| public static SafeDelete ( string path ) : void | ||
| path | string | |
| Результат | void | |
private void DoTestImportSim(bool asSmallMolecules)
{
if (asSmallMolecules && !RunSmallMoleculeTestVersions)
{
System.Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath(DOCUMENT_NAME);
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var pepdoc = doc;
if (asSmallMolecules)
{
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(pepdoc, TestContext.ResultsDirectory);
}
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the mzML file and verify Mz range
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME), 510, 512);
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME2), 555, 557);
}
}
public void CreateDb(string fileName)
{
// If the file exists, then the user chose to overwrite,
// so delete the existing file.
try
{
FileEx.SafeDelete(fileName);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
Settings.Default.ProteomeDbDirectory = Path.GetDirectoryName(fileName);
try
{
ProteomeDb.CreateProteomeDb(fileName);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(
Resources
.BuildBackgroundProteomeDlg_btnCreate_Click_An_error_occurred_attempting_to_create_the_proteome_file__0__,
fileName), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
if (textName.Text.Length == 0)
{
textName.Text = Path.GetFileNameWithoutExtension(fileName);
}
textPath.Text = fileName; // This will cause RefreshStatus()
}
public void CreateDatabase(string path)
{
//The file that was just created does not have a schema, so SQLite won't touch it.
//The file must have a schema or not exist for use with SQLite, so we'll delete
//it and install a schema
try
{
FileEx.SafeDelete(path);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
//Create file, initialize db
try
{
IonMobilityDb.CreateIonMobilityDb(path);
textDatabase.Text = path;
}
catch (DatabaseOpeningException x)
{
MessageDlg.ShowException(this, x);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.EditIonMobilityLibraryDlg_CreateDatabase_The_ion_mobility_library_file__0__could_not_be_created, path),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
private static void DeleteFiles(TestFilesDir testFilesDir, IEnumerable <string> fileNames)
{
foreach (var fileName in fileNames)
{
FileEx.SafeDelete(testFilesDir.GetTestPath(fileName));
}
}
public void WatersLockmassCmdlinePerfTest()
{
if (IsPerfTest && !RunPerfTests)
{
return; // Don't want to run this lengthy test right now
}
TestFilesZip = "https://skyline.gs.washington.edu/perftests/PerfTestLockmass.zip";
TestFilesPersistent = new[] { "ID19638_01_UCA195_2533_082715.raw" }; // List of files that we'd like to unzip alongside parent zipFile, and (re)use in place
TestFilesDir = new TestFilesDir(TestContext, TestFilesZip, "CmdlineTest", TestFilesPersistent);
var skyfile = GetTestPath("2533_FattyAcids.sky");
var rawPath = GetTestPath(TestFilesPersistent[0]);
const double lockmassNegative = 554.2615;
// Exercise the commandline
var outPathUncorrected = TestFilesDir.GetTestPath("cmdlineTestUncorrected.sky");
var outPathCorrected = TestFilesDir.GetTestPath("cmdlineTestCorrected.sky");
RunCommand("--in=" + skyfile,
"--import-file=" + rawPath,
"--out=" + outPathUncorrected);
FileEx.SafeDelete(Path.ChangeExtension(skyfile, ChromatogramCache.EXT));
var cmdDocUncorrected = ResultsUtil.DeserializeDocument(outPathUncorrected);
RunCommand("--in=" + skyfile,
"--import-file=" + rawPath,
"--import-lockmass-negative=" + lockmassNegative,
"--out=" + outPathCorrected);
var cmdDocCorrected = ResultsUtil.DeserializeDocument(outPathCorrected);
ComparePeaks(cmdDocCorrected, cmdDocUncorrected);
}
private void BuildLibraryError(string inputFile, string libraryPath, params string[] messageParts)
{
string redundantBuildPath = TestFilesDir.GetTestPath(_libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT);
FileEx.SafeDelete(redundantBuildPath);
string nonredundantBuildPath = TestFilesDir.GetTestPath(_libraryName + BiblioSpecLiteSpec.EXT);
FileEx.SafeDelete(nonredundantBuildPath);
ReportLibraryBuildFailures = false;
BuildLibrary(TestFilesDir.GetTestPath("library_errors"), new[] { inputFile }, libraryPath, false, false,
false, false, null);
var messageDlg = WaitForOpenForm <MessageDlg>();
Assert.IsNotNull(messageDlg, "No message box shown");
AssertEx.Contains(messageDlg.Message, "ERROR");
if (messageParts.Length == 0)
{
AssertEx.Contains(messageDlg.Message, inputFile, "line");
}
else
{
AssertEx.Contains(messageDlg.Message, messageParts);
}
OkDialog(messageDlg, messageDlg.OkDialog);
CheckLibraryExistence(redundantBuildPath, false);
CheckLibraryExistence(nonredundantBuildPath, false);
WaitForConditionUI(() => !PeptideSettingsUI.IsBuildingLibrary);
}
public BiblioSpecLiteBuilder GetLibBuilder(SrmDocument doc, string docFilePath, bool includeAmbiguousMatches)
{
string outputPath = BiblioSpecLiteSpec.GetLibraryFileName(docFilePath);
// Check to see if the library is already there, and if it is,
// "Append" instead of "Create"
bool libraryExists = File.Exists(outputPath);
var libraryBuildAction = LibraryBuildAction.Create;
if (libraryExists)
{
if (doc.Settings.HasDocumentLibrary)
{
libraryBuildAction = LibraryBuildAction.Append;
}
else
{
// If the document does not have a document library, then delete the one that we have found
// CONSIDER: it may be that user is trying to re-import, in which case this file is probably in use
FileEx.SafeDelete(outputPath);
FileEx.SafeDelete(Path.ChangeExtension(outputPath, BiblioSpecLiteSpec.EXT_REDUNDANT));
}
}
string name = Path.GetFileNameWithoutExtension(docFilePath);
return(new BiblioSpecLiteBuilder(name, outputPath, SearchFilenames)
{
Action = libraryBuildAction,
KeepRedundant = true,
CutOffScore = CutoffScore,
Id = Helpers.MakeId(name),
IncludeAmbiguousMatches = includeAmbiguousMatches
});
}
private void RemovePartialCacheFiles(string[] files)
{
WaitForChromatogramManagerQuiet();
foreach (var file in files)
{
string cacheFile = ChromatogramCache.PartPathForName(SkylineWindow.DocumentFilePath, new MsDataFilePath(file));
FileEx.SafeDelete(cacheFile, true);
}
}
private void btnCreate_Click(object sender, EventArgs e)
{
string filterProtDb = TextUtil.FileDialogFiltersAll(FILTER_PROTDB);
string fileName;
using (var saveFileDialog = new SaveFileDialog
{
Filter = filterProtDb,
InitialDirectory = Settings.Default.ProteomeDbDirectory,
Title = Resources.BuildBackgroundProteomeDlg_btnCreate_Click_Create_Background_Proteome,
OverwritePrompt = true,
})
{
if (saveFileDialog.ShowDialog(this) == DialogResult.Cancel)
{
return;
}
fileName = saveFileDialog.FileName;
}
// If the file exists, then the user chose to overwrite,
// so delete the existing file.
try
{
FileEx.SafeDelete(fileName);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
Settings.Default.ProteomeDbDirectory = Path.GetDirectoryName(fileName);
textPath.Text = fileName;
if (textName.Text.Length == 0)
{
textName.Text = Path.GetFileNameWithoutExtension(fileName);
}
try
{
ProteomeDb.CreateProteomeDb(fileName);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildBackgroundProteomeDlg_btnCreate_Click_An_error_occurred_attempting_to_create_the_proteome_file__0__,
fileName), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
RefreshStatus();
}
public void SafeDeleteTest()
{
// Test ArgumentException.
