public void ConsoleImportDocTest()
{
TestFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string[] documentPaths =
{
TestFilesDir.GetTestPath("document1.sky"), // subject1, subject2, buffer (waters calcurv - annotations, manual integration, removed peak)
TestFilesDir.GetTestPath("document2.sky"), // subject1, buffer (waters calcurve - annotations + custom, manual integration)
TestFilesDir.GetTestPath("document3.sky"), // subject2 (waters calcurve - node notes, manual integration)
TestFilesDir.GetTestPath("document4.sky"), // subject2 (agilent bovine1 - manual integration)
TestFilesDir.GetTestPath("document5.sky"), // opt1, opt2 (thermo bovine2 optimization data)
};
int[] groupCounts = { 36, 24, 12, 6, 10 };
int[] tranCounts = { 72, 48, 24, 23, 440 };
int[] peakCounts = { 518, 310, 162, 52, 3608 };
string[] cachePaths = new string[documentPaths.Length];
long[] cacheSizes = new long[documentPaths.Length];
for (int i = 0; i < documentPaths.Length; i++)
{
cachePaths[i] = ChromatogramCache.FinalPathForName(documentPaths[i], null);
cacheSizes[i] = new FileInfo(cachePaths[i]).Length; // Actual length of the file
}
const int firstIndex = 1;
string firstDocPath = documentPaths[firstIndex];
string emptyDocPath = TestFilesDir.GetTestPath("in_document.sky");
var docEmpty = new SrmDocument(SrmSettingsList.GetDefault());
docEmpty.SerializeToFile(emptyDocPath, emptyDocPath, SkylineVersion.CURRENT, null);
string docPersistPath = TestFilesDir.GetTestPath("out_document.sky");
string cachePersistPath = ChromatogramCache.FinalPathForName(docPersistPath, null);
string msg = RunCommand("--in=" + emptyDocPath,
"--import-document=" + firstDocPath,
"--import-document-results=" + MeasuredResults.MergeAction.merge_names,
"--out=" + docPersistPath);
CheckRunCommandOutputContains(string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(firstDocPath)), msg);
var doc = ResultsUtil.DeserializeDocument(docPersistPath);
var docImported = ResultsUtil.DeserializeDocument(documentPaths[firstIndex]);
Assert.IsTrue(doc.Settings.HasResults);
// Make sure original cache file is still on disk
Assert.IsTrue(File.Exists(cachePaths[firstIndex]));
Assert.IsTrue(File.Exists(cachePersistPath));
// The cache version of the original test file is 3.
// The cache file just created is version 4 or higher.
long startCacheLen = ResultsUtil.CacheSize(doc, cacheSizes[firstIndex],
groupCounts[firstIndex], tranCounts[firstIndex], peakCounts[firstIndex]);
AssertEx.IsDocumentState(doc, null, docImported.MoleculeGroupCount, docImported.MoleculeCount,
docImported.MoleculeTransitionGroupCount, docImported.MoleculeTransitionCount);
long singleCacheLen = new FileInfo(cachePersistPath).Length;
Assert.AreEqual(startCacheLen, singleCacheLen);
// Import a document removing the results
string docPersistPath2 = TestFilesDir.GetTestPath("out_document2.sky");
string lastDocPath = documentPaths[3];
msg = RunCommand("--in=" + docPersistPath,
"--import-document=" + lastDocPath,
"--import-document-results=" + MeasuredResults.MergeAction.remove,
"--out=" + docPersistPath2);
CheckRunCommandOutputContains(string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(lastDocPath)), msg);
// Skyd file should not have changed, but new molecules should have been added
var doc2 = ResultsUtil.DeserializeDocument(docPersistPath2);
var docImported2 = ResultsUtil.DeserializeDocument(lastDocPath);
// One protein should get merged
int groups2 = docImported.MoleculeGroupCount + docImported2.MoleculeTransitionGroupCount - 1;
int mols = docImported.MoleculeCount + docImported2.MoleculeCount;
int trans = docImported.MoleculeTransitionCount + docImported2.MoleculeTransitionCount;
AssertEx.IsDocumentState(doc2, null, groups2, mols, trans);
Assert.AreEqual(doc.MeasuredResults, doc2.MeasuredResults);
Assert.AreEqual(startCacheLen, new FileInfo(cachePersistPath).Length);
// Try again importing both at the same time without any results
string docPersistPath3 = TestFilesDir.GetTestPath("out_document3.sky");
string cachePersistPath3 = ChromatogramCache.FinalPathForName(docPersistPath3, null);
msg = RunCommand("--in=" + emptyDocPath,
