public new void InitializeWorkflow()
{
_resultsFolder = string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase) ? RunUtilities.GetDatasetParentFolder(DatasetPath) : GetResultsFolder(ExecutorParameters.OutputFolderBase);
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
var currentTargetsFilePath = targetsFilePathIsEmpty ? TryFindTargetsForCurrentDataset() : ExecutorParameters.TargetsFilePath;
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
public void InitializeWorkflow()
{
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
_resultsFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
}
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
string currentTargetsFilePath;
if (targetsFilePathIsEmpty)
{
currentTargetsFilePath = TryFindTargetsForCurrentDataset(); //check for a _targets file specifically associated with dataset
}
else
{
currentTargetsFilePath = ExecutorParameters.TargetsFilePath;
}
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
Check.Ensure(Targets != null && Targets.TargetList.Count > 0,
"Target massTags is empty (or all peptides contain unknown modifications). Check the path to the massTag data file.");
IqLogger.Log.Info("Total targets loaded= " + Targets.TargetList.Count);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (TargetedWorkflow == null)
{
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
else
{
_workflowParameters = TargetedWorkflow.WorkflowParameters;
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
}
/// <summary>
/// A factory method for creating the WorkflowParameters class. Based on the 'WorkflowType' parameter of the xml file.
/// </summary>
/// <param name="xmlFilepath"></param>
/// <returns></returns>
public static WorkflowParameters CreateParameters(string xmlFilepath)
{
Check.Require(File.Exists(xmlFilepath), "Workflow parameter file could not be loaded. File not found: " + xmlFilepath);
var doc = XDocument.Load(xmlFilepath);
var xElement = doc.Element("WorkflowParameters");
if (xElement == null)
{
throw new Exception("WorkflowParameters element not found in " + xmlFilepath);
}
var query = xElement.Elements();
var parameterTableFromXML = new Dictionary <string, string>();
foreach (var item in query)
{
var paramName = item.Name.ToString();
var paramValue = item.Value;
if (!parameterTableFromXML.ContainsKey(paramName))
{
parameterTableFromXML.Add(paramName, paramValue);
}
}
Globals.TargetedWorkflowTypes workflowType;
var successfulEnum = Enum.TryParse(parameterTableFromXML["WorkflowType"], out workflowType);
WorkflowParameters workflowParameters;
if (successfulEnum)
{
switch (workflowType)
{
case Globals.TargetedWorkflowTypes.Undefined:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.UnlabelledTargeted1:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.O16O18Targeted1:
workflowParameters = new O16O18WorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.N14N15Targeted1:
workflowParameters = new N14N15Workflow2Parameters();
break;
case Globals.TargetedWorkflowTypes.SipperTargeted1:
workflowParameters = new SipperTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.TargetedAlignerWorkflow1:
workflowParameters = new TargetedAlignerWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.BasicTargetedWorkflowExecutor1:
workflowParameters = new BasicTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.LcmsFeatureTargetedWorkflowExecutor1:
workflowParameters = new LcmsFeatureTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.SipperWorkflowExecutor1:
workflowParameters = new SipperWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.TopDownTargeted1:
workflowParameters = new TopDownTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.TopDownTargetedWorkflowExecutor1:
workflowParameters = new TopDownTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.UIMFTargetedMSMSWorkflowCollapseIMS:
workflowParameters = new UIMFTargetedMSMSWorkflowCollapseIMSParameters();
break;
default:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
}
}
else
{
throw new ArgumentOutOfRangeException(
"Tried to create WorkflowParameter object. But WorkflowType is unknown.");
}
workflowParameters.LoadParameters(xmlFilepath);
return(workflowParameters);
}