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(null));
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete("")); // Not L10N
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(" ")); // Not L10N
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete("<path with illegal chars>")); // Not L10N
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(null, true));
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete("", true)); // Not L10N
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(" ", true)); // Not L10N
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete("<path with illegal chars>", true)); // Not L10N
// Test DirectoryNotFoundException.
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(@"c:\blah-blah-blah\blah.txt")); // Not L10N
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(@"c:\blah-blah-blah\blah.txt", true)); // Not L10N
// Test PathTooLongException.
var pathTooLong = "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx".Replace("x", "xxxxxxxxxx"); // Not L10N
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(pathTooLong));
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(pathTooLong, true));
// Test IOException.
const string busyFile = "TestBusyDelete.txt"; // Not L10N
using (File.CreateText(busyFile))
{
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(busyFile));
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(busyFile, true));
}
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(busyFile));
// Test UnauthorizedAccessException.
const string readOnlyFile = "TestReadOnlyFile.txt"; // Not L10N
// ReSharper disable LocalizableElement
File.WriteAllText(readOnlyFile, "Testing read only file delete.\n"); // Not L10N
// ReSharper restore LocalizableElement
var fileInfo = new FileInfo(readOnlyFile)
{
IsReadOnly = true
};
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(readOnlyFile));
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(readOnlyFile, true));
fileInfo.IsReadOnly = false;
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(readOnlyFile));
var directory = Environment.CurrentDirectory;
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(directory));
AssertEx.NoExceptionThrown <IOException>(() => FileEx.SafeDelete(directory, true));
}
private void Download(SkypFile skyp, IProgressMonitor progressMonitor, FormEx parentWindow = null)
{
var progressStatus =
new ProgressStatus(string.Format(Resources.SkypSupport_Download_Downloading__0_, skyp.SkylineDocUri));
progressMonitor.UpdateProgress(progressStatus);
if (DownloadClient == null)
{
DownloadClient = new WebDownloadClient(progressMonitor, progressStatus);
}
DownloadClient.Download(skyp.SkylineDocUri, skyp.DownloadPath, skyp.Server?.Username, skyp.Server?.Password);
if (progressMonitor.IsCanceled || DownloadClient.IsError)
{
FileEx.SafeDelete(skyp.DownloadPath, true);
}
if (DownloadClient.IsError)
{
var message =
string.Format(
Resources
.SkypSupport_Download_There_was_an_error_downloading_the_Skyline_document_specified_in_the_skyp_file___0__,
skyp.SkylineDocUri);
if (DownloadClient.Error != null)
{
var exceptionMsg = DownloadClient.Error.Message;
message = TextUtil.LineSeparate(message, exceptionMsg);
if (exceptionMsg.Contains(ERROR401))
{
message = TextUtil.LineSeparate(message,
string.Format(
Resources
.SkypSupport_Download_You_may_have_to_add__0__as_a_Panorama_server_from_the_Tools___Options_menu_in_Skyline_,
skyp.SkylineDocUri.Host));
}
else if (exceptionMsg.Contains(ERROR403))
{
message = TextUtil.LineSeparate(message,
string.Format(
Resources.SkypSupport_Download_You_do_not_have_permissions_to_download_this_file_from__0__,
skyp.SkylineDocUri.Host));
}
}
throw new Exception(message, DownloadClient.Error);
}
}
private void DoTestAgilentCEOpt()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath(DOCUMENT_NAME);
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the .wiff file
ExportImport(docContainer, testFilesDir.GetTestPath(RESULTS_NAME));
}
}
private static void ValidateRelativeRT(RelativeRT relativeRT, SrmDocument doc, string docPath, List <ChromatogramSet> listChromatograms)
{
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
SrmSettings settings = doc.Settings.ChangePeptideModifications(mods =>
mods.ChangeHeavyModifications(
mods.HeavyModifications.Select(m => m.ChangeRelativeRT(relativeRT)).ToArray()));
var docMods = doc.ChangeSettings(settings);
var docResults = docMods.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainer = new ResultsTestDocumentContainer(docMods, docPath);
Assert.IsTrue(docContainer.SetDocument(docResults, docMods, true));
docContainer.AssertComplete();
docContainer.Release();
}
public void ThermoMixedPeptidesTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument docMixed = InitMixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
SrmDocument docUnmixed = InitUnmixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
new ChromatogramSet("rep05", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_05" + extRaw))
})
};
var docResults = docMixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerMixed = new ResultsTestDocumentContainer(docMixed, docPath);
Assert.IsTrue(docContainerMixed.SetDocument(docResults, docMixed, true));
docContainerMixed.AssertComplete();
docMixed = docContainerMixed.Document;
SrmDocument docMixedUnmixed = (SrmDocument)docMixed.ChangeChildren(new DocNode[0]);
IdentityPath tempPath;
docMixedUnmixed = docMixedUnmixed.AddPeptideGroups(docUnmixed.PeptideGroups, true, IdentityPath.ROOT,
out tempPath, out tempPath);
docResults = docUnmixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerUnmixed = new ResultsTestDocumentContainer(docUnmixed, docPath);
Assert.IsTrue(docContainerUnmixed.SetDocument(docResults, docUnmixed, true));
docContainerUnmixed.AssertComplete();
docUnmixed = docContainerUnmixed.Document;
AssertEx.DocumentCloned(docMixedUnmixed, docUnmixed);
docContainerMixed.Release();
docContainerUnmixed.Release();
}
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
TestSmallMolecules = false; // We test small molecules explicitly in this test
LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("TROUBLED_File.sky");
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, testFilesDir.FullPath, asSmallMolecules);
const int expectedMoleculeCount = 1; // At first small molecules did not support multiple label types
AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 6);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("Rush_p3_96_21May16_Smeagol.mzML");
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) });
{
// Import with symmetric isolation window
var docResults =
docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 3, 3);
var nodeGroup = docResults.MoleculeTransitionGroups.First();
double ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// The expected ratio is 1.0, but the symmetric isolation window should produce poor results
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(0.008, ratio, 0.001);
}
}
}
testFilesDir.Dispose();
}
private void DoTestAgilentCEOpt()
{
// The special mode for exercising non-proteomic molecules just doesn't make sense with this test
TestSmallMolecules = false;
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath(DOCUMENT_NAME);
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the .wiff file
ExportImport(docContainer, testFilesDir.GetTestPath(RESULTS_NAME));
}
}
private void TestExportTransitionList()
{
var filePathActual = GetTestPath("actual.csv");
FileEx.SafeDelete(filePathActual);
var exportDialog = ShowDialog <ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
// Export CE optimization transition list
RunUI(() =>
{
exportDialog.InstrumentType = ExportInstrumentType.THERMO_QUANTIVA;
exportDialog.ExportStrategy = ExportStrategy.Single;
exportDialog.MethodType = ExportMethodType.Standard;
exportDialog.OptimizeType = ExportOptimize.NONE;
exportDialog.WriteCompensationVoltages = true;
});
MultiButtonMsgDlg errDlg1 = null;
RunDlg <MultiButtonMsgDlg>(() => exportDialog.OkDialog(filePathActual),
// Expect The_settings_for_this_document_do_not_match_the_instrument_type...
