JAL-1889 unit test tweaks for running on server

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
index 4d904cf..99394dc 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
@@ -41,7 +41,7 @@ public class ChimeraConnect
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "External" })
   public void testLaunchAndExit()
   {
     final StructureManager structureManager = new StructureManager(true);

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 5ed0cac..7801250 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -277,7 +277,7 @@ public class AlignViewportTest
    * Test for JAL-1306 - conservation thread should run even when only Quality
    * (and not Conservation) is enabled in Preferences
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, timeOut=2000)
   public void testUpdateConservation_qualityOnly()
   {
     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
@@ -292,7 +292,24 @@ public class AlignViewportTest
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+    /*
+     * wait for Conservation thread to complete
+     */
+    AlignViewport viewport = af.getViewport();
+    synchronized (this)
+    {
+      while (viewport.getAlignmentConservationAnnotation() != null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+    AlignmentAnnotation[] anns = viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
     assertEquals("More than one annotation found", 1, anns.length);

diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index 2819dbf..e84b87a 100644 (file)
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -222,7 +222,7 @@ public class AlignmentPanelTest
 
   /**
    * Test that update layout reverts to original (unwrapped) values for endRes
-   * and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
+   * when switching from wrapped back to unwrapped mode (JAL-2739)
    */
   @Test(groups = "Functional")
   public void TestUpdateLayout_endRes()
@@ -235,14 +235,14 @@ public class AlignmentPanelTest
     af.alignPanel.getAlignViewport().setWrapAlignment(true);
     af.alignPanel.updateLayout();
 
-    // endRes changes
+    // endRes has changed
     assertNotEquals(ranges.getEndRes(), endres);
 
     // unwrap
     af.alignPanel.getAlignViewport().setWrapAlignment(false);
     af.alignPanel.updateLayout();
 
-    // endRes and endSeq back to original values
+    // endRes back to original value
     assertEquals(ranges.getEndRes(), endres);
 
   }

diff --git a/test/jalview/io/IdentifyFileTest.java b/test/jalview/io/IdentifyFileTest.java
index dd4f6ba..5be7968 100644 (file)
--- a/test/jalview/io/IdentifyFileTest.java
+++ b/test/jalview/io/IdentifyFileTest.java
@@ -94,7 +94,7 @@ public class IdentifyFileTest
         { "examples/plantfdx.fa", FileFormat.Fasta },
         { "examples/dna_interleaved.phy", FileFormat.Phylip },
         { "examples/2GIS.pdb", FileFormat.PDB },
-        { "examples/rf00031_folded.stk", FileFormat.Stockholm },
+        { "examples/RF00031_folded.stk", FileFormat.Stockholm },
         { "examples/testdata/test.rnaml", FileFormat.Rnaml },
         { "examples/testdata/test.aln", FileFormat.Clustal },
         { "examples/testdata/test.pfam", FileFormat.Pfam },

diff --git a/test/jalview/io/cache/JvCacheableInputBoxTest.java b/test/jalview/io/cache/JvCacheableInputBoxTest.java
index dfd7973..010a4b2 100644 (file)
--- a/test/jalview/io/cache/JvCacheableInputBoxTest.java
+++ b/test/jalview/io/cache/JvCacheableInputBoxTest.java
@@ -55,10 +55,9 @@ public class JvCacheableInputBoxTest
     cacheBox.updateCache();
     try
     {
-      // This 1ms delay is essential to prevent the
-      // assertion below from executing before
-      // cacheBox.updateCache() finishes updating the cache
-      Thread.sleep(100);
+      // This delay is to let
+      // cacheBox.updateCache() finish updating the cache
+      Thread.sleep(200);
     } catch (InterruptedException e)
     {
       e.printStackTrace();

diff --git a/test/jalview/viewmodel/styles/ViewStyleTest.java b/test/jalview/viewmodel/styles/ViewStyleTest.java
index 26c3574..2fcfe1a 100644 (file)
--- a/test/jalview/viewmodel/styles/ViewStyleTest.java
+++ b/test/jalview/viewmodel/styles/ViewStyleTest.java
@@ -114,6 +114,11 @@ public class ViewStyleTest
   {
     Class<?> type = field.getType();
 
+    if (type.toString().contains("com_atlassian_clover"))
+    {
+      // instrumentation added for test coverage - ignore
+      return;
+    }
     if (type.equals(boolean.class) || type.equals(Boolean.class))
     {
       boolean value = (Boolean) field.get(vs);