public RemoteChromDataProvider(SrmDocument document, IRetentionTimePredictor retentionTimePredictor, ChromFileInfo chromFileInfo, ProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
_document = document;
ChorusUrl chorusUrl = (ChorusUrl)chromFileInfo.FilePath;
_chorusAccount = chorusUrl.FindChorusAccount(Settings.Default.ChorusAccountList);
var chromatogramRequestProviders = new List<ChromatogramRequestProvider>();
foreach (bool firstPass in new[] {true, false})
{
if (null == retentionTimePredictor && !firstPass)
{
continue;
}
var chromatogramRequestProvider = new ChromatogramRequestProvider(document, chorusUrl,
retentionTimePredictor, firstPass);
if (0 == chromatogramRequestProvider.ChromKeys.Count)
{
continue;
}
chromatogramRequestProviders.Add(chromatogramRequestProvider);
}
_chromatogramRequestProviders = chromatogramRequestProviders.ToArray();
_chromTaskLists = new ChromTaskList[_chromatogramRequestProviders.Length];
}
private BlibDb(String path)
{
FilePath = path;
SessionFactory = BlibSessionFactoryFactory.CreateSessionFactory(path, false);
DatabaseLock = new ReaderWriterLock();
_progressStatus = new ProgressStatus(string.Empty);
}
public const string EXE_BLIB_FILTER = "BlibFilter"; // Not L10N
public bool Filter(string sourceFile, string destinationFile, IProgressMonitor progressMonitor, ref ProgressStatus status)
{
// ReSharper disable NonLocalizedString
var argv = new List<string>
{
"-b true",
"\"" + sourceFile + "\"",
"\"" + destinationFile + "\""
};
// ReSharper restore NonLocalizedString
var psiBlibFilter = new ProcessStartInfo(EXE_BLIB_FILTER)
{
CreateNoWindow = true,
UseShellExecute = false,
WorkingDirectory = Path.GetDirectoryName(destinationFile) ?? string.Empty,
Arguments = string.Join(" ", argv.ToArray()), // Not L10N
RedirectStandardOutput = true,
RedirectStandardError = true
};
var processRunner = new ProcessRunner();
processRunner.Run(psiBlibFilter, null, progressMonitor, ref status);
return status.IsComplete;
}
public static void RunProcess(this ProcessStartInfo psi, string stdin, string messagePrefix, IProgressMonitor progress, ref ProgressStatus status)
{
var processRunner = new ProcessRunner
{
StatusPrefix = messagePrefix,
};
processRunner.Run(psi, stdin, progress, ref status);
}
public ChromCacheJoiner(string cachePath, IPooledStream streamDest,
IList<string> cacheFilePaths, ILoadMonitor loader, ProgressStatus status,
Action<ChromatogramCache, Exception> completed)
: base(cachePath, loader, status, completed)
{
_destinationStream = streamDest;
CacheFilePaths = cacheFilePaths;
}
public static ProgressMonitorImpl NewProgressMonitorImpl(ProgressStatus currentStatus, Func<int, bool> updateProgress)
{
return new ProgressMonitorImpl(
() => !updateProgress.Invoke(currentStatus.PercentComplete),
status => {
currentStatus = status;
updateProgress(status.PercentComplete);
});
}
protected ChromCacheWriter(string cachePath, ILoadMonitor loader, ProgressStatus status,
Action<ChromatogramCache, Exception> completed)
{
CachePath = cachePath;
_fs = new FileSaver(CachePath);
_fsScans = new FileSaver(CachePath + ChromatogramCache.SCANS_EXT, true);
_fsPeaks = new FileSaver(CachePath + ChromatogramCache.PEAKS_EXT, true);
_fsScores = new FileSaver(CachePath + ChromatogramCache.SCORES_EXT, true);
_loader = loader;
_status = status;
_completed = completed;
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
double lastPrecursor = 0;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
continue;
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
var ki = new KeyValuePair<ChromKey, int>(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
FixCEOptForShimadzu();
if (_chromIds.Count == 0)
throw new NoSrmDataException(dataFile.FilePath);
SetPercentComplete(50);
}
public ChorusResponseChromDataProvider(SrmDocument document, ChromFileInfo chromFileInfo, ProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
ChromatogramCache.RawData rawData;
MsDataFilePath msDataFilePath = (MsDataFilePath) chromFileInfo.FilePath;
IPooledStream stream = loader.StreamManager.CreatePooledStream(msDataFilePath.FilePath, false);
ChromatogramCache.LoadStructs(stream.Stream, out rawData);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
new ChromCachedFile(chromFileInfo.FilePath, chromCacheFile.Flags, chromCacheFile.FileWriteTime,
chromCacheFile.RunStartTime, chromCacheFile.MaxRetentionTime, chromCacheFile.MaxIntensity,
chromCacheFile.InstrumentInfoList),
};
var cache = new ChromatogramCache("cachePath", rawData, stream); // Not L10N
