DIA search workflow UI changes (#3134)

- reworked DIA workflow radio button to work with and without DIA-Umpire
- added DIA-Umpire checkbox to converter settings page, which is now always shown for DIA workflow
- added GPF checkbox to extract chromatograms page, which is now always shown for DIA workflow
- fixed MsFraggerSearchEngine to fill in percolator_qvalue from DIA searches properly, and if a PSM id in pepXML can't be found in the percolator TSV file, to put in percolator_qvalue=1
- changed MsFraggerSearchEngine to use Alexey's recommended DDA search settings for low resolution DIA data (e.g. Stellar) when the workflow is DIA
- fixed support for MSFragger output_report_topN > 1 but limited it to 1 for DIA until the output format changes to keep all ranks in the same pepXML
* added faster TestDiaSearch test (sharing TestDiaSearch DiaUmpire code)
* updated audit logs
* removed default value from audit log for IsGpf and UseDiaUmpire
* fixed MSFragger to look for correct pepXML file extension based on data_type parameter instead of workflow setting
* fixed compile error with C++17
* added cleanup of DIA Umpire output files for Test*DiaUmpireTutorial
* added tracking of Default (initial) values to AbstractDdaSearchEngine.Setting
* fixed expat warnings
* fixed copy button for KeyValueGridDlg and SimpleFileDownloaderDlg
* removed no longer necessary PIN file scan number adjustment logic

libraries/expat.jam

@@ -108,6 +108,7 @@ rule init ( version ? : location : options * )
             <location-prefix>expat
             <toolset>msvc:<define>_CRT_SECURE_NO_DEPRECATE
             <toolset>msvc:<define>_SCL_SECURE_NO_DEPRECATE
+            <toolset>msvc:<cxxflags>/wd4100 # warning C4100: 'enc': unreferenced formal parameter
             <define>HAVE_EXPAT_CONFIG_H
             <define>XML_LARGE_SIZE
             <implicit-dependency>expat_config.h

pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs

@@ -221,10 +221,10 @@ public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, r
                         ? Path.Combine(Environment.CurrentDirectory, psi.FileName)
                         : psi.FileName;
                     // ReSharper disable LocalizableElement
-                    sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath,
+                    sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}\r\nExit code: {4}", processPath,
                         // ReSharper restore LocalizableElement
                         string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory,
-                        stdin != null ? "\r\nStandard input:\r\n" + stdin : "");
+                        stdin != null ? "\r\nStandard input:\r\n" + stdin : "", exit);
                     throw new IOException(sbError.ToString());
                 }
 

pwiz_tools/Skyline/Alerts/KeyValueGridDlg.cs

@@ -20,6 +20,7 @@
 using System.Collections.Generic;
 using System.Drawing;
 using System.Linq;
+using System.Text;
 using System.Windows.Forms;
 using pwiz.Skyline.Properties;
 using pwiz.Skyline.Util;
@@ -73,6 +74,7 @@ public static void Show<TValue>(IWin32Window parent, string title, IDictionary<s
             var keyToControl = new Dictionary<string, Control>();
             var controlToSetting = new Dictionary<object, TValue>();
             int row = 1;
+            var ctlTextRepresentation = new StringBuilder();
             foreach (var kvp in gridValues.OrderBy(kvp => kvp.Key))
             {
                 var lbl = new Label
@@ -140,13 +142,14 @@ public static void Show<TValue>(IWin32Window parent, string title, IDictionary<s
                 layout.Controls.Add(valueControl, 1, row);
                 keyToControl[kvp.Key] = valueControl;
                 controlToSetting[valueControl] = kvp.Value;
+                ctlTextRepresentation.AppendLine($@"{kvp.Key} = {valueToString(kvp.Value)}");
                 row++;
             }
 
             var activeScreen = parent == null ? Screen.PrimaryScreen : Screen.FromHandle(parent.Handle); 
             int defaultHeight = Math.Min(3 * activeScreen.Bounds.Height / 4, layout.GetRowHeights().Sum() + 50);
 
-            using (var dlg = new MultiButtonMsgDlg(layout, Resources.OK))
+            using (var dlg = new MultiButtonMsgDlg(layout, Resources.OK, ctlTextRepresentation.ToString()))
             {
                 dlg.Text = title;
                 dlg.ClientSize = new Size(400, defaultHeight);

pwiz_tools/Skyline/Alerts/MultiButtonMsgDlg.cs

@@ -75,7 +75,8 @@ public MultiButtonMsgDlg(string message, string btnYesText, string btnNoText, bo
         /// </summary>
         /// <param name="ctl">The control to show</param>
         /// <param name="btnText">The text to show in the non-Cancel button (DialogResult.OK)</param>
-        public MultiButtonMsgDlg(Control ctl, string btnText) : this(string.Empty, btnText)
+        /// <param name="ctlContentAsText">A text representation of the control's contents.</param>
+        public MultiButtonMsgDlg(Control ctl, string btnText, string ctlContentAsText) : this(ctlContentAsText, btnText)
         {
             messageScrollPanel.Hide();
             splitContainer.Panel1.Controls.Add(ctl);
@@ -119,8 +120,9 @@ public MultiButtonMsgDlg(string message, MessageBoxButtons buttons, DialogResult
         /// <param name="btnNoText">The text to show in the second, non-default button (DialogResult.No)</param>
         /// <param name="allowCancel">When this is true a Cancel button is the button furthest to the
         /// right. Otherwise, only the two named buttons are visible.</param>
-        public MultiButtonMsgDlg(Control ctl, string btnYesText, string btnNoText, bool allowCancel)
-        : this(string.Empty, btnYesText, btnNoText, allowCancel)
+        /// <param name="ctlContentAsText">A text representation of the control's contents.</param>
+        public MultiButtonMsgDlg(Control ctl, string btnYesText, string btnNoText, bool allowCancel, string ctlContentAsText)
+        : this(ctlContentAsText, btnYesText, btnNoText, allowCancel)
         {
             messageScrollPanel.Hide();
             splitContainer.Panel1.Controls.Add(ctl);

