WIFF2 file extension in OpenDataSourceDialog and import test (#318)

- added support for WIFF2 file extension to OpenDataSourceDialog
* added import results test for a WIFF2 file in SmallWiffTest
* fixed smartBuildTrigger.py to trigger Container builds for Skyline
- fixed missing userSettings configGroup
* disabled offscreen testing on TeamCity so some troublesome tests will run there, e.g. Shimadzu TOF and WIFF2
* moved WIFF2 test disabling logic to ExtensionTestContext.CanImportAbWiff2
* changed ExtensionTestContext.CanImportShimadzuRaw to be conditioned on Program.SkylineOffscreen

pwiz_tools/SeeMS/app.config

@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <configuration>
   <configSections>
+		<sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089">
+			<section name="seems.Properties.Settings" type="System.Configuration.ClientSettingsSection, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false"/>
+		</sectionGroup>
   </configSections>
 	<userSettings>
 		<seems.Properties.Settings>

pwiz_tools/Skyline/Jamfile.jam

@@ -32,7 +32,7 @@ if [ modules.peek : NT ] && --i-agree-to-the-vendor-licenses in [ modules.peek :
     .teamcity-test-decoration = "" ;
     if --teamcity-test-decoration in [ modules.peek : ARGV ]
     {
-        .teamcity-test-decoration = "teamcitytestdecoration=1" ;
+        .teamcity-test-decoration = "offscreen=0 teamcitytestdecoration=1" ;
     }
 
     rule build-properties ( targets + : sources * : properties * )

pwiz_tools/Skyline/TestData/PwizFileInfoTest.cs

@@ -17,11 +17,9 @@
  * limitations under the License.
  */
 
-using System.Globalization;
 using System.Linq;
 using Microsoft.VisualStudio.TestTools.UnitTesting;
 using pwiz.ProteowizardWrapper;
-using pwiz.Skyline;
 using pwiz.SkylineTestUtil;
 
 namespace pwiz.SkylineTestData
@@ -54,12 +52,12 @@ public void TestInstrumentInfo()
             {
                 VerifyInstrumentInfo(testFilesDir.GetTestPath("051309_digestion.wiff"),
                     "4000 QTRAP", "electrospray ionization", "quadrupole/quadrupole/axial ejection linear ion trap", "electron multiplier");
-                if (System.DateTime.Now.Year > 2018 /* start failing after the new year */ ||
-                    (System.Environment.Is64BitProcess && !Program.SkylineOffscreen &&  /* wiff2 access leaks thread and event handles, so avoid it during nightly tests when offscreen */
-                     (CultureInfo.CurrentCulture.NumberFormat.NumberDecimalSeparator != "," || /* wiff2 access fails under french language settings */
-                      CultureInfo.CurrentCulture.NumberFormat.NumberGroupSeparator != "\xA0")) /* no break space */ )
-                    VerifyInstrumentInfo(testFilesDir.GetTestPath("OnyxTOFMS.wiff2"),
-                        "TripleTOF 5600", "electrospray ionization", "quadrupole/quadrupole/time-of-flight", "electron multiplier");
+            }
+
+            if (ExtensionTestContext.CanImportAbWiff2)
+            {
+                VerifyInstrumentInfo(testFilesDir.GetTestPath("OnyxTOFMS.wiff2"),
+                    "TripleTOF 5600", "electrospray ionization", "quadrupole/quadrupole/time-of-flight", "electron multiplier");
             }
 
             // MzWiff generated mzXML files

pwiz_tools/Skyline/TestData/Results/SmallWiffTest.cs

@@ -42,27 +42,73 @@ public class SmallWiffTest : AbstractUnitTest
     {
         private const string ZIP_FILE = @"TestData\Results\SmallWiff.zip";
 
+        // TODO: Next time SmallWiff.zip is updated, remove the suffix shenanigans below and rename the mzML files in the zip
         [TestMethod]
         public void FileTypeTest()
         {
             var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
 
-            string extWiff = ExtensionTestContext.ExtAbWiff;
-            string suffix = ExtensionTestContext.CanImportAbWiff ? "" : "-test";
-
-            // Do file type checks
-            using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion" + suffix + extWiff)))
+            // wiff1
             {
-                Assert.IsTrue(msData.IsABFile);
+                string extWiff = ExtensionTestContext.ExtAbWiff;
+                string suffix = ExtensionTestContext.CanImportAbWiff ? "" : "-test";
+
+                // Do file type checks
+                using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion" + suffix + extWiff)))
+                {
+                    Assert.IsTrue(msData.IsABFile);
+                }
+
+                using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")))
+                {
+                    Assert.IsTrue(msData.IsABFile);
+                    Assert.IsTrue(msData.IsMzWiffXml);
+                }
             }
 
-            using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")))
+            // wiff2
             {
-                Assert.IsTrue(msData.IsABFile);
-                Assert.IsTrue(msData.IsMzWiffXml);
+                string extWiff2 = ExtensionTestContext.ExtAbWiff2;
+                string suffix = ExtensionTestContext.CanImportAbWiff2 ? "" : "-sample";
+
+                // Do file type checks
+                using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("OnyxTOFMS" + suffix + extWiff2)))
+                {
+                    Assert.IsTrue(msData.IsABFile);
+                }
             }
         }
 
