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Result Text and Individual File Result Cleanup (#2397)
* Updated to MzLib 1.0.548 and fixed custom ions in search tasks * reverted calibration task change * merged in master bbbyy * Spectral Library from Command Line (#2386) * Updated to MzLib 1.0.548 and fixed custom ions in search tasks * reverted calibration task change * merged in master bbbyy * Enabled Library Loading from command line * replaced "Peptides" with GlobalVariables.AnalyteType * built lazy loading search result structure for post search analysis task * Finsihed test case strucutre, added test for result files. Added top-down test case * changed access modifier * Refactored test case setup * Added more test cases to hopefully up coverage
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,192 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.Diagnostics.CodeAnalysis; | ||
| using System.IO; | ||
| using System.Linq; | ||
| using Nett; | ||
| using NUnit.Framework; | ||
| using TaskLayer; | ||
|
|
||
| namespace Test | ||
| { | ||
| public enum EverythingRunnerEngineTestCases | ||
| { | ||
| BottomUpQValue, | ||
| BottomUpQValueNoIndividualFilesWriteMzId, | ||
| BottomUpQValueNoIndividualFilesWritePepXml, | ||
| BottomUpQValueSingle, | ||
| BottomUpPepQValue, | ||
| TopDownQValue, | ||
| TopDownQValueSingle | ||
| } | ||
|
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||
| /// <summary> | ||
| /// Test cases for the post search analysis task. These test cases are used to verify that the post search analysis task is functioning correctly. | ||
| /// This structure ensures that the database search is only ran once, and only ran once called. | ||
| /// These directories are cleaned up in the Global Cleanup found in SetUpTests.GlobalTearDown | ||
| /// </summary> | ||
| [ExcludeFromCodeCoverage] | ||
| internal class EverythingRunnerEngineTestCase : IDisposable | ||
| { | ||
| internal EverythingRunnerEngineTestCases TestCase { get; init; } | ||
| internal List<(string, MetaMorpheusTask)> TaskList { get; init; } | ||
| internal List<DbForTask> DatabaseList { get; init; } | ||
| internal List<string> DataFileList { get; init; } | ||
| internal string OutputDirectory => Path.Combine(ResultDirectory, TestCase.ToString()); | ||
| internal bool IsTopDown { get; init; } | ||
| internal bool HasRun { get; private set; } | ||
| internal bool WriteIndividualResults { get; init; } | ||
| internal bool WritePepXml { get; init; } | ||
| internal bool WriteMzId { get; init; } | ||
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| internal EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases testCase, | ||
| List<(string, MetaMorpheusTask)> taskList, List<string> dataFileList, | ||
| List<DbForTask> databaseList, bool isTopDown) | ||
| { | ||
| TestCase = testCase; | ||
| TaskList = taskList; | ||
| DatabaseList = databaseList; | ||
| DataFileList = dataFileList; | ||
| IsTopDown = isTopDown; | ||
| HasRun = false; | ||
|
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||
| var firstSearchTask = taskList.Select(p => p.Item2).FirstOrDefault(p => p.TaskType == MyTask.Search); | ||
| if (firstSearchTask is null) return; | ||
|
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| var searchTask = (SearchTask)firstSearchTask; | ||
| WriteIndividualResults = searchTask.SearchParameters.WriteIndividualFiles; | ||
| WritePepXml = searchTask.SearchParameters.WritePepXml; | ||
| WriteMzId = searchTask.SearchParameters.WriteMzId; | ||
| } | ||
|
|
||
| internal void Run() | ||
| { | ||
| if (Directory.Exists(OutputDirectory)) | ||
| Directory.Delete(OutputDirectory, true); | ||
|
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| var runner = new EverythingRunnerEngine(TaskList, DataFileList, DatabaseList, OutputDirectory); | ||
| runner.Run(); | ||
| HasRun = true; | ||
| } | ||
|
|
||
| public void Dispose() | ||
| { | ||
| if (Directory.Exists(OutputDirectory)) | ||
| Directory.Delete(OutputDirectory, true); | ||
| } | ||
|
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| #region Case Setup | ||
|
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| internal static string ResultDirectory => | ||
| Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PostSearchAnalysisTaskTest"); | ||
|
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| private static Dictionary<EverythingRunnerEngineTestCases, EverythingRunnerEngineTestCase> _cases; | ||
|
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| internal static bool TryGetTestCase(EverythingRunnerEngineTestCases testCase, | ||
| out EverythingRunnerEngineTestCase outCase) | ||
| { | ||
| if (!_cases.TryGetValue(testCase, out outCase)) return false; | ||
|
|
||
| if (!outCase.HasRun) | ||
| outCase.Run(); | ||
| return true; | ||
| } | ||
|
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| internal static EverythingRunnerEngineTestCase GetTestCase(EverythingRunnerEngineTestCases testCase) | ||
| { | ||
| if (!TryGetTestCase(testCase, out var outCase)) | ||