_cachedChromatogramDataProvider = new CachedChromatogramDataProvider(cache, document,
chromFileInfo.FilePath, chromFileInfo, null, progressStatus, startPercent, endPercent, loader);
}
public CachedChromatogramDataProvider(ChromatogramCache cache,
SrmDocument document,
MsDataFileUri dataFilePath,
ChromFileInfo fileInfo,
bool? singleMatchMz,
ProgressStatus status,
int startPercent,
int endPercent,
ILoadMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_cache = cache;
_fileIndex = cache.CachedFiles.IndexOf(f => Equals(f.FilePath, dataFilePath));
_chromKeyIndices = cache.GetChromKeys(dataFilePath).OrderBy(v => v.LocationPoints).ToArray();
_cache.GetStatusDimensions(dataFilePath, out _maxRetentionTime, out _maxIntensity);
_singleMatchMz = singleMatchMz.HasValue
? singleMatchMz.Value
// Unfortunately, before the single matching status was
// written into the cache file, we can only guess about its
// status based on the overall document settings
: document.Settings.TransitionSettings.FullScan.IsEnabled;
}
public UpdateProgressResponse UpdateProgress(ProgressStatus status)
{
return UpdateProgressResponse.normal;
}
//Throws DatabaseOpeningException
public static IrtDb GetIrtDb(string path, IProgressMonitor loadMonitor)
{
var status = new ProgressStatus(string.Format(Resources.IrtDb_GetIrtDb_Loading_iRT_database__0_, path));
if (loadMonitor != null)
loadMonitor.UpdateProgress(status);
try
{
if (path == null)
throw new DatabaseOpeningException(Resources.IrtDb_GetIrtDb_Database_path_cannot_be_null);
if (!File.Exists(path))
throw new DatabaseOpeningException(String.Format(Resources.IrtDb_GetIrtDb_The_file__0__does_not_exist_, path));
string message;
Exception xInner = null;
try
{
//Check for a valid SQLite file and that it has our schema
//Allow only one thread at a time to read from the same path
using (var sessionFactory = GetSessionFactory(path))
{
lock (sessionFactory)
{
return new IrtDb(path, sessionFactory).Load(loadMonitor, status);
}
}
}
catch (UnauthorizedAccessException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_You_do_not_have_privileges_to_access_the_file__0_, path);
xInner = x;
}
catch (DirectoryNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_path_containing__0__does_not_exist, path);
xInner = x;
}
catch (FileNotFoundException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_created_Perhaps_you_do_not_have_sufficient_privileges, path);
xInner = x;
}
catch (SQLiteException x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__is_not_a_valid_iRT_database_file, path);
xInner = x;
}
catch (Exception x)
{
message = string.Format(Resources.IrtDb_GetIrtDb_The_file__0__could_not_be_opened, path);
xInner = x;
}
throw new DatabaseOpeningException(message, xInner);
}
catch (DatabaseOpeningException x)
{
if (loadMonitor == null)
throw;
loadMonitor.UpdateProgress(status.ChangeErrorException(x));
return null;
}
}
public void ExportChromatograms(string chromatogramsFile, bool precursors, bool products, bool basePeaks, bool tics)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Exporting_chromatograms_file__0____, chromatogramsFile);
var chromExtractors = new List<ChromExtractor>();
if (tics)
chromExtractors.Add(ChromExtractor.summed);
if (basePeaks)
chromExtractors.Add(ChromExtractor.base_peak);
var chromSources = new List<ChromSource>();
if (precursors)
chromSources.Add(ChromSource.ms1);
if (products)
chromSources.Add(ChromSource.fragment);
if (chromExtractors.Count == 0 && chromSources.Count == 0)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__At_least_one_chromatogram_type_must_be_selected);
return;
}
var filesToExport = Document.Settings.HasResults
? Document.Settings.MeasuredResults.MSDataFilePaths.Select(f => f.GetFileName()).ToList()
: new List<string>();
if (filesToExport.Count == 0)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__The_document_must_have_imported_results);
return;
}
try
{
var chromExporter = new ChromatogramExporter(Document);
using (var saver = new FileSaver(chromatogramsFile))
using (var writer = new StreamWriter(saver.SafeName))
{
var status = new ProgressStatus(string.Empty);
IProgressMonitor broker = new CommandProgressMonitor(_out, status);
chromExporter.Export(writer, broker, filesToExport, LocalizationHelper.CurrentCulture, chromExtractors, chromSources);
writer.Close();
broker.UpdateProgress(status.Complete());
saver.Commit();
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Chromatograms_file__0__exported_successfully_, chromatogramsFile);
