public void AreEqual(SrmDocument document)
{
var state = new DocResultsState(document);
Assert.AreEqual(PeptideResults, state.PeptideResults);
Assert.AreEqual(TransitionGroupResults, state.TransitionGroupResults);
Assert.AreEqual(TransitionResults, state.TransitionResults);
Assert.AreEqual(UserSetCount, state.UserSetCount);
Assert.AreEqual(NoteCount, state.NoteCount);
Assert.AreEqual(AnnotationCount, state.AnnotationCount);
}
/// <summary>
/// Test import document functionality with results importing
/// </summary>
protected override void DoTest()
{
_documentPaths = new[]
{
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)
};
_groupCounts = new[] { 36, 24, 12, 6, 10 };
_tranCounts = new[] { 72, 48, 24, 23, 440 };
_cachePaths = new string[_documentPaths.Length];
_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
}
var docEmpty = SkylineWindow.Document;
var state = new DocResultsState(docEmpty);
// Import a document into the empty document attempt to keep the results and fail
var importDlg = ShowDialog <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[1]));
RunUI(() => importDlg.Action = MeasuredResults.MergeAction.merge_names);
var messageDlg = ShowDialog <MessageDlg>(importDlg.OkDialog);
// Allow results to be removed
RunUI(messageDlg.OkDialog);
WaitForClosedForm(messageDlg);
RunUI(importDlg.OkDialog);
WaitForClosedForm(importDlg);
var docFirstAttempt = WaitForDocumentChange(docEmpty);
// Results state should not have changed
state.AreEqual(docFirstAttempt);
// Undo and save
string docPersistPath = TestFilesDir.GetTestPath("out_document.sky");
string cachePersistPath = ChromatogramCache.FinalPathForName(docPersistPath, null);
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.SaveDocument(docPersistPath);
});
// Document now changes because of document GUID
Assert.AreNotSame(docEmpty, SkylineWindow.Document);
Assert.AreNotSame(docEmpty.Settings.DataSettings, SkylineWindow.Document.Settings.DataSettings);
Assert.AreSame(docEmpty.Children, SkylineWindow.Document.Children);
Assert.AreSame(docEmpty.Settings.PeptideSettings, SkylineWindow.Document.Settings.PeptideSettings);
Assert.AreSame(docEmpty.Settings.TransitionSettings, SkylineWindow.Document.Settings.TransitionSettings);
Assert.IsTrue(File.Exists(docPersistPath));
Assert.IsFalse(File.Exists(cachePersistPath));
// Try again
const int firstIndex = 1;
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[firstIndex]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_names;
dlg.OkDialog();
});
var docInitial = WaitForDocumentChangeLoaded(docEmpty);
state = new DocResultsState(docInitial);
Assert.IsTrue(state.HasResults);
// Make sure cache is where it is expected to be
Assert.AreEqual(cachePersistPath, docInitial.Settings.MeasuredResults.CachePaths.ToArray()[0]);
// 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 = GetCacheSize(firstIndex, docInitial);
long singleCacheLen = new FileInfo(cachePersistPath).Length;
Assert.AreEqual(startCacheLen, singleCacheLen);
RunUI(() =>
{
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
});
// Import a document removing the results
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[3]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.remove;
dlg.OkDialog();
});
var docRemove = WaitForDocumentChange(docInitial);
// Results state should not have changed
state.AreEqual(docRemove);
RunUI(SkylineWindow.Undo);
Assert.AreSame(docInitial, SkylineWindow.Document);
// Import a document adding all replicates
const int nextIndex = 0;
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[nextIndex]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.add;
dlg.OkDialog();