errDlg =>
{
errDlg1 = errDlg;
RunUI(errDlg.ClickNo);
});
// Expect You_are_missing_compensation_voltages_for_the_following...
var errDlg2 = FindOpenForms <MultiButtonMsgDlg>().FirstOrDefault(f => f != errDlg1);
// ReSharper disable once PossibleNullReferenceException
RunUI(errDlg2.ClickOk);
WaitForCondition(() => File.Exists(filePathActual));
var actual = File.ReadAllLines(filePathActual);
var expected = File.ReadAllLines(GetTestPath("expected.csv"));
for (var i = 0; i < Math.Min(expected.Length, actual.Length); i++)
{
AssertEx.AreEqual(expected[i], actual[i], $@"transitions differ at line {i}");
}
AssertEx.AreEqual(expected.Length, actual.Length, @"different transition count");
}
public static void CreateIrtDatabase(string path)
{
FileEx.SafeDelete(path);
//Create file, initialize db
try
{
IrtDb.CreateIrtDb(path);
}
catch (DatabaseOpeningException)
{
throw;
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.EditIrtCalcDlg_CreateDatabase_The_file__0__could_not_be_created, path),
x.Message);
throw new IOException(message, x);
}
}
/// <summary>
/// Given a list of packages it determines which need to be installed and which are already installed.
/// </summary>
/// <param name="packages">Collection of package names to check for</param>
/// <param name="pathToR">Path to R</param>
/// <returns>Collection of packages that need to be installed</returns>
public static ICollection <ToolPackage> WhichPackagesToInstall(ICollection <ToolPackage> packages, string pathToR)
{
List <ToolPackage> packagesToInstall = new List <ToolPackage>();
string pathToScript = WriteCheckForPackagesFile(packages);
string response = RunRscript(pathToR, pathToScript);
string[] lines = response.Split('\n');
foreach (var line in lines.Where(l => !string.IsNullOrEmpty(l)))
{
string[] split = line.Split('-');
if (split.Length > 1 && split[1].Contains(@"FALSE"))
{
string packageName = split[0].Trim();
var toInstall = packages.First(packageContainer => Equals(packageContainer.Name, packageName));
packagesToInstall.Add(toInstall);
}
}
FileEx.SafeDelete(pathToScript);
return(packagesToInstall);
}
public void DoTestDemux(bool asSmallMolecules)
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPathMsx = testFilesDir.GetTestPath("MsxTest.sky");
string dataPathMsx = testFilesDir.GetTestPath("MsxTest.mzML");
string cachePathMsx = ChromatogramCache.FinalPathForName(docPathMsx, null);
FileEx.SafeDelete(cachePathMsx);
SrmDocument docMsx = ResultsUtil.DeserializeDocument(docPathMsx);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docMsx = refine.ConvertToSmallMolecules(docMsx);
}
var fullScanInitialMsx = docMsx.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitialMsx.IsEnabledMsMs);
TestMsx(docMsx, dataPathMsx);
string docPathOverlap = testFilesDir.GetTestPath("OverlapTest.sky");
string dataPathOverlap = testFilesDir.GetTestPath("OverlapTest.mzML");
string cachePathOverlap = ChromatogramCache.FinalPathForName(docPathOverlap, null);
FileEx.SafeDelete(cachePathOverlap);
SrmDocument docOverlap = ResultsUtil.DeserializeDocument(docPathOverlap);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOverlap = refine.ConvertToSmallMolecules(docOverlap);
}
var fullScanInitialOverlap = docMsx.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitialOverlap.IsEnabledMsMs);
TestOverlap(docOverlap, dataPathOverlap);
}
private void DoTestImportSim(bool asSmallMolecules)
{
TestSmallMolecules = false; // Don't need that magic extra node
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath(DOCUMENT_NAME);
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var pepdoc = doc;
if (asSmallMolecules)
{
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(pepdoc);
}
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
// Import the mzML file and verify Mz range
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME), 510, 512);
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME2), 555, 557);
}
public void WatersCacheTest()
{
// First test transition from per-replicate caching strategy to
// single cache per document strategy.
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
// Open the replicate document, and let it reload the data from mzML
// showing the document can find data files by name in its own directory,
// since the document paths will not match those on disk.
string docPath;
var doc = InitWatersDocument(testFilesDir, out docPath);
var docReload = InitWatersDocument(testFilesDir, "160109_Mix1_calcurve_rep.sky", out docPath);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
var streamManager = docContainer.ChromatogramManager.StreamManager;
Assert.IsTrue(docContainer.SetDocument(docReload, doc, true));
docContainer.AssertComplete();
docReload = docContainer.Document;
// Release file handles to cache files created during load
Assert.IsTrue(docContainer.SetDocument(doc, docReload));
// Delete the cache
string cachePath = Path.ChangeExtension(docPath, ".skyd");
FileEx.SafeDelete(cachePath);
// Then try using cached replicate files
// Move per-replicate cache files into place
var replicateCacheNames = new[]
{
"160109_Mix1_calcurve_rep_calcurve_070.skyd",
"160109_Mix1_calcurve_rep_calcurve_073.skyd"
};
GetCacheFiles(testFilesDir, replicateCacheNames);
// Delete the files these cache
DeleteFiles(testFilesDir,
new[]
{
"160109_Mix1_calcurve_070.mzML",
"160109_Mix1_calcurve_073.mzML",
});
var docCached = InitWatersDocument(testFilesDir, "160109_Mix1_calcurve_rep.sky", out docPath);
Assert.IsTrue(docContainer.SetDocument(docCached, doc, true));
docContainer.AssertComplete();
docCached = docContainer.Document;
// The document with data from the .mzML files should be the same as
// the one loaded from the .skyd files.
// Unfortunately, this is to hard to maintain when cache changes are made.
