Skyline: Improvements to tutorial screenshots based on testing

pwiz_tools/Skyline/Controls/Databinding/DocumentGridViewContext.cs

@@ -20,6 +20,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Windows.Forms;
+using pwiz.Common;
 using pwiz.Common.DataBinding;
 using pwiz.Common.DataBinding.Controls;
 using pwiz.Common.DataBinding.Controls.Editor;
@@ -46,7 +47,7 @@ protected override ViewEditor CreateViewEditor(ViewGroup viewGroup, ViewSpec vie
             viewEditor.SetViewTransformer(new DocumentViewTransformer());
             viewEditor.AddViewEditorWidget(new PivotReplicateAndIsotopeLabelWidget {Dock = DockStyle.Left});
 #if DEBUG
-            viewEditor.ShowSourceTab = true;
+            viewEditor.ShowSourceTab = CommonApplicationSettings.PauseSeconds == 0; // not when taking screenshots
 #else
             viewEditor.ShowSourceTab = false;
 #endif

pwiz_tools/Skyline/Controls/Graphs/AllChromatogramsGraph.cs

@@ -159,6 +159,9 @@ protected override void Dispose(bool disposing)
 
         private void ElapsedTimer_Tick(object sender, EventArgs e)
         {
+            if (IsProgressFrozen())
+                return;
+
             // Update timer and overall progress bar.
             // ReSharper disable LocalizableElement
             lblDuration.Text = _stopwatch.Elapsed.ToString(@"hh\:mm\:ss");
@@ -376,8 +379,34 @@ private void WindowMove(object sender, EventArgs e)
         /// <summary>
         /// Display chromatogram data. 
         /// </summary>
-        /// <param name="status"></param>
+        /// <param name="status">The <see cref="MultiProgressStatus"/> to update the UI to.</param>
         public void UpdateStatus(MultiProgressStatus status)
+        {
+            lock (_missedProgressStatusList)
+            {
+                // If a freeze percent is set, freeze once all status is 
+                if (IsProgressFrozen(status))
+                {
+                    // Play this back later when progress is unfrozen
+                    _missedProgressStatusList.Add(status);
+                    lblDuration.Text = _elapsedTimeAtFreeze;
+                    return;
+                }
+                if (_missedProgressStatusList.Count > 0)
+                {
+                    // Play the missed progress before the current status
+                    foreach (var multiProgressStatus in _missedProgressStatusList)
+                    {
+                        UpdateStatusInternal(multiProgressStatus);
+                    }
+                    _missedProgressStatusList.Clear();
+                }
+            }
+
+            UpdateStatusInternal(status);
+        }
+
+        private void UpdateStatusInternal(MultiProgressStatus status)
         {
             // Update overall progress bar.
             if (_partialProgressList.Count == 0)
@@ -752,6 +781,39 @@ private void btnCopyText_Click(object sender, EventArgs e)
 
         #region Testing Support
 
+        private int? _freezeProgressPercent;
+        private string _elapsedTimeAtFreeze;
+        private List<MultiProgressStatus> _missedProgressStatusList = new List<MultiProgressStatus>();
+
+        /// <summary>
+        /// Provide enough information for a consistent screenshot. Set values to null to resume.
+        /// </summary>
+        /// <param name="percent">Percent to freeze at when all processing threads match this percent or greater</param>
+        /// <param name="elapsedTime">Text for an elapsed time during the freeze</param>
+        public void SetFreezeProgressPercent(int? percent, string elapsedTime)
+        {
+            lock (_missedProgressStatusList)
+            {
+                _freezeProgressPercent = percent;
+                _elapsedTimeAtFreeze = elapsedTime;
+            }
+        }
+
+        public bool IsProgressFrozen(MultiProgressStatus status = null)
+        {
+            lock (_missedProgressStatusList)
+            {
+                if (!_freezeProgressPercent.HasValue)
+                    return false;
+
+                if (status == null)
+                    return _missedProgressStatusList.Count > 0;
+
+                // Stop when anything goes over the limit
+                return status.ProgressList.Any(loadingStatus => loadingStatus.PercentComplete > _freezeProgressPercent);
+            }
+        }
+
         public int ProgressTotalPercent
         {
             get

