protected override void DoTest()
{
// Formerly this little .sky file would not update its (unsearchable) protein metdata on load
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Mutant Peptides with Braf AG A00Y - Cut Down.sky")));
var doc = WaitForDocumentLoaded();
var nodeProt = doc.MoleculeGroups.First();
var metadata = nodeProt.ProteinMetadata;
Assert.IsFalse(metadata.NeedsSearch());
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ProteinMetadataFunctionalTests.sky")));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First();
metadata = nodeProt.ProteinMetadata;
// Examine the various View | Targets | By* modes
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
ProteinMetadataManager.ProteinDisplayMode arg = mode;
RunUI(() => SkylineWindow.UpdateTargetsDisplayMode(arg)); // This should alter the text displayed by the node in the sequence tree view
WaitForConditionUI(() =>
{
var displayText = SkylineWindow.SequenceTree.GetSequenceNodes().First().Text;
if (arg != ProteinMetadataManager.ProteinDisplayMode.ByName &&
Equals(displayText, GetDisplayText(ProteinMetadataManager.ProteinDisplayMode.ByName, metadata)))
{
return(false);
}
return(Equals(displayText, GetDisplayText(arg, metadata)));
});
}
// Examine the various Edit | Refine | Sort Proteins | By* modes
Assert.AreEqual("YIL075C", nodeProt.Name); // unsorted
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
string expectedTopName = null;
switch (mode)
{
case ProteinMetadataManager.ProteinDisplayMode.ByName:
expectedTopName = "YAL003W";
RunUI(() => SkylineWindow.sortProteinsByNameToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByAccession:
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YFL038C";
RunUI(() => SkylineWindow.sortProteinsByAccessionToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByPreferredName:
RunUI(() => SkylineWindow.sortProteinsByPreferredNameToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YAL016W";
break;
case ProteinMetadataManager.ProteinDisplayMode.ByGene:
RunUI(() => SkylineWindow.sortProteinsByGeneToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YGL234W";
break;
}
var actualTopName = WaitForDocumentLoaded().MoleculeGroups.First().Name.ToUpperInvariant();
Assert.AreEqual(expectedTopName, actualTopName);
}
// Now paste in our fake fasta test data, and handle it with our fake webaccess handler
var protdbLoader = SkylineWindow.BackgroundProteomeManager;
protdbLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
var treeLoader = SkylineWindow.ProteinMetadataManager;
treeLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
const int maxEntries = 5;
var fastaText = CommonTest.FastaImporterTest.GetFastaTestText(maxEntries); // Just get the first few
SetClipboardTextUI(fastaText);
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteFastaDlg); // Show the paste dialog
RunDlg <EmptyProteinsDlg>(() => // Anticpate the EmptyProteinsDialog as a side effect
{
pasteDlg.PasteFasta(); // Doing this in pastDlg...
pasteDlg.OkDialog();
},
dlg =>
{
Assert.AreEqual(maxEntries, dlg.EmptyProteins);
dlg.KeepEmptyProteins();
dlg.OkDialog(); // ... will cause EmptyProteinsDlg to pop up, so OK it.