});
var docAdd = WaitForDocumentChangeLoaded(docInitial);
var docAdded = ResultsUtil.DeserializeDocument(_documentPaths[nextIndex]);
long expectCacheLen = startCacheLen
+ GetCacheSize(nextIndex, docAdded)
- ChromatogramCache.HeaderSize; // Only one header between the two caches
// No peptide merging should have happened
AssertEx.IsDocumentState(docAdd, null,
docInitial.PeptideGroupCount + docAdded.PeptideGroupCount,
docInitial.PeptideCount + docAdded.PeptideCount,
docInitial.PeptideTransitionCount + docAdded.PeptideTransitionCount);
Assert.AreEqual(3, docAdded.Settings.MeasuredResults.Chromatograms.Count);
var chromatograms = docAdd.Settings.MeasuredResults.Chromatograms;
var chromatogramsInitial = docInitial.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);
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(cachePersistPath).Length;
Assert.AreEqual(expectCacheLen, newCacheLen);
// An undo followed by a redo should not change that
Assert.AreEqual(9, SkylineWindow.Document.RevisionIndex);
RunUI(SkylineWindow.Undo);
WaitForDocumentLoaded(5000);
Assert.AreEqual(6, SkylineWindow.Document.RevisionIndex);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
RunUI(SkylineWindow.Redo);
WaitForDocumentLoaded(5000); // Necessary? Have seen intermittent failures in this area
Assert.AreEqual(9, SkylineWindow.Document.RevisionIndex);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
// Undo followed by a save, should reduce cache to previous size
RunUI(SkylineWindow.Undo);
WaitForDocumentLoaded(5000); // Necessary? Have seen intermittent failures in this area
Assert.AreEqual(6, SkylineWindow.Document.RevisionIndex);
RunUI(() => SkylineWindow.SaveDocument());
Assert.AreEqual(startCacheLen, new FileInfo(cachePersistPath).Length);
Assert.AreEqual(7, SkylineWindow.Document.RevisionIndex);
Thread.Sleep(1000); // Wait 10 ms to make sure the cache change in Redo registers as a cache modification
// After which, a redo should return the document to the add state and
// restore the cache
RunUI(SkylineWindow.Redo);
var docRedo = WaitForDocumentLoaded();
Assert.AreEqual(10, docRedo.RevisionIndex);
stateAdd.AreEqual(docRedo);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
// Import matching replicates by name
var docPreUndo = SkylineWindow.Document;
RunUI(SkylineWindow.Undo);
var docUndoLoaded = WaitForDocumentChangeLoaded(docPreUndo);
Assert.AreEqual(8, docUndoLoaded.RevisionIndex);
Assert.AreNotSame(docInitial, docUndoLoaded);
Assert.AreEqual(docInitial, docUndoLoaded); // Cache optimization changes document
docInitial = docUndoLoaded;
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_names;
dlg.OkDialog();
});
var docNames = WaitForDocumentChangeLoaded(docInitial);
// Should have the same impact on state as adding all replicates. The information
// just gets stored differently.
chromatograms = docNames.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(3, chromatograms.Count);
Assert.AreEqual(chromatogramsInitial[0].Name, chromatograms[0].Name);
Assert.AreEqual(2, chromatograms[0].MSDataFileInfos.Count);
Assert.AreEqual(chromatogramsInitial[1].Name, chromatograms[1].Name);
Assert.AreEqual(2, chromatograms[1].MSDataFileInfos.Count);
var missingNames = (from chromatogramSet in docAdded.Settings.MeasuredResults.Chromatograms
where !chromatogramsInitial.Any(cs => Equals(cs.Name, chromatogramSet.Name))
select chromatogramSet.Name).ToArray();
Assert.AreEqual(missingNames[0], chromatograms[2].Name);
Assert.AreEqual(1, chromatograms[2].MSDataFileInfos.Count);
stateAdd.AreEqual(docNames);
foreach (var nodeGroup in docNames.PeptideTransitionGroups)
{
Assert.AreEqual(2, nodeGroup.Results[0].Count);