// AssertEx.Cloned(docCached, docReload);
// The one cache should be present
Assert.IsTrue(File.Exists(cachePath));
// And the replicate cache files should have been removed
foreach (var cacheName in replicateCacheNames)
{
var path = testFilesDir.GetTestPath(cacheName);
Assert.IsFalse(File.Exists(path));
}
// Save the cache file time stamp
// ReSharper disable once AssignNullToNotNullAttribute
var cacheInfo = new FileInfo(cachePath);
long cacheSize = cacheInfo.Length;
// Adding files already in the document should have no impact on the cache.
string extRaw = ExtensionTestContext.ExtWatersRaw;
var listChromatograms = new List <ChromatogramSet>(docCached.Settings.MeasuredResults.Chromatograms)
{
new ChromatogramSet("extra1",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("160109_Mix1_calcurve_075" + extRaw)) }),
new ChromatogramSet("extra2",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("160109_Mix1_calcurve_078.mzML")) })
};
// Adding a new file should cause the cache to grow.
var settings = docCached.Settings.MeasuredResults.ChangeChromatograms(listChromatograms);
var docGrow = docCached.ChangeMeasuredResults(settings);
Assert.IsTrue(docContainer.SetDocument(docGrow, docCached, true));
docContainer.AssertComplete();
docGrow = docContainer.Document;
cacheInfo = new FileInfo(cachePath);
Assert.IsTrue(cacheSize < cacheInfo.Length);
cacheSize = cacheInfo.Length;
var writeTime = cacheInfo.LastWriteTime;
listChromatograms.Add(
new ChromatogramSet("double",
new[]
{
testFilesDir.GetTestPath("160109_Mix1_calcurve_075" + extRaw),
testFilesDir.GetTestPath("160109_Mix1_calcurve_078.mzML")
}));
settings = docGrow.Settings.MeasuredResults.ChangeChromatograms(listChromatograms);
var docNoCacheChange1 = docGrow.ChangeMeasuredResults(settings);
Assert.IsTrue(docContainer.SetDocument(docNoCacheChange1, docGrow, true));
docContainer.AssertComplete();
docNoCacheChange1 = docContainer.Document;
Assert.AreEqual(writeTime, File.GetLastWriteTime(cachePath));
// Removing files should have no impact, until optimized
listChromatograms.RemoveRange(listChromatograms.Count - 2, 2);
listChromatograms.RemoveAt(1);
settings = docNoCacheChange1.Settings.MeasuredResults.ChangeChromatograms(listChromatograms);
var docNoCacheChange2 = docNoCacheChange1.ChangeMeasuredResults(settings);
Assert.IsTrue(docContainer.SetDocument(docNoCacheChange2, docNoCacheChange1, true));
docContainer.AssertComplete();
docNoCacheChange2 = docContainer.Document;
Assert.AreEqual(writeTime, File.GetLastWriteTime(cachePath));
// Optimizing should shrink the cache
var results = docNoCacheChange2.Settings.MeasuredResults.OptimizeCache(docPath, streamManager);
var docOptimized = docNoCacheChange2.ChangeSettings(docNoCacheChange2.Settings.ChangeMeasuredResults(results));
// This should not cause a reload
Assert.IsTrue(docContainer.SetDocument(docOptimized, docNoCacheChange2, false));
cacheInfo = new FileInfo(cachePath);
Assert.IsTrue(cacheSize > cacheInfo.Length);
// Test file caches
// First reload the files from .mzML
docReload = InitWatersDocument(testFilesDir, "160109_Mix1_calcurve_file.sky", out docPath);
// Change the path to use the right .skyd file
docContainer.DocumentFilePath = docPath;
Assert.IsTrue(docContainer.SetDocument(docReload, docOptimized, true));
docContainer.AssertComplete();
docReload = docContainer.Document;
// Release file handles to cache files created during load
Assert.IsTrue(docContainer.SetDocument(doc, docReload));
// Delete the cache
cachePath = Path.ChangeExtension(docPath, ".skyd");
FileEx.SafeDelete(cachePath);
// Then try using cached files
// Move per-file cache files into place
var fileCacheNames = new[]
{
"160109_Mix1_calcurve_075.mzML.skyd",
"160109_Mix1_calcurve_078.mzML.skyd"
};
GetCacheFiles(testFilesDir, fileCacheNames);
// Swap the mzML files, so the test will fail, if not reading from the cache
// CONSIDER: Should this really work, since they have different time stamps?
string file075 = testFilesDir.GetTestPath("160109_Mix1_calcurve_075.mzML");
string file078 = testFilesDir.GetTestPath("160109_Mix1_calcurve_078.mzML");
string fileTemp = file075 + ".tmp";
File.Move(file075, fileTemp);
File.Move(file078, file075);
File.Move(fileTemp, file078);
docCached = InitWatersDocument(testFilesDir, "160109_Mix1_calcurve_file.sky", out docPath);
// Make sure cache files exactly match the names the loader will look for
var listResultsFiles = new List <MsDataFileUri>();
foreach (var chromatogram in docCached.Settings.MeasuredResults.Chromatograms)
{
listResultsFiles.AddRange(chromatogram.MSDataFilePaths);
}
for (int i = 0; i < fileCacheNames.Length; i++)
{
string partPath = ChromatogramCache.PartPathForName(docPath, listResultsFiles[i]);
File.Move(testFilesDir.GetTestPath(fileCacheNames[i]), partPath);
}
Assert.IsTrue(docContainer.SetDocument(docCached, doc, true));
docContainer.AssertComplete();
// docCached = docContainer.Document;
// The document with data from the .mzML files should be the same as
// the one loaded from the .skyd files.
// Unfortunately, this is to hard to maintain when cache changes are made.
// AssertEx.Cloned(docCached, docReload);
// The one cache should be present
Assert.IsTrue(File.Exists(Path.ChangeExtension(docPath, ".skyd")));
// And the replicate cache files should have been removed
foreach (var cacheName in fileCacheNames)
{
Assert.IsFalse(File.Exists(testFilesDir.GetTestPath(cacheName)));
}
}
testFilesDir.Dispose();
}
public void ThermoCancelImportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
string resultsPath = testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03" +
ExtensionTestContext.ExtThermoRaw);
string dirPath = Path.GetDirectoryName(resultsPath) ?? "";
// Remove any existing temp and cache files
foreach (var path in Directory.GetFiles(dirPath))
{
if (IsCacheOrTempFile(path))
{
FileEx.SafeDelete(path);
}
}
string name = Path.GetFileNameWithoutExtension(resultsPath);
var listChromatograms = new List <ChromatogramSet> {
new ChromatogramSet(name, new[] { MsDataFileUri.Parse(resultsPath) })
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
// Start cache load, but don't wait for completion
Assert.IsTrue(docContainer.SetDocument(docResults, doc));
// Wait up to 1 second for the cache to start being written
for (int i = 0; i < 100; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1)
{
break;
}
Thread.Sleep(10);
}
Assert.IsTrue(Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1, "Failed to create cache file");
// Cancel by reverting to the original document
Assert.IsTrue(docContainer.SetDocument(doc, docResults));
// Wait up to 5 seconds for cancel to occur
for (int i = 0; i < 50; i++)
{
if (docContainer.LastProgress.IsCanceled)
{
break;
}
Thread.Sleep(100);
}
if (!docContainer.LastProgress.IsCanceled)
{
Assert.Fail("Attempt to cancel results load failed. {0}", docContainer.LastProgress.ErrorException != null
? docContainer.LastProgress.ErrorException.Message : string.Empty);
}
// Wait up to 20 seconds for the cache to be removed
for (int i = 0; i < 200; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1)
{
break;
}
Thread.Sleep(100);
}
// Cache file has been removed
Assert.IsTrue(Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1, "Failed to remove cache file");
testFilesDir.Dispose();
}
public void WatersMultiReplicateTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument docOriginal = InitWatersDocument(testFilesDir, out docPath);
SrmDocument doc = docOriginal;
var listCachePaths = new List <string>();
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
string extRaw = ExtensionTestContext.ExtWatersRaw;
string[] replicatePaths =
{
testFilesDir.GetTestPath("160109_Mix1_calcurve_070.mzML"),
testFilesDir.GetTestPath("160109_Mix1_calcurve_073.mzML"),
testFilesDir.GetTestPath("160109_Mix1_calcurve_075" + extRaw),
testFilesDir.GetTestPath("160109_Mix1_calcurve_078.mzML")
};
// Count peaks where higher concentration replicates show less area
int outOfOrder = 0;
foreach (string path in replicatePaths)
{
var listChromatograms = new List <ChromatogramSet>();
if (doc.Settings.HasResults)
{
listChromatograms.AddRange(doc.Settings.MeasuredResults.Chromatograms);
}
string name = Path.GetFileNameWithoutExtension(path);
if (name != null)
{
name = name.Substring(name.Length - 12);
}
listChromatograms.Add(new ChromatogramSet(name, new[] { MsDataFileUri.Parse(path) }));
int len = listChromatograms.Count;
var docResults = doc.ChangeMeasuredResults(doc.Settings.MeasuredResults != null
? doc.Settings.MeasuredResults.ChangeChromatograms(listChromatograms)
: new MeasuredResults(listChromatograms));
// Adding unloaded results should add a new null result.