});
// Check that IPI:IPI00197700.1 got an accession number P04638
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals("IPI:IPI00197700.1", pg.Name)));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First(pg => Equals("IPI:IPI00197700.1", pg.Name));
Assert.AreEqual("P04638", nodeProt.ProteinMetadata.Accession);
// Now make our fake fasta into a protdb file, and check statement completion against that
const string basename = "fake.fasta";
var protdbPath = TestFilesDir.GetTestPath(basename + ProteomeDb.EXT_PROTDB);
var fastapath = TestFilesDir.GetTestPath(basename);
using (StreamWriter outfile = new StreamWriter(fastapath))
{
outfile.Write(CommonTest.FastaImporterTest.GetFastaTestText()); // write them all
}
BackgroundProteomeTest.CreateBackgroundProteome(protdbPath, basename, fastapath);
doc = WaitForDocumentChange(doc);
// Test for getting accession info from protdb
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "NP_313205";
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals("NP_313205", pg.Name));
Assert.AreEqual("P0A7T9", nodeProt.ProteinMetadata.Accession);
var snapshot = SkylineWindow.Document;
// Test for getting protein from protdb by preferredName
const string uniRef100A5Di11 = "UniRef100_A5DI11";
const string a5Di11 = "A5DI11";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "EF2_PICGU"; // PreferredName for UniRef100_A5DI11
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// Paste in some junk and make sure we handle the View Targets By* gracefully
const string badname = "badname";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = badname;
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
var nodeText = SkylineWindow.SequenceTree.GetSequenceNodes().Last(n => !SrmDocument.IsSpecialNonProteomicTestDocNode(n.DocNode)).Text;
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, badname); // As in PeptideGroupTreeNode.cs
Assert.AreEqual(failsafe, nodeText);
// Revert those changes, so we can insert another way
Assert.IsTrue(SkylineWindow.SetDocument(snapshot, doc));
WaitForCondition(() => !SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = SkylineWindow.Document;
// Test for pasting accession number in protein paste dialog, and having it populate with correct name
SetClipboardTextUI(a5Di11);
PasteDlg pasteProteinsDlgA = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgA.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgA.PasteProteins();
});
OkDialog(pasteProteinsDlgA, pasteProteinsDlgA.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// See what happens when you paste in a gene name shared by a couple of proteins
const string dupeGene = "Apoa2";
const string ipi00197700 = "IPI:IPI00197700.1";
SetClipboardTextUI(dupeGene);
PasteDlg pasteProteinsDlgB = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgB.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgB.PasteProteins();
});
OkDialog(pasteProteinsDlgB, pasteProteinsDlgB.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(ipi00197700, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(ipi00197700, pg.Name));
Assert.AreEqual(dupeGene, nodeProt.ProteinMetadata.Gene);
// Test for pasting in protein PasteDlg with sequence and metadata - metadata values are same as DocumentGrid column names
const string pasteProteinName = "Protein";
const string pasteProteinDescription = "Description";
const string pasteProteinAccession = "Accession";
const string pasteProteinPreferredName = "PreferredName";
const string pasteProteinGene = "Gene";
const string pasteProteinSpecies = "Species";
var pasteProteinText = String.Join("\t", pasteProteinName, pasteProteinDescription,
"MFEQFDLDSELLASINK IGYTKPTSIQELVIPQAMV", pasteProteinAccession, pasteProteinPreferredName, // Note the whitespace embedded in the sequence - UI should deal with that
pasteProteinGene, pasteProteinSpecies);
SetClipboardTextUI(pasteProteinText);
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(pasteProteinName, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(pasteProteinName, pg.Name));
Assert.AreEqual(pasteProteinAccession, nodeProt.ProteinMetadata.Accession);
// Verify DocumentGrid's use of protein metadata - last line should agree with var pasteProteinText
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Proteins));
WaitForCondition(() => (documentGrid.RowCount > 0)); // Let it initialize
foreach (var colName in new[]
{
pasteProteinAccession,
pasteProteinPreferredName,
pasteProteinGene,
pasteProteinSpecies
})
{ // Column content should match column name, for pasteProteinText as input
string value = null;
string name = colName;
RunUI(() =>
{
var col = documentGrid.FindColumn(PropertyPath.Parse(name));
value =
documentGrid.DataGridView.Rows[documentGrid.RowCount - 1].Cells[col.Index].Value.ToString();
});
Assert.AreEqual(colName, value);
}
}
protected override void DoTest()
{
var protdbPath = TestFilesDir.GetTestPath(_backgroundProteomeName + ProteomeDb.EXT_PROTDB);