+        [TestMethod]
+        public void Wiff2ResultsTest()
+        {
+            TestFilesDir testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
+
+            string docPath = testFilesDir.GetTestPath("OnyxTOFMS.sky");
+            SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
+            AssertEx.IsDocumentState(doc, 0, 1, 1, 4);
+
+            using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
+            {
+                const string replicateName = "Wiff2Test";
+                string extRaw = ExtensionTestContext.ExtAbWiff2;
+                string suffix = ExtensionTestContext.CanImportAbWiff2 ? "" : "-sample";
+                var chromSets = new[]
+                {
+                    new ChromatogramSet(replicateName, new[]
+                        { new MsDataFilePath(testFilesDir.GetTestPath("OnyxTOFMS" + suffix + extRaw)),  }),
+                };
+                var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
+                Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
+                docContainer.AssertComplete();
+                docResults = docContainer.Document;
+                AssertResult.IsDocumentResultsState(docResults, replicateName,
+                    doc.MoleculeCount, doc.MoleculeTransitionGroupCount, 0, doc.MoleculeTransitionCount, 0);
+            }
+
+            testFilesDir.Dispose();
+        }
+
         [TestMethod]
         public void MsDataFileUriEncodingTest()
         {

pwiz_tools/Skyline/TestUtil/ExtensionTestContext.cs

@@ -17,6 +17,7 @@
  * limitations under the License.
  */
 using System;
+using System.Globalization;
 using System.IO;
 using System.Linq;
 using System.Reflection;
@@ -146,6 +147,23 @@ public static bool CanImportAbWiff
             }
         }
 
+        public static string ExtAbWiff2
+        {
+            get { return CanImportAbWiff2 ? DataSourceUtil.EXT_WIFF2 : ExtMzml; }
+        }
+
+        public static bool CanImportAbWiff2
+        {
+            get
+            {
+                // return false to import mzML
+                return (DateTime.Now.Year > 2018 /* start failing after the new year */ ||
+                        (Environment.Is64BitProcess && !Program.SkylineOffscreen &&  /* wiff2 access leaks thread and event handles, so avoid it during nightly tests when offscreen */
+                         (CultureInfo.CurrentCulture.NumberFormat.NumberDecimalSeparator != "," || /* wiff2 access fails under french language settings */
+                          CultureInfo.CurrentCulture.NumberFormat.NumberGroupSeparator != "\xA0")) /* no break space */ ) ;
+            }
+        }
+
         public static string ExtAgilentRaw
         {
             get { return CanImportAgilentRaw ? DataSourceUtil.EXT_AGILENT_BRUKER_RAW : ExtMzml; }
@@ -156,7 +174,7 @@ public static bool CanImportShimadzuRaw
             get
             {
                 // return false to import mzML
-                return false;    // TODO: Currently leaks to process heap
+                return !Program.SkylineOffscreen;    // currently leaks to process heap, so avoid it during nightly tests when offscreen
             }
         }
 

pwiz_tools/Skyline/Util/DataSourceUtil.cs

@@ -33,6 +33,7 @@ public static class DataSourceUtil
         // ReSharper disable NonLocalizedString
         public const string EXT_THERMO_RAW = ".raw";
         public const string EXT_WIFF = ".wiff";
+        public const string EXT_WIFF2 = ".wiff2";
         public const string EXT_SHIMADZU_RAW = ".lcd";
         public const string EXT_MZXML =  ".mzxml";
         public const string EXT_MZDATA = ".mzdata";
@@ -113,6 +114,7 @@ public static string GetSourceType(FileInfo fileInfo)
             {
                 case EXT_THERMO_RAW: return TYPE_THERMO_RAW;
                 case EXT_WIFF: return TYPE_WIFF;
+                case EXT_WIFF2: return TYPE_WIFF;
                 case EXT_SHIMADZU_RAW: return TYPE_SHIMADZU;
                 //case ".mgf": return "Mascot Generic";
                 //case ".dta": return "Sequest DTA";

scripts/misc/smartBuildTrigger.py

@@ -119,7 +119,7 @@ def merge(a, *b):
     ("scripts/.*", targets['All']),
     ("pwiz_tools/BiblioSpec/.*", merge(targets['Core'], targets['Skyline'], targets['Container'])),
     ("pwiz_tools/Bumbershoot/.*", targets['Bumbershoot']),
-    ("pwiz_tools/Skyline/.*", targets['Skyline'], targets['Container']),
+    ("pwiz_tools/Skyline/.*", merge(targets['Skyline'], targets['Container'])),
     ("pwiz_tools/Topograph/.*", targets['Skyline']),
     ("pwiz_tools/Shared/.*", merge(targets['Skyline'], targets['BumbershootRelease'], targets['Container'])),
     ("pwiz_tools/.*", targets['All']),