pwiz_tools/Skyline/FileUI/PeptideSearch/ImportFastaControl.cs

@@ -296,7 +296,12 @@ private void tbxFasta_TextChanged(object sender, EventArgs e)
                 FastaFile = tbxFasta.Text;
                 if (!File.Exists(FastaFile))
                     ImportFastaHelper.ShowFastaError(Resources.ToolDescription_RunTool_File_not_found_);
+            }
         }
+
+        public void ScrollFastaTextToEnd()
+        {
+            tbxFasta.Select(tbxFasta.Text.Length, 0);
         }
 
         public void SetFastaContent(string fastaFilePath, bool forceFastaAsFilepath = false)

pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.cs

@@ -44,6 +44,14 @@ public ImportResultsDIAControl(IModifyDocumentContainer documentContainer, strin
             listResultsFiles.DisplayMember = @"Name";
             SimultaneousFiles = Settings.Default.ImportResultsSimultaneousFiles;
             DoAutoRetry = Settings.Default.ImportResultsDoAutoRetry;
+
+            // Hide the GPF checkbox during screenshots until we branch for 24.1 docs
+            if (Program.PauseSeconds != 0)
+            {
+                btnBrowse.Top = cbGpf.Top;
+                btnRemove.Top = cbGpf.Top;
+                cbGpf.Visible = false;
+            }
         }
 
         private BindingList<ImportPeptideSearch.FoundResultsFile> _foundResultsFiles;

pwiz_tools/Skyline/Skyline.cs

@@ -4075,8 +4075,12 @@ private void UpdateProgressUI(object sender = null, EventArgs e = null)
                     if (!ImportingResultsWindow.IsUserCanceled)
                         Settings.Default.AutoShowAllChromatogramsGraph = ImportingResultsWindow.Visible;
                     ImportingResultsWindow.Finish();
-                    if (!ImportingResultsWindow.HasErrors && Settings.Default.ImportResultsAutoCloseWindow)
+                    if (!ImportingResultsWindow.HasErrors &&
+                        !ImportingResultsWindow.IsProgressFrozen() &&
+                        Settings.Default.ImportResultsAutoCloseWindow)
+                    {
                         DestroyAllChromatogramsGraph();
+                    }
                 }
             }
 

pwiz_tools/Skyline/SkylineTester/Main.cs

@@ -364,9 +364,10 @@ private IEnumerable<string> GetLanguageNames()
         {
             foreach (var language in GetLanguages())
             {
-                string name;
-                if (_languageNames.TryGetValue(language, out name))
-                    yield return name;
+                yield return _languageNames
+                    .Where(lang => lang.Key.StartsWith(language))
+                    .Select(lang => lang.Value)
+                    .First();
             }
         }
 

pwiz_tools/Skyline/SkylineTester/SkylineTesterWindow.cs

@@ -87,9 +87,9 @@ public Button DefaultButton
 
         private readonly Dictionary<string, string> _languageNames = new Dictionary<string, string>
         {
-            {"en", "English"},
-            {"fr", "French"},
-            {"tr", "Turkish"},
+            {"en-US", "English"},
+            {"fr-FR", "French"},
+            {"tr-TR", "Turkish"},
             {"ja", "Japanese"},
             {"zh-CHS", "Chinese"}
         };
@@ -390,6 +390,9 @@ private void BackgroundLoad(object sender, DoWorkEventArgs e)
 
                 RunUI(() =>
                 {
+                    if (!Equals(testSet.SelectedItem, testSetValue))
+                        return;
+
                     testsTree.Nodes.Clear();
                     testsTree.Nodes.Add(skylineNode);
                     skylineNode.Expand();

pwiz_tools/Skyline/TestPerf/DdaTutorialTest.cs

@@ -206,6 +206,7 @@ private void TestMsFraggerSearch()
                 Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
                 importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 0;
                 importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("DdaSearchMs1Filtering\\2014_01_HUMAN_UPS.fasta"));
+                importPeptideSearchDlg.ImportFastaControl.ScrollFastaTextToEnd();   // So that the FASTA file name is visible
                 //importPeptideSearchDlg.ImportFastaControl.SetFastaContent(@"D:\test\Skyline\downloads\Tutorials\DdaSearchMs1Filtering\DdaSearchMS1Filtering\2021-11-09-decoys-2014_01_HUMAN_UPS.fasta");
             });
             PauseForScreenShot<ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", tutorialPage++);

