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();
}
