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(); }