Assert.AreEqual(2, nodeGroup.Results[1].Count);
Assert.AreEqual(1, nodeGroup.Results[2].Count);
}
// Import merging by order
RunUI(() =>
{
SkylineWindow.Undo();
var docCurrent = SkylineWindow.DocumentUI;
if (ReferenceEquals(docInitial, docCurrent))
{
Assert.AreEqual(8, docInitial.RevisionIndex);
}
else
{
// Attempt to report more information when the test fails here
AssertEx.DocsEqual(docInitial, docCurrent);
Assert.AreEqual(docInitial.Id.GlobalIndex, docCurrent.Id.GlobalIndex);
Assert.AreEqual(docInitial.UserRevisionIndex, docCurrent.UserRevisionIndex);
Assert.AreEqual(docInitial.RevisionIndex, docCurrent.RevisionIndex);
Assert.AreSame(docInitial, docCurrent);
}
});
Assert.AreSame(docInitial, SkylineWindow.Document);
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[3]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_indices;
dlg.OkDialog();
});
var docOrder = WaitForDocumentChangeLoaded(docInitial);
var docOrderAdded = ResultsUtil.DeserializeDocument(_documentPaths[3]);
chromatograms = docOrder.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(2, chromatograms.Count);
AssertEx.AreEqualDeep(chromatogramsInitial.Select(chrom => chrom.Name).ToArray(),
chromatogramsInitial.Select(chrom => chrom.Name).ToArray());
var stateOrder = new DocResultsState(docOrder);
var stateOrderAdded = new DocResultsState(docOrderAdded);
Assert.AreEqual(stateOrder.NoteCount, state.NoteCount + stateOrderAdded.NoteCount);
Assert.AreEqual(stateOrder.AnnotationCount, state.AnnotationCount + stateOrderAdded.AnnotationCount);
Assert.AreEqual(stateOrder.UserSetCount, state.UserSetCount + stateOrderAdded.UserSetCount);
Assert.AreEqual(stateOrder.PeptideResults, state.PeptideResults + stateOrderAdded.PeptideResults);
Assert.AreEqual(stateOrder.TransitionGroupResults,
state.TransitionGroupResults + stateOrderAdded.TransitionGroupResults);
Assert.AreEqual(stateOrder.TransitionResults,
state.TransitionResults + stateOrderAdded.TransitionResults);
foreach (var nodeGroup in docOrder.PeptideTransitionGroups)
{
Assert.AreEqual(1, nodeGroup.Results[0].Count);
}
// Import merging by order with overflow and multiple files
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0], _documentPaths[2]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_indices;
dlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count > 2);
var docOrder2 = WaitForDocumentLoaded();
var docAdded2 = ResultsUtil.DeserializeDocument(_documentPaths[2]);
// No peptide merging should have happened
AssertEx.IsDocumentState(docOrder2, null,
docInitial.PeptideGroupCount + docAdded.PeptideGroupCount + docAdded2.PeptideGroupCount,
docInitial.PeptideCount + docAdded.PeptideCount + docAdded2.PeptideCount,
docInitial.PeptideTransitionCount + docAdded.PeptideTransitionCount + docAdded2.PeptideTransitionCount);
chromatograms = docOrder2.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(3, chromatograms.Count);
Assert.AreEqual(chromatogramsInitial[0].Name, chromatograms[0].Name);
Assert.AreEqual(chromatogramsInitial[1].Name, chromatograms[1].Name);
Assert.AreEqual("buffer1", chromatograms[2].Name);
var stateOrder2 = new DocResultsState(docOrder2);
var stateAdded2 = new DocResultsState(docAdded2);
Assert.AreEqual(stateOrder2.NoteCount, stateAdd.NoteCount + stateAdded2.NoteCount);
Assert.AreEqual(stateOrder2.AnnotationCount, stateAdd.AnnotationCount + stateAdded2.AnnotationCount);
Assert.AreEqual(stateOrder2.UserSetCount, stateAdd.UserSetCount + stateAdded2.UserSetCount);
// Because the data all 3 documents actually cover the same results,
// some calculation is required to determine the number of chromInfo objects
// expected.