}
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__Failure_attempting_to_save_chromatograms_file__0_, chromatogramsFile);
_out.WriteLine(x.Message);
}
}
public SrmDocument Import(TextReader reader, IProgressMonitor progressMonitor, long lineCount, bool isMinutes, bool removeMissing = false, bool changePeaks = true)
{
var status = new ProgressStatus(Resources.PeakBoundaryImporter_Import_Importing_Peak_Boundaries);
double timeConversionFactor = isMinutes ? 1.0 : 60.0;
int linesRead = 0;
int progressPercent = 0;
var docNew = (SrmDocument) Document.ChangeIgnoreChangingChildren(true);
var docReference = docNew;
var sequenceToNode = new Dictionary<Tuple<string, bool>, IList<IdentityPath>>();
var fileNameToFileMatch = new Dictionary<string, ChromSetFileMatch>();
var trackAdjustedResults = new HashSet<ResultsKey>();
var modMatcher = new ModificationMatcher();
// Make the dictionary of modified peptide strings to doc nodes and paths
for (int i = 0; i < Document.MoleculeCount; ++i)
{
IdentityPath peptidePath = Document.GetPathTo((int) SrmDocument.Level.Molecules, i);
PeptideDocNode peptideNode = (PeptideDocNode) Document.FindNode(peptidePath);
var peptidePair = new Tuple<string, bool>(peptideNode.RawTextId, peptideNode.IsDecoy);
IList<IdentityPath> idPathList;
// Each (sequence, isDecoy) pair can be associated with more than one peptide,
// to handle the case of duplicate peptides in the doucment.
if (sequenceToNode.TryGetValue(peptidePair, out idPathList))
{
idPathList.Add(peptidePath);
sequenceToNode[peptidePair] = idPathList;
}
else
{
idPathList = new List<IdentityPath> { peptidePath };
sequenceToNode.Add(peptidePair, idPathList);
}
}
// Add annotations as possible columns
var allFieldNames = new List<string[]>(FIELD_NAMES);
allFieldNames.AddRange(from def in Document.Settings.DataSettings.AnnotationDefs
where def.AnnotationTargets.Contains(AnnotationDef.AnnotationTarget.precursor_result)
select new[] { def.Name });
string line = reader.ReadLine();
linesRead++;
int[] fieldIndices;
int fieldsTotal;
// If we aren't changing peaks, allow start and end time to be missing
var requiredFields = changePeaks ? REQUIRED_FIELDS : REQUIRED_NO_CHROM;
char correctSeparator = ReadFirstLine(line, allFieldNames, requiredFields, out fieldIndices, out fieldsTotal);
while ((line = reader.ReadLine()) != null)
{
linesRead++;
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return Document;
int progressNew = (int) (linesRead*100/lineCount);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
var dataFields = new DataFields(fieldIndices, line.ParseDsvFields(correctSeparator), allFieldNames);
if (dataFields.Length != fieldsTotal)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Line__0__field_count__1__differs_from_the_first_line__which_has__2_,
linesRead, dataFields.Length, fieldsTotal));
}
string modifiedPeptideString = dataFields.GetField(Field.modified_peptide);
modMatcher.CreateMatches(Document.Settings,
new List<string> {modifiedPeptideString},
Settings.Default.StaticModList,
Settings.Default.HeavyModList);
// Convert the modified peptide string into a standardized form that
// converts unimod, names, etc, into masses, eg [+57.0]
var nodeForModPep = modMatcher.GetModifiedNode(modifiedPeptideString);
if (nodeForModPep == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Peptide_has_unrecognized_modifications__0__at_line__1_, modifiedPeptideString, linesRead));
}
nodeForModPep = nodeForModPep.ChangeSettings(Document.Settings, SrmSettingsDiff.ALL);
modifiedPeptideString = nodeForModPep.RawTextId; // Modified sequence, or custom ion name
string fileName = dataFields.GetField(Field.filename);
bool isDecoy = dataFields.IsDecoy(linesRead);
var peptideIdentifier = new Tuple<string, bool>(modifiedPeptideString, isDecoy);
int charge;
bool chargeSpecified = dataFields.TryGetCharge(linesRead, out charge);
string sampleName = dataFields.GetField(Field.sample_name);
double? startTime = null;
double? endTime = null;
if (changePeaks)
{
startTime = dataFields.GetTime(Field.start_time, Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_, linesRead);
if (startTime.HasValue)
startTime = startTime / timeConversionFactor;
endTime = dataFields.GetTime(Field.end_time, Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_end_time_, linesRead);
if (endTime.HasValue)
endTime = endTime / timeConversionFactor;
}
// Error if only one of startTime and endTime is null
if (startTime == null && endTime != null)