pwiz_tools/Skyline/Alerts/SimpleFileDownloaderDlg.cs

@@ -20,6 +20,7 @@
 using System.Collections.Generic;
 using System.Drawing;
 using System.Linq;
+using System.Text;
 using System.Windows.Forms;
 using pwiz.Skyline.Controls;
 using pwiz.Skyline.Util;
@@ -34,6 +35,7 @@ public static class SimpleFileDownloaderDlg
         /// </summary>
         public static DialogResult Show(Control parent, string title, IEnumerable<FileDownloadInfo> requiredFiles)
         {
+            var ctlTextRepresentation = new StringBuilder();
             var layout = new TableLayoutPanel
             {
                 Anchor = AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right | AnchorStyles.Top,
@@ -63,6 +65,7 @@ public static DialogResult Show(Control parent, string title, IEnumerable<FileDo
             };
             layout.Controls.Add(downloadMessageLabel, 0, 0);
             layout.SetColumnSpan(downloadMessageLabel, 2);
+            ctlTextRepresentation.AppendLine(downloadMessage);
 
             int row = 2;
             var gridLabels = new List<Label>();
@@ -90,6 +93,7 @@ public static DialogResult Show(Control parent, string title, IEnumerable<FileDo
                 gridLabels.Add(name);
                 gridLabels.Add(url);
                 ++row;
+                ctlTextRepresentation.AppendFormat(@"{0}{1}{2}{3}", name.Text, '\t', url.Text, Environment.NewLine);
             }
 
             var activeScreen = parent == null ? Screen.PrimaryScreen : Screen.FromHandle(parent.Handle);
@@ -102,7 +106,7 @@ public static DialogResult Show(Control parent, string title, IEnumerable<FileDo
                 label.Width += 10;
             }
 
-            using (var dlg = new MultiButtonMsgDlg(layout, AlertsResources.AlertDlg_GetDefaultButtonText__Yes, AlertsResources.AlertDlg_GetDefaultButtonText__No, false))
+            using (var dlg = new MultiButtonMsgDlg(layout, AlertsResources.AlertDlg_GetDefaultButtonText__Yes, AlertsResources.AlertDlg_GetDefaultButtonText__No, false, ctlTextRepresentation.ToString()))
             {
                 dlg.Text = title;
                 dlg.ClientSize = new Size(defaultWidth, defaultHeight);

pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs

@@ -72,9 +72,10 @@ public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContain
             if (_isRunPeptideSearch)
             {
                 panel1.Hide();
-                radioDIA.Text = SkylineResources.BuildPeptideSearchLibraryControl_RunPeptideSearchRadioDIAText_DIA_with_DIA_Umpire;
-                helpTip.SetToolTip(radioDIA, SkylineResources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibraryControl_Library_from_DIA_deconvoluted_to_single_precursor_MS_MS_spectra_and_chromatograms_from_raw_DIA_spectra_of_same_runs);
-                InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw;
+                if (ImportPeptideSearch.IsDIASearch)
+                    InputFileType = ImportPeptideSearchDlg.InputFile.dia_raw;
+                else
+                    InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw;
             }
             else
             {
@@ -115,7 +116,8 @@ public BuildPeptideSearchLibrarySettings(BuildPeptideSearchLibraryControl contro
 
             public BuildPeptideSearchLibrarySettings(IEnumerable<BuildLibraryGridView.File> files, IrtStandard standard,
                 bool includeAmbiguousMatches, bool filterForDocumentPeptides,
-                ImportPeptideSearchDlg.Workflow workFlow, ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType)
+                ImportPeptideSearchDlg.Workflow workFlow,
+                ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType)
             {
                 SearchFileNames = files?.ToArray() ?? Array.Empty<BuildLibraryGridView.File>();
                 Standard = standard;
@@ -669,8 +671,6 @@ public bool PerformDDASearch
             get { return InputFileType != ImportPeptideSearchDlg.InputFile.search_result; }
         }
 
-        public bool DIAConversionNeeded => InputFileType == ImportPeptideSearchDlg.InputFile.dia_raw;
-
         private void OnGridChange(object sender, EventArgs e)
         {
             if (!PerformDDASearch)

pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx

@@ -129,7 +129,7 @@
     <value>6, 42</value>
   </data>
   <data name="radioDIA.Size" type="System.Drawing.Size, System.Drawing">
-    <value>369, 17</value>
+    <value>84, 17</value>
   </data>
   <assembly alias="mscorlib" name="mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" />
   <data name="radioDIA.TabIndex" type="System.Int32, mscorlib">
@@ -468,7 +468,7 @@ like BiblioSpec .blib, EncyclopeDIA .elib, SpectraST .sqt</value>
     <value>gridSearchFiles</value>
   </data>
   <data name="&gt;&gt;gridSearchFiles.Type" xml:space="preserve">
-    <value>pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null</value>
+    <value>pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline-daily, Version=24.1.1.263, Culture=neutral, PublicKeyToken=null</value>
   </data>
   <data name="&gt;&gt;gridSearchFiles.Parent" xml:space="preserve">
     <value>panelPeptideSearch</value>