JAL-2154 testNG like assertAlignmentDatasetRefs static wrappers and allow a message...

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 9434569..003f2aa 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -104,6 +104,29 @@ public class AlignmentTest
   }
 
   /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, null);
+  }
+
+  /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   * @param message
+   *          - prefixed to any assert failed messages
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment,
+          String message)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, message);
+  }
+
+  /**
    * verify sequence and dataset references are properly contained within
    * dataset
    * 
@@ -111,16 +134,19 @@ public class AlignmentTest
    *          - the alignmentI object to verify (either alignment or dataset)
    * @param raiseAssert
    *          - when set, testng assertions are raised.
+   *          @param message
+   *          - null or a string message to prepend to the assert failed messages.
    * @return true if alignment references were in order, otherwise false.
    */
   public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
-          boolean raiseAssert)
+          boolean raiseAssert, String message)
   {
+    if (message==null) { message = ""; }
     if (alignment == null)
     {
       if (raiseAssert)
       {
-        Assert.fail("Alignment for verification was null.");
+        Assert.fail(message+"Alignment for verification was null.");
       }
       return false;
     }
@@ -135,7 +161,7 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail("Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+            Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference.");
           }
           return false;
         }
@@ -143,12 +169,12 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail("Alignment contained a sequence who's dataset sequence was not in the dataset.");
+            Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset.");
           }
           return false;
         }
       }
-      return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert);
+      return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message);
     }
     else
     {
@@ -159,7 +185,7 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail("Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+            Assert.fail(message+" Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
           }
           return false;
         }
@@ -176,7 +202,7 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail("DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
                   }
                   return false;
 
@@ -185,7 +211,7 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail("DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -205,7 +231,7 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-FromSeq is not a dataset sequence");
+                Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence");
               }
               return false;
             }
@@ -214,7 +240,7 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-FromSeq is not contained in dataset");
+                Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset");
               }
               return false;
             }
@@ -222,7 +248,7 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
               }
               return false;
             }
@@ -231,7 +257,7 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
               }
               return false;
             }
@@ -258,7 +284,7 @@ public class AlignmentTest
       try
       {
 
-        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true),
+        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
                 "Valid test alignment failed when raiseAsserts enabled:"
                         + msg);
       } catch (AssertionError ae)
@@ -269,7 +295,7 @@ public class AlignmentTest
                         + msg, ae);
       }
       // also check validation passes with asserts disabled
-      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false),
+      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
               "Valid test alignment failed when raiseAsserts disabled:"
                       + msg);
     }
@@ -277,7 +303,7 @@ public class AlignmentTest
     {
       try
       {
-        Assert.assertFalse(verifyAlignmentDatasetRefs(al, true));
+        Assert.assertFalse(verifyAlignmentDatasetRefs(al, true, null));
         Assert.fail("Invalid test alignment passed but no assertion raised when raiseAsserts enabled:"
                 + msg);
       } catch (AssertionError ae)
@@ -285,7 +311,7 @@ public class AlignmentTest
         // expected behaviour
       }
       // also check validation passes with asserts disabled
-      Assert.assertFalse(verifyAlignmentDatasetRefs(al, false),
+      Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
               "Invalid test alignment passed when raiseAsserts disabled:"
                       + msg);
     }

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 154abc0..d1821f1 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -99,8 +99,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           assertTrue("Didn't retrieve " + first, af != null);
 
           // verify references for retrieved data
-          AlignmentTest.verifyAlignmentDatasetRefs(af.getViewport()
-                  .getAlignment(), true);
+          AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Fetch " + first + ":");
 
           // store project to recover on next pass
           stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
@@ -113,8 +114,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                   .get(first).toString(), FormatAdapter.FILE);
 
           // verify references for recovered data
-          AlignmentTest.verifyAlignmentDatasetRefs(af.getViewport()
-                  .getAlignment(), true);
+          AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Recover " + first + ":");
 
         }
 
@@ -186,12 +188,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             }
             for (AlignmentViewPanel avp : cra_views)
             {
+              nextxref = first + " -> " + db + "{" + p++ + "}";
+
               // verify references for this panel
-              AlignmentTest.verifyAlignmentDatasetRefs(avp.getAlignment(),
-                      true);
+              AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+                      "" + "Pass (" + pass1 + "," + pass2 + "): For "
+                              + nextxref + ":");
 
               SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
-              nextxref = first + " -> " + db + "{" + p++ + "}";
 
               viewsourcedb.put(avp, nextxref);
               stringify(dbtoviewBit, savedProjects, nextxref, avp);
@@ -263,8 +267,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                             + xrefdb + "{" + q++ + "}";
 
                     // verify references for this panel
-                    AlignmentTest.verifyAlignmentDatasetRefs(
-                            nextavp.getAlignment(), true);
+                    AlignmentTest.assertAlignmentDatasetRefs(
+                            nextavp.getAlignment(), "" + "Pass (" + pass1
+                                    + "," + pass2 + "): For "
+                                    + nextnextxref + ":");
 
                     viewsourcedb.put(nextavp, nextnextxref);
                     stringify(dbtoviewBit, savedProjects, nextnextxref,