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_start_time_on_line__0_, linesRead));
if (startTime != null && endTime == null)
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_end_time_on_line__0_, linesRead));
// Add filename to second dictionary if not yet encountered
ChromSetFileMatch fileMatch;
if (!fileNameToFileMatch.TryGetValue(fileName, out fileMatch))
{
fileMatch = Document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(fileName));
fileNameToFileMatch.Add(fileName, fileMatch);
}
if (fileMatch == null)
{
UnrecognizedFiles.Add(fileName);
continue;
}
var chromSet = fileMatch.Chromatograms;
string nameSet = chromSet.Name;
ChromFileInfoId[] fileIds;
if (sampleName == null)
{
fileIds = chromSet.MSDataFileInfos.Select(x => x.FileId).ToArray();
}
else
{
var sampleFile = chromSet.MSDataFileInfos.FirstOrDefault(info => Equals(sampleName, info.FilePath.GetSampleName()));
if (sampleFile == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Sample__0__on_line__1__does_not_match_the_file__2__, sampleName, linesRead, fileName));
}
fileIds = new[] {sampleFile.FileId};
}
// Look up the IdentityPath of peptide in first dictionary
IList<IdentityPath> pepPaths;
if (!sequenceToNode.TryGetValue(peptideIdentifier, out pepPaths))
{
UnrecognizedPeptides.Add(modifiedPeptideString);
continue;
}
// Define the annotations to be added
var annotations = dataFields.GetAnnotations();
AnnotationsAdded = annotations.Keys.ToList();
// Loop over all the transition groups in that peptide to find matching charge,
// or use all transition groups if charge not specified
bool foundSample = false;
foreach (var pepPath in pepPaths)
{
var nodePep = (PeptideDocNode)docNew.FindNode(pepPath);
for(int i = 0; i < nodePep.Children.Count; ++i)
{
var groupRelPath = nodePep.GetPathTo(i);
var groupNode = (TransitionGroupDocNode) nodePep.FindNode(groupRelPath);
if (!chargeSpecified || charge == groupNode.TransitionGroup.PrecursorCharge)
{
var groupFileIndices =
new HashSet<int>(groupNode.ChromInfos.Select(x => x.FileId.GlobalIndex));
// Loop over the files in this groupNode to find the correct sample
// Change peak boundaries for the transition group
foreach (var fileId in fileIds)
{
if (groupFileIndices.Contains(fileId.GlobalIndex))
{
var groupPath = new IdentityPath(pepPath, groupNode.Id);
// Attach annotations
docNew = docNew.AddPrecursorResultsAnnotations(groupPath, fileId, annotations);
// Change peak
var filePath = chromSet.GetFileInfo(fileId).FilePath;
if (changePeaks)
{
docNew = docNew.ChangePeak(groupPath, nameSet, filePath,
null, startTime, endTime, UserSet.IMPORTED, null, false);
}
// For removing peaks that are not in the file, if removeMissing = true
trackAdjustedResults.Add(new ResultsKey(fileId.GlobalIndex, groupNode.Id));
foundSample = true;
}
}
}
}
}
if (!foundSample)
{
UnrecognizedChargeStates.Add(new UnrecognizedChargeState(charge, fileName, modifiedPeptideString));
}
}
// Remove peaks from the document that weren't in the file.
if (removeMissing)
docNew = RemoveMissing(docNew, trackAdjustedResults, changePeaks);
// If nothing has changed, return the old Document before ChangeIgnoreChangingChildren was turned off
if (!ReferenceEquals(docNew, docReference))
Document = (SrmDocument) Document.ChangeIgnoreChangingChildren(false).ChangeChildrenChecked(docNew.Children);
return Document;
}
UpdateProgressResponse IProgressMonitor.UpdateProgress(ProgressStatus status)
{
UpdateProgress(status);
return UpdateProgressResponse.normal;
}
private void UpdateProgress(ProgressStatus status)
{
if (status.PercentComplete != -1)
{
// Stop the waiting thread if it is running.
_waiting = false;
if(_waitingThread != null && _waitingThread.IsAlive)
{
_waitingThread.Join();
}
}
var currentTime = DateTime.Now;
// Show progress at least every 2 seconds and at 100%, if any other percentage
// output has been shown.
if ((currentTime - _lastOutput).Seconds < 2 && !status.IsError && (status.PercentComplete != 100 || _lastOutput == _waitStart))
{
return;
}
bool writeMessage = !string.IsNullOrEmpty(status.Message) &&
(_lastMessage == null || !ReferenceEquals(status.Message, _lastMessage));
if (status.IsError)
{
_out.WriteLine(Resources.CommandLine_GeneralException_Error___0_, status.ErrorException.Message);
writeMessage = false;
}
else if (status.PercentComplete == -1)
{
_out.Write(Resources.CommandWaitBroker_UpdateProgress_Waiting___);
_waiting = true;
// Start a thread that will indicate "waiting" progress to the console every few seconds.