"--import-document=" + firstDocPath,
"--import-document=" + lastDocPath,
"--import-document-results=" + MeasuredResults.MergeAction.remove,
"--out=" + docPersistPath3);
CheckRunCommandOutputContains(string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(firstDocPath)), msg);
CheckRunCommandOutputContains(string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(lastDocPath)), msg);
// Skyd file should not have changed, but new molecules should have been added
var doc3 = ResultsUtil.DeserializeDocument(docPersistPath3);
AssertEx.IsDocumentState(doc2, null, groups2, mols, trans);
Assert.IsFalse(doc3.Settings.HasResults);
Assert.IsFalse(File.Exists(cachePersistPath3));
var moleculeGroups2 = doc2.MoleculeGroups.ToArray();
var moleculeGroups3 = doc3.MoleculeGroups.ToArray();
// Make sure the order is the same
for (int i = 0; i < groups2; i++)
{
Assert.AreEqual(moleculeGroups2[i].Id, moleculeGroups3[i].Id);
}
// Import a document adding all replicates
const int nextIndex = 0;
string nextDocPath = documentPaths[nextIndex];
string docPersistPath4 = TestFilesDir.GetTestPath("out_document4.sky");
string cachePersistPath4 = ChromatogramCache.FinalPathForName(docPersistPath4, null);
msg = RunCommand("--in=" + docPersistPath,
"--import-document=" + nextDocPath,
"--import-document-results=" + MeasuredResults.MergeAction.add,
"--out=" + docPersistPath4);
CheckRunCommandOutputContains(string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(nextDocPath)), msg);
var docAdd = ResultsUtil.DeserializeDocument(docPersistPath4);
var docAdded = ResultsUtil.DeserializeDocument(nextDocPath);
long expectCacheLen = startCacheLen
+ ResultsUtil.CacheSize(docAdded, cacheSizes[nextIndex], groupCounts[nextIndex], tranCounts[nextIndex], peakCounts[nextIndex])
- ChromatogramCache.HeaderSize; // Only one header between the two caches
// No peptide merging should have happened
AssertEx.IsDocumentState(docAdd, null,
doc.PeptideGroupCount + docAdded.PeptideGroupCount,
doc.PeptideCount + docAdded.PeptideCount,
doc.PeptideTransitionCount + docAdded.PeptideTransitionCount);
Assert.AreEqual(3, docAdded.Settings.MeasuredResults.Chromatograms.Count);
var chromatograms = docAdd.Settings.MeasuredResults.Chromatograms;
var chromatogramsInitial = doc.Settings.MeasuredResults.Chromatograms;
int chromCount = chromatograms.Count;
Assert.AreEqual(chromatogramsInitial.Count + 3, chromatograms.Count);
Assert.AreEqual("buffer1", chromatograms[chromCount - 1].Name);
Assert.AreEqual("subject3", chromatograms[chromCount - 2].Name);
Assert.AreEqual("subject2", chromatograms[chromCount - 3].Name);
// Make sure annotations and user set peaks were added and not lost
var stateAdd = new DocResultsState(docAdd);
var stateAdded = new DocResultsState(docAdded);
var state = new DocResultsState(doc);
Assert.IsTrue(stateAdd.HasResults && stateAdded.HasResults);
Assert.AreEqual(stateAdd.NoteCount, state.NoteCount + stateAdded.NoteCount);
Assert.AreEqual(stateAdd.AnnotationCount, state.AnnotationCount + stateAdded.AnnotationCount);
Assert.AreEqual(stateAdd.UserSetCount, state.UserSetCount + stateAdded.UserSetCount);
// Because the data in the two documents actually cover the same results,
// some calculation is required to determine the number of chromInfo objects
// expected.
double fOld = chromCount / (double)chromatogramsInitial.Count;
double fAdded = chromCount / (double)docAdded.Settings.MeasuredResults.Chromatograms.Count;
Assert.AreEqual(stateAdd.PeptideResults,
(int)(state.PeptideResults * fOld + stateAdded.PeptideResults * fAdded));
Assert.AreEqual(stateAdd.TransitionGroupResults,
(int)(state.TransitionGroupResults * fOld + stateAdded.TransitionGroupResults * fAdded));
Assert.AreEqual(stateAdd.TransitionResults,
(int)(state.TransitionResults * fOld + stateAdded.TransitionResults * fAdded));
foreach (var nodeGroup in docAdd.PeptideTransitionGroups)
{
for (int i = 0; i < 5; i++)
{
Assert.AreEqual(1, nodeGroup.Results[i].Count);
}
}
// Cache should now contain results for both documents
long newCacheLen = new FileInfo(cachePersistPath4).Length;
Assert.AreEqual(expectCacheLen, newCacheLen);
}
