public void temp_ExecuteSipper() { var paramFile = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.FolderPathForCopiedRawDataset = @"D:\data\temp"; var testDataset = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile), Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml"); parameters.SaveParametersToXML(outputParameterFile); var executor = new SipperWorkflowExecutor(parameters, testDataset); executor.Execute(); }
public void ExecuteSipper_FindAssociatedTargetsFile() { var paramFile = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.DbName = String.Empty; parameters.DbServer = String.Empty; parameters.DbTableName = String.Empty; parameters.CopyRawFileLocal = false; //parameters.ReferenceDataForTargets = // @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Targets\massTag_reference_file.txt"; parameters.TargetsBaseFolder = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Targets"; var testDataset = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile), Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml"); parameters.SaveParametersToXML(outputParameterFile); var executor = new SipperWorkflowExecutor(parameters, testDataset); executor.Execute(); }
public void ExecuteSipper_UsingTargetsWithEmpiricalFormulaOnly() { var paramFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.DbName = String.Empty; parameters.DbServer = String.Empty; parameters.DbTableName = String.Empty; parameters.CopyRawFileLocal = false; parameters.TargetsFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_10practice_targets_empFormula_noMonoMass.txt"; var testDataset = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executor = new SipperWorkflowExecutor(parameters, testDataset); executor.Execute(); }
public void loadPreviousResultsAndReProcess() { var paramFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperExecutorParams_importedFeaturesWithEmpFormula.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.TargetsFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Results\Yellow_C13_070_23Mar10_Griffin_10-01-28_copy_results.txt"; //string exportedParameterFile = // @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperExecutorParams1.xml"; //parameters.SaveParametersToXML(exportedParameterFile); var testDataset = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executor = new SipperWorkflowExecutor(parameters, testDataset); Assert.IsTrue(executor.ExecutorParameters.WorkflowType == Globals.TargetedWorkflowTypes.SipperWorkflowExecutor1); executor.Execute(); }
public void loadLCMSFeaturesNotIdentifiedAndProcess2() { var paramFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperExecutorParams_importedFeaturesWithEmpFormula.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.TargetsToFilterOn = String.Empty; parameters.TargetsFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_select_unidentified_LCMSFeatures.txt"; parameters.ReferenceDataForTargets = String.Empty; var testDataset = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executor = new SipperWorkflowExecutor(parameters, testDataset); Assert.IsTrue(executor.ExecutorParameters.WorkflowType == Globals.TargetedWorkflowTypes.SipperWorkflowExecutor1); executor.Execute(); }
public void ExecuteSipper() { var paramFile = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.CopyRawFileLocal = false; //parameters.FolderPathForCopiedRawDataset = @"D:\data\temp"; var testDataset = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile), Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml"); parameters.SaveParametersToXML(outputParameterFile); var executor = new SipperWorkflowExecutor(parameters, testDataset); var targetsOfInterest = new int[] { 5555 }; executor.Targets.TargetList = (executor.Targets.TargetList.Where(n => targetsOfInterest.Contains(n.ID))).ToList(); executor.Execute(); var workflow = executor.TargetedWorkflow as SipperTargetedWorkflow; var result = workflow.Result as SipperLcmsTargetedResult; Assert.IsNotNull(result); Assert.IsNotNull(result.ChromCorrelationData); Assert.IsNotNull(result.ChromCorrelationData.CorrelationDataItems); Assert.IsTrue(result.ChromCorrelationData.CorrelationDataItems.Count > 0); //foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems) //{ // Console.WriteLine(dataItem.CorrelationRSquaredVal); //} foreach (var fitScoreDataItem in workflow.FitScoreData) { Console.WriteLine(fitScoreDataItem.Key + "\t" + fitScoreDataItem.Value); } }
public AutoprocessorViewModel() { ExecutorParameters = new SipperWorkflowExecutorParameters(); ExecutorParameters.TargetType = Globals.TargetType.LcmsFeature; SipperWorkflowParameters = new SipperTargetedWorkflowParameters(); StatusCollection = new ObservableCollection<string>(); ProgressInfos = new ObservableCollection<TargetedWorkflowExecutorProgressInfo>(); FileInputs = new FileInputsViewModel(null); }
public void Test1() { var outputFile = Path.Combine(FileRefs.OutputFolderPath, "SipperExecutorParameters1.xml"); var parameters = new SipperWorkflowExecutorParameters(); parameters.DeleteLocalDatasetAfterProcessing = false; parameters.FolderPathForCopiedRawDataset = String.Empty; parameters.ReferenceDataForTargets = @"C:\Sipper\SipperDemo\SipperInputs\Sample_ReferenceDataForTargets.txt"; parameters.TargetedAlignmentIsPerformed = false; parameters.TargetedAlignmentWorkflowParameterFile = String.Empty; parameters.TargetsBaseFolder = @"C:\Sipper\SipperDemo\SipperInputs\Targets"; parameters.TargetsFilePath = @"C:\Sipper\SipperDemo\SipperInputs\Targets\sample_targets.txt"; parameters.TargetsToFilterOn = String.Empty; parameters.WorkflowParameterFile = @"C:\Sipper\SipperDemo\SipperInputs\SipperWorkflowParameters.xml"; parameters.SaveParametersToXML(outputFile); }
public void test2() { var paramFile = @"\\protoapps\UserData\Slysz\Data\Yellowstone\SIPPER\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); var testDataset = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executor = new SipperWorkflowExecutor(parameters, testDataset); Assert.IsTrue(executor.ExecutorParameters.WorkflowType == Globals.TargetedWorkflowTypes.SipperWorkflowExecutor1); executor.Execute(); }
public void ExecuteSipper_UsingSpecifiedTargets() { var paramFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperExecutorParams1.xml"; var parameters = new SipperWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.DbName = String.Empty; parameters.DbServer = String.Empty; parameters.DbTableName = String.Empty; parameters.CopyRawFileLocal = false; parameters.ReferenceDataForTargets = @"\\protoapps\DataPkgs\Public\2012\548_YSIP_C12_C13_data_analysis\massTag_reference_file.txt"; parameters.TargetsFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_10practice_targets.txt"; var testDataset = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executor = new SipperWorkflowExecutor(parameters, testDataset); executor.Execute(); }