public void CopyToScanner(clsMSFileInfoScanner scanner)
{
// Note: These values will be overridden if /P was used and they are defined in the parameter file
scanner.UseCacheFiles = UseCacheFiles;
scanner.ReprocessExistingFiles = ReprocessingExistingFiles;
scanner.ReprocessIfCachedSizeIsZero = ReprocessIfCachedSizeIsZero;
scanner.PlotWithPython = PlotWithPython;
scanner.SaveTICAndBPIPlots = SaveTICAndBPIPlots;
scanner.SaveLCMS2DPlots = SaveLCMS2DPlots;
scanner.LCMS2DPlotMaxPointsToPlot = LCMS2DMaxPointsToPlot;
scanner.LCMS2DOverviewPlotDivisor = LCMS2DOverviewPlotDivisor;
scanner.TestLCMSGradientColorSchemes = TestLCMSGradientColorSchemes;
scanner.CheckCentroidingStatus = CheckCentroidingStatus;
scanner.MS2MzMin = MS2MzMin;
scanner.DisableInstrumentHash = DisableInstrumentHash;
scanner.ScanStart = ScanStart;
scanner.ScanEnd = ScanEnd;
scanner.ShowDebugInfo = ShowDebugInfo;
scanner.ComputeOverallQualityScores = ComputeOverallQualityScores;
scanner.CreateDatasetInfoFile = CreateDatasetInfoFile;
scanner.CreateScanStatsFile = CreateScanStatsFile;
scanner.UpdateDatasetStatsTextFile = UpdateDatasetStatsTextFile;
scanner.DatasetStatsTextFileName = DatasetStatsTextFileName;
scanner.CheckFileIntegrity = CheckFileIntegrity;
scanner.RecheckFileIntegrityForExistingDirectories = ReprocessingExistingFiles;
scanner.MaximumTextFileLinesToCheck = MaximumTextFileLinesToCheck;
scanner.ComputeFileHashes = ComputeFileHashes;
scanner.ZipFileCheckAllData = ZipFileCheckAllData;
scanner.IgnoreErrorsWhenRecursing = IgnoreErrorsWhenRecursing;
if (LogFilePath.Length > 0)
{
scanner.LogMessagesToFile = true;
scanner.LogFilePath = LogFilePath;
}
scanner.DatasetIDOverride = DatasetID;
scanner.DSInfoDBPostingEnabled = PostResultsToDMS;
if (!string.IsNullOrEmpty(ParameterFilePath))
{
scanner.LoadParameterFileSettings(ParameterFilePath);
}
}
public static int Main(string[] args)
{
var exeName = System.Reflection.Assembly.GetEntryAssembly()?.GetName().Name;
var exePath = PRISM.FileProcessor.ProcessFilesOrDirectoriesBase.GetAppPath();
var cmdLineParser = new CommandLineParser <CommandLineOptions>(exeName, GetAppVersion());
var scannerInfo = new clsMSFileInfoScanner();
cmdLineParser.ProgramInfo = "This program will scan a series of MS data files (or data directories) and " +
"extract the acquisition start and end times, number of spectra, and the " +
"total size of the data, saving the values in the file " +
clsMSFileInfoScanner.DefaultAcquisitionTimeFilename + ". " +
"Supported file types are Thermo .RAW files, Agilent Ion Trap (.D directories), " +
"Agilent or QStar/QTrap .WIFF files, MassLynx .Raw directories, Bruker 1 directories, " +
"Bruker XMass analysis.baf files, .UIMF files (IMS), " +
"zipped Bruker imaging datasets (with 0_R*.zip files), and " +
"DeconTools _isos.csv files" + Environment.NewLine + Environment.NewLine +
"Known file extensions: " + CollapseList(scannerInfo.GetKnownFileExtensionsList()) + Environment.NewLine +
"Known directory extensions: " + CollapseList(scannerInfo.GetKnownDirectoryExtensionsList());
cmdLineParser.ContactInfo = "Program written by Matthew Monroe for PNNL (Richland, WA) in 2005" + Environment.NewLine +
"E-mail: [email protected] or [email protected]" + Environment.NewLine + "Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/";
cmdLineParser.UsageExamples.Add("Program syntax:" + Environment.NewLine + Path.GetFileName(exePath) +