foreach (var nodeTran in docResults.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(listChromatograms.Count, nodeTran.Results.Count);
Assert.IsTrue(nodeTran.Results[len - 1].IsEmpty);
}
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true),
string.Format("Failed adding results for {0}.", path));
docContainer.AssertComplete();
docResults = docContainer.Document;
Assert.IsTrue(docResults.Settings.MeasuredResults.IsLoaded);
var transOld = doc.PeptideTransitions.ToArray();
var transNew = docResults.PeptideTransitions.ToArray();
Assert.AreEqual(transOld.Length, transNew.Length);
int countPeaks = 0;
for (int i = 0; i < transNew.Length; i++)
{
// Make sure new peak was added to each transition
var nodeTranNew = transNew[i];
Assert.IsTrue(nodeTranNew.HasResults);
Assert.AreEqual(len, nodeTranNew.Results.Count);
var chromInfo = nodeTranNew.Results[len - 1][0];
Assert.IsNotNull(chromInfo);
if (!chromInfo.IsEmpty)
{
countPeaks++;
}
// Make sure previously loaded peaks did not change
for (int j = 0; j < len - 1; j++)
{
var chromInfoPrevious = transOld[i].Results[j][0];
Assert.AreSame(chromInfoPrevious, nodeTranNew.Results[j][0]);
if ((chromInfo.IsEmpty && !chromInfoPrevious.IsEmpty) ||
(!chromInfo.IsEmpty && chromInfoPrevious.Area >= chromInfo.Area))
{
outOfOrder++;
}
}
}
// Allow 2 missed peaks
Assert.IsTrue(countPeaks >= transNew.Length - (TestSmallMolecules ? 1 : 0) - 2);
// Check results calculations for peptides and groups
foreach (var nodePep in docResults.Peptides)
{
Assert.AreEqual(len, nodePep.Results.Count);
Assert.IsTrue(nodePep.HasResults);
var chromInfo = nodePep.Results[len - 1][0];
Assert.AreEqual(1, nodePep.Children.Count);
var nodeGroup = (TransitionGroupDocNode)nodePep.Children[0];
Assert.IsTrue(nodeGroup.HasResults);
Assert.AreEqual(len, nodeGroup.Results.Count);
var chromInfoGroup = nodeGroup.Results[len - 1][0];
Assert.IsTrue(chromInfoGroup.PeakCountRatio >= 0.5);
Assert.IsTrue(chromInfoGroup.RetentionTime.HasValue);
Assert.IsTrue(chromInfoGroup.Area.HasValue && chromInfoGroup.Area > 290);
Assert.AreEqual(chromInfo.RetentionTime, chromInfoGroup.RetentionTime);
Assert.AreEqual(chromInfo.PeakCountRatio, chromInfoGroup.PeakCountRatio);
}
doc = docResults;
}
Assert.AreEqual(13, outOfOrder, 1);
// Remove the original data
foreach (string path in replicatePaths)
{
if (File.Exists(path))
{
FileEx.SafeDelete(path);
}
else
{
DirectoryEx.SafeDelete(path);
}
}
FileEx.SafeDelete(docPath);
// Save the document
string xmlSaved = null;
var docPersisted = AssertEx.RoundTrip(doc, ref xmlSaved);
Assert.IsTrue(!docPersisted.Settings.MeasuredResults.IsLoaded);
// Make sure the persisted document round-trips.
// The orginal doesn't because of changing precision in the results info.
