuild.BuildLibrary(LibraryBuildAction.Create, progressMonitorImpl, ref status, out ambiguousPeptides);
return(ReadBiblioSpecDatabase(tempFile, progressMonitor));
}
finally
{
try
{
if (tempFile != null)
{
File.Delete(tempFile);
}
}
catch (Exception exception)
{
Trace.TraceWarning("Exception deleting temp file {0}", exception);
}
}
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return(false);
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
PreferEmbeddedSpectra = PreferEmbeddedSpectra,
DebugMode = DebugMode,
};
bool retry = true;
do
{
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status,
out _buildCommandArgs, out _buildOutput, out _ambiguousMatches))
{
return(false);
}
retry = false;
}
catch (IOException x)
{
if (IsLibraryMissingExternalSpectraError(x, out string spectrumFilename, out string resultsFilepath))
{
// replace the relative path to the results file (e.g. msms.txt) with the absolute path
string fullResultsFilepath = InputFiles.SingleOrDefault(o => o.EndsWith(resultsFilepath)) ??
throw new InvalidDataException(@"no results filepath from BiblioSpec error message", x);
// TODO: this will break if BiblioSpec output is translated to other languages
string messageWithFullFilepath =
x.Message.Replace(@"search results file '" + resultsFilepath,
@"search results file '" + fullResultsFilepath);
var response =
progress.UpdateProgress(
status.ChangeErrorException(new IOException(messageWithFullFilepath, x)));
if (response == UpdateProgressResponse.cancel)
{
return(false);
}
else if (response == UpdateProgressResponse.normal)
{
blibBuilder.PreferEmbeddedSpectra = true;
}
continue;
}
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
} while (retry);
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