pwiz_tools/Skyline/TestPerf/DiaSwathTutorialTest.cs

@@ -23,6 +23,8 @@
 using System.Globalization;
 using System.IO;
 using System.Linq;
+using System.Threading;
+using System.Windows.Forms;
 using Microsoft.VisualStudio.TestTools.UnitTesting;
 using pwiz.Common.Chemistry;
 using pwiz.Common.DataBinding;
@@ -587,6 +589,13 @@ protected override void DoTest()
                 Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches);
             });
             WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
+            RunUIForScreenShot(() =>
+            {
+                var cols = importPeptideSearchDlg.BuildPepSearchLibControl.Grid.Columns;
+                cols[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.None;
+                cols[0].Width = 175;    // just "interact.pep.xml"
+                cols[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill; // To show the full PeptideProphet confidence
+            });
             PauseForScreenShot<ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", screenshotPage++);
 
             AddIrtPeptidesDlg addIrtPeptidesDlg;
@@ -852,8 +861,10 @@ protected override void DoTest()
             OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
 
             var allChrom = WaitForOpenForm<AllChromatogramsGraph>();
-            WaitForConditionUI(() => allChrom.ProgressTotalPercent >= 20);
+            allChrom.SetFreezeProgressPercent(41, @"00:00:22");
+            WaitForCondition(() => allChrom.IsProgressFrozen());
             PauseForScreenShot<AllChromatogramsGraph>("Loading chromatograms window", screenshotPage++, 30*1000); // 30 second timeout to avoid getting stuck
+            allChrom.SetFreezeProgressPercent(null, null);
             WaitForDocumentChangeLoaded(doc, 20 * 60 * 1000); // 20 minutes
 
             var peakScoringModelDlg = WaitForOpenForm<EditPeakScoringModelDlg>();
@@ -937,6 +948,11 @@ protected override void DoTest()
                 RunUI(() =>
                 {
                     SkylineWindow.Size = new Size(900, 900);
+                    SkylineWindow.ForceOnScreen();  // Avoid this shifting the window under the floating window later
+                });
+                Thread.Sleep(200);  // Give layout time to adjust
+                RunUI(() =>
+                {
                     var chromPane1 = SkylineWindow.GetGraphChrom(SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[0].Name);
                     var chromPane2 = SkylineWindow.GetGraphChrom(SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[1].Name);
                     var rtGraphFrame = FindFloatingWindow(SkylineWindow.GraphRetentionTime);

pwiz_tools/Skyline/TestPerf/HiResMetabolomicsTutorial.cs

@@ -163,14 +163,48 @@ protected override void DoTest()
                 });
                 RestoreViewOnScreen(5);
 
-                PauseForScreenShot("Skyline with 14 transition - show the right-click menu for setting DHA to be a surrogate standard", 9);
+                PauseForScreenShot("Skyline with 14 transition", 9);
 
                 // Set the standard type of the surrogate standards to StandardType.SURROGATE_STANDARD
                 SelectNode(SrmDocument.Level.Molecules, 3);
 
