Skyline: First draft of TestDdaTutorial and TestPeakPickingTutorial… (#…

…3256)

* Skyline: First draft of TestDdaTutorial and TestPeakPickingTutorial for auto-screenshots
- fixed a gap in file locking testing that cause TestDdaTutorial to fail with a strange message

pwiz_tools/Skyline/FileUI/PeptideSearch/SearchControl.cs

@@ -174,6 +174,8 @@ public void SetProgressBarText(string message)
             }
         }
 
+        public int PercentComplete => progressBar.Value;
+
         protected CancellationTokenSource _cancelToken;
 
         public abstract void RunSearch();

pwiz_tools/Skyline/SettingsUI/EditPeakScoringModelDlg.cs

@@ -1184,6 +1184,18 @@ public int SelectedGraphTab
             set { tabControl1.SelectTab(value); }
         }
 
+        #region screenshot helpers
+
+        public Control GraphsControl => tabControl1;
+        public Control SelectedGraphControl => tabControl1.TabPages[tabControl1.SelectedIndex];
+
+        public void ShowFindButton(bool show)
+        {
+            findPeptidesButton.Visible = show;
+        }
+
+        #endregion
+
         public SimpleGridViewDriver<PeakCalculatorWeight> PeakCalculatorsGrid
         {
             get { return _gridViewDriver; }

pwiz_tools/Skyline/TestPerf/DdaTutorialTest.cs

@@ -25,6 +25,7 @@
 using pwiz.Common.Chemistry;
 using pwiz.Skyline.Alerts;
 using pwiz.Skyline.Controls;
+using pwiz.Skyline.Controls.Graphs;
 using pwiz.Skyline.EditUI;
 using pwiz.Skyline.FileUI;
 using pwiz.Skyline.FileUI.PeptideSearch;
@@ -267,6 +268,7 @@ private void TestMsFraggerSearch()
             {
 
                 WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_page);
+                WaitForConditionUI(() => importPeptideSearchDlg.SearchControl.PercentComplete > 25);
                 PauseForScreenShot<ImportPeptideSearchDlg.DDASearchPage>("Import Peptide Search - DDA Search Progress page", tutorialPage++);
 
                 // Wait for search to finish
@@ -297,6 +299,7 @@ private void TestMsFraggerSearch()
             else
             {
                 var ambiguousDlg = ShowDialog<MessageDlg>(() => importPeptideSearchDlg.ClickNextButton());
+                RunUIForScreenShot(() => ambiguousDlg.Height = 448);
                 PauseForScreenShot<MessageDlg>("Import Peptide Search - Ambiguous Peptides dialog", tutorialPage++);
                 RunUI(() => AssertEx.Contains(ambiguousDlg.Message,
                     Resources.BiblioSpecLiteBuilder_AmbiguousMatches_The_library_built_successfully__Spectra_matching_the_following_peptides_had_multiple_ambiguous_peptide_matches_and_were_excluded_));
@@ -351,7 +354,7 @@ private void TestMsFraggerSearch()
                     }
                 }
             });
-            PauseForScreenShot("Import Peptide Search - Empty Proteins dialog", tutorialPage++);
+            PauseForScreenShot<AssociateProteinsDlg>("Import Peptide Search - Associate Proteins dialog", tutorialPage++);
 
             using (new WaitDocumentChange(null, true, 600 * 1000))
             {
@@ -376,7 +379,7 @@ private void TestMsFraggerSearch()
 
             RunUI(() => SkylineWindow.ShowPeakAreaReplicateComparison());
             RefreshGraphs();
-            PauseForScreenShot("Peak Areas - Replicate Comparison", tutorialPage++);
+            PauseForScreenShot<GraphSummary.AreaGraphView>("Peak Areas - Replicate Comparison", tutorialPage++);
 
             RunUI(() =>
             {
@@ -406,6 +409,10 @@ private void TestMsFraggerSearch()
             RunUI(() => SkylineWindow.SaveDocument());
 
             DirectoryEx.SafeDelete(Path.Combine(Path.GetDirectoryName(SearchFiles.First())!, "converted"));
+            foreach (var searchFile in SearchFiles)
+            {
+                FileEx.SafeDelete(Path.ChangeExtension(searchFile, ".mzid.gz"));
+            }
         }
 
         private void RefreshGraphs()

pwiz_tools/Skyline/TestTutorial/PeakPickingTutorialTest.cs

@@ -22,6 +22,7 @@
 using System.Globalization;
 using System.IO;
 using System.Linq;
+using System.Windows.Forms;
 using Microsoft.VisualStudio.TestTools.UnitTesting;
 using pwiz.Common.DataBinding;
 using pwiz.Common.DataBinding.Controls.Editor;
@@ -118,8 +119,12 @@ protected override void DoTest()
             OkDialog(generateDecoysDlg, generateDecoysDlg.OkDialog);
 