_waitingThread = new Thread(Wait){IsBackground = true};
_waitingThread.Start();
}
else if (_currentProgress != null && status.PercentComplete != _currentProgress.PercentComplete)
{
// If writing a message at the same time as updating percent complete,
// put them both on the same line
if (writeMessage)
_out.WriteLine("{0}% - {1}", status.PercentComplete, status.Message); // Not L10N
else
_out.WriteLine("{0}%", status.PercentComplete); // Not L10N
}
else if (writeMessage)
{
_out.WriteLine(status.Message);
}
if (writeMessage)
_lastMessage = status.Message;
_lastOutput = currentTime;
_currentProgress = status;
}
private void ExportLiveReport(string reportName, string reportFile, char reportColSeparator, bool reportInvariant)
{
var viewContext = DocumentGridViewContext.CreateDocumentGridViewContext(_doc, reportInvariant
? DataSchemaLocalizer.INVARIANT
: SkylineDataSchema.GetLocalizedSchemaLocalizer());
var viewInfo = viewContext.GetViewInfo(PersistedViews.MainGroup.Id.ViewName(reportName));
if (null == viewInfo)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__does_not_exist__If_it_has_spaces_in_its_name__use__double_quotes__around_the_entire_list_of_command_parameters_, reportName);
return;
}
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Exporting_report__0____, reportName);
try
{
using (var saver = new FileSaver(reportFile))
{
if (!saver.CanSave())
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__could_not_be_saved_to__1__, reportName, reportFile);
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Check_to_make_sure_it_is_not_read_only_);
}
var status = new ProgressStatus(string.Empty);
IProgressMonitor broker = new CommandProgressMonitor(_out, status);
using (var writer = new StreamWriter(saver.SafeName))
{
viewContext.Export(broker, ref status, viewInfo, writer,
new DsvWriter(reportInvariant ? CultureInfo.InvariantCulture : LocalizationHelper.CurrentCulture, reportColSeparator));
}
broker.UpdateProgress(status.Complete());
saver.Commit();
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Report__0__exported_successfully_to__1__, reportName, reportFile);
}
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__Failure_attempting_to_save__0__report_to__1__, reportName, reportFile);
_out.WriteLine(x.Message);
}
}
public CommandProgressMonitor(TextWriter outWriter, ProgressStatus status)
{
_out = outWriter;
_waitStart = _lastOutput = DateTime.Now;
UpdateProgress(status);
}
private static void ConvertBrukerToMzml(string filePathBruker,
string outputPath, IProgressMonitor monitor, ProgressStatus status)
{
// We use CompassXport, if it is installed, to convert a Bruker raw file to mzML. This solves two
// issues: the Bruker reader can't be called on any thread other than the main thread, and there
// is no 64-bit version of the reader. So we start CompassXport in its own 32-bit process,
// and use it to convert the raw data to mzML in a temporary file, which we read back afterwards.
var key = Registry.LocalMachine.OpenSubKey(KEY_COMPASSXPORT, false);
string compassXportExe = (key != null) ? (string)key.GetValue(string.Empty) : null;
if (compassXportExe == null)
throw new IOException(Resources.VendorIssueHelper_ConvertBrukerToMzml_CompassXport_software_must_be_installed_to_import_Bruker_raw_data_files_);
// CompassXport arguments
// ReSharper disable NonLocalizedString
var argv = new[]
{
"-a \"" + filePathBruker + "\"", // input file (directory)
"-o \"" + outputPath + "\"", // output file (directory)
"-mode 2", // mode 2 (mzML)
"-raw 0" // export line spectra (profile data is HUGE and SLOW!)
};
// ReSharper restore NonLocalizedString
// Start CompassXport in its own process.
var psi = new ProcessStartInfo(compassXportExe)
{
CreateNoWindow = true,
UseShellExecute = false,
// Common directory includes the directory separator
WorkingDirectory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) ?? string.Empty,
Arguments = string.Join(" ", argv), // Not L10N
RedirectStandardError = true,
RedirectStandardOutput = true,
};
var proc = new Process { StartInfo = psi };
proc.Start();
// CompassXport starts by calculating a hash of the input file. This takes a long time, and there is
// no intermediate output during this time. So we set the progress bar some fraction of the way and
// let it sit there and animate while we wait for the start of spectra processing.
