internal Project CreateProject(Process process)
{
var project = new Project(process.Provenance.QualifierId);
// All projects in a msbuild file must use the same BuildXL value.
// TODO: Check whether this is the same BuildXL value as the other projects in this msbuild file
var value = process.Provenance.OutputValueSymbol.ToString(Context.SymbolTable);
project.SetProperty("DominoValue", value);
project.SetProperty("ProjectGuid", Guid);
project.SetProperty("SpecRoot", SpecDirectory);
var relativeSpecFile = Context.GetRelativePath(SpecFilePath).ToString(Context.StringTable);
project.SetProperty("DominoSpecFile", relativeSpecFile);
project.AddItem("None", SpecFilePath);
var dirString = SpecFilePath.GetParent(Context.PathTable).ToString(Context.PathTable);
var packagePath = System.IO.Path.Combine(dirString, "package" + Names.DotDscExtension);
var packageConfigPath = System.IO.Path.Combine(dirString, Names.PackageConfigDsc);
if (System.IO.File.Exists(packagePath))
{
project.AddItem("DominoPackageFile", AbsolutePath.Create(Context.PathTable, packagePath));
}
if (System.IO.File.Exists(packageConfigPath))
{
project.AddItem("DominoPackageConfigFile", AbsolutePath.Create(Context.PathTable, packageConfigPath));
}
return(project);
}
internal Project CreateProject(Process process)
{
string qualifierString = Context.QualifierTable.GetCanonicalDisplayString(process.Provenance.QualifierId);
var project = new Project(qualifierString);
// All projects in a msbuild file must use the same BuildXL value.
// TODO: Check whether this is the same BuildXL value as the other projects in this msbuild file
var value = process.Provenance.OutputValueSymbol.ToString(Context.SymbolTable);
project.SetProperty("DominoValue", value);
project.SetProperty("ProjectGuid", Guid);
project.SetProperty("SpecRoot", SpecDirectory);
// Try to get the target framework:
var qualifier = Context.QualifierTable.GetQualifier(process.Provenance.QualifierId);
if (qualifier.TryGetValue(Context.StringTable, "targetFramework", out var targetFramework))
{
// MsBuild has its own version number so do a custom
if (targetFramework.StartsWith("net") && targetFramework.Substring(3).ToCharArray().All(char.IsDigit))
{
var msbuildStyleTf = "v" + string.Join(".", targetFramework.Substring(3).ToCharArray());
project.SetProperty("TargetFrameworkVersion", msbuildStyleTf);
project.SetProperty("TargetFrameworkProfile", string.Empty);
}
}
var relativeSpecFile = Context.GetRelativePath(SpecFilePath).ToString(Context.StringTable);
project.SetProperty("DominoSpecFile", relativeSpecFile);
project.AddItem("None", SpecFilePath);
var dirString = SpecFilePath.GetParent(Context.PathTable).ToString(Context.PathTable);
var packagePath = System.IO.Path.Combine(dirString, "package" + Names.DotDscExtension);
var packageConfigPath = System.IO.Path.Combine(dirString, Names.PackageConfigDsc);
if (System.IO.File.Exists(packagePath))
{
project.AddItem("DominoPackageFile", AbsolutePath.Create(Context.PathTable, packagePath));
}
if (System.IO.File.Exists(packageConfigPath))
{
project.AddItem("DominoPackageConfigFile", AbsolutePath.Create(Context.PathTable, packageConfigPath));
}
return(project);
}
internal override void VisitProcess(Process process, ProcessType pipCategory)
{
string friendlyQualifier = Context.QualifierTable.GetCanonicalDisplayString(process.Provenance.QualifierId);
// TODO: After fixing the qualifier in the DS, I will start using the qualifier id instead of friendly qualifier name
// Context.QualifierTable.GetQualifiedOutputDirectoryPart(Context.StringTable, qualifierId).ToString(Context.StringTable);
var arguments = Context.GetArgumentsDataFromProcess(process);
Project project;
if (!ProjectsByQualifier.TryGetValue(friendlyQualifier, out project))
{
project = CreateProject(process);
project.SetProperty("PlatformToolset", "v140");
FillProjectConfigurations(project);
AddHeaderFiles(project);
ProjectsByQualifier.Add(friendlyQualifier, project);
}
switch (pipCategory)
{
case ProcessType.Cl:
IterateClArguments(project, arguments);
break;
case ProcessType.Link:
IterateLinkArguments(project, arguments);
// If this is DS, use WorkingDirectory as an output folder.
var outputDir = ExtensionUtilities.IsScriptExtension(SpecFilePath.GetExtension(Context.PathTable).ToString(Context.StringTable)) ?
process.WorkingDirectory :
process.UniqueOutputDirectory;
SetOutputDirectory(project, outputDir, OutputDirectoryType.Build);
break;
}
}
public bool Validate()
{
// Spec file path validation
if (string.IsNullOrWhiteSpace(SpecFilePath))
{
PrintError("Missing parameter for spectrum file path");
return(false);
}
// Check for folder-type datasets, and replace specFilePath with the directory name if it is.
