skyline: Fixed the small-molecule conversion tests racing the library loader

pwiz_tools/Skyline/TestUtil/AsSmallMoleculeTestUtil.cs

@@ -226,6 +226,13 @@ public static SrmDocument ConvertToSmallMolecules(SrmDocument doc, ref string do
                     {
                         docContainer.SetDocument(docLoad, null, true);
                         docContainer.AssertComplete();
+                        // ConvertToSmallMolecules skips library conversion entirely unless
+                        // Libraries.IsLoaded, so the conversion under test depends on winning a
+                        // race with the library loader. Whichever conversion test ran first in a
+                        // process lost it: no converted .blib was written, the converted document
+                        // had no library dot product where the original did, and the comparison
+                        // below failed. Later tests in the same process passed on a warm cache.
+                        docContainer.WaitForLibrariesLoaded();
                         doc = docContainer.Document;
                     }
                 }
@@ -280,6 +287,7 @@ public static SrmDocument ConvertToSmallMolecules(SrmDocument doc, ref string do
             {
                 docContainer.SetDocument(docResults, null, true);
                 docContainer.AssertComplete();
+                docContainer.WaitForLibrariesLoaded();
                 doc = docContainer.Document;
             }
             AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(docOriginal, doc, Path.GetDirectoryName(docPath), mode);

pwiz_tools/Skyline/TestUtil/ResultsUtil.cs

@@ -254,6 +254,7 @@ public ResultsTestDocumentContainer(SrmDocument docInitial, string pathInitial,
 
         private const int SLEEP_INTERVAL = 10;
         public const int WAIT_TIME = 5 * 1000;    // 5 seconds
+        public const int WAIT_TIME_LIBRARIES = 60 * 1000;    // 60 seconds
 
         private static int GetWaitCycles(int millis = WAIT_TIME)
         {
@@ -277,6 +278,34 @@ public bool AnyProcessing
             get { return BackgroundLoaders.Any(l => l.AnyProcessing()); }
         }
 
+        /// <summary>
+        /// Waits for the document's spectral libraries to finish loading.
+        /// <see cref="AssertComplete"/> only inspects the chromatogram loader's progress, so it
+        /// can return while the library manager is still working. A caller that then reads
+        /// Settings.PeptideSettings.Libraries.IsLoaded sees false purely because it got there
+        /// first, and silently takes whatever path the code has for a library-less document.
+        /// A document with no libraries reports itself loaded, so this returns immediately.
+        /// </summary>
+        public void WaitForLibrariesLoaded(int millis = WAIT_TIME_LIBRARIES)
+        {
+            int waitCycles = GetWaitCycles(millis);
+            for (int i = 0; i < waitCycles; i++)
+            {
+                if (Document.Settings.PeptideSettings.Libraries.IsLoaded)
+                    return;
+                Thread.Sleep(SLEEP_INTERVAL);
+            }
+            // One last look: the loop sleeps after its final check, so the libraries may have
+            // finished during that sleep, and a timeout below SLEEP_INTERVAL yields no cycles
+            // at all and must still get one check rather than failing without ever looking.
+            if (Document.Settings.PeptideSettings.Libraries.IsLoaded)
+                return;
+
+            Assert.Fail("Libraries still not loaded after {0} seconds: {1}",
+                waitCycles*SLEEP_INTERVAL/1000,
+                Document.Settings.PeptideSettings.Libraries.IsNotLoadedExplained);
+        }
+
         public void AssertComplete()
         {
             if (LastProgress == null || LastProgress.IsComplete) return;