int fileCount = docOrder2.Settings.MeasuredResults.Chromatograms.SelectMany(chrom => chrom.MSDataFileInfos).Count();
fOld = fileCount / (double)chromatogramsInitial.Count;
fAdded = fileCount / (double)docAdded.Settings.MeasuredResults.Chromatograms.Count;
double fAdded2 = fileCount / (double)docAdded2.Settings.MeasuredResults.Chromatograms.Count;
Assert.AreEqual(stateOrder2.PeptideResults,
(int)(state.PeptideResults * fOld + stateAdded.PeptideResults * fAdded + stateAdded2.PeptideResults * fAdded2));
Assert.AreEqual(stateOrder2.TransitionGroupResults,
(int)(state.TransitionGroupResults * fOld + stateAdded.TransitionGroupResults * fAdded + stateAdded2.TransitionGroupResults * fAdded2));
Assert.AreEqual(stateOrder2.TransitionResults,
(int)(state.TransitionResults * fOld + stateAdded.TransitionResults * fAdded + stateAdded2.TransitionResults * fAdded2));
foreach (var nodeGroup in docOrder2.PeptideTransitionGroups)
{
Assert.AreEqual(3, nodeGroup.Results[0].Count);
Assert.AreEqual(2, nodeGroup.Results[1].Count);
Assert.AreEqual(1, nodeGroup.Results[2].Count);
// Make sure files are ordered as expected
Assert.AreEqual(docInitial.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][0].FileId).FilePath);
Assert.AreEqual(docAdded.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][1].FileId).FilePath);
Assert.AreEqual(docAdded2.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][2].FileId).FilePath);
}
// Now import allowing matching peptides to be merged
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
RunDlg <ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0], _documentPaths[2]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.add;
dlg.IsMergePeptides = true;
dlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count > 2);
var docMerged = WaitForDocumentLoaded();
chromatograms = docMerged.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(6, chromatograms.Count);
var dictPeptides = docInitial.Peptides.ToDictionary(nodePep => nodePep.Key);
foreach (var nodePep in docAdded.Peptides.Where(p => !dictPeptides.ContainsKey(p.Key)))
{
dictPeptides.Add(nodePep.Key, nodePep);
}
foreach (var nodePep in docAdded2.Peptides.Where(p => !dictPeptides.ContainsKey(p.Key)))
{
dictPeptides.Add(nodePep.Key, nodePep);
}
AssertEx.IsDocumentState(docMerged, null, 3, dictPeptides.Count,
dictPeptides.Values.Sum(nodePep => nodePep.TransitionCount));
var stateMerged = new DocResultsState(docMerged);
Assert.AreEqual(stateMerged.NoteCount, stateAdd.NoteCount + stateAdded2.NoteCount);
Assert.AreEqual(stateMerged.AnnotationCount, stateAdd.AnnotationCount + stateAdded2.AnnotationCount);
Assert.AreEqual(stateMerged.UserSetCount, stateAdd.UserSetCount + stateAdded2.UserSetCount);
var setColors = new HashSet <int>();
foreach (var nodePep in docMerged.Peptides.Take(4))
{
setColors.Add(nodePep.Annotations.ColorIndex);
}
Assert.AreEqual(4, setColors.Count);
Assert.IsFalse(setColors.Contains(-1));
// TODO: Import optimization data
// Check cache sizes
// At this point, the main cache should be about the size of the sum of
// the caches it has incorporated.