             RestoreViewOnScreen(3);
-            RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[11]);
-            PauseForScreenShot("Targets view clipped from main window", 3);
+            RunUIForScreenShot(() =>
+            {
+                SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[11];
+                SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[12];
+            });
+            PauseForTargetsScreenShot("Targets view clipped from main window");
 
             // Open the file with decoys
             RunUI(() => SkylineWindow.OpenFile(GetTestPath("SRMCourse_DosR-hDP__20130501-tutorial-empty-decoys.sky")));
@@ -193,15 +198,24 @@ protected override void DoTest()
             PauseForScreenShot<EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form trained model", 6);
             RunUI(() => Assert.AreEqual(0.5893, editDlg.PeakCalculatorsGrid.Items[3].PercentContribution ?? 0, 0.005));
 
-            RunUI(() => editDlg.SelectedGraphTab = 2);
-            PauseForScreenShot<EditPeakScoringModelDlg.PvalueTab>("Edit Peak Scoring Model form p value graph metafile", 7);
+            Control selectedGraphControl = null;
+            RunUI(() =>
+            {
+                editDlg.SelectedGraphTab = 2;
+                selectedGraphControl = editDlg.SelectedGraphControl;
+            });
+            PauseForGraphScreenShot("Edit Peak Scoring Model form p value graph metafile", selectedGraphControl);
 
-            RunUI(() => editDlg.SelectedGraphTab = 3);
-            PauseForScreenShot<EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph metafile", 8);
+            RunUI(() =>
+            {
+                editDlg.SelectedGraphTab = 3;
+                selectedGraphControl = editDlg.SelectedGraphControl;
+            });
+            PauseForGraphScreenShot("Edit Peak Scoring Model form q value graph metafile", selectedGraphControl);
 
             RunUI(() => editDlg.SelectedGraphTab = 1);
-            RunUI(() => editDlg.PeakCalculatorsGrid.SelectRow(3));
-            PauseForScreenShot<EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form feature score", 10);
+            RunUI(() => editDlg.PeakCalculatorsGrid.SelectRow(2));
+            PauseForScreenShot<EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form library dotp feature score", 10);
 
             RunUI(() =>
             {
@@ -215,15 +229,26 @@ protected override void DoTest()
                 editDlg.FindMissingValues(2);   // Retention time
                 editDlg.PeakScoringModelName = "test1";
             });
-            PauseForScreenShot<EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form find missing scores", 11);
+            RunUIForScreenShot(() => editDlg.ShowFindButton(true));
+            PauseForScreenShot(editDlg.GraphsControl, "Edit Peak Scoring Model form find missing scores", null, null, bmp =>
+                DrawLArrowCursorOnBitmap(bmp, 0.88, 0.7));
+            RunUIForScreenShot(() => editDlg.ShowFindButton(false));
 
             OkDialog(editDlg, editDlg.OkDialog);
             OkDialog(reintegrateDlg, reintegrateDlg.CancelDialog);
 
+            var findResultsForm = FindOpenForm<FindResultsForm>();
+            int oldSkylineWindowHeight = SkylineWindow.Height;
+            RunUIForScreenShot(() =>
+            {
+                SkylineWindow.Height = 715;
+                findResultsForm.ActivateItem(0);
+                findResultsForm.Focus();
+            });
             PauseForScreenShot<FindResultsForm>("Find Results view clipped from main window", 12);
+            RunUIForScreenShot(() => SkylineWindow.Height = oldSkylineWindowHeight);
 
             // Remove the peptide with no library dot product, and train again
-            FindResultsForm findResultsForm = null;
             var missingPeptides = new List<string> { "LGGNEQVTR", "IPVDSIYSPVLK", "YFNDGDIVEGTIVK", 
                                                      "DFDSLGTLR", "GGYAGMLVGSVGETVAQLAR", "GGYAGMLVGSVGETVAQLAR"};
             var isDecoys = new List<bool> {false, false, false, false, false, true};
@@ -287,8 +312,12 @@ protected override void DoTest()
                 });
             PauseForScreenShot<EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form with library score", 13);
 
-            RunUI(() => editDlgLibrary.SelectedGraphTab = 3);
-            PauseForScreenShot<EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph with library score metafile", 14);
+            RunUI(() =>
+            {
+                editDlgLibrary.SelectedGraphTab = 3;
+                selectedGraphControl = editDlgLibrary.SelectedGraphControl;
+            });
+            PauseForGraphScreenShot("Edit Peak Scoring Model form q value graph with library score metafile", selectedGraphControl);
 
             OkDialog(editDlgLibrary, editDlgLibrary.OkDialog);
 