" /I:InputFileNameOrDirectoryPath [/O:OutputDirectoryName]" +
" [/P:ParamFilePath] [/S[:MaxLevel]] [/IE] [/L:LogFilePath]" +
" [/LC[:MaxPointsToPlot]] [/NoTIC] [/LCGrad]" +
" [/DI] [/SS] [/QS] [/CC]" +
" [/MS2MzMin:MzValue] [/NoHash]" +
" [/DST:DatasetStatsFileName]" +
" [/ScanStart:0] [/ScanEnd:0] [/Debug]" +
" [/C] [/M:nnn] [/H] [/QZ]" +
" [/CF] [/R] [/Z]" +
" [/PostToDMS] [/PythonPlot]");
var result = cmdLineParser.ParseArgs(args);
var options = result.ParsedResults;
if (!result.Success || !options.Validate())
{
// Delay for 750 msec in case the user double clicked this file from within Windows Explorer (or started the program via a shortcut)
System.Threading.Thread.Sleep(750);
return(-1);
}
mLastProgressTime = DateTime.UtcNow;
try
{
var scanner = new clsMSFileInfoScanner();
scanner.DebugEvent += MSFileScanner_DebugEvent;
scanner.ErrorEvent += MSFileScanner_ErrorEvent;
scanner.WarningEvent += MSFileScanner_WarningEvent;
scanner.StatusEvent += MSFileScanner_MessageEvent;
scanner.ProgressUpdate += MSFileScanner_ProgressUpdate;
options.CopyToScanner(scanner);
scanner.ShowCurrentProcessingOptions();
bool processingError;
int returnCode;
if (options.RecurseDirectories)
{
if (scanner.ProcessMSFilesAndRecurseDirectories(options.InputDataFilePath, options.OutputDirectoryName, options.MaxLevelsToRecurse))
{
returnCode = 0;
processingError = false;
}
else
{
returnCode = (int)scanner.ErrorCode;
processingError = true;
}
}
else
{
if (scanner.ProcessMSFileOrDirectoryWildcard(options.InputDataFilePath, options.OutputDirectoryName, true))
{
returnCode = 0;
processingError = false;
}
else
{
returnCode = (int)scanner.ErrorCode;
processingError = true;
}
}
if (processingError)
{
if (returnCode != 0)
{
ShowErrorMessage("Error while processing: " + scanner.GetErrorMessage());
}
else
{
ShowErrorMessage("Unknown error while processing (ProcessMSFileOrDirectoryWildcard returned false but the ErrorCode is 0)");
}
System.Threading.Thread.Sleep(1500);
}
else if (scanner.ErrorCode == iMSFileInfoScanner.eMSFileScannerErrorCodes.MS2MzMinValidationWarning)
{
ConsoleMsgUtils.ShowWarning("MS2MzMin validation warning: " + scanner.MS2MzMinValidationMessage);
}
scanner.SaveCachedResults();
return(returnCode);
}
catch (Exception ex)
{
ShowErrorMessage("Error occurred in modMain->Main", ex);
return(-1);
}
}
public static int Main()
{
int intReturnCode;
var objParseCommandLine = new clsParseCommandLine();
mInputDataFilePath = string.Empty;
mOutputFolderName = string.Empty;
mParameterFilePath = string.Empty;
mLogFilePath = string.Empty;
mRecurseFolders = false;
mRecurseFoldersMaxLevels = 2;
mIgnoreErrorsWhenRecursing = false;
mReprocessingExistingFiles = false;
mReprocessIfCachedSizeIsZero = false;
mUseCacheFiles = false;
mSaveTICandBPIPlots = true;
mSaveLCMS2DPlots = false;
mLCMS2DMaxPointsToPlot = clsLCMSDataPlotterOptions.DEFAULT_MAX_POINTS_TO_PLOT;
mLCMS2DOverviewPlotDivisor = clsLCMSDataPlotterOptions.DEFAULT_LCMS2D_OVERVIEW_PLOT_DIVISOR;
mTestLCMSGradientColorSchemes = false;
mCheckCentroidingStatus = false;
mScanStart = 0;
mScanEnd = 0;
mShowDebugInfo = false;
mComputeOverallQualityScores = false;
mCreateDatasetInfoFile = false;
mCreateScanStatsFile = false;
mUpdateDatasetStatsTextFile = false;
mDatasetStatsTextFileName = string.Empty;
mCheckFileIntegrity = false;
mComputeFileHashes = false;