Assert.AreEqual(newCacheLen + GetCacheSize(2) + GetCacheSize(3) - 2 * ChromatogramCache.HeaderSize,
new FileInfo(cachePersistPath).Length, 200);
// Undo and save should have set the main cache back to the initial state
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SaveDocument());
Assert.AreEqual(startCacheLen, new FileInfo(cachePersistPath).Length);
// And the original caches should remain unchanged
for (int i = 0; i < _cachePaths.Length; i++)
{
Assert.AreEqual(_cacheSizes[i], new FileInfo(_cachePaths[i]).Length);
}
// Another undo and save should remove the results cache for the active document
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.SaveDocument();
});
Assert.IsFalse(File.Exists(cachePersistPath));
}
/// <summary>
/// Test import document functionality with results importing
/// </summary>
protected override void DoTest()
{
_documentPaths = new[]
{
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)
};
_groupCounts = new[] {36, 24, 12, 6, 10};
_tranCounts = new[] {72, 48, 24, 23, 440};
_cachePaths = new string[_documentPaths.Length];
_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;
}
var docEmpty = SkylineWindow.Document;
var state = new DocResultsState(docEmpty);
// Import a document into the empty document attempt to keep the results and fail
var importDlg = ShowDialog<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[1]));
RunUI(() => importDlg.Action = MeasuredResults.MergeAction.merge_names);
var messageDlg = ShowDialog<MessageDlg>(importDlg.OkDialog);
// Allow results to be removed
RunUI(messageDlg.OkDialog);
WaitForClosedForm(messageDlg);
RunUI(importDlg.OkDialog);
WaitForClosedForm(importDlg);
var docFirstAttempt = WaitForDocumentChange(docEmpty);
// Results state should not have changed
state.AreEqual(docFirstAttempt);
// Undo and save
string docPersistPath = TestFilesDir.GetTestPath("out_document.sky");
string cachePersistPath = ChromatogramCache.FinalPathForName(docPersistPath, null);
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.SaveDocument(docPersistPath);
});
// Document now changes because of document GUID
Assert.AreNotSame(docEmpty, SkylineWindow.Document);
Assert.AreNotSame(docEmpty.Settings.DataSettings, SkylineWindow.Document.Settings.DataSettings);
Assert.AreSame(docEmpty.Children, SkylineWindow.Document.Children);
Assert.AreSame(docEmpty.Settings.PeptideSettings, SkylineWindow.Document.Settings.PeptideSettings);
Assert.AreSame(docEmpty.Settings.TransitionSettings, SkylineWindow.Document.Settings.TransitionSettings);
Assert.IsTrue(File.Exists(docPersistPath));
Assert.IsFalse(File.Exists(cachePersistPath));
// Try again
const int firstIndex = 1;
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[firstIndex]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_names;
dlg.OkDialog();
});
var docInitial = WaitForDocumentChangeLoaded(docEmpty);
state = new DocResultsState(docInitial);
Assert.IsTrue(state.HasResults);
// Make sure cache is where it is expected to be
Assert.AreEqual(cachePersistPath, docInitial.Settings.MeasuredResults.CachePaths.ToArray()[0]);
// 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 = GetCacheSize(firstIndex, docInitial);
long singleCacheLen = new FileInfo(cachePersistPath).Length;
Assert.AreEqual(startCacheLen, singleCacheLen);
RunUI(() =>
{
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
});
// Import a document removing the results
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[3]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.remove;
dlg.OkDialog();
});
var docRemove = WaitForDocumentChange(docInitial);
// Results state should not have changed
state.AreEqual(docRemove);
RunUI(SkylineWindow.Undo);