AssertEx.Serializable(docPersisted, AssertEx.DocumentCloned);
// Make sure the loaded document has reasonable results info
// before the cache files are loaded
for (int i = 0; i < doc.Children.Count; i++)
{
PeptideGroupDocNode nodePepGroup1 = (PeptideGroupDocNode)doc.Children[i];
if (TestSmallMolecules && nodePepGroup1.Name.Equals(SrmDocument.TestingNonProteomicMoleculeGroupName))
{
continue;
}
PeptideGroupDocNode nodePepGroup2 = (PeptideGroupDocNode)docPersisted.Children[i];
Assert.AreNotSame(nodePepGroup1, nodePepGroup2);
for (int j = 0; j < nodePepGroup1.Children.Count; j++)
{
PeptideDocNode nodePep1 = (PeptideDocNode)nodePepGroup1.Children[j];
PeptideDocNode nodePep2 = (PeptideDocNode)nodePepGroup2.Children[j];
Assert.AreNotSame(nodePep1, nodePep2);
Assert.AreEqual(nodePep1.Results.Count, nodePep2.Results.Count);
for (int k = 0; k < nodePep1.Results.Count; k++)
{
Assert.AreEqual(nodePep1.Results[k][0].PeakCountRatio, nodePep2.Results[k][0].PeakCountRatio);
}
for (int k = 0; k < nodePep1.Children.Count; k++)
{
TransitionGroupDocNode nodeGroup1 = (TransitionGroupDocNode)nodePep1.Children[k];
TransitionGroupDocNode nodeGroup2 = (TransitionGroupDocNode)nodePep2.Children[k];
Assert.AreNotSame(nodeGroup1, nodeGroup2);
Assert.AreEqual(nodeGroup1.Results.Count, nodeGroup2.Results.Count);
for (int l = 0; l < nodeGroup1.Results.Count; l++)
{
Assert.AreEqual(nodeGroup1.Results[l][0].PeakCountRatio,
nodeGroup2.Results[l][0].PeakCountRatio);
}
for (int l = 0; l < nodeGroup1.Children.Count; l++)
{
TransitionDocNode nodeTran1 = (TransitionDocNode)nodeGroup1.Children[l];
TransitionDocNode nodeTran2 = (TransitionDocNode)nodeGroup2.Children[l];
Assert.AreNotSame(nodeTran1, nodeTran2);
Assert.AreEqual(nodeTran1.Results.Count, nodeTran2.Results.Count);
for (int m = 0; m < nodeTran1.Results.Count; m++)
{
if (!nodeTran1.Results[m].IsEmpty && !nodeTran2.Results[m].IsEmpty)
{
Assert.AreEqual(nodeTran1.Results[m][0].IsEmpty, nodeTran2.Results[m][0].IsEmpty);
}
else
{
Assert.AreEqual(nodeTran1.Results[m], nodeTran2.Results[m]); // both null
}
}
}
}
}
}
// Reload data from .skyd files
Assert.IsTrue(docContainer.SetDocument(docPersisted, doc, true));
docContainer.AssertComplete();
doc = docContainer.Document;
var results = doc.Settings.MeasuredResults;
const float tolerance = (float)TransitionInstrument.DEFAULT_MZ_MATCH_TOLERANCE;
foreach (var pair in doc.PeptidePrecursorPairs)
{
foreach (var chromSet in results.Chromatograms)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(chromSet, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
}
}
// The single final cache path should be open now
listCachePaths.AddRange(doc.Settings.MeasuredResults.CachePaths);
// Should only have one cache file at this point
Assert.AreEqual(1, listCachePaths.Count);
foreach (var cachePath in listCachePaths)
{
// Attempting to delete should throw
string path = cachePath;
AssertEx.ThrowsException <IOException>(() => FileEx.SafeDelete(path));
}
}
foreach (var cachePath in listCachePaths)
{
// Cache files should be closed now, and delete successfully.
FileEx.SafeDelete(cachePath);
}
testFilesDir.Dispose();
}
public void ThermoCancelImportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string resultsPath = testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03" +
ExtensionTestContext.ExtThermoRaw);
string dirPath = Path.GetDirectoryName(resultsPath) ?? "";
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
// Give this two chances to succeed. It can succeed tens of thousands of times
// in a row, but it still occasionally fails on nightly tests. Hopefully two
// tries will make this extremely unlikely.
for (int tries = 0; tries < 2; tries++)
{
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Remove any existing temp and cache files
foreach (var path in Directory.GetFiles(dirPath))
{
if (IsCacheOrTempFile(path))
{
FileEx.SafeDelete(path);
}
}
string name = Path.GetFileNameWithoutExtension(resultsPath);
var listChromatograms = new List <ChromatogramSet> {
new ChromatogramSet(name, new[] { MsDataFileUri.Parse(resultsPath) })
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
// Start cache load, but don't wait for completion
Assert.IsTrue(docContainer.SetDocument(docResults, doc));
// Wait up to 10 second for the cache to start being written
bool cacheFound = false;
for (int i = 0; i < 1000; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1)
{
cacheFound = true;
break;
}
Thread.Sleep(10);
}
if (!cacheFound)
{
Assert.Fail(TextUtil.LineSeparate("Failed to create cache file. Found files:", TextUtil.LineSeparate(Directory.GetFiles(dirPath))));
}
// Cancel by reverting to the original document
Assert.IsTrue(docContainer.SetDocument(doc, docResults));
// Wait up to 10 seconds for cancel to occur
bool cancelOccurred = false;
for (int i = 0; i < 1000; i++)
{
if (docContainer.LastProgress != null && docContainer.LastProgress.IsCanceled)
{
cancelOccurred = true;
break;
}
Thread.Sleep(10);
}
// Wait up to 20 seconds for the cache to be removed
bool cacheRemoved = false;
for (int i = 0; i < 200; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1)
{
cacheRemoved = true;
break;
}
Thread.Sleep(100);
}
if (!cacheRemoved)
{
if (tries == 0 && File.Exists(Path.ChangeExtension(docPath, ChromatogramCache.EXT)))
{
// Allow a single failure where we end up with the final cache instead of a cancelation
FileEx.SafeDelete(docPath);
continue; // Try again
}
if (!cancelOccurred)
{
Assert.Fail("Attempt to cancel results load failed on try {0}. {1}", tries + 1,
docContainer.LastProgress != null && docContainer.LastProgress.ErrorException != null
? docContainer.LastProgress.ErrorException.Message : string.Empty);
}
Assert.Fail(TextUtil.LineSeparate("Failed to remove cache file. Found files:", TextUtil.LineSeparate(Directory.GetFiles(dirPath))));
}
break; // If we make it here then, successful
}
}
// Cache file has been removed
testFilesDir.Dispose();
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return(false);
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
public bool BuildLibrary(IProgressMonitor progress)
{
RetentionTimeRegression regr = null;
var standardSpectra = new List <SpectrumMzInfo>();
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY))
{
// Align Prosit iRTs with iRT standard
var standardPeptidesToAdd = SkylineWindow.ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
var original = standardIRTMap.ToDictionary(p => p.Key.ModifiedTarget, p => p.Value);
var target = IrtStandard.Peptides.ToDictionary(p => p.ModifiedTarget, p => p.Irt);
var aligned = AlignedRetentionTimes.AlignLibraryRetentionTimes(target, original, 0.0, RegressionMethodRT.linear,
CancellationToken.None);
regr = aligned.Regression;
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, _nce)).ToArray(),
CancellationToken.None);
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctPeps = _peptides.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p).Distinct(
new SystemLinqExtensionMethods.FuncEqualityComparer <PrositRetentionTimeModel.PeptideDocNodeWrapper>(
(p1, p2) => p1.Node.ModifiedSequence == p2.Node.ModifiedSequence)).ToArray();
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, _document.Settings,
distinctPeps, CancellationToken.None);
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = regr?.Conversion?.GetY(iRT) ?? iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List <SrmDocument>();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
var expectedPepCount = 7;
var expectedTransGroupCount = 7;
var expectedTransCount = 49;
var doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
if (centroided && ExtensionTestContext.CanImportThermoRaw)
{
const double ppm20 = 20.0;
doc = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm20, 0)));
}
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { new MsDataFilePath(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
docCheckpoints.Add(docResults);
// Refilter allowing multiple precursors per spectrum
SrmDocument docMulti = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(
fs => fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, new IsolationScheme("Test", 2))));
AssertEx.Serializable(docMulti, AssertEx.DocumentCloned);
// Release data cache file
Assume.IsTrue(docContainer.SetDocument(docMulti, docResults));
// And remove it
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 6, 6, 38));
// Import full scan Orbi-Velos data
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_long_acc_template.sky");
expectedPepCount = 3;
expectedTransGroupCount = 3;
expectedTransCount = 21;
doc = InitFullScanDocument(ref docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
docCheckpoints.Add(doc);
Assume.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
// Make sure saving this type of document works
AssertEx.Serializable(doc, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(doc, docContainer.Document));
rawPath = testFilesDir.GetTestPath("ah_20101029r_BSA_CID_FT_centroid_3uscan_3" +
ExtensionTestContext.ExtThermoRaw);
measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Accurate", new[] { rawPath }) });
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21));
// Import LTQ data with MS1 and MS/MS
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_test4.sky");
expectedPepCount = 3;
expectedTransGroupCount = 4;
expectedTransCount = 32;
doc = InitFullScanDocument(ref docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
docCheckpoints.Add(doc);
var docBoth = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.Targeted, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, TransitionFullScan.DEFAULT_RES_QIT, null)));
docCheckpoints.Add(docBoth);
AssertEx.Serializable(docBoth, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docBoth, docContainer.Document));
string dataPath = testFilesDir.GetTestPath("klc_20100329v_Protea_Peptide_Curve_200fmol_uL_tech1.mzML");
var listResults = new List <ChromatogramSet>
{
new ChromatogramSet("MS1 and MS/MS", new[] { dataPath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount, expectedTransGroupCount, expectedTransCount - 6));
// The mzML was filtered for the m/z range 410 to 910.
