public void Wiff2ResultsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("OnyxTOFMS.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
//AssertEx.IsDocumentState(doc, 0, 1, 1, 4);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
const string replicateName = "Wiff2Test";
string extRaw = ExtensionTestContext.ExtAbWiff2;
string suffix = ExtensionTestContext.CanImportAbWiff2 ? "" : "-sample-centroid";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.ABI, "swath.api" + suffix + extRaw)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
//AssertResult.IsDocumentResultsState(docResults, replicateName,
// doc.MoleculeCount, doc.MoleculeTransitionGroupCount, 0, doc.MoleculeTransitionCount, 0);
}
testFilesDir.Dispose();
}
public void FileTypeTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
// wiff1
{
string extWiff = ExtensionTestContext.ExtAbWiff;
string suffix = ExtensionTestContext.CanImportAbWiff ? "" : "-test";
// Do file type checks
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion" + suffix + extWiff)))
{
Assert.IsTrue(msData.IsABFile);
}
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")))
{
Assert.IsTrue(msData.IsABFile);
Assert.IsTrue(msData.IsMzWiffXml);
}
}
// wiff2
{
string extWiff2 = ExtensionTestContext.ExtAbWiff2;
string suffix = ExtensionTestContext.CanImportAbWiff2 ? "" : "-sample-centroid";
// Do file type checks
using (var msData = new MsDataFileImpl(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.ABI, "swath.api" + suffix + extWiff2)))
{
Assert.IsTrue(msData.IsABFile);
}
}
}
public void TestScanDescription()
{
if (Skyline.Program.NoVendorReaders)
{
return;
}
string path = TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Thermo, "IT-HCD-SPS.raw");
using (var msDataFile = new MsDataFileImpl(path))
{
Assert.AreEqual("sps", msDataFile.GetScanDescription(0));
}
}
public void TestInstrumentInfo()
{
const string testZipPath = @"TestData\PwizFileInfoTest.zip";
var testFilesDir = new TestFilesDir(TestContext, testZipPath);
// Waters file (.raw directory) and mz5 equivalent
foreach (
var ext in
new[]
{ ExtensionTestContext.ExtWatersRaw, ExtensionTestContext.ExtMz5 })
{
VerifyInstrumentInfo(testFilesDir.GetTestPath("160109_Mix1_calcurve_075" + ext),
"Waters instrument model", "", "", "");
}
// ABI .wiff file
VerifyInstrumentInfo(testFilesDir.GetTestPath("051309_digestion" + ExtensionTestContext.ExtAbWiff),
"4000 QTRAP", "electrospray ionization", "quadrupole/quadrupole/axial ejection linear ion trap", "electron multiplier");
// Sciex .wiff2 file
string wiff2Ext = ExtensionTestContext.CanImportAbWiff2 ? ".wiff2" : "-sample-centroid.mzML";
VerifyInstrumentInfo(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.ABI, "swath.api" + wiff2Ext),
"X500R QTOF", "electrospray ionization", "quadrupole/quadrupole/time-of-flight", "electron multiplier");
// MzWiff generated mzXML files
VerifyInstrumentInfo(testFilesDir.GetTestPath("051309_digestion-s3.mzXML"),
"4000 Q Trap", "electrospray ionization", "TOFMS", "");
// Agilent file (.d directory)
VerifyInstrumentInfo(testFilesDir.GetTestPath("081809_100fmol-MichromMix-05" + ExtensionTestContext.ExtAgilentRaw),
"Agilent instrument model", "nanoelectrospray", "quadrupole/quadrupole/quadrupole", "electron multiplier");
// Shimadzu TOF file (.lcd file)
VerifyInstrumentInfo(testFilesDir.GetTestPath("10nmol_Negative_MS_ID_ON_055" + ExtensionTestContext.ExtShimadzuRaw),
"Shimadzu instrument model", "electrospray ionization", "quadrupole/quadrupole/time-of-flight", "microchannel plate detector");
// Thermo .raw|mzML file
foreach (
var ext in
new[]
{ ExtensionTestContext.ExtThermoRaw, ExtensionTestContext.ExtMzml })
{