Assert.AreSame(docInitial, SkylineWindow.Document);
// Import a document adding all replicates
const int nextIndex = 0;
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[nextIndex]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.add;
dlg.OkDialog();
});
var docAdd = WaitForDocumentChangeLoaded(docInitial);
var docAdded = ResultsUtil.DeserializeDocument(_documentPaths[nextIndex]);
long expectCacheLen = startCacheLen
+ GetCacheSize(nextIndex, docAdded)
- ChromatogramCache.HeaderSize; // Only one header between the two caches
// No peptide merging should have happened
AssertEx.IsDocumentState(docAdd, null,
docInitial.PeptideGroupCount + docAdded.PeptideGroupCount,
docInitial.PeptideCount + docAdded.PeptideCount,
docInitial.PeptideTransitionCount + docAdded.PeptideTransitionCount);
Assert.AreEqual(3, docAdded.Settings.MeasuredResults.Chromatograms.Count);
var chromatograms = docAdd.Settings.MeasuredResults.Chromatograms;
var chromatogramsInitial = docInitial.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);
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(cachePersistPath).Length;
Assert.AreEqual(expectCacheLen, newCacheLen);
// An undo followed by a redo should not change that
Assert.AreEqual(9, SkylineWindow.Document.RevisionIndex);
RunUI(SkylineWindow.Undo);
Assert.AreEqual(6, SkylineWindow.Document.RevisionIndex);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
RunUI(SkylineWindow.Redo);
Assert.AreEqual(9, SkylineWindow.Document.RevisionIndex);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
// Undo followed by a save, should reduce cache to previous size
RunUI(SkylineWindow.Undo);
Assert.AreEqual(6, SkylineWindow.Document.RevisionIndex);
RunUI(() => SkylineWindow.SaveDocument());
Assert.AreEqual(startCacheLen, new FileInfo(cachePersistPath).Length);
Assert.AreEqual(7, SkylineWindow.Document.RevisionIndex);
Thread.Sleep(10); // Wait 10 ms to make sure the cache change in Redo registers as a cache modification
// After which, a redo should return the document to the add state and
// restore the cache
RunUI(SkylineWindow.Redo);
var docRedo = WaitForDocumentLoaded();
Assert.AreEqual(10, docRedo.RevisionIndex);
stateAdd.AreEqual(docRedo);
Assert.AreEqual(newCacheLen, new FileInfo(cachePersistPath).Length);
// Import matching replicates by name
var docPreUndo = SkylineWindow.Document;
RunUI(SkylineWindow.Undo);
var docUndoLoaded = WaitForDocumentChangeLoaded(docPreUndo);
Assert.AreEqual(8, docUndoLoaded.RevisionIndex);
Assert.AreNotSame(docInitial, docUndoLoaded);
Assert.AreEqual(docInitial, docUndoLoaded); // Cache optimization changes document
docInitial = docUndoLoaded;
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_names;
dlg.OkDialog();
});
var docNames = WaitForDocumentChangeLoaded(docInitial);
// Should have the same impact on state as adding all replicates. The information
// just gets stored differently.
chromatograms = docNames.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(3, chromatograms.Count);
Assert.AreEqual(chromatogramsInitial[0].Name, chromatograms[0].Name);
Assert.AreEqual(2, chromatograms[0].MSDataFileInfos.Count);
Assert.AreEqual(chromatogramsInitial[1].Name, chromatograms[1].Name);
Assert.AreEqual(2, chromatograms[1].MSDataFileInfos.Count);
var missingNames = (from chromatogramSet in docAdded.Settings.MeasuredResults.Chromatograms
where !chromatogramsInitial.Any(cs => Equals(cs.Name, chromatogramSet.Name))
select chromatogramSet.Name).ToArray();
Assert.AreEqual(missingNames[0], chromatograms[2].Name);
Assert.AreEqual(1, chromatograms[2].MSDataFileInfos.Count);
stateAdd.AreEqual(docNames);
foreach (var nodeGroup in docNames.PeptideTransitionGroups)