-                // TODO: Show right-click menu with "Surrogate Standard" selected
+                if (IsPauseForScreenShots)
+                {
+                    RunUI(() => SkylineWindow.Height = 720);    // Taller for context menu
+
+                    var sequenceTree = SkylineWindow.SequenceTree;
+                    ToolStripDropDown menuStrip = null, subMenuStrip = null;
+
+                    RunUI(() =>
+                    {
+                        var rectSelectedItem = sequenceTree.SelectedNode.Bounds;
+                        SkylineWindow.ContextMenuTreeNode.Show(sequenceTree.PointToScreen(
+                            new Point(rectSelectedItem.X + rectSelectedItem.Width / 2,
+                                rectSelectedItem.Y + rectSelectedItem.Height / 2)));
+                        var setStandardTypeMenu = SkylineWindow.ContextMenuTreeNode.Items.OfType<ToolStripMenuItem>()
+                            .First(i => Equals(i.Name, @"setStandardTypeContextMenuItem"));
+                        setStandardTypeMenu.ShowDropDown();
+                        setStandardTypeMenu.DropDownItems.OfType<ToolStripMenuItem>()
+                            .First(i => Equals(i.Name, @"surrogateStandardContextMenuItem")).Select();
+
+                        menuStrip = SkylineWindow.ContextMenuTreeNode;
+                        subMenuStrip = setStandardTypeMenu.DropDown;
+                        menuStrip.Closing += DenyMenuClosing;
+                        subMenuStrip.Closing += DenyMenuClosing;
+                    });
+
+                    // Should all land on the SkylineWindow, so just screenshot the whole window
+                    PauseForScreenShot("Skyline with 4 molecules with menu and submenu showing for surrogate standard setting");
+
+                    RunUI(() =>
+                    {
+                        menuStrip.Closing -= DenyMenuClosing;
+                        subMenuStrip.Closing -= DenyMenuClosing;
+                        menuStrip.Close();
+                    });
+                }
+
                 RunUI(() => SkylineWindow.SetStandardType(StandardType.SURROGATE_STANDARD));
-                PauseForScreenShot("Skyline with 4 molecules and one set as surrogate standard");
                 RunUI(() => SkylineWindow.SaveDocument(GetTestPath("FattyAcids_demo.sky")));
 
                 using (new WaitDocumentChange(1, true))

pwiz_tools/Skyline/TestRunner/Program.cs

@@ -61,8 +61,8 @@ internal static class Program
         private static readonly string[] TEST_DLLS = { "Test.dll", "TestData.dll", "TestConnected.dll", "TestFunctional.dll", "TestTutorial.dll", "CommonTest.dll", "TestPerf.dll" };
 
         private static readonly string executingDirectory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
-        private static readonly string[] allLanguages = new FindLanguages(executingDirectory, "en", "fr", "tr").Enumerate().ToArray(); // Languages used in pass 1, and in pass 2 perftets
-        private static readonly string[] qualityLanguages = new FindLanguages(executingDirectory, "en", "fr").Enumerate().ToArray(); // "fr" and "tr" pretty much test the same thing, so just use fr in pass 2
+        private static readonly string[] allLanguages = new FindLanguages(executingDirectory, "en-US", "fr-FR", "tr-TR").Enumerate().ToArray(); // Languages used in pass 1, and in pass 2 perftets
+        private static readonly string[] qualityLanguages = allLanguages.Where(l => !l.StartsWith("tr")).ToArray(); // "fr" and "tr" pretty much test the same thing, so just use fr in pass 2
 
         private const int LeakTrailingDeltas = 7;   // Number of trailing deltas to average and check against thresholds below
         // CONSIDER: Ideally these thresholds would be zero, but memory and handle retention are not stable enough to support that
@@ -896,7 +896,7 @@ private static bool PushToTestQueue(List<TestInfo> testList, List<TestInfo> unfi
             if (commandLineArgs.ArgAsBool("buildcheck"))
             {
                 loop = 1;
-                languages = new[] { "en" };
+                languages = new[] { "en-US" };
             }
 
             Action<string, StreamWriter, int> LogTestOutput = (testOutput, testLog, pass) =>
@@ -1285,7 +1285,19 @@ private static string[] GetLanguages(CommandLineArgs args)
             string value = args.ArgAsString("language");
             if (value == "all")
                 return allLanguages;
-            return value.Split(',');
+            return value.Split(',').Select(GetCanonicalLanguage).ToArray();
+        }
+
+        private static string GetCanonicalLanguage(string rawLanguage)
+        {
+            // If the raw language is a prefix of something from allLanguages, use
+            // the full name.
+            foreach (var language in allLanguages)
+            {
+                if (language.StartsWith(rawLanguage))
+                    return language;
+            }
+            return rawLanguage;
         }
 
         private static DirectoryInfo GetSkylineDirectory()
@@ -1492,7 +1504,7 @@ private static bool RunTestPasses(
 
                 // Get list of languages
                 var languages = buildMode
-                    ? new[] { "en" }
+                    ? new[] { "en-US" }
                     : GetLanguages(commandLineArgs);
 
                 if (showFormNames)