public void importTest1()
{
var testFile = Path.Combine(FileRefs.ImportedData, "ImportedSipperResults1.txt");
var importer = new SipperResultFromTextImporter(testFile);
var results = importer.Import();
Assert.IsNotNull(results);
Assert.IsTrue(results.Results.Count > 0);
var testResult1 = results.Results.First() as SipperLcmsFeatureTargetedResultDTO;
Assert.IsNotNull(testResult1);
Assert.IsNotNull(testResult1.LabelDistributionVals);
Assert.IsTrue(testResult1.LabelDistributionVals.Length > 0);
Console.WriteLine(testResult1.ToStringWithDetailsAsRow());
}
public void executeWorkflow1()
{
var executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\workflowExecutor_parameters.xml";
WorkflowExecutorBaseParameters executorParameters = new LcmsFeatureTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var testDatasetPath = FileRefs.SipperRawDataFile;
var testDatasetName = "Yellow_C13_070_23Mar10_Griffin_10-01-28";
var expectedResultsFilename = executorParameters.OutputFolderBase + "\\Results" + "\\" + testDatasetName + "_results.txt";
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
TargetedWorkflowExecutor executor = new LcmsFeatureTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new SipperResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(9, repository.Results.Count);
var result1 = repository.Results[2];
Assert.AreEqual(8586, result1.TargetID);
Assert.AreEqual(2, result1.ChargeState);
Assert.AreEqual(6512, result1.ScanLC);
Assert.AreEqual(1543.82565m, (decimal)Math.Round(result1.MonoMass, 5));
}
public void LoadResults(string resultFile)
{
_resultRepositorySource.Results.Clear();
FileInfo fileInfo = new FileInfo(resultFile);
if (fileInfo.Exists)
{
SipperResultFromTextImporter importer = new SipperResultFromTextImporter(resultFile);
var tempResults = importer.Import();
_resultRepositorySource.Results.AddRange(tempResults.Results);
}
SetResults(_resultRepositorySource.Results);
}
public void process_test1()
{
AutoprocessorViewModel viewModel=new AutoprocessorViewModel();
// Instrument data file
string testRawDataFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
string expectedResultsFile = Path.GetDirectoryName(testRawDataFile) + "\\Results\\" +
RunUtilities.GetDatasetName(testRawDataFile) + "_results.txt";
if (File.Exists(expectedResultsFile)) File.Delete(expectedResultsFile);
// Parameter file
string testWorkflowFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\SipperTargetedWorkflowParameters1.xml";
// Targets file
string testTargetFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_testing_results.txt";
viewModel.FileInputs.CreateFileLinkage(testRawDataFile);
viewModel.FileInputs.CreateFileLinkage(testTargetFile1);
viewModel.FileInputs.CreateFileLinkage(testWorkflowFile);
viewModel.Execute();
Thread.Sleep(12000); // the viewModel has a background worker and we need to pause to let the processing complete in the background
Assert.That(File.Exists(expectedResultsFile));
SipperResultFromTextImporter importer = new SipperResultFromTextImporter(expectedResultsFile);
var resultRepo = importer.Import();
Assert.AreEqual(19, resultRepo.Results.Count);
var testResult = (DeconTools.Workflows.Backend.Results.SipperLcmsFeatureTargetedResultDTO)resultRepo.Results[1];
Assert.AreEqual("Yellow_C13_070_23Mar10_Griffin_10-01-28", testResult.DatasetName);
Assert.AreEqual(7585, testResult.TargetID);
Assert.AreEqual("C63H109N17O21", testResult.EmpiricalFormula);
Assert.AreEqual(11805, testResult.ScanLC);
}
public void Execute()
{
//Load results
SipperResultFromTextImporter importer = new SipperResultFromTextImporter(_fileInputs.TargetsFilePath);
_resultRepositorySource = importer.Import();
//Load Parameters
WorkflowParameters.LoadParameters(_fileInputs.ParameterFilePath);
//Sort by dataset
var sortedDatasets = (from n in _resultRepositorySource.Results orderby n.DatasetName select n);
//Set output folder
//iterate over results
int resultCounter = 0;
foreach (SipperLcmsFeatureTargetedResultDTO result in sortedDatasets)
{
resultCounter++;
CurrentResult = result;
if (result.DatasetName != CurrentDatasetName)
{
if (Run != null)
{
Run.Close();
}
InitializeRun(result.DatasetName);
}
SetCurrentWorkflowTarget(result);
Workflow.Execute();
double fwhm;
if (Workflow.Result.IsotopicProfile != null)
{
fwhm = Workflow.Result.IsotopicProfile.GetFWHM();
}
else
{
fwhm = DefaultMSPeakWidth;
}
TheorProfileXYData = TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData(Workflow.Result.Target.IsotopicProfile, fwhm);
if (resultCounter % NumResultsPerFolder == 0)
{
_subFolderCounter++;
}
OutputImages();
}
}
public void LoadUnlabeledResults(string filePath)
{
SipperResultFromTextImporter importer = new SipperResultFromTextImporter(filePath);
UnlabeledResults = (from SipperLcmsFeatureTargetedResultDTO n in importer.Import().Results select n).ToList();
}
