From 6f9b0cd13d25cf041aed033652e87f2d547cba52 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 22 Aug 2016 16:42:53 +0100
Subject: [PATCH] JAL-2154 - rejig test pass code for breadth-first (or top
 down) repetition of fetch/fetch crossref/fetch crossref.

* First iteration, all pass counters at zero, process through all crossrefs.
* Next iteration, pass1=1 - recover, process through all crossers
* Next iteration, pass2=1 - recover each first crossref result and process through
* Last iteration, pass3=1 - recover each second crossref result and process.
---
 test/jalview/io/CrossRef2xmlTests.java |   43 ++++++++++++++++++++++----------
 1 file changed, 30 insertions(+), 13 deletions(-)

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 64c800b..20a95d0 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -20,8 +20,6 @@
  */
 package jalview.io;
 
-import static org.testng.AssertJUnit.assertTrue;
-
 import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignedCodonFrame;
@@ -100,7 +98,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
           af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
                   .get(0);
-          assertTrue("Didn't retrieve " + first, af != null);
+          Assert.assertTrue(af != null, "Didn't retrieve " + first);
 
           // verify references for retrieved data
           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
@@ -140,8 +138,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
         // start of pass2: retrieve each cross-ref for fetched or restored
         // project.
-        pass2 = 0;
-        do // second cross ref and recover crossref loop
+        do // first cross ref and recover crossref loop
         {
 
           for (String db : ptypes)
@@ -153,6 +150,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             // perform crossref action, or retrieve stored project
             List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
             CrossRefAction cra = null;
+            
             if (pass2 == 0)
             { // retrieve and show cross-refs in this thread
               cra = new CrossRefAction(af, seqs, dna, db);
@@ -164,6 +162,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             else
             {
               Desktop.instance.closeAll_actionPerformed(null);
+              pass3 = 0;
               // recover stored project
               AlignFrame af2 = new FileLoader(false)
                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
@@ -213,11 +212,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               xrptypes.put(nextxref, _xrptypes);
 
             }
-            // now do the next xref pass starting from either saved or just
+
+            // now do the second xref pass starting from either saved or just
             // recovered split pane, in sequence
-            pass3 = 0;
-            do // 3rd cross ref and recover crossref loop, for each view from
-               // second xref view set or recover viewset
+            do // retrieve second set of cross refs or recover and verify
             {
               firstcr_ap = 0;
               for (AlignmentViewPanel avp : cra_views)
@@ -302,20 +300,39 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 } // end of loop around showing all xrefdb for crossrf2
 
               } // end of loop around all viewpanels from crossrf1
-            } while (pass3++ < 2 && pass2 < 1);
+            } while (pass2 == 2 && pass3++ < 2);
             // fetchdb->crossref1->crossref-2->verify for xrefs we
             // either loop twice when pass2=0, or just once when pass2=1
             // (recovered project from previous crossref)
 
-          }
+          } // end of loop over db-xrefs for crossref-2
+
           // fetchdb-->crossref1
           // for each xref we try to retrieve xref, store and verify when
           // pass1=0, or just retrieve and verify when pass1=1
-        } while (pass2++ < 2 && pass1 < 1);
+        } while (pass1 == 1 && pass2++ < 2);
         // fetchdb
         // for each ref we
         // loop twice: first, do the retrieve, second recover from saved project
-      } while (pass1++ < 2);
+
+        // increment pass counters, so we repeat traversal starting from the
+        // oldest saved project first.
+        if (pass1 == 0)
+        {
+          // verify stored projects for first set of cross references
+          pass1 = 1;
+          // and verify cross-references retrieved from stored projects
+          pass2 = 0;
+          pass3 = 0;
+        }
+        else
+        {
+          // verify stored projects for second set of cross references
+          pass2 = 1;
+          // and verify cross-references retrievable from those stored projects.
+          pass3 = 0;
+        }
+      } while (pass3 < 2);
     }
   }
 
-- 
1.7.10.2