CreateBackgroundProteome(protdbPath, _backgroundProteomeName, TestFilesDir.GetTestPath("celegans_mini.fasta"));
WaitForProteinMetadataBackgroundLoaderCompleted();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = "Y18D10A.20"; // Not L10N
sequenceTree.CommitEditBox(false);
});
WaitForProteinMetadataBackgroundLoaderCompleted();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = "AccessionWithout";
});
WaitForOpenForm <StatementCompletionForm>();
Assert.IsNotNull(FindOpenForm <StatementCompletionForm>());
RunUI(() =>
{
var statementCompletionForm = FindOpenForm <StatementCompletionForm>();
Assert.IsNotNull(statementCompletionForm);
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
Assert.IsNotNull(sequenceTree.StatementCompletionEditBox);
sequenceTree.StatementCompletionEditBox.OnSelectionMade(
(StatementCompletionItem)statementCompletionForm.ListView.Items[0].Tag);
});
WaitForProteinMetadataBackgroundLoaderCompleted();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = "TISEVIAQGK"; // Not L10N
});
WaitForOpenForm <StatementCompletionForm>();
RunUI(() =>
{
var statementCompletionForm = FindOpenForm <StatementCompletionForm>();
Assert.IsNotNull(statementCompletionForm);
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
Assert.IsNotNull(sequenceTree.StatementCompletionEditBox);
sequenceTree.StatementCompletionEditBox.OnSelectionMade(
(StatementCompletionItem)statementCompletionForm.ListView.Items[0].Tag);
});
var peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual(3, peptideGroups.Count);
Assert.AreEqual("Y18D10A.20", peptideGroups[0].Name);
Assert.IsTrue(peptideGroups[0].AutoManageChildren);
Assert.AreEqual("AccessionWithoutDescription", peptideGroups[1].Name);
Assert.IsTrue(peptideGroups[1].AutoManageChildren);
Assert.AreEqual("C37A2.7", peptideGroups[2].Name);
Assert.IsFalse(peptideGroups[2].AutoManageChildren);
// Save and re-open with prot db moved to see MissingFileDlg
int pepCount = SkylineWindow.Document.PeptideCount;
string documentPath = TestFilesDir.GetTestPath("BackgroundProtDoc.sky");
RunUI(() =>
{
SkylineWindow.SaveDocument(documentPath);
SkylineWindow.SwitchDocument(new SrmDocument(SrmSettingsList.GetDefault()), null);
});
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
// Wait until protein metadata manager is finished before trying to rename the background proteome database.
WaitForCondition(() => !SkylineWindow.BackgroundLoaders.OfType <ProteinMetadataManager>()
.Any(loader => loader.AnyProcessing()));
File.Move(protdbPath, TestFilesDir.GetTestPath(_backgroundProteomeName + "-copy" + ProteomeDb.EXT_PROTDB));
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.OkDialog());
Assert.AreEqual(pepCount, SkylineWindow.Document.PeptideCount);
RunUI(() => SkylineWindow.NewDocument());
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.CancelDialog());
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
}
protected override void DoTest()
{
var protdbPath = TestFilesDir.GetTestPath(_backgroundProteomeName + ProteomeDb.EXT_PROTDB);
CreateBackgroundProteome(protdbPath, _backgroundProteomeName, TestFilesDir.GetTestPath("celegans_mini.fasta"));
WaitForProteinMetadataBackgroundLoaderCompleted();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "Y18D10A.20"; // Not L10N
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
WaitForProteinMetadataBackgroundLoaderCompleted();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "TISEVIAQGK"; // Not L10N
// ReSharper restore LocalizableElement
});
var statementCompletionForm = WaitForOpenForm <StatementCompletionForm>();
Assert.IsNotNull(statementCompletionForm);
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
Assert.IsNotNull(sequenceTree.StatementCompletionEditBox);
sequenceTree.StatementCompletionEditBox.OnSelectionMade(
(StatementCompletionItem)statementCompletionForm.ListView.Items[0].Tag);
});
WaitForProteinMetadataBackgroundLoaderCompleted();
var peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual(2, peptideGroups.Count);
Assert.AreEqual("Y18D10A.20", peptideGroups[0].Name);
Assert.IsTrue(peptideGroups[0].AutoManageChildren);
Assert.AreEqual("C37A2.7", peptideGroups[1].Name);
Assert.IsFalse(peptideGroups[1].AutoManageChildren);
// Save and re-open with prot db moved to see MissingFileDlg
int pepCount = SkylineWindow.Document.PeptideCount;
string documentPath = TestFilesDir.GetTestPath("BackgroundProtDoc.sky");
RunUI(() =>
{
SkylineWindow.SaveDocument(documentPath);
SkylineWindow.SwitchDocument(new SrmDocument(SrmSettingsList.GetDefault()), null);
});
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
File.Move(protdbPath, TestFilesDir.GetTestPath(_backgroundProteomeName + "-copy" + ProteomeDb.EXT_PROTDB));
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.OkDialog());
Assert.AreEqual(pepCount, SkylineWindow.Document.PeptideCount);
RunUI(() => SkylineWindow.NewDocument());
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.CancelDialog());
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
}