mZipFileCheckAllData = true;
mMaximumTextFileLinesToCheck = clsFileIntegrityChecker.DEFAULT_MAXIMUM_TEXT_FILE_LINES_TO_CHECK;
mPostResultsToDMS = false;
mPlotWithPython = false;
mLastProgressTime = DateTime.UtcNow;
try
{
var blnProceed = false;
if (objParseCommandLine.ParseCommandLine())
{
if (SetOptionsUsingCommandLineParameters(objParseCommandLine))
{
blnProceed = true;
}
}
if (mInputDataFilePath == null)
{
mInputDataFilePath = string.Empty;
}
if (!blnProceed || objParseCommandLine.NeedToShowHelp || objParseCommandLine.ParameterCount + objParseCommandLine.NonSwitchParameterCount == 0 || mInputDataFilePath.Length == 0)
{
ShowProgramHelp();
return(-1);
}
var scanner = new clsMSFileInfoScanner();
scanner.DebugEvent += mMSFileScanner_DebugEvent;
scanner.ErrorEvent += mMSFileScanner_ErrorEvent;
scanner.WarningEvent += mMSFileScanner_WarningEvent;
scanner.StatusEvent += mMSFileScanner_MessageEvent;
scanner.ProgressUpdate += mMSFileScanner_ProgressUpdate;
if (mCheckFileIntegrity)
{
mUseCacheFiles = true;
}
// Note: These values will be overridden if /P was used and they are defined in the parameter file
scanner.UseCacheFiles = mUseCacheFiles;
scanner.ReprocessExistingFiles = mReprocessingExistingFiles;
scanner.ReprocessIfCachedSizeIsZero = mReprocessIfCachedSizeIsZero;
scanner.PlotWithPython = mPlotWithPython;
scanner.SaveTICAndBPIPlots = mSaveTICandBPIPlots;
scanner.SaveLCMS2DPlots = mSaveLCMS2DPlots;
scanner.LCMS2DPlotMaxPointsToPlot = mLCMS2DMaxPointsToPlot;
scanner.LCMS2DOverviewPlotDivisor = mLCMS2DOverviewPlotDivisor;
scanner.TestLCMSGradientColorSchemes = mTestLCMSGradientColorSchemes;
scanner.CheckCentroidingStatus = mCheckCentroidingStatus;
scanner.ScanStart = mScanStart;
scanner.ScanEnd = mScanEnd;
scanner.ShowDebugInfo = mShowDebugInfo;
scanner.ComputeOverallQualityScores = mComputeOverallQualityScores;
scanner.CreateDatasetInfoFile = mCreateDatasetInfoFile;
scanner.CreateScanStatsFile = mCreateScanStatsFile;
scanner.UpdateDatasetStatsTextFile = mUpdateDatasetStatsTextFile;
scanner.DatasetStatsTextFileName = mDatasetStatsTextFileName;
scanner.CheckFileIntegrity = mCheckFileIntegrity;
scanner.MaximumTextFileLinesToCheck = mMaximumTextFileLinesToCheck;
scanner.ComputeFileHashes = mComputeFileHashes;
scanner.ZipFileCheckAllData = mZipFileCheckAllData;
scanner.IgnoreErrorsWhenRecursing = mIgnoreErrorsWhenRecursing;
if (mLogFilePath.Length > 0)
{
scanner.LogMessagesToFile = true;
scanner.LogFilePath = mLogFilePath;
}
scanner.DatasetIDOverride = mDatasetID;
scanner.DSInfoDBPostingEnabled = mPostResultsToDMS;
if (!string.IsNullOrEmpty(mParameterFilePath))
{
scanner.LoadParameterFileSettings(mParameterFilePath);
}
if (mRecurseFolders)
{
if (scanner.ProcessMSFilesAndRecurseFolders(mInputDataFilePath, mOutputFolderName, mRecurseFoldersMaxLevels))
{
intReturnCode = 0;
}
else
{
intReturnCode = (int)scanner.ErrorCode;
}
}
else
{
if (scanner.ProcessMSFileOrFolderWildcard(mInputDataFilePath, mOutputFolderName, true))
{
intReturnCode = 0;
}
else
{
intReturnCode = (int)scanner.ErrorCode;
if (intReturnCode != 0)
{
ShowErrorMessage("Error while processing: " + scanner.GetErrorMessage());
}
}
}
scanner.SaveCachedResults();
}
catch (Exception ex)
{
ShowErrorMessage("Error occurred in modMain->Main: " + Environment.NewLine + ex.Message);
intReturnCode = -1;
}
return(intReturnCode);
}
