public void InitializeRun(string dataset)
{
string runFilename;
if (this.ExecutorParameters.CopyRawFileLocal)
{
ReportGeneralProgress("Started copying raw data to local folder: " + this.ExecutorParameters.FolderPathForCopiedRawDataset);
var attr = File.GetAttributes(dataset);
DirectoryInfo sourceDirInfo;
DirectoryInfo targetDirInfo;
if ((attr & FileAttributes.Directory) == FileAttributes.Directory)
{
sourceDirInfo = new DirectoryInfo(dataset);
runFilename = Path.Combine(this.ExecutorParameters.FolderPathForCopiedRawDataset, sourceDirInfo.Name);
targetDirInfo = new DirectoryInfo(runFilename);
FileUtilities.CopyAll(sourceDirInfo, targetDirInfo);
ReportGeneralProgress("Copying complete.");
}
else
{
var fileinfo = new FileInfo(dataset);
sourceDirInfo = fileinfo.Directory;
runFilename = Path.Combine(this.ExecutorParameters.FolderPathForCopiedRawDataset, Path.GetFileName(dataset));
targetDirInfo = new DirectoryInfo(this.ExecutorParameters.FolderPathForCopiedRawDataset);
if (!File.Exists(runFilename))
{
FileUtilities.CopyAll(fileinfo, targetDirInfo);
ReportGeneralProgress("Copying complete.");
}
else
{
ReportGeneralProgress("Datafile already exists on local drive. Using existing datafile.");
}
}
}
else
{
runFilename = dataset;
}
//create Run
var rf = new RunFactory();
Run = rf.CreateRun(runFilename);
var runInstantiationFailed = (Run == null);
if (runInstantiationFailed)
{
ReportGeneralProgress("Run initialization FAILED. Likely a filename problem. Or missing manufacturer .dlls");
return;
}
else
{
ReportGeneralProgress("Run initialized successfully.");
}
//Retrieve alignment data if it exists
CopyAlignmentInfoIfExists();
//check and load chrom source data (_peaks.txt)
var peaksFileExists = CheckForPeaksFile();
if (!peaksFileExists)
{
ReportGeneralProgress("Creating _Peaks.txt file for extracted ion chromatogram (XIC) source data ... takes 1-5 minutes");
CreatePeaksForChromSourceData();
ReportGeneralProgress("Done creating _Peaks.txt file");
}
else
{
ReportGeneralProgress("Using existing _Peaks.txt file");
}
ReportGeneralProgress("Peak loading started...");
var baseFileName = Path.Combine(this.Run.DataSetPath, this.Run.DatasetName);
var possibleFilename1 = baseFileName + "_peaks.txt";
if (File.Exists(possibleFilename1))
{
//create background worker so that updates don't go out to console.
//BackgroundWorker bw = new BackgroundWorker();
//bw.WorkerSupportsCancellation = true;
//bw.WorkerReportsProgress = true;
//TODO: keep an eye on errors connected to background worker here.
var peakImporter = new PeakImporterFromText(possibleFilename1, _backgroundWorker);
peakImporter.ImportPeaks(this.Run.ResultCollection.MSPeakResultList);
}
else
{
ReportGeneralProgress("CRITICAL FAILURE. Chrom source data (_peaks.txt) file not loaded.");
return;
}
// Grab the primary LC Scan numbers if they are not already filled out
if (!Run.PrimaryLcScanNumbers.Any())
{
Run.PrimaryLcScanNumbers = RunUtilities.FindPrimaryLcScanNumbers(this.Run.ResultCollection.MSPeakResultList);
}
ReportGeneralProgress("Peak Loading complete.");
return;
}