JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinqu...

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

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index ef7615b..ae5ed25 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
 import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignedCodonFrame;
@@ -29,8 +33,8 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.CrossRefAction;
 import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
+import jalview.project.Jalview2XML;
 import jalview.util.DBRefUtils;
 
 import java.io.File;
@@ -39,12 +43,15 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 @Test(singleThreaded = true)
 public class CrossRef2xmlTests extends Jalview2xmlBase
 {
@@ -57,6 +64,51 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @Test(groups = { "Functional" }, enabled = true)
+  public void openCrossrefsForEnsemblTwice()
+  {
+    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+            "examples/testdata/CantShowEnsemblCrossrefsTwice.jvp",
+            DataSourceType.FILE);
+    assertNotNull(af, "Couldn't load test's project.");
+    AlignmentI origAlig = af.getViewport().getAlignment();
+    List<String> source = new CrossRef(origAlig.getSequencesArray(),
+            origAlig.getDataset()).findXrefSourcesForSequences(true);
+    assertEquals(source.size(), 1, "Expected just one crossref to show.");
+    List<AlignmentViewPanel> views;
+    {
+      // try to show once - in a code block so handler is forgotten about
+      CrossRefAction xref1 = CrossRefAction.getHandlerFor(
+              origAlig.getSequencesArray(), true, source.get(0), af);
+      try
+      {
+        xref1.run();
+        views = (List<AlignmentViewPanel>) PA.getValue(xref1, "xrefViews");
+        assertTrue(views.size() > 0,
+                "Couldn't get cross ref on first attempt (SERIOUS FAIL).");
+      } catch (Exception ex)
+      {
+        Assert.fail("Unexpected Exception for first xref action", ex);
+      }
+    }
+
+    views = null;
+    // now just try it again
+    CrossRefAction xref2 = CrossRefAction.getHandlerFor(
+            origAlig.getSequencesArray(), true, source.get(0), af);
+    try
+    {
+      xref2.run();
+      views = (List<AlignmentViewPanel>) PA.getValue(xref2, "xrefViews");
+      assertTrue(views.size() > 0,
+              "Couldn't get cross ref on second attempt (SERIOUS FAIL).");
+    } catch (Exception ex)
+    {
+      Assert.fail("Unexpected Exception for second xref action", ex);
+    }
+    // TODO : check that both views contain the same data
+  }
+
   @DataProvider(name = "initialAccessions")
   static Object[][] getAccessions()
   {
@@ -104,9 +156,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    Map<String, String> dbtoviewBit = new HashMap<>();
     List<String> keyseq = new ArrayList<>();
-    HashMap<