private void RemovePartialCacheFiles(string[] files)
{
WaitForChromatogramManagerQuiet();
foreach (var file in files)
{
string cacheFile = ChromatogramCache.PartPathForName(SkylineWindow.DocumentFilePath, new MsDataFilePath(file));
FileEx.SafeDelete(cacheFile, true);
}
}
public void TestCommandLineNoJoin()
{
if (!ExtensionTestContext.CanImportWatersRaw)
{
return;
}
var testFilesDir = new TestFilesDir(TestContext, @"TestA\CommandLineNoJoinTest.zip");
string inDocPath = testFilesDir.GetTestPath("test.sky");
string rawFileRoot = testFilesDir.GetTestPath("RawFiles");
string[] rawFiles =
{
Path.Combine(rawFileRoot, "160109_Mix1_calcurve_071.raw"),
Path.Combine(rawFileRoot, "160109_Mix1_calcurve_074.raw")
};
Assert.IsTrue(Directory.Exists(rawFileRoot));
List <string> partialSkydFiles = new List <string>();
// First, create the partial .skyd files for each of the replicates.
for (int iFile = 0; iFile < rawFiles.Length; iFile++)
{
string rawFile = rawFiles[iFile];
Assert.IsTrue(Directory.Exists(rawFile), rawFile);
string outFile = testFilesDir.GetTestPath("partial" + iFile + ".sky");
RunCommand("--in=" + inDocPath, "--import-file=" + rawFile, "--out=" + outFile, "--import-no-join");
Assert.IsTrue(File.Exists(outFile), rawFile);
string partialSkydFile = ChromatogramCache.PartPathForName(outFile, new MsDataFilePath(rawFile));
Assert.IsTrue(File.Exists(partialSkydFile), rawFile);
partialSkydFiles.Add(partialSkydFile);
File.Delete(outFile);
}
// Delete the raw files since we no longer need them, since we have the .skyd files
Directory.Delete(rawFileRoot, true);
Assert.IsFalse(Directory.Exists(rawFileRoot));
string completeFile = testFilesDir.GetTestPath("complete.sky");
Assert.IsNotNull(completeFile);
string completeSkyd = Path.ChangeExtension(completeFile, "skyd");
Assert.IsFalse(File.Exists(completeFile));
Assert.IsFalse(File.Exists(completeSkyd));
List <string> args = new List <string>
{
"--in=" + inDocPath,
"--out=" + completeFile
};
args.AddRange(rawFiles.Select(file => "--import-file=" + file));
RunCommand(args.ToArray());
Assert.IsTrue(File.Exists(completeFile));
Assert.IsTrue(File.Exists(completeSkyd));
foreach (var partialSkydFile in partialSkydFiles)
{
Assert.IsFalse(File.Exists(partialSkydFile), partialSkydFile);
}
using (var stream = new FileStream(completeFile, FileMode.Open))
{
var srmDocument = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(stream);
Assert.IsTrue(srmDocument.Settings.HasResults);
Assert.AreEqual(rawFiles.Length, srmDocument.MeasuredResults.Chromatograms.Count);
for (int iFile = 0; iFile < rawFiles.Length; iFile++)
{
var msDataFilePath = srmDocument.MeasuredResults.Chromatograms[iFile].MSDataFilePaths.First() as MsDataFilePath;
Assert.IsNotNull(msDataFilePath);
Assert.AreEqual(rawFiles[iFile], msDataFilePath.FilePath);
}
}
}
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();
}