Added new SkylineCmd arguments for building ion mobility libraries: -…

pwiz_tools/Skyline/CommandArgUsage.resx

@@ -123,6 +123,12 @@
   <data name="_add_library_path" xml:space="preserve">
     <value>Specify a spectral library to be added to the open document.</value>
   </data>
+  <data name="_ionmobility_create_library" xml:space="preserve">
+    <value>Add an ion mobility library to the open document, based on its currently loaded chromatograms.</value>
+  </data>
+  <data name="_ionmobility_create_library_name" xml:space="preserve">
+    <value>Name to give the ion mobility library in an –-ionmobility-create-library operation.</value>
+  </data>
   <data name="_batch_commands" xml:space="preserve">
     <value>Runs a file line by line treating each line like a SkylineRunner/Cmd input. Useful for automating the execution of multiple commands.  The open Skyline file remains active through all commands.</value>
   </data>
@@ -387,6 +393,9 @@
   <data name="CommandArgs_GROUP_IMPORT_Importing_results_replicates" xml:space="preserve">
     <value>Importing results replicates</value>
   </data>
+  <data name="CommandArgs_GROUP_CREATE_IMSDB_Ion_Mobility_Library" xml:space="preserve">
+    <value>Creating an ion mobility library</value>
+  </data>
   <data name="CommandArgs_GROUP_REMOVE_Removing_results_replicates" xml:space="preserve">
     <value>Removing results replicates</value>
   </data>

pwiz_tools/Skyline/CommandArgs.cs

@@ -215,6 +215,17 @@ public bool Saving
         public string SharedFile { get; private set; }
         public ShareType SharedFileType { get; private set; }
 
+        // For creating a .imsdb ion mobility library
+        public static readonly Argument ARG_CREATE_IMSDB = new DocArgument(@"ionmobility-create-library", PATH_TO_FILE,
+            (c, p) => c.CreateIMSDB(p));
+
+        // For creating a .imsdb ion mobility library
+        public static readonly Argument ARG_CREATE_IMSDB_NAME = new DocArgument(@"ionmobility-create-library-name", NAME_VALUE,
+            (c, p) => c.IMSDbName = p.Value);
+
+        private static readonly ArgumentGroup GROUP_CREATE_IMSDB = new ArgumentGroup(() => CommandArgUsage.CommandArgs_GROUP_CREATE_IMSDB_Ion_Mobility_Library, false,
+            ARG_CREATE_IMSDB, ARG_CREATE_IMSDB_NAME);
+
         public static readonly Argument ARG_IMPORT_FILE = new DocArgument(@"import-file", PATH_TO_FILE,
             (c, p) => c.ParseImportFile(p));
         public static readonly Argument ARG_IMPORT_REPLICATE_NAME = new DocArgument(@"import-replicate-name", NAME_VALUE,
@@ -337,6 +348,8 @@ private bool ValidateMinimizeResultsArgs()
             return true;
         }
 
+        public MsDataFileUri IMSDbFile { get; private set; }
+        public string IMSDbName { get; private set; }
 
         public List<MsDataFileUri> ReplicateFile { get; private set; }
         public string ReplicateName { get; private set; }
@@ -362,6 +375,11 @@ private bool ValidateMinimizeResultsArgs()
         public double? LockmassTolerance { get; private set; }
         public LockMassParameters LockMassParameters { get { return new LockMassParameters(LockmassPositive, LockmassNegative, LockmassTolerance); } }
 
+        private void CreateIMSDB(NameValuePair pair)
+        {
+            IMSDbFile = new MsDataFilePath(pair.ValueFullPath);
+        }
+
         private void ParseImportFile(NameValuePair pair)
         {
             ReplicateFile.Add(new MsDataFilePath(pair.ValueFullPath));
@@ -556,6 +574,10 @@ public bool AddDecoys
         {
             get { return !string.IsNullOrEmpty(AddDecoysType); }
         }
+        public bool CreatingIMSDB
+        {
+            get { return IMSDbFile != null; }
+        }
         public bool ImportingResults
         {
             get { return ImportingReplicateFile || ImportingSourceDirectory; }
@@ -1784,6 +1806,7 @@ public static IEnumerable<IUsageBlock> UsageBlocks
                     GROUP_IMPORT_SEARCH,
                     GROUP_IMPORT_LIST,
                     GROUP_ADD_LIBRARY,
+                    GROUP_CREATE_IMSDB,
                     GROUP_DECOYS,
                     GROUP_REFINEMENT,
                     GROUP_REFINEMENT_W_RESULTS,

pwiz_tools/Skyline/CommandLine.cs

@@ -376,6 +376,11 @@ private bool ProcessDocument(CommandArgs commandArgs)
                 return false;
             }
 