private static void ShowProgramHelp()
{
try
{
var scanner = new clsMSFileInfoScanner();
Console.WriteLine("This program will scan a series of MS data files (or data folders) and " + "extract the acquisition start and end times, number of spectra, and the " + "total size of the data, saving the values in the file " + clsMSFileInfoScanner.DefaultAcquisitionTimeFilename + ". " + "Supported file types are Finnigan .RAW files, Agilent Ion Trap (.D folders), " + "Agilent or QStar/QTrap .WIFF files, Masslynx .Raw folders, Bruker 1 folders, " + "Bruker XMass analysis.baf files, .UIMF files (IMS), " + "zipped Bruker imaging datasets (with 0_R*.zip files), and " + "DeconTools _isos.csv files");
Console.WriteLine();
Console.WriteLine("Program syntax:" + Environment.NewLine + Path.GetFileName(System.Reflection.Assembly.GetExecutingAssembly().Location));
Console.WriteLine(" /I:InputFileNameOrFolderPath [/O:OutputFolderName]");
Console.WriteLine(" [/P:ParamFilePath] [/S[:MaxLevel]] [/IE] [/L:LogFilePath]");
Console.WriteLine(" [/LC[:MaxPointsToPlot]] [/NoTIC] [/LCGrad]");
Console.WriteLine(" [/DI] [/SS] [/QS] [/CC]");
Console.WriteLine(" [/DST:DatasetStatsFileName]");
Console.WriteLine(" [/ScanStart:0] [/ScanEnd:0] [/Debug]");
Console.WriteLine(" [/C] [/M:nnn] [/H] [/QZ]");
Console.WriteLine(" [/CF] [/R] [/Z]");
Console.WriteLine(" [/PostToDMS] [/PythonPlot]");
Console.WriteLine();
Console.WriteLine("Use /I to specify the name of a file or folder to scan; the path can contain the wildcard character *");
Console.WriteLine("The output folder name is optional. If omitted, the output files will be created in the program directory.");
Console.WriteLine();
Console.WriteLine("The param file switch is optional. If supplied, it should point to a valid XML parameter file. If omitted, defaults are used.");
Console.WriteLine("Use /S to process all valid files in the input folder and subfolders. Include a number after /S (like /S:2) to limit the level of subfolders to examine. Use /IE to ignore errors when recursing.");
Console.WriteLine("Use /L to specify the file path for logging messages.");
Console.WriteLine();
Console.WriteLine("Use /LC to create 2D LCMS plots (this process could take several minutes for each dataset). By default, plots the top " + clsLCMSDataPlotterOptions.DEFAULT_MAX_POINTS_TO_PLOT + " points. To plot the top 20000 points, use /LC:20000.");
Console.WriteLine("Use /LCDiv to specify the divisor to use when creating the overview 2D LCMS plots. By default, uses /LCDiv:" + clsLCMSDataPlotterOptions.DEFAULT_LCMS2D_OVERVIEW_PLOT_DIVISOR + "; use /LCDiv:0 to disable creation of the overview plots.");
Console.WriteLine("Use /NoTIC to not save TIC and BPI plots.");
Console.WriteLine("Use /LCGrad to save a series of 2D LC plots, each using a different color scheme. The default color scheme is OxyPalettes.Jet");
Console.WriteLine();
Console.WriteLine("Use /DatasetID:# to define the dataset's DatasetID value (where # is an integer); only appropriate if processing a single dataset");
Console.WriteLine("Use /DI to create a dataset info XML file for each dataset.");
Console.WriteLine();
Console.WriteLine("Use /SS to create a _ScanStats.txt file for each dataset.");
Console.WriteLine("Use /QS to compute an overall quality score for the data in each datasets.");
Console.WriteLine("Use /CC to check spectral data for whether it is centroided or profile");
