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);
}