{
Assert.AreEqual(2, nodeGroup.Results[0].Count);
Assert.AreEqual(2, nodeGroup.Results[1].Count);
Assert.AreEqual(1, nodeGroup.Results[2].Count);
}
// Import merging by order
RunUI(() =>
{
SkylineWindow.Undo();
var docCurrent = SkylineWindow.DocumentUI;
if (ReferenceEquals(docInitial, docCurrent))
Assert.AreEqual(8, docInitial.RevisionIndex);
else
{
// Attempt to report more information when the test fails here
AssertEx.DocsEqual(docInitial, docCurrent);
Assert.AreEqual(docInitial.Id.GlobalIndex, docCurrent.Id.GlobalIndex);
Assert.AreEqual(docInitial.UserRevisionIndex, docCurrent.UserRevisionIndex);
Assert.AreEqual(docInitial.RevisionIndex, docCurrent.RevisionIndex);
Assert.AreSame(docInitial, docCurrent);
}
});
Assert.AreSame(docInitial, SkylineWindow.Document);
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[3]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_indices;
dlg.OkDialog();
});
var docOrder = WaitForDocumentChangeLoaded(docInitial);
var docOrderAdded = ResultsUtil.DeserializeDocument(_documentPaths[3]);
chromatograms = docOrder.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(2, chromatograms.Count);
AssertEx.AreEqualDeep(chromatogramsInitial.Select(chrom => chrom.Name).ToArray(),
chromatogramsInitial.Select(chrom => chrom.Name).ToArray());
var stateOrder = new DocResultsState(docOrder);
var stateOrderAdded = new DocResultsState(docOrderAdded);
Assert.AreEqual(stateOrder.NoteCount, state.NoteCount + stateOrderAdded.NoteCount);
Assert.AreEqual(stateOrder.AnnotationCount, state.AnnotationCount + stateOrderAdded.AnnotationCount);
Assert.AreEqual(stateOrder.UserSetCount, state.UserSetCount + stateOrderAdded.UserSetCount);
Assert.AreEqual(stateOrder.PeptideResults, state.PeptideResults + stateOrderAdded.PeptideResults);
Assert.AreEqual(stateOrder.TransitionGroupResults,
state.TransitionGroupResults + stateOrderAdded.TransitionGroupResults);
Assert.AreEqual(stateOrder.TransitionResults,
state.TransitionResults + stateOrderAdded.TransitionResults);
foreach (var nodeGroup in docOrder.PeptideTransitionGroups)
{
Assert.AreEqual(1, nodeGroup.Results[0].Count);
}
// Import merging by order with overflow and multiple files
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0], _documentPaths[2]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.merge_indices;
dlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count > 2);
var docOrder2 = WaitForDocumentLoaded();
var docAdded2 = ResultsUtil.DeserializeDocument(_documentPaths[2]);
// No peptide merging should have happened
AssertEx.IsDocumentState(docOrder2, null,
docInitial.PeptideGroupCount + docAdded.PeptideGroupCount + docAdded2.PeptideGroupCount,
docInitial.PeptideCount + docAdded.PeptideCount + docAdded2.PeptideCount,
docInitial.PeptideTransitionCount + docAdded.PeptideTransitionCount + docAdded2.PeptideTransitionCount);
chromatograms = docOrder2.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(3, chromatograms.Count);
Assert.AreEqual(chromatogramsInitial[0].Name, chromatograms[0].Name);
Assert.AreEqual(chromatogramsInitial[1].Name, chromatograms[1].Name);
Assert.AreEqual("buffer1", chromatograms[2].Name);
var stateOrder2 = new DocResultsState(docOrder2);
var stateAdded2 = new DocResultsState(docAdded2);
Assert.AreEqual(stateOrder2.NoteCount, stateAdd.NoteCount + stateAdded2.NoteCount);
Assert.AreEqual(stateOrder2.AnnotationCount, stateAdd.AnnotationCount + stateAdded2.AnnotationCount);
Assert.AreEqual(stateOrder2.UserSetCount, stateAdd.UserSetCount + stateAdded2.UserSetCount);
// Because the data all 3 documents actually cover the same results,
// some calculation is required to determine the number of chromInfo objects
// expected.