Console.WriteLine();
Console.WriteLine("Use /DST to update (or create) a tab-delimited text file with overview stats for the dataset. " +
"If /DI is used, will include detailed scan counts; otherwise, will just have the dataset name, " +
"acquisition date, and (if available) sample name and comment. " +
"By default, the file is named " + clsDatasetStatsSummarizer.DEFAULT_DATASET_STATS_FILENAME + "; " +
"to override, add the file name after the /DST switch, for example /DST:DatasetStatsFileName.txt");
Console.WriteLine();
Console.WriteLine("Use /ScanStart and /ScanEnd to limit the scan range to process; useful for files where the first few scans are corrupt. " +
"For example, to start processing at scan 10, use /ScanStart:10");
Console.WriteLine("Use /Debug to display debug information at the console, including showing the scan number prior to reading each scan's data");
Console.WriteLine();
Console.WriteLine("Use /C to perform an integrity check on all known file types; this process will open known file types and " +
"verify that they contain the expected This option is only used if you specify an Input Folder and use a wildcard; you will typically also want to use /S when using /C.");
Console.WriteLine(("Use /M to define the maximum number of lines to process when checking text or csv files;" +
" default is /M:" + clsFileIntegrityChecker.DEFAULT_MAXIMUM_TEXT_FILE_LINES_TO_CHECK));
Console.WriteLine();
Console.WriteLine("Use /H to compute Sha-1 file hashes when verifying file integrity.");
Console.WriteLine("Use /QZ to run a quick zip-file validation test when verifying file integrity (the test does not check all data in the .Zip file).");
Console.WriteLine();
Console.WriteLine("Use /CF to save/load information from the acquisition time file (cache file). This option is auto-enabled if you use /C.");
Console.WriteLine("Use /R to reprocess files that are already defined in the acquisition time file.");
Console.WriteLine("Use /Z to reprocess files that are already defined in the acquisition time file only if their cached size is 0 bytes.");
Console.WriteLine();
Console.WriteLine("Use /PostToDMS to store the dataset info in the DMS database. To customize the server name and/or stored procedure to use for posting, use an XML parameter file with settings DSInfoConnectionString, DSInfoDBPostingEnabled, and DSInfoStoredProcedure");
Console.WriteLine();
Console.WriteLine("Use /PythonPlot to create plots with Python instead of OxyPlot");
Console.WriteLine();
Console.WriteLine("Known file extensions: " + CollapseList(scanner.GetKnownFileExtensionsList()));
Console.WriteLine("Known folder extensions: " + CollapseList(scanner.GetKnownFolderExtensionsList()));
Console.WriteLine();
Console.WriteLine("Program written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA) in 2005");
Console.WriteLine("Version: " + GetAppVersion());
Console.WriteLine();
Console.WriteLine("E-mail: [email protected] or [email protected]");
Console.WriteLine("Website: http://omics.pnl.gov/ or http://panomics.pnnl.gov/");
Console.WriteLine();
// Delay for 750 msec in case the user double clicked this file from within Windows Explorer (or started the program via a shortcut)
System.Threading.Thread.Sleep(750);
}
catch (Exception ex)
{
ShowErrorMessage("Error displaying the program syntax: " + ex.Message);
}
}
