X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=838aa7a09a12ff0e25f08063ab089758d55b4769;hb=ec58d7c6a3ceadb413a2e11247adef2eaee3382b;hp=24074d0b371779579967e34aee075ad70a09435e;hpb=bcdd444ed0efcf2d3f0112402a7c780994e6305b;p=jalview.git

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 24074d0..838aa7a 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -52,6 +52,11 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Operational" }, enabled = true)
   public void testRetrieveAndShowCrossref() throws Exception
   {
+
+    List<String> failedDBRetr = new ArrayList<String>();
+    List<String> failedXrefMenuItems = new ArrayList<String>();
+    List<String> failedProjectRecoveries = new ArrayList<String>();
+
     // for every set of db queries
     // retrieve db query
     // verify presence of expected xrefs
@@ -94,11 +99,15 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
         {
           // retrieve dbref
 
+          List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+                  did[0], did[1]);
+          if (afs.size() == 0)
+          {
+            failedDBRetr.add("Didn't retrieve " + first);
+            break;
+          }
           keyseq.add(first);
-
-          af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
-                  .get(0);
-          Assert.assertTrue(af != null, "Didn't retrieve " + first);
+          af = afs.get(0);
 
           // verify references for retrieved data
           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
@@ -155,8 +164,12 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             { // retrieve and show cross-refs in this thread
               cra = new CrossRefAction(af, seqs, dna, db);
               cra.run();
-              Assert.assertTrue(cra.getXrefViews().size() > 0,
-                      "No crossrefs retrieved for " + db);
+              if (cra.getXrefViews().size() == 0)
+              {
+                failedXrefMenuItems.add("No crossrefs retrieved for "
+                        + first + " -> " + db);
+                continue;
+              }
               cra_views = cra.getXrefViews();
               assertNucleotide(cra_views.get(0),
                       "Nucleotide panel included proteins for " + first
@@ -170,6 +183,15 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               Desktop.instance.closeAll_actionPerformed(null);
               pass3 = 0;
               // recover stored project
+              File storedProject = savedProjects.get(nextxref);
+              if (storedProject == null)
+              {
+                failedProjectRecoveries.add("Failed to store a view for '"
+                        + nextxref + "'");
+                continue;
+              }
+
+              // recover stored project
               AlignFrame af2 = new FileLoader(false)
                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
                               .toString(), FormatAdapter.FILE);
@@ -245,11 +267,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     cra = new CrossRefAction(nextaf, xrseqs, avp
                             .getAlignViewport().isNucleotide(), xrefdb);
                     cra.run();
-                    Assert.assertTrue(
-                            cra.getXrefViews().size() > 0,
-                            "No crossrefs found for '" + nextnextxref
-                                    + "' to " + xrefdb + " via '"
-                                    + nextaf.getTitle() + "'");
+                    if (cra.getXrefViews().size() == 0)
+                    {
+                      failedXrefMenuItems
+                              .add("No crossrefs retrieved for '"
+                              + nextxref + "' to " + xrefdb + " via '"
+                              + nextaf.getTitle() + "'");
+                      continue;
+                    }
                     cra_views2 = cra.getXrefViews();
                     assertNucleotide(cra_views2.get(0),
                             "Nucleotide panel included proteins for '"
@@ -265,6 +290,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                   {
                     Desktop.instance.closeAll_actionPerformed(null);
                     // recover stored project
+                    File storedProject = savedProjects.get(nextnextxref);
+                    if (storedProject == null)
+                    {
+                      failedProjectRecoveries
+                              .add("Failed to store a view for '"
+                                      + nextnextxref + "'");
+                      continue;
+                    }
                     AlignFrame af2 = new FileLoader(false)
                             .LoadFileWaitTillLoaded(
                                     savedProjects.get(nextnextxref)
@@ -342,13 +375,45 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
         }
         else
         {
-          // verify stored projects for second set of cross references
-          pass2 = 1;
+          pass1++;
+          if (pass1 < 2)
+          {
+            // verify stored projects for second set of cross references
+            pass2 = 1;
           // and verify cross-references retrievable from those stored projects.
-          pass3 = 0;
+            pass3 = 0;
+          }
         }
       } while (pass3 < 2);
     }
+    if (failedXrefMenuItems.size() > 0)
+    {
+      for (String s : failedXrefMenuItems)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+              + " counts)");
+    }
+    if (failedProjectRecoveries.size() > 0)
+    {
+
+      for (String s : failedProjectRecoveries)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
+              + failedProjectRecoveries.size() + " counts)");
+    }
+    if (failedDBRetr.size() > 0)
+    {
+      for (String s : failedProjectRecoveries)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+              + failedDBRetr.size() + " counts)");
+    }
   }
 
   private void assertProtein(AlignmentViewPanel alignmentViewPanel,