int fileCount = docOrder2.Settings.MeasuredResults.Chromatograms.SelectMany(chrom => chrom.MSDataFileInfos).Count();
fOld = fileCount/(double) chromatogramsInitial.Count;
fAdded = fileCount/(double) docAdded.Settings.MeasuredResults.Chromatograms.Count;
double fAdded2 = fileCount/(double) docAdded2.Settings.MeasuredResults.Chromatograms.Count;
Assert.AreEqual(stateOrder2.PeptideResults,
(int)(state.PeptideResults*fOld + stateAdded.PeptideResults*fAdded + stateAdded2.PeptideResults*fAdded2));
Assert.AreEqual(stateOrder2.TransitionGroupResults,
(int)(state.TransitionGroupResults*fOld + stateAdded.TransitionGroupResults*fAdded + stateAdded2.TransitionGroupResults*fAdded2));
Assert.AreEqual(stateOrder2.TransitionResults,
(int)(state.TransitionResults*fOld + stateAdded.TransitionResults*fAdded + stateAdded2.TransitionResults*fAdded2));
foreach (var nodeGroup in docOrder2.PeptideTransitionGroups)
{
Assert.AreEqual(3, nodeGroup.Results[0].Count);
Assert.AreEqual(2, nodeGroup.Results[1].Count);
Assert.AreEqual(1, nodeGroup.Results[2].Count);
// Make sure files are ordered as expected
Assert.AreEqual(docInitial.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][0].FileId).FilePath);
Assert.AreEqual(docAdded.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][1].FileId).FilePath);
Assert.AreEqual(docAdded2.Settings.MeasuredResults.Chromatograms[0].MSDataFileInfos[0].FilePath,
chromatograms[0].GetFileInfo(nodeGroup.Results[0][2].FileId).FilePath);
}
// Now import allowing matching peptides to be merged
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
RunDlg<ImportDocResultsDlg>(() => SkylineWindow.ImportFiles(_documentPaths[0], _documentPaths[2]), dlg =>
{
dlg.Action = MeasuredResults.MergeAction.add;
dlg.IsMergePeptides = true;
dlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count > 2);
var docMerged = WaitForDocumentLoaded();
chromatograms = docMerged.Settings.MeasuredResults.Chromatograms;
Assert.AreEqual(6, chromatograms.Count);
var dictPeptides = docInitial.Peptides.ToDictionary(nodePep => nodePep.Key);
foreach(var nodePep in docAdded.Peptides.Where(p => !dictPeptides.ContainsKey(p.Key)))
dictPeptides.Add(nodePep.Key, nodePep);
foreach (var nodePep in docAdded2.Peptides.Where(p => !dictPeptides.ContainsKey(p.Key)))
dictPeptides.Add(nodePep.Key, nodePep);
AssertEx.IsDocumentState(docMerged, null, 3, dictPeptides.Count,
dictPeptides.Values.Sum(nodePep => nodePep.TransitionCount));
var stateMerged = new DocResultsState(docMerged);
Assert.AreEqual(stateMerged.NoteCount, stateAdd.NoteCount + stateAdded2.NoteCount);
Assert.AreEqual(stateMerged.AnnotationCount, stateAdd.AnnotationCount + stateAdded2.AnnotationCount);
Assert.AreEqual(stateMerged.UserSetCount, stateAdd.UserSetCount + stateAdded2.UserSetCount);
var setColors = new HashSet<int>();
foreach (var nodePep in docMerged.Peptides.Take(4))
{
setColors.Add(nodePep.Annotations.ColorIndex);
}
Assert.AreEqual(4, setColors.Count);
Assert.IsFalse(setColors.Contains(-1));
// TODO: Import optimization data
// Check cache sizes
// At this point, the main cache should be about the size of the sum of
// the caches it has incorporated.
Assert.AreEqual(newCacheLen + GetCacheSize(2) + GetCacheSize(3) - 2*ChromatogramCache.HeaderSize,
new FileInfo(cachePersistPath).Length, 200);
// Undo and save should have set the main cache back to the initial state
RunUI(SkylineWindow.Undo);
Assert.AreEqual(docInitial, SkylineWindow.Document);
RunUI(() => SkylineWindow.SaveDocument());
Assert.AreEqual(startCacheLen, new FileInfo(cachePersistPath).Length);
// And the original caches should remain unchanged
for (int i = 0; i < _cachePaths.Length; i++)
{
Assert.AreEqual(_cacheSizes[i], new FileInfo(_cachePaths[i]).Length);
}
// Another undo and save should remove the results cache for the active document
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.SaveDocument();
});
Assert.IsFalse(File.Exists(cachePersistPath));
}
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);
}
public void AreEqual(SrmDocument document)
{
var state = new DocResultsState(document);
Assert.AreEqual(PeptideResults, state.PeptideResults);
Assert.AreEqual(TransitionGroupResults, state.TransitionGroupResults);
Assert.AreEqual(TransitionResults, state.TransitionResults);
Assert.AreEqual(UserSetCount, state.UserSetCount);
Assert.AreEqual(NoteCount, state.NoteCount);
Assert.AreEqual(AnnotationCount, state.AnnotationCount);
}