SpecFilePath = MassSpecDataReaderFactory.GetDatasetName(SpecFilePath);
var isDirectoryDataset = MassSpecDataReaderFactory.IsADirectoryDataset(SpecFilePath);
// True if specFilePath is a directory that is NOT a supported folder-type dataset.
var specPathIsDirectory = Directory.Exists(SpecFilePath) && !isDirectoryDataset;
if (!File.Exists(SpecFilePath) && !specPathIsDirectory && !isDirectoryDataset)
{
PrintError("File not found: " + SpecFilePath);
return(false);
}
var types = MassSpecDataReaderFactory.MassSpecDataTypeFilterList;
if (!specPathIsDirectory && !(types.Select(ext => SpecFilePath.ToLower().EndsWith(ext)).Any()))
{
PrintError("Invalid file extension for spectrum file: (" + Path.GetExtension(SpecFilePath) + ") " + SpecFilePath);
return(false);
}
// TODO: Handle non-.raw files in the subfolder
SpecFilePaths = Directory.Exists(SpecFilePath) && !MassSpecDataReaderFactory.IsADirectoryDataset(SpecFilePath) ? Directory.GetFiles(SpecFilePath, "*.raw") : new[] { SpecFilePath };
// Database path validation
if (string.IsNullOrWhiteSpace(DatabaseFilePath))
{
PrintError("Missing parameter for database file path");
return(false);
}
if (!File.Exists(DatabaseFilePath))
{
PrintError("File not found: " + DatabaseFilePath);
return(false);
}
var dbExtension = Path.GetExtension(DatabaseFilePath).ToLower();
if (!dbExtension.Equals(".fa") &&
!dbExtension.Equals(".fasta"))
{
PrintError("Invalid extension for the database file path (" + dbExtension + ")");
return(false);
}
// Output directory validation
if (string.IsNullOrWhiteSpace(OutputDir))
{
// Must use "Path.GetFullPath" to return the absolute path when the source file is in the working directory
// But, it could cause problems with too-long paths.
OutputDir = specPathIsDirectory ? SpecFilePath : Path.GetDirectoryName(Path.GetFullPath(SpecFilePath));
}
if (string.IsNullOrWhiteSpace(OutputDir))
{
PrintError("Invalid output file directory: " + OutputDir);
return(false);
}
if (!Directory.Exists(OutputDir))
{
if (File.Exists(OutputDir) && !File.GetAttributes(OutputDir).HasFlag(FileAttributes.Directory))
{
PrintError("OutputDir \"" + OutputDir + "\" is not a directory!");
return(false);
}
Directory.CreateDirectory(OutputDir);
}
// Mods file validation
if (!string.IsNullOrWhiteSpace(ModsFilePath) && !File.Exists(ModsFilePath))
{
PrintError("Modifications file not found: " + ModsFilePath);
return(false);
}
try
{
var errorMessage = LoadModsFile(ModsFilePath);
if (!string.IsNullOrWhiteSpace(errorMessage))
{
PrintError(errorMessage);
return(false);
}
}
catch (Exception ex)
{
PrintError("Exception parsing the file for parameter -mod: " + ex.Message);
return(false);
}
// Scans file validation
if (!string.IsNullOrWhiteSpace(ScansFilePath) && !File.Exists(ScansFilePath))
{
PrintError("Scans File file not found: " + ScansFilePath);
return(false);
}
try
{
var errorMessage = LoadScansFile(ScansFilePath);
if (!string.IsNullOrWhiteSpace(errorMessage))
{
PrintError(errorMessage);
return(false);
}
}
catch (Exception ex)
{
PrintError("Exception parsing the file for parameter -scansFile: " + ex.Message);
return(false);
}
// Feature file validation
if (!string.IsNullOrWhiteSpace(FeatureFilePath) && !File.Exists(FeatureFilePath))
{
PrintError("Feature File not found: " + FeatureFilePath);
return(false);
}
if (!string.IsNullOrWhiteSpace(FeatureFilePath) &&
!Path.GetExtension(FeatureFilePath).ToLower().Equals(".csv") &&
!Path.GetExtension(FeatureFilePath).ToLower().Equals(".ms1ft") &&
!Path.GetExtension(FeatureFilePath).ToLower().Equals(".msalign"))
{
PrintError("Invalid extension for the Feature file path (" + Path.GetExtension(FeatureFilePath) + ")");
return(false);
}
// MinX/MaxX validation
if (MinSequenceLength > MaxSequenceLength)
{
PrintError("MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!");
return(false);
}
if (MinProductIonCharge > MaxProductIonCharge)
{
PrintError("MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!");
return(false);
}
if (MinSequenceMass > MaxSequenceMass)
{
PrintError("MinSequenceMassInDa (" + MinSequenceMass + ") is larger than MaxSequenceMassInDa (" + MaxSequenceMass + ")!");
return(false);
}
MaxNumThreads = GetOptimalMaxThreads(MaxNumThreads);
return(true);
}