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.IsNotNull(nodeTran.Results[0]);
if (410 > nodeTran.Mz || nodeTran.Mz > 910)
{
Assume.IsTrue(nodeTran.Results[0][0].IsForcedIntegration);
}
else
{
Assume.IsFalse(nodeTran.Results[0][0].IsForcedIntegration);
}
}
// Import LTQ data with MS1 and MS/MS using multiple files for a single replicate
listResults.Add(new ChromatogramSet("Multi-file", new[]
{
testFilesDir.GetTestPath("both_DRV.mzML"),
testFilesDir.GetTestPath("both_KVP.mzML"),
}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount - 1, expectedTransGroupCount - 1, expectedTransCount - 6));
if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
return; // Can't work with isotope distributions when we don't have ion formulas
}
int indexResults = listResults.Count - 1;
var matchIdentifierDRV = "DRV";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierDRV = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierDRV;
}
int index = 0;
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(listResults.Count, nodeTran.Results.Count);
var peptide = nodeTran.Transition.Group.Peptide;
if (peptide.IsCustomMolecule && index == 24)
{
// Conversion to small molecule loses some of the nuance of "Sequence" vs "FastaSequence", comparisons are inexact
Assume.AreEqual("pep_DRVY[+80.0]IHPF", nodeTran.PrimaryCustomIonEquivalenceKey);
break;
}
// DRV without FASTA sequence should not have data for non-precursor transitions
if (!peptide.TextId.StartsWith(matchIdentifierDRV) ||
(!peptide.IsCustomMolecule && !peptide.Begin.HasValue))
{
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
}
else if (nodeTran.Transition.IonType != IonType.precursor)
{
Assert.IsTrue(nodeTran.Results[indexResults].IsEmpty);
}
else
{
// Random, bogus peaks chosen in both files
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.AreEqual(2, nodeTran.Results[indexResults].Count);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
Assume.IsFalse(nodeTran.Results[indexResults][1].IsEmpty);
}
index++;
}
// Verify handling of bad request for vendor centroided data - out-of-range PPM
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docBad = doc;
AssertEx.ThrowsException <InvalidDataException>(() =>
docBad.ChangeSettings(docBad.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, 50 * 1000, 400))),
string.Format(Resources.TransitionFullScan_ValidateRes_Mass_accuracy_must_be_between__0__and__1__for_centroided_data_,
TransitionFullScan.MIN_CENTROID_PPM, TransitionFullScan.MAX_CENTROID_PPM));
// Verify relationship between PPM and resolving power
const double ppm = 20.0; // Should yield same filter width as resolving power 50,000 in TOF
var docNoCentroid = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0)));
AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document));
const double mzTest = 400.0;
var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth);
// Verify relationship between normal and high-selectivity extraction
var docTofNormal = docNoCentroid.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
AssertEx.Serializable(docTofNormal, AssertEx.DocumentCloned);
var docTofSelective = docTofNormal.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 25 * 1000, null)
.ChangeUseSelectiveExtraction(true)));
AssertEx.Serializable(docTofSelective, AssertEx.DocumentCloned);
var filterWidthTof = docTofNormal.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
var filterWidthSelective = docTofSelective.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(filterWidth, filterWidthTof);
Assume.AreEqual(filterWidth, filterWidthSelective);
// Verify handling of bad request for vendor centroided data - ask for centroiding in mzML
const string fileName = "S_2_LVN.mzML";
var filePath = testFilesDir.GetTestPath(fileName);
AssertEx.ThrowsException <AssertFailedException>(() =>
{
listResults = new List <ChromatogramSet> {
new ChromatogramSet("rep1", new[] { new MsDataFilePath(filePath) }),
};
docContainer.ChangeMeasuredResults(new MeasuredResults(listResults.ToArray()), 1, 1, 1);
},
string.Format(Resources.NoCentroidedDataException_NoCentroidedDataException_No_centroided_data_available_for_file___0_____Adjust_your_Full_Scan_settings_, filePath));
// Import FT data with only MS1
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
Assume.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest));
docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest)));
AssertEx.Serializable(docMs1, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docMs1, docContainer.Document));
const string rep1 = "rep1";
listResults = new List <ChromatogramSet>
{
new ChromatogramSet(rep1, new[] { filePath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
var matchIdentifierLVN = "LVN";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierLVN = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierLVN;
}
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(1, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
else
{
Assume.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
}
}
const string rep2 = "rep2";
listResults.Add(new ChromatogramSet(rep2, new[] { testFilesDir.GetTestPath("S_2_NVN.mzML") }));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(2, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsTrue(nodeTran.Results[1][0].IsEmpty);
}
else
{
Assume.IsFalse(nodeTran.Results[1][0].IsEmpty);
}
}
}
// Chromatograms should be present in the cache for a number of isotopes.