| throw new KeyNotFoundException($"Test case {testCase} not found"); | ||
| return outCase; | ||
| } | ||
|
|
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| internal static void DisposeAll() | ||
| { | ||
| foreach (var testCase in _cases.Values) | ||
| testCase.Dispose(); | ||
| } | ||
|
|
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| static EverythingRunnerEngineTestCase() | ||
| { | ||
| // Directory GlobalSetup | ||
| if (Directory.Exists(ResultDirectory)) | ||
| Directory.Delete(ResultDirectory, true); | ||
|
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||
| if (!Directory.Exists(ResultDirectory)) | ||
| Directory.CreateDirectory(ResultDirectory); | ||
|
|
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| // Test Case Instantiation | ||
| _cases = new(); | ||
|
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| string myTomlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TestData\Task1-SearchTaskconfig.toml"); | ||
| SearchTask searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig); | ||
| string myFile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TestData\TaGe_SA_A549_3_snip.mzML"); | ||
| string myFile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TestData\TaGe_SA_A549_3_snip_2.mzML"); | ||
| string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TestData\TaGe_SA_A549_3_snip.fasta"); | ||
| _cases.Add(EverythingRunnerEngineTestCases.BottomUpQValue, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile1, myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, | ||
| false)); | ||
| _cases.Add(EverythingRunnerEngineTestCases.BottomUpQValueSingle, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.BottomUpQValueSingle, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile2 }, | ||
| new List<DbForTask> { new DbForTask(myDatabase, false) }, false)); | ||
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| searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig); | ||
| searchTaskLoaded.SearchParameters.WriteIndividualFiles = false; | ||
| searchTaskLoaded.SearchParameters.WriteMzId = true; | ||
| searchTaskLoaded.SearchParameters.WritePepXml = false; | ||
| _cases.Add(EverythingRunnerEngineTestCases.BottomUpQValueNoIndividualFilesWriteMzId, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.BottomUpQValueNoIndividualFilesWriteMzId, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile1, myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, | ||
| false)); | ||
|
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| searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig); | ||
| searchTaskLoaded.SearchParameters.WriteIndividualFiles = false; | ||
| searchTaskLoaded.SearchParameters.WriteMzId = false; | ||
| searchTaskLoaded.SearchParameters.WritePepXml = true; | ||
| _cases.Add(EverythingRunnerEngineTestCases.BottomUpQValueNoIndividualFilesWritePepXml, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.BottomUpQValueNoIndividualFilesWritePepXml, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile1, myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, | ||
| false)); | ||
|
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| myTomlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TestData\Task2-SearchTaskconfig.toml"); | ||
| searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig); | ||
| // TODO: Uncomment this line and change values for PR 2394 | ||
| //searchTaskLoaded.CommonParameters.QValueCutoffForPepCalculation = 0.01; | ||
| _cases.Add(EverythingRunnerEngineTestCases.BottomUpPepQValue, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.BottomUpPepQValue, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile1, myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, | ||
| false)); | ||
|
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| myTomlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, | ||
| @"TopDownTestData\TopDownSearchToml.toml"); | ||
| searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig); | ||
| myFile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"); | ||
| myFile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TopDownTestData\slicedTDYeast.mzML"); | ||
| myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta"); | ||
| _cases.Add(EverythingRunnerEngineTestCases.TopDownQValue, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.TopDownQValue, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile1, myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, | ||
| true)); | ||
| _cases.Add(EverythingRunnerEngineTestCases.TopDownQValueSingle, | ||
| new EverythingRunnerEngineTestCase(EverythingRunnerEngineTestCases.TopDownQValueSingle, | ||
| new List<(string, MetaMorpheusTask)> { ("postSearchAnalysisTaskTestOutput", searchTaskLoaded) }, | ||
| new List<string> { myFile2 }, new List<DbForTask> { new DbForTask(myDatabase, false) }, true)); | ||
| } | ||
|
|
||
| #endregion | ||
| } | ||
| } | ||
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