VerifyInstrumentInfo(testFilesDir.GetTestPath("CE_Vantage_15mTorr_0001_REP1_01" + ext),
"TSQ Vantage", "nanoelectrospray", "quadrupole/quadrupole/quadrupole", "electron multiplier");
}
}
public void TestTicChromatogram()
{
if (Skyline.Program.NoVendorReaders)
{
return;
}
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.ABI, "PressureTrace1.wiff"), 0, 0);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Agilent, "ImsSynthAllIons.d"), 49, 369032);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Agilent, "GFb_4Scan_TimeSegs_1530_100ng.d"), 63, 56163792);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Bruker, "Hela_QC_PASEF_Slot1-first-6-frames.d"), 1, 23340182);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Thermo, "090701-LTQVelos-unittest-01.raw"), 30, 32992246);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Waters, "MSe_Short.raw"), 2, 3286253);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Waters, "HDMRM_Short_noLM.raw"), 0, 0);
VerifyTicChromatogram(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.Waters, "HDDDA_Short_noLM.raw"), 1, 3692876);
}
public void TestInstrumentSerialNumbers()
{
if (Skyline.Program.NoVendorReaders)
{
return;
}
const string testZipPath = @"TestData\PwizFileInfoTest.zip";
var testFilesDir = new TestFilesDir(TestContext, testZipPath);
if (ExtensionTestContext.CanImportAbWiff2)
{
VerifySerialNumber(TestFilesDir.GetVendorTestData(TestFilesDir.VendorDir.ABI, "swath.api.wiff2"), "CI231606PT"); // WIFF2 file with empty serial number
}
if (ExtensionTestContext.CanImportAbWiff)
{
VerifySerialNumber(testFilesDir.GetTestPath("051309_digestion.wiff"), "U016050603");
}
if (ExtensionTestContext.CanImportAgilentRaw)
{
VerifySerialNumber(testFilesDir.GetTestPath("081809_100fmol-MichromMix-05.d"), "50331873");
}
if (ExtensionTestContext.CanImportShimadzuRaw)
{
VerifySerialNumber(testFilesDir.GetTestPath("10nmol_Negative_MS_ID_ON_055.lcd"), null); // Shimadzu does not provide serial number
}
if (ExtensionTestContext.CanImportWatersRaw)
{
VerifySerialNumber(testFilesDir.GetTestPath("160109_Mix1_calcurve_075.raw"), null); // Waters does not provide serial number
}
if (ExtensionTestContext.CanImportThermoRaw)
{
VerifySerialNumber(testFilesDir.GetTestPath("CE_Vantage_15mTorr_0001_REP1_01.raw"), null); // Thermo RAW file with empty serial number
const string testZipPath2 = @"TestData\Results\ThermoQuant.zip";
var testFilesDir2 = new TestFilesDir(TestContext, testZipPath2);
VerifySerialNumber(testFilesDir2.GetTestPath("Site20_STUDY9P_PHASEII_QC_03.raw"), "TQU00490");
}
}
public static void CreateZipFile(string zipPath)
{
zipPath = zipPath ?? string.Empty; // For quiet ReSharper code inspection
Console.WriteLine();
Console.WriteLine("# Creating " + Path.GetFileName(zipPath) + "...");
Console.WriteLine();
if (File.Exists(zipPath))
{
File.Delete(zipPath);
}
var exeDirectory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) ?? "";
Directory.SetCurrentDirectory(exeDirectory);
var solutionDirectory = exeDirectory;
while (!File.Exists(Path.Combine(solutionDirectory, "Skyline.sln")))
{
solutionDirectory = Path.GetDirectoryName(solutionDirectory);
if (string.IsNullOrEmpty(solutionDirectory))
{
throw new ApplicationException("Can't find solution directory");
}
}
using (var zipFile = new ZipFile(zipPath))
{
// DotNetZip has a _bug_ which causes an extraction error without this
// (see http://stackoverflow.com/questions/15337186/dotnetzip-badreadexception-on-extract)
zipFile.ParallelDeflateThreshold = -1;
zipFile.AlternateEncodingUsage = ZipOption.Always;
zipFile.AlternateEncoding = System.Text.Encoding.UTF8;
if ((String.Empty + Path.GetFileName(zipPath)).ToLower() == "skylinenightly.zip")
{
// Add files to top level of zip file.