+            if (!CreateIMSDB(commandArgs))
+            {
+                return false;
+            }
+
             if (commandArgs.Saving)
             {
                 var saveFile = commandArgs.SaveFile ?? _skylineFile;
@@ -588,6 +593,42 @@ private bool RefineDocument(CommandArgs commandArgs)
             }
         }
 
+        private bool CreateIMSDB(CommandArgs commandArgs)
+        {
+            if (commandArgs.IMSDbFile == null)
+            {
+                return true;  // Nothing to do
+            }
+            _out.WriteLine(Resources.CommandLine_CreateIMSDB_Creating_an_ion_mobility_library___);
+            try
+            {
+                ModifyDocumentWithLogging(doc => doc.ChangeSettings(doc.Settings.ChangeTransitionSettings(p =>
+                {
+                    var progressMonitor = new CommandProgressMonitor(_out, new ProgressStatus(string.Empty));
+                    var path = commandArgs.IMSDbFile.GetFilePath();
+                    var name = commandArgs.IMSDbName ?? Path.GetFileNameWithoutExtension(path);
+                    var lib = IonMobilityLibrary.CreateFromResults(
+                        doc, null, false, name, path,
+                        progressMonitor);
+
+                    return p.ChangeIonMobilityFiltering(p.IonMobilityFiltering.ChangeLibrary(lib));
+                })), AuditLogEntry.SettingsLogFunction);
+                return true;
+            }
+            catch (Exception x)
+            {
+                if (!_out.IsErrorReported)
+                {
+                    _out.WriteLine(Resources.CommandLine_GeneralException_Error___0_, x.Message);
+                }
+                else
+                {
+                    _out.WriteLine(x.Message);
+                }
+                return false;
+            }
+        }
+
         private IsotopeLabelType GetLabelTypeHelper(string label)
         {
             var mods = _doc.Settings.PeptideSettings.Modifications;

pwiz_tools/Skyline/Properties/Resources.resx

@@ -11838,4 +11838,7 @@ If you do not have the original file, you may build the library with embedded sp
   <data name="SkylineWindow_submitErrorReportMenuItem_Click_Submitting_an_unhandled_error_report" xml:space="preserve">
 	  <value>Submitting an unhandled error report</value>
   </data>
+  <data name="CommandLine_CreateIMSDB_Creating_an_ion_mobility_library___" xml:space="preserve">
+	  <value>Creating an ion mobility library...</value>
+  </data>
 </root>

pwiz_tools/Skyline/TestPerf/PerfMeasuredInverseK0.cs

@@ -200,18 +200,24 @@ private void TestCommandlineImport(string skyFile, string testPath)
         {
             if (File.Exists(testPath))
                 File.Delete(testPath);
+            var imsdbPath = TestFilesDir.GetTestPath("testlib.imsdb");
 
             // Show anyone watching that work is being performed
+            // Create an ion mobility library after import just to exercise that code
             RunUI(() => {
                 using (var longWait = new LongWaitDlg(SkylineWindow) { Message = "Running command-line import" })
                 {
                     longWait.PerformWork(SkylineWindow, 500, () =>
+                    {
                         RunCommand("--in=" + skyFile,
                             "--import-file=" + TestFilesDir.GetTestPath(BSA_50fmol_TIMS_InfusionESI_10precd),
-                            "--out=" + testPath));
+                            "--ionmobility-create-library=" + imsdbPath,
+                            "--ionmobility-create-library-name=testlib",
+                            "--out=" + testPath);
+                    });
                 }
             });
-
+            AssertEx.FileExists(imsdbPath);
             VerifySerialization(testPath, false);
         }