const int hashPercent = 25; // percentage of import time allocated to calculating the input file hash
int spectrumCount = 0;
var sbOut = new StringBuilder();
var reader = new ProcessStreamReader(proc);
string line;
while ((line = reader.ReadLine()) != null)
{
if (monitor.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
sbOut.AppendLine(line);
line = line.Trim();
// The main part of conversion starts with the hash calculation.
if (line.StartsWith("Calculating hash")) // Not L10N
{
status = status.ChangeMessage(Resources.VendorIssueHelper_ConvertBrukerToMzml_Calculating_hash_of_input_file)
.ChangePercentComplete(hashPercent);
monitor.UpdateProgress(status);
continue;
}
// Determine how many spectra will be converted so we can track progress.
var match = Regex.Match(line, @"Converting (\d+) spectra"); // Not L10N
if (match.Success)
{
spectrumCount = int.Parse(match.Groups[1].Value);
continue;
}
// Update progress as each spectra batch is converted.
match = Regex.Match(line, @"Spectrum \d+ - (\d+)"); // Not L10N
if (match.Success)
{
var spectrumEnd = int.Parse(match.Groups[1].Value);
var percentComplete = hashPercent + (100-hashPercent)*spectrumEnd/spectrumCount;
status = status.ChangeMessage(line).ChangePercentComplete(percentComplete);
monitor.UpdateProgress(status);
}
}
while (!proc.WaitForExit(200))
{
if (monitor.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
}
if (proc.ExitCode != 0)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.VendorIssueHelper_ConvertBrukerToMzml_Failure_attempting_to_convert__0__to_mzML_using_CompassXport_,
filePathBruker), string.Empty, sbOut.ToString()));
}
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status, TextWriter writer)
{
if (shouldCancel)
{
status.Cancel();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(stringToWriteToWriter))
{
writer.WriteLine(stringToWriteToWriter);
}
status.ChangePercentComplete(100);
progress.UpdateProgress(status);
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status, TextWriter writer)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
var proc = Process.Start(psi);
if (proc == null)
throw new IOException(string.Format("Failure starting {0} command.", psi.FileName)); // Not L10N
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")) // Not L10N
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (line.EndsWith("%")) // Not L10N
{
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 (MessagePrefix == null || line.StartsWith(MessagePrefix))
{
// Remove prefix, if there is one.
if (MessagePrefix != null)
line = line.Substring(MessagePrefix.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)
throw new IOException("Error occurred running process."); // Not L10N
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);
}
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status, TextWriter writer)
{
if (shouldCancel)
{
status.Cancel();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(stringToWriteToWriter))
writer.WriteLine(stringToWriteToWriter);
status.ChangePercentComplete(100);
progress.UpdateProgress(status);
}
private IrtDb Load(IProgressMonitor loadMonitor, ProgressStatus status)
{
var result = ChangeProp(ImClone(this), im => im.LoadPeptides(im.GetPeptides()));
// Not really possible to show progress, unless we switch to raw reading
if (loadMonitor != null)
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
return result;
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status)
{
Run(psi, stdin, progress, ref status, null);
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
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()) != null)
{
if (progress == null || line.ToLower().StartsWith("error"))
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
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 (MessagePrefix == null || line.StartsWith(MessagePrefix))
{
// Remove prefix, if there is one.
if (MessagePrefix != null)
{
line = line.Substring(MessagePrefix.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)
{
throw new IOException("Error occurred running process.");
}
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
else if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
{
status = status.NextSegment();
}
if (progress != null)
{
progress.UpdateProgress(status);
}
}
}
// ReSharper restore NonLocalizedString
/// <summary>
/// Executes an export for all chromatograms in the document
/// with file names matching one of the files in filesToExport
/// writer = location to write the chromatogram data to
/// longWaitBroker = progress bar (can be null)
/// filesToExport = file names for which to write chromatograms
/// cultureInfo = local culture