var docMs1Isotopes = docContainer.Document.ChangeSettings(doc.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count,
3, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionFilter(filter => filter.ChangePeptideIonTypes(new[] { IonType.precursor })
.ChangeSmallMoleculeIonTypes(new[] { IonType.precursor })));
docCheckpoints.Add(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 2); // Need to reset auto-manage for transitions
var refineAutoSelect = new RefinementSettings {
AutoPickChildrenAll = PickLevel.transitions
};
docMs1Isotopes = refineAutoSelect.Refine(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 6);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep1, 1, 1, 0, 3, 0);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep2, 1, 1, 0, 3, 0);
docCheckpoints.Add(docMs1Isotopes);
// Add M-1 transitions, and verify that they have chromatogram data also, but
// empty peaks in all cases
var docMs1All = docMs1Isotopes.ChangeSettings(docMs1Isotopes.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent,
0, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionIntegration(i => i.ChangeIntegrateAll(false))); // For compatibility with v2.5 and earlier
docCheckpoints.Add(docMs1All);
AssertEx.IsDocumentState(docMs1All, null, 2, 2, 10);
AssertResult.IsDocumentResultsState(docMs1All, rep1, 1, 1, 0, 4, 0);
AssertResult.IsDocumentResultsState(docMs1All, rep2, 1, 1, 0, 4, 0);
var ms1AllTranstions = docMs1All.MoleculeTransitions.ToArray();
var tranM1 = ms1AllTranstions[0];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsForcedIntegration);
tranM1 = ms1AllTranstions[5];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsForcedIntegration && tranM1.Results[1][0].IsEmpty);
}
}
public void WiffResultsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
SrmDocument doc = InitWiffDocument(testFilesDir);
using (var docContainer = new ResultsTestDocumentContainer(doc,
testFilesDir.GetTestPath("SimpleWiffTest.sky")))
{
FileEx.SafeDelete(ChromatogramCache.FinalPathForName(docContainer.DocumentFilePath, null));
var listChromatograms = new List <ChromatogramSet>();
if (ExtensionTestContext.CanImportAbWiff)
{
string pathWiff = testFilesDir.GetTestPath("051309_digestion.wiff");
string[] dataIds = MsDataFileImpl.ReadIds(pathWiff);
for (int i = 0; i < dataIds.Length; i++)
{
string nameSample = dataIds[i];
if (!Equals(nameSample, "test") && listChromatograms.Count == 0)
{
continue;
}
string pathSample = SampleHelp.EncodePath(pathWiff, nameSample, i, LockMassParameters.EMPTY, false, false);
listChromatograms.Add(new ChromatogramSet(nameSample, new[] { MsDataFileUri.Parse(pathSample) }));
}
}
else
{
listChromatograms.Add(new ChromatogramSet("test",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-test.mzML")) }));
listChromatograms.Add(new ChromatogramSet("rfp9,before,h,1",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-rfp9,before,h,1.mzML")) }));
}
// Should have added test and one after
Assert.AreEqual(2, listChromatograms.Count);
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
AssertEx.IsDocumentState(docResults, 6, 9, 9, 18, 54);
Assert.IsTrue(docResults.Settings.MeasuredResults.IsLoaded);
foreach (var nodeTran in docResults.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(2, nodeTran.Results.Count);
}
// Remove the last chromatogram
listChromatograms.RemoveAt(1);
var docResultsSingle = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
AssertResult.IsDocumentResultsState(docResultsSingle, "test", 9, 2, 9, 8, 27);
// Add mzXML version of test sample
listChromatograms.Add(new ChromatogramSet("test-mzXML", new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")) }));
var docMzxml = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docMzxml, docResults, true));
docContainer.AssertComplete();
docMzxml = docContainer.Document;
// Verify mzXML and native contained same results
// Unfortunately mzWiff produces chromatograms with now zeros, which
// need to be interpolated into place. This means a .wiff file and
// its mzWiff mzXML file will never be the same.
AssertResult.MatchChromatograms(docMzxml, 0, 1, -1, 0);
}
// TODO: Switch to a using clause when PWiz is fixed, and this assertion fails
// AssertEx.ThrowsException<IOException>(() => testFilesDir.Dispose());
}
protected override void DoTest()
{
var skyfile = TestFilesDir.GetTestPath("2533_FattyAcids.sky");
const double lockmassNegative = 554.2615;
const double lockmassToler = 0.25; // Per Hans Vissers @ Waters
SrmDocument corrected = null, uncorrected2 = null, uncorrected1 = null;
for (var testloop = 2; testloop >= 0; testloop--)
{
RunUI(() => SkylineWindow.OpenFile(skyfile));
var doc0 = WaitForDocumentLoaded();
AssertEx.IsDocumentState(doc0, null, 1, 11, 11, 22);
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
ImportResults(GetTestPath(TestFilesPersistent[0]),
(testloop == 0)
? new LockMassParameters(0, lockmassNegative, lockmassToler) // ESI- data
: LockMassParameters.EMPTY);
var document = WaitForDocumentLoaded(400000);
loadStopwatch.Stop();
if (testloop < 2)
{
DebugLog.Info("lockmass {0} load time = {1}", (testloop == 0) ? "corrected" : "uncorrected", loadStopwatch.ElapsedMilliseconds);
}
if (testloop == 0)
{
corrected = document;
}
else if (testloop == 1)
{
uncorrected1 = document;
}
else
{
uncorrected2 = document;
}
if (testloop > 0)
{
RunUI(() => SkylineWindow.NewDocument(true));
}
}
Assert.AreNotEqual(corrected, uncorrected2); // Corrected pass should differ
Assert.AreEqual(uncorrected2, uncorrected1); // Both uncorrected passes should agree
Assert.IsNotNull(corrected);
Assert.IsNotNull(uncorrected2);
ComparePeaks(corrected, uncorrected2);
var correctedPeaks = Peaks(corrected);
var uncorrectedPeaks = Peaks(uncorrected1);
// Verify roundtrip with and without .skyd
for (var loop = 0; loop < 2; loop++)
{
var outfile = TestFilesDirs[0].GetTestPath("test" + loop + ".sky");
var withoutCache = (loop == 0);
RunUI(() =>
{
SkylineWindow.SaveDocument(outfile, !withoutCache);
SkylineWindow.NewDocument(true);
if (withoutCache)
{
FileEx.SafeDelete(Path.ChangeExtension(outfile, ChromatogramCache.EXT)); // kill the .skyd file
}
SkylineWindow.OpenFile(outfile);
});
var reopened = WaitForDocumentLoaded();
var reopenedPeaks = Peaks(reopened);
Assert.AreEqual(correctedPeaks.Count, reopenedPeaks.Count);
for (var i = 0; i < correctedPeaks.Count; i++)
{
var correctedPeak = correctedPeaks[i];
var uncorrectedPeak = uncorrectedPeaks[i];
var reopenedPeak = reopenedPeaks[i];
Assert.AreNotEqual(uncorrectedPeak, reopenedPeak, "reopened peaks should have lockmass correction");
Assert.AreEqual(correctedPeak, reopenedPeak, "reopened peaks should agree");
}
}
// And finally, verify that reimport successfully uses the lockmass values cached in the chromatograms
Settings.Default.LockmassParameters = LockMassParameters.EMPTY; // Make sure we aren't pulling from settngs
var manageResults = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RunUI(() =>
{
manageResults.SelectedChromatograms = new[] { SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[0] };
manageResults.ReimportResults();
manageResults.OkDialog();
});
WaitForDocumentChange(corrected);
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
var reimportedPeaks = Peaks(SkylineWindow.Document);
Assert.AreEqual(correctedPeaks.Count, reimportedPeaks.Count);
for (var i = 0; i < correctedPeaks.Count; i++)
{
var correctedPeak = correctedPeaks[i];
var uncorrectedPeak = uncorrectedPeaks[i];
var reimportedPeak = reimportedPeaks[i];
Assert.AreNotEqual(uncorrectedPeak, reimportedPeak, "reimported peaks should have lockmass correction");
Assert.AreEqual(correctedPeak, reimportedPeak, "reimported peaks should agree");
}
}
