JAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignm...

[jalview.git] / test / jalview / io / CrossRef2xmlTests.java

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 24074d0..080bda8 100644 (file)
--- 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
@@ -72,7 +77,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     List<String> keyseq = new ArrayList<String>();
     HashMap<String, File> savedProjects = new HashMap<String, File>();
 
-    for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+    for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+    { "UNIPROT", "P01731" } })
     {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
@@ -94,16 +100,23 @@ 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()
                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
                   + pass3 + "): Fetch " + first + ":");
+          AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Fetch " + first + ":");
           dna = af.getViewport().getAlignment().isNucleotide();
           retral = af.getViewport().getAlignment();
           dataset = retral.getDataset();
@@ -127,6 +140,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
                   + pass3 + "): Recover " + first + ":");
+          AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Recover " + first + ":");
 
         }
 
@@ -155,8 +171,12 @@ 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 +190,15 @@ 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);
@@ -206,6 +235,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                       "Pass (" + pass1 + "," + pass2 + "," + pass3
                               + "): before start of pass3: " + nextxref
                               + ":");
+              AlignmentTest.assertDatasetIsNormalised(avp.getAlignment(),
+                      "Pass (" + pass1 + "," + pass2 + "," + pass3
+                              + "): before start of pass3: " + nextxref
+                              + ":");
 
               SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
 
@@ -245,11 +278,14 @@ 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 +301,14 @@ 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)
@@ -307,6 +351,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                             nextavp.getAlignment(), "" + "Pass (" + pass1
                                     + "," + pass2 + "): For "
                                     + nextnextxref + ":");
+                    AlignmentTest.assertDatasetIsNormalised(
+                            nextavp.getAlignment(), "" + "Pass (" + pass1
+                                    + "," + pass2 + "): For "
+                                    + nextnextxref + ":");
 
                     stringify(dbtoviewBit, savedProjects, nextnextxref,
                             nextavp);
@@ -342,13 +390,45 @@ 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,