/// chromExtractors = list of special chromatogram types to include (base peak, etc)
/// chromSources = type of ions to include (precursor, product)
/// </summary>
public void Export(TextWriter writer,
IProgressMonitor longWaitBroker,
IList<string> filesToExport,
CultureInfo cultureInfo,
IList<ChromExtractor> chromExtractors,
IList<ChromSource> chromSources)
{
int currentReplicates = 0;
int totalReplicates = _chromatogramSets.Count;
var status = new ProgressStatus(string.Empty);
FormatHeader(writer, FIELD_NAMES);
foreach (var chromatograms in _chromatogramSets)
{
if (longWaitBroker != null)
{
int percentComplete = currentReplicates++ * 100 / totalReplicates;
if (percentComplete < 100)
{
longWaitBroker.UpdateProgress(status = status.ChangeMessage(string.Format(Resources.ChromatogramExporter_Export_Exporting_Chromatograms_for__0_,
chromatograms.Name)).ChangePercentComplete(percentComplete));
}
}
foreach (var extractor in chromExtractors)
{
ChromatogramGroupInfo[] arrayChromSpecial;
if (!_measuredResults.TryLoadAllIonsChromatogram(chromatograms, extractor, true, out arrayChromSpecial))
{
// TODO: need error determination here
continue;
}
foreach (var chromInfo in arrayChromSpecial)
{
string fileName = chromInfo.FilePath.GetFileName();
// Skip the files that have not been selected for export
if (!filesToExport.Contains(fileName))
continue;
IList<float> times = chromInfo.Times;
IList<float> intensities = chromInfo.IntensityArray[0];
float tic = CalculateTic(times, intensities);
string extractorName = GetExtractorName(extractor);
string[] fieldArray =
{
fileName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
extractorName,
TextUtil.EXCEL_NA,
TextUtil.EXCEL_NA,
System.Convert.ToString(tic, cultureInfo)
};
FormatChromLine(writer, fieldArray, times, intensities, cultureInfo);
}
}
foreach (var peptideNode in Document.Molecules)
{
foreach (TransitionGroupDocNode groupNode in peptideNode.Children)
ExportGroupNode(peptideNode, groupNode, chromatograms, filesToExport, chromSources, writer, cultureInfo);
}
}
}
public SrmSettingsChangeMonitor(IProgressMonitor progressMonitor, string formatString,
IDocumentContainer documentContainer = null, SrmDocument startDocument = null)
{
_progressMonitor = progressMonitor;
_documentContainer = documentContainer;
_startDocument = startDocument;
if (_startDocument == null && documentContainer != null)
_startDocument = documentContainer.Document;
if (!formatString.Contains('{'))
_status = new ProgressStatus(formatString);
else
{
_formatString = formatString;
// Set status string to empty, since it should be reset very quickly
_status = new ProgressStatus(string.Empty);
}
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref ProgressStatus status)
{
Run(psi, stdin, progress,ref status, null);
}
public void Dispose()
{
if (_seenGroupCount + _seenMoleculeCount > 0)
_progressMonitor.UpdateProgress(_status = _status.Complete());
}
private string GetReportRows(SrmDocument document, ViewSpec viewSpec, IProgressMonitor progressMonitor)
{
var container = new MemoryDocumentContainer();
container.SetDocument(document, container.Document);
var dataSchema = new SkylineDataSchema(container, DataSchemaLocalizer.INVARIANT);
var viewContext = new DocumentGridViewContext(dataSchema);
var status = new ProgressStatus(string.Format(Resources.ReportSpec_ReportToCsvString_Exporting__0__report,
viewSpec.Name));
var writer = new StringWriter();
if (viewContext.Export(progressMonitor, ref status, viewContext.GetViewInfo(null, viewSpec), writer,
new DsvWriter(CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV)))
{
return writer.ToString();
}
return null;
}
public void ProcessGroup(PeptideGroupDocNode nodeGroup)
{
bool messageChange = _formatString != null;
if (messageChange)
_status = _status.ChangeMessage(string.Format(_formatString, nodeGroup.Name));
int? percentComplete = ProgressStatus.ThreadsafeIncementPercent(ref _seenGroupCount, GroupCount);
UpdateProgress(percentComplete, messageChange);
}
// ReSharper restore NonLocalizedString
public static List<string> ConvertPilotFiles(IList<string> inputFiles, IProgressMonitor progress, ProgressStatus status)
{
string groupConverterExePath = null;
var inputFilesPilotConverted = new List<string>();
for (int index = 0; index < inputFiles.Count; index++)
{
string inputFile = inputFiles[index];
if (!inputFile.EndsWith(BiblioSpecLiteBuilder.EXT_PILOT))
{
inputFilesPilotConverted.Add(inputFile);
continue;
}
string outputFile = Path.ChangeExtension(inputFile, BiblioSpecLiteBuilder.EXT_PILOT_XML);
// Avoid re-converting files that have already been converted
if (File.Exists(outputFile))
{
// Avoid duplication, in case the user accidentally adds both .group and .group.xml files
// for the same results
