Skyline: Update small molecule tutorials to remove the word "peptide"…

… and update screenshots (#2747) (#2750)
ProteoWizard · Oct 13, 2023 · 85202be · 85202be
1 parent bde6557
commit 85202be
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Showing 8 changed files with 27 additions and 23 deletions.
diff --git a/pwiz_tools/Skyline/Controls/Startup/TutorialLinkResources.Designer.cs b/pwiz_tools/Skyline/Controls/Startup/TutorialLinkResources.Designer.cs
diff --git a/pwiz_tools/Skyline/Controls/Startup/TutorialLinkResources.resx b/pwiz_tools/Skyline/Controls/Startup/TutorialLinkResources.resx
@@ -266,23 +266,23 @@
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="SmallMoleculeMethodDevCEOpt_pdf" xml:space="preserve">
-    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/SmallMoleculeMethodDevCEOpt-20_1.pdf</value>
+    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/SmallMoleculeMethodDevCEOpt-23_1.pdf</value>
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="SmallMoleculeQuantification_zip" xml:space="preserve">
     <value>https://skyline.ms/tutorials/SmallMoleculeQuantification.zip</value>
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="SmallMoleculeQuantification_pdf" xml:space="preserve">
-    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/SmallMoleculeQuant-20_1.pdf</value>
+    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/SmallMoleculeQuant-23_1.pdf</value>
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="HiResMetabolomics_zip" xml:space="preserve">
     <value>https://skyline.ms/tutorials/HiResMetabolomics.zip</value>
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="HiResMetabolomics_pdf" xml:space="preserve">
-    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/HiResMetabolomics-20_1.pdf</value>
+    <value>https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/HiResMetabolomics-23_1.pdf</value>
     <comment>Not to be localized with other Skyline content.  Skyline developers will take care of localizing these.</comment>
   </data>
   <data name="SmallMolLibraries_zip" xml:space="preserve">

diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Hi-Res Metabolomics.docx b/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Hi-Res Metabolomics.docx
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Small Molecule Method Dev and CE Opt.docx b/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Small Molecule Method Dev and CE Opt.docx
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Small Molecule Quantification.docx b/pwiz_tools/Skyline/Documentation/Tutorials/Skyline Small Molecule Quantification.docx
diff --git a/pwiz_tools/Skyline/TestPerf/HiResMetabolomicsTutorial.cs b/pwiz_tools/Skyline/TestPerf/HiResMetabolomicsTutorial.cs
@@ -202,7 +202,7 @@ protected override void DoTest()
 
                 var expectedTransCount = new Dictionary<string, int[]>
                 {
-                    // peptides, transition groups, heavy transition groups, tranistions, heavy transitions
+                    // peptides, transition groups, heavy transition groups, transitions, heavy transitions
                     {"default", new[] {4, 4, 3, 8, 6}}, // Most have these values
                     {"ID31609_01_E749_4745_091517", new[] {4, 4, 3, 7, 6}},
 
@@ -233,7 +233,7 @@ protected override void DoTest()
                     documentGrid = FindOpenForm<DocumentGridForm>();
                 }
                 if (!IsCoverShotMode)
-                    RunUI(() => documentGrid.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification));
+                    RunUI(() => documentGrid.ChooseView(Resources.PersistedViews_GetDefaults_Molecule_Quantification));
                 else
                 {
                     RunUI(() => documentGrid.DataboundGridControl.ChooseView(new ViewName(ViewGroup.BUILT_IN.Id,
@@ -286,7 +286,7 @@ protected override void DoTest()
                         peptideSettingsUI.QuantUnits = "uM";
                     });
 
-                    PauseForScreenShot<PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 13);
+                    PauseForScreenShot<PeptideSettingsUI.QuantificationTab>("Molecule Settings - Quantitation", 13);
                     OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
                 }
 
@@ -316,30 +316,34 @@ protected override void DoTest()
                 });
                 // Make sure the edits have flowed to the document
                 WaitForConditionUI(() => SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms.Where(c => c.Name.StartsWith("GW")).All(c => c.SampleType.Equals(SampleType.QC)));
+                RestoreViewOnScreen(14);
                 PauseForScreenShot<DocumentGridForm>("Document Grid - replicates", 14);
 
