public void O16O18Workflow_ProblemCaseTesting1()
{
//This is a nice case where the O16 is quite low and can be missed. In the current settings
//the O16Chrom is null (by itself), so the chrom correlation fails.
//Thus quant based on chrom corr fails, but quant based on O16O18 feature finding succeeds.
//7673789
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
var testTarget = 7415;
executor.Targets.TargetList =
executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList();
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase,
"Results",
executor.TargetedWorkflow.Run.DatasetName + "_results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import().Results;
var result1 = results.First();
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
public void O16O18Workflow_ProblemCaseTesting2()
{
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
executorParameters.TargetsFilePath =
@"\\protoapps\DataPkgs\Public\2012\641_Alz_O16O18_dataprocessing2\Targets\MT_Human_ALZ_O18_P852\MassTags_PMT2.txt";
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
//int testTarget = 7673789;
//executor.Targets.TargetList =executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState==3).ToList();
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "Results",
executor.TargetedWorkflow.Run.DatasetName + "_results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import().Results;
var result1 = results.First();
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
public void StandardO16O18Testing_VladAlz()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
var testTarget = 9282;
executor.Targets.TargetList =
executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList();
//executor.InitializeRun(testDatasetPath);
//executor.TargetedWorkflow.Run = executor.Run;
//foreach (var targetBase in executor.Targets.TargetList)
//{
// executor.Run.CurrentMassTag = targetBase;
// var workflow = (O16O18Workflow)executor.TargetedWorkflow;
// workflow.Execute();
// var result = workflow.Result as DeconTools.Backend.Core.Results.LcmsFeatureTargetedResult;
//}
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase,
"Results",
executor.TargetedWorkflow.Run.DatasetName + "_Results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(3, repository.Results.Count);
var result1 = repository.Results[1] as O16O18TargetedResultDTO;
Assert.AreEqual(9282, result1.TargetID);
Assert.AreEqual(2, result1.ChargeState);
Assert.AreEqual(4537, result1.ScanLC);
Assert.AreEqual(0.32514m, (decimal)Math.Round(result1.NET, 5));
Assert.AreEqual(-0.001662m, (decimal)Math.Round(result1.NETError, 6));
Assert.AreEqual(0.274m, (decimal)Math.Round(result1.Ratio, 3));
Assert.IsTrue(result1.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