if (!inputFiles.Contains(outputFile))
inputFilesPilotConverted.Add(outputFile);
continue;
}
string message = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Converting__0__to_xml, Path.GetFileName(inputFile));
int percent = index * 100 / inputFiles.Count;
progress.UpdateProgress(status = status.ChangeMessage(message).ChangePercentComplete(percent));
if (groupConverterExePath == null)
{
var key = Registry.LocalMachine.OpenSubKey(KEY_PROTEIN_PILOT, false);
if (key != null)
{
string proteinPilotCommandWithArgs = (string)key.GetValue(string.Empty);
var proteinPilotCommandWithArgsSplit =
proteinPilotCommandWithArgs.Split(new[] { "\" \"" }, StringSplitOptions.RemoveEmptyEntries); // Remove " "%1" // Not L10N
string path = Path.GetDirectoryName(proteinPilotCommandWithArgsSplit[0].Trim(new[] { '\\', '\"' })); // Remove preceding "
if (path != null)
{
var groupFileExtractorPath = Path.Combine(path, EXE_GROUP_FILE_EXTRACTOR);
if (File.Exists(groupFileExtractorPath))
{
groupConverterExePath = groupFileExtractorPath;
}
else
{
var group2XmlPath = Path.Combine(path, EXE_GROUP2_XML);
if (File.Exists(group2XmlPath))
{
groupConverterExePath = group2XmlPath;
}
else
{
string errorMessage = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Unable_to_find__0__or__1__in_directory__2____Please_reinstall_ProteinPilot_software_to_be_able_to_handle__group_files_,
EXE_GROUP_FILE_EXTRACTOR, EXE_GROUP2_XML, path);
throw new IOException(errorMessage);
}
}
}
}
if (groupConverterExePath == null)
{
throw new IOException(Resources.VendorIssueHelper_ConvertPilotFiles_ProteinPilot_software__trial_or_full_version__must_be_installed_to_convert___group__files_to_compatible___group_xml__files_);
}
}
// run group2xml
// ReSharper disable NonLocalizedString
var argv = new[]
{
"XML",
"\"" + inputFile + "\"",
"\"" + outputFile + "\""
};
// ReSharper restore NonLocalizedString
var psi = new ProcessStartInfo(groupConverterExePath)
{
CreateNoWindow = true,
UseShellExecute = false,
// Common directory includes the directory separator
WorkingDirectory = Path.GetDirectoryName(groupConverterExePath) ?? string.Empty,
Arguments = string.Join(" ", argv.ToArray()), // Not L10N
RedirectStandardError = true,
RedirectStandardOutput = true,
};
var sbOut = new StringBuilder();
var proc = new Process {StartInfo = psi};
proc.Start();
var reader = new ProcessStreamReader(proc);
string line;
while ((line = reader.ReadLine()) != null)
{
if (progress.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
sbOut.AppendLine(line);
}
while (!proc.WaitForExit(200))
{
if (progress.IsCanceled)
{
proc.Kill();
return inputFilesPilotConverted;
}
}
if (proc.ExitCode != 0)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Failure_attempting_to_convert_file__0__to__group_xml_,
inputFile), string.Empty, sbOut.ToString()));
}
inputFilesPilotConverted.Add(outputFile);
}
progress.UpdateProgress(status.ChangePercentComplete(100));
return inputFilesPilotConverted;
}
/// <summary>
/// This function will add the given replicate, from dataFile, to the given document. If the replicate
/// does not exist, it will be added. If it does exist, it will be appended to.
/// </summary>
public static SrmDocument ImportResults(SrmDocument doc, string docPath, string replicate, MsDataFileUri dataFile,
OptimizableRegression optimize, IProgressMonitor progressMonitor, out ProgressStatus status)
{
using (var docContainer = new ResultsMemoryDocumentContainer(null, docPath) {ProgressMonitor = progressMonitor})
{
// Make sure library loading happens, which may not happen, if the doc
// parameter is used as the baseline document.
docContainer.SetDocument(doc, null);
SrmDocument docAdded;
do
{
doc = docContainer.Document;
var listChromatograms = new List<ChromatogramSet>();
if (doc.Settings.HasResults)
listChromatograms.AddRange(doc.Settings.MeasuredResults.Chromatograms);
int indexChrom = listChromatograms.IndexOf(chrom => chrom.Name.Equals(replicate));
if (indexChrom != -1)
{
var chromatogram = listChromatograms[indexChrom];
var paths = chromatogram.MSDataFilePaths;
var listFilePaths = paths.ToList();
listFilePaths.Add(dataFile);
listChromatograms[indexChrom] = chromatogram.ChangeMSDataFilePaths(listFilePaths);
}
else
{
listChromatograms.Add(new ChromatogramSet(replicate, new[] {dataFile.Normalize()},
Annotations.EMPTY, optimize));
}
var results = doc.Settings.HasResults
? doc.Settings.MeasuredResults.ChangeChromatograms(listChromatograms)
: new MeasuredResults(listChromatograms, doc.Settings.IsResultsJoiningDisabled);
docAdded = doc.ChangeMeasuredResults(results);
}
while (!docContainer.SetDocument(docAdded, doc, true));
status = docContainer.LastProgress;
return docContainer.Document;
}
}
