public new void InitializeWorkflow()
{
var executorParams = (LcmsFeatureTargetedWorkflowExecutorParameters)ExecutorParameters;
//_loggingFileName = GetLogFileName(ExecutorParameters.LoggingFolder);
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
Targets = GetLcmsFeatureTargets(ExecutorParameters.TargetsFilePath);
MassTagsForReference = GetMassTagTargets(executorParams.MassTagsForReference);
UpdateTargetsWithMassTagInfo(Targets, MassTagsForReference);
Check.Ensure(Targets != null && Targets.TargetList.Count > 0,
"Target massTags is empty. Check the path to the massTag data file.");
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
//TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
//TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
protected TargetedWorkflowExecutor(WorkflowExecutorBaseParameters parameters, WorkflowParameters workflowParameters, string datasetPath, BackgroundWorker backgroundWorker = null)
{
this.DatasetPath = datasetPath;
RunIsDisposed = true;
_backgroundWorker = backgroundWorker;
this.WorkflowParameters = parameters;
_workflowParameters = workflowParameters;
ResultRepository = new TargetedResultRepository();
InitializeWorkflow();
}
/// <summary>
/// Factory method for creating the Workflow object using the WorkflowType information in the parameter object
/// </summary>
/// <param name="workflowParameters"></param>
/// <returns></returns>
public static TargetedWorkflow CreateWorkflow(WorkflowParameters workflowParameters)
{
TargetedWorkflow wf;
switch (workflowParameters.WorkflowType)
{
case Globals.TargetedWorkflowTypes.Undefined:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.UnlabelledTargeted1:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.O16O18Targeted1:
wf = new O16O18Workflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.N14N15Targeted1:
wf = new N14N15Workflow2(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.SipperTargeted1:
wf = new SipperTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.TargetedAlignerWorkflow1:
wf = new TargetedAlignerWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.TopDownTargeted1:
wf = new TopDownTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.PeakDetectAndExportWorkflow1:
throw new System.NotImplementedException("Cannot create this workflow type here.");
case Globals.TargetedWorkflowTypes.BasicTargetedWorkflowExecutor1:
throw new System.NotImplementedException("Cannot create this workflow type here.");
case Globals.TargetedWorkflowTypes.UIMFTargetedMSMSWorkflowCollapseIMS:
wf = new UIMFTargetedMSMSWorkflowCollapseIMS(workflowParameters as TargetedWorkflowParameters);
break;
default:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
}
return(wf);
}
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 BasicTargetedWorkflowExecutor(WorkflowExecutorBaseParameters workflowExecutorParameters, WorkflowParameters workflowParameters, string datasetPath) : base(workflowExecutorParameters, workflowParameters, datasetPath)
{
}
public new void InitializeWorkflow()
{
//_loggingFileName = GetLogFileName(ExecutorParameters.LoggingFolder);
Check.Require(WorkflowParameters is SipperWorkflowExecutorParameters, "Parameters are not of the right type.");
var db = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbName;
var server = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbServer;
var table = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbTableName;
var massTagIDsForFiltering =
GetMassTagsToFilterOn(((SipperWorkflowExecutorParameters)WorkflowParameters).TargetsToFilterOn).Distinct().ToList();
_loggingFileName = Path.Combine(ExecutorParameters.OutputFolderBase, "Logs", RunUtilities.GetDatasetName(DatasetPath) + "_log.txt");
TargetsAreFromPeakMatchingDataBase = (!String.IsNullOrEmpty(db) && !String.IsNullOrEmpty(server));
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
if (TargetsAreFromPeakMatchingDataBase)
{
Targets = LoadTargetsFromPeakMatchingResultsForGivenDataset(RunUtilities.GetDatasetName(DatasetPath));
}
else
{
if (targetsFilePathIsEmpty)
{
var currentTargetsFilePath = TryFindTargetsForCurrentDataset(); //check for a _targets file specifically associated with dataset
if (String.IsNullOrEmpty(currentTargetsFilePath))
{
Targets = null;
}
else
{
Targets = GetLcmsFeatureTargets(currentTargetsFilePath);
}
}
else
{
Targets = GetLcmsFeatureTargets(ExecutorParameters.TargetsFilePath);
}
}
Check.Ensure(Targets != null && Targets.TargetList.Count > 0, "Failed to initialize - Target list is empty. Please check parameter file.");
if (massTagIDsForFiltering.Count > 0)
{
Targets.TargetList =
(from n in Targets.TargetList
where massTagIDsForFiltering.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
}
MassTagIDsinTargets = Targets.TargetList.Select(p => (long)((LcmsFeatureTarget)p).FeatureToMassTagID).Where(n => n > 0).ToList();
if (TargetsAreFromPeakMatchingDataBase)
{
var mtImporter = new MassTagFromSqlDbImporter(db, server, MassTagIDsinTargets);
MassTagsForReference = mtImporter.Import();
}
else
{
MassTagsForReference = GetMassTagTargets(((SipperWorkflowExecutorParameters)WorkflowParameters).ReferenceDataForTargets, MassTagIDsinTargets.Select(p => (int)p).ToList());
}
MassTagsForReference.TargetList = (from n in MassTagsForReference.TargetList
group n by new
{
n.ID,
n.ChargeState
}
into grp
select grp.First()).ToList();
UpdateTargetMissingInfo();
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
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);
}
}
public TopDownTargetedWorkflowExecutor(WorkflowExecutorBaseParameters parameters, WorkflowParameters workflowParameters, string datasetPath, BackgroundWorker backgroundWorker = null)
: base(parameters, workflowParameters, datasetPath, backgroundWorker)
{
}