                 // Finish setting up quant
                 var documentGrid3 = FindOpenForm<DocumentGridForm>();
                 RunUI(() =>
                 {
-                    documentGrid3.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification);
+                    documentGrid3.ChooseView(Resources.PersistedViews_GetDefaults_Molecule_Quantification);
                 });
-                WaitForConditionUI(() => (documentGrid3.RowCount > 0 &&
-                                          documentGrid3.ColumnCount > 6)); // Let it initialize
+                WaitForConditionUI(() => documentGrid3.IsComplete);
 
                 RunUI(() =>
                 {
+                    var colNormal = documentGrid3.FindColumn(PropertyPath.Root.Property("NormalizationMethod"));
+                    var colMultiplier = documentGrid3.FindColumn(PropertyPath.Root.Property("ConcentrationMultiplier"));
+                    const int indexOfHeavyDha = 6;
                     var gridView = documentGrid3.DataGridView;
-                    var methods = ((DataGridViewComboBoxCell) gridView.Rows[0].Cells[6]).Items;
-                    var ratioToSurrogateHeavyDHA = ((Tuple<String, NormalizationMethod>)methods[6]).Item2;
-                    gridView.Rows[0].Cells[5].Value = 2838.0;
-                    gridView.Rows[1].Cells[5].Value = 54.0;
-                    gridView.Rows[1].Cells[6].Value = ratioToSurrogateHeavyDHA;
-                    gridView.Rows[2].Cells[5].Value = 984.0;
-                    gridView.Rows[3].Cells[5].Value = 118.0;
+                    var methods = ((DataGridViewComboBoxCell) gridView.Rows[0].Cells[colNormal.Index]).Items;
+                    var ratioToSurrogateHeavyDHA = ((Tuple<String, NormalizationMethod>)methods[indexOfHeavyDha]).Item2;
+                    gridView.Rows[0].Cells[colMultiplier.Index].Value = 2838.0;
+                    gridView.Rows[1].Cells[colMultiplier.Index].Value = 54.0;
+                    gridView.Rows[1].Cells[colNormal.Index].Value = ratioToSurrogateHeavyDHA;
+                    gridView.Rows[2].Cells[colMultiplier.Index].Value = 984.0;
+                    gridView.Rows[3].Cells[colMultiplier.Index].Value = 118.0;
                 });
 
-                PauseForScreenShot<DocumentGridForm>("Document Grid - peptide quant again", 15);
+                RestoreViewOnScreen(15);
+                PauseForScreenShot<DocumentGridForm>("Document Grid - molecule quant again", 15);
 
                 RunUI(() => SkylineWindow.ShowCalibrationForm());
                 SelectNode(SrmDocument.Level.Molecules, 0);

diff --git a/pwiz_tools/Skyline/TestPerf/HiResMetabolomicsViews.zip b/pwiz_tools/Skyline/TestPerf/HiResMetabolomicsViews.zip
diff --git a/pwiz_tools/Skyline/TestTutorial/SmallMoleculesQuantificationTutorial.cs b/pwiz_tools/Skyline/TestTutorial/SmallMoleculesQuantificationTutorial.cs
@@ -253,7 +253,7 @@ protected override void DoTest()
                         peptideSettingsUI.QuantMsLevel = null; // All
                         peptideSettingsUI.QuantUnits = "uM";
                     });
-                    PauseForScreenShot<PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 17);
+                    PauseForScreenShot<PeptideSettingsUI.QuantificationTab>("Molecule Settings - Quantification", 17);
                     OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
                 }
 
@@ -394,14 +394,14 @@ protected override void DoTest()
 
                 ImportReplicates(false); // Import the rest of the replicates
 
-                RunUI(() => documentGrid.ChooseView(Resources.ReportSpecList_GetDefaults_Peptide_Ratio_Results));
+                RunUI(() => documentGrid.ChooseView(Resources.PersistedViews_GetDefaults_Molecule_Ratio_Results));
                 WaitForConditionUI(() => documentGrid.ColumnCount > 6);
                 RunUI(() => {
                     var colReplicate = documentGrid.FindColumn(PropertyPath.Parse("Results!*.Value.ResultFile.Replicate"));
                     documentGrid.DataGridView.Sort(colReplicate, ListSortDirection.Ascending);
                 });
 
-                PauseForScreenShot<DocumentGridForm>("Document Grid - Peptide Ratio Results - manually widen to show all columns", 25);
+                PauseForScreenShot<DocumentGridForm>("Document Grid - Molecule Ratio Results - manually widen to show all columns", 25);
                 Settings.Default.CalibrationCurveOptions.LogXAxis = true;
                 Settings.Default.CalibrationCurveOptions.LogYAxis = true;