var files = new[]
{
"SkylineNightlyShim.exe",
"SkylineNightly.exe",
"SkylineNightly.pdb",
"Microsoft.Win32.TaskScheduler.dll",
"DotNetZip.dll"
};
foreach (var file in files)
{
Console.WriteLine(file);
zipFile.AddFile(file);
}
}
else if ((String.Empty + Path.GetFileName(zipPath)).ToLower() == "bibliospec.zip")
{
// Create a BiblioSpec distro
var files = new List <string>
{
"BlibBuild.exe",
"BlibFilter.exe",
"MassLynxRaw.dll",
"timsdata.dll",
"baf2sql_c.dll",
"cdt.dll",
"modifications.xml",
"quantitation_1.xsd",
"quantitation_2.xsd",
"unimod_2.xsd"
};
var dir = Directory.GetCurrentDirectory();
files.Add(dir.Contains("Debug") ? "msparserD.dll" : "msparser.dll");
// Locate BlibToMS2
var parent = dir.IndexOf("Skyline\\", StringComparison.Ordinal);
if (parent > 0)
{
dir = dir.Substring(0, parent);
var blib2ms2 = dir + "Shared\\BiblioSpec\\obj\\x64\\BlibToMs2.exe";
if (File.Exists(blib2ms2)) // Don't worry about this for a 32 bit build, we don't distribute that
{
files.Add(blib2ms2);
}
}
foreach (var file in files)
{
Console.WriteLine(file);
zipFile.AddFile(file, string.Empty);
}
}
else
{
// Add SkylineTester at top level of zip file.
Console.WriteLine("SkylineTester.exe");
zipFile.AddFile("SkylineTester.exe");
// Add .skytr files at top level of zip file.
var skytrDirectory = Path.Combine(solutionDirectory, @"SkylineTester\Run files");
foreach (var skytrFile in Directory.EnumerateFiles(skytrDirectory, "*.skytr"))
{
AddFile(skytrFile, zipFile, ".");
}
// Add each subdirectory in the bin directory.
foreach (var directory in Directory.EnumerateDirectories("."))
{
if (Include(directory))
{
var name = Path.GetFileName(directory) ?? "";
Console.WriteLine(Path.Combine(SkylineTesterWindow.SkylineTesterFiles, name));
zipFile.AddDirectory(directory, Path.Combine(SkylineTesterWindow.SkylineTesterFiles, name));
}
}
// Add each file in the bin directory.
foreach (var file in Directory.EnumerateFiles("."))
{
if (Include(file))
{
AddFile(file, zipFile);
}
}
// Add test zip files.
var zipFilesList = new List <string>();
FindZipFiles(solutionDirectory, zipFilesList);
var zipFilesDirectory = Path.Combine(SkylineTesterWindow.SkylineTesterFiles, "TestZipFiles");
foreach (var testZipFile in zipFilesList)
{
var testZipDirectory = Path.GetDirectoryName(testZipFile);
if (string.IsNullOrEmpty(testZipDirectory))
{
continue;
}
testZipDirectory = Path.Combine(zipFilesDirectory,
testZipDirectory.Substring(solutionDirectory.Length + 1));
AddFile(testZipFile, zipFile, testZipDirectory);
}
// Add pwiz vendor reader test data
var vendorTestData = new List <string>();
foreach (TestFilesDir.VendorDir vendorDir in Enum.GetValues(typeof(TestFilesDir.VendorDir)))
{
FindVendorReaderTestData(TestFilesDir.GetVendorTestData(vendorDir), vendorTestData);
}
foreach (var file in vendorTestData)
{
var parentDirectory = Path.GetDirectoryName(file);
if (string.IsNullOrEmpty(parentDirectory))
{
continue;
}
int relativePathStart = parentDirectory.LastIndexOf('\\',
parentDirectory.IndexOf(@"Test.data", StringComparison.InvariantCulture));
parentDirectory = parentDirectory.Substring(relativePathStart + 1);
AddFile(file, zipFile, Path.Combine(SkylineTesterWindow.SkylineTesterFiles, parentDirectory));
}
// Add the file that we use to determine which branch this is from
AddFile(Path.Combine(solutionDirectory, "..\\..\\pwiz\\Version.cpp"), zipFile);
// Add unit testing DLL.
const string relativeUnitTestingDll =
@"PublicAssemblies\Microsoft.VisualStudio.QualityTools.UnitTestFramework.dll";
var unitTestingDll = SkylineTesterWindow.GetExistingVsIdeFilePath(relativeUnitTestingDll);
if (unitTestingDll == null)
{
throw new ApplicationException(string.Format("Can't find {0}", relativeUnitTestingDll));
}
AddFile(unitTestingDll, zipFile);
}
Console.WriteLine();
Console.WriteLine("# Saving...");
zipFile.Save();
Console.WriteLine();
Console.WriteLine("# {0} size: {1:F1} MB", Path.GetFileName(zipPath), new FileInfo(PathEx.SafePath(zipPath)).Length / (1024.0 * 1024));
Console.WriteLine("# Done.");
Console.WriteLine();
}
}