@@ -334,7 +363,8 @@ protected override void DoTest()
                 Assert.AreEqual(18.0, chromGroupInfo.RetentionTime.Value, 0.1);
             });
             FindNode(peptideSeqHighlight);
-            PauseForScreenShot<GraphChromatogram>("Chromatogram graph metafile corrected peak at 18.0", 17);
+            const string screenshotReplicate = "006_StC-DosR_B2";
+            PauseForChromGraphScreenShot("Chromatogram graph metafile corrected peak at 18.0", screenshotReplicate);
 
             // Reintegrate slightly differently, with a q value cutoff
             var reintegrateDlgQ = ShowDialog<ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
@@ -345,11 +375,20 @@ protected override void DoTest()
                     reintegrateDlgQ.OverwriteManual = true;
                 });
             OkDialog(reintegrateDlgQ, reintegrateDlgQ.OkDialog);
-            PauseForScreenShot("Targets view with some null peaks clipped from main window", 17);
-            PauseForScreenShot<GraphChromatogram>("Chromatogram graph metafile with no picked peak", 18);
+            RunUIForScreenShot(() => SkylineWindow.SequenceTree.TopNode =
+                SkylineWindow.SequenceTree.SelectedNode.PrevVisibleNode.PrevVisibleNode);
+            FocusDocument();
+            PauseForTargetsScreenShot("Targets view with some null peaks clipped from main window", true, 4);
+            PauseForChromGraphScreenShot("Chromatogram graph metafile with no picked peak", screenshotReplicate);
 
             RestoreViewOnScreen(14);
             FindNode((622.3086).ToString(CultureInfo.CurrentCulture) + "++");
+            WaitForGraphs();
+            RunUIForScreenShot(() =>
+            {
+                SkylineWindow.GetGraphChrom(screenshotReplicate).ZoomTo(17.5, 18.4, 2E+5);
+                SkylineWindow.Width = 863;
+            });
             PauseForScreenShot("Main window with interference on transition", 19);
 
             // Export the mProphet features

pwiz_tools/Skyline/TestUtil/TestFilesDir.cs

@@ -396,10 +396,11 @@ string GetProcessNamesLockingFile(string lockedDirectory, Exception exceptionSho
                 try
                 {
                     Helpers.TryTwice(() => Directory.Delete(path, true));
+                    return; // If this succeeds then the lock was only temporary and we don't have a GUID folder to move back.
                 }
                 catch (Exception e)
                 {
-                    throw new IOException($@"Directory.Move(""{path}"",""{guidName}"") failed, attempt to delete instead resulted in ""{e.Message}""{GetProcessNamesLockingFile(path, e)}");
+                    throw new IOException($@"Directory.Move(""{path}"", ""{guidName}"") failed, attempt to delete instead resulted in ""{e.Message}""{GetProcessNamesLockingFile(path, e)}");
                 }
             }
 
@@ -417,7 +418,7 @@ string GetProcessNamesLockingFile(string lockedDirectory, Exception exceptionSho
                 }
                 catch (Exception e)
                 {
-                    throw new IOException($@"Directory.Move(""{guidName}"",(""{path}"") failed, attempt to delete instead resulted in ""{e.Message}""{GetProcessNamesLockingFile(path, e)}");
+                    throw new IOException($@"Directory.Move(""{guidName}"", ""{path}"") failed, attempt to delete instead resulted in ""{e.Message}""{GetProcessNamesLockingFile(path, e)}");
                 }
             }
         }

pwiz_tools/Skyline/TestUtil/TestFunctional.cs

@@ -289,10 +289,10 @@ protected static TDlg ShowDialog<TDlg>(Action act, int millis = -1) where TDlg :
             // Making sure if the form has a visible icon it's Skyline release icon, not daily one.
             if (IsRecordingScreenShots && dlg.ShowIcon && !ReferenceEquals(dlg, SkylineWindow))
             {
-                var ico = dlg.Icon.Handle;
                 if (dlg.FormBorderStyle != FormBorderStyle.FixedDialog ||
-                    ico == Resources.Skyline_Daily.Handle)
+                    dlg.Icon != null)    // Normally a fixed dialog will not have the Skyline icon handle
                 {
+                    var ico = dlg.Icon.Handle;
                     if (ico != SkylineWindow.Icon.Handle)
                         RunUI(() => dlg.Icon = SkylineWindow.Icon);
                 }
@@ -1504,6 +1504,8 @@ protected Bitmap ClipTargets(Bitmap targetsBmp, int? countTargets = null, bool f
             var sequenceTreeRect = sequenceTree.Bounds;
 
             sequenceTreeRect.Inflate(-1, -1);   // Borders outside parent rect
+            sequenceTreeRect.X += 1;
+            sequenceTreeRect.Y += 1;
 
             const int GWL_STYLE = -16;
             const int WS_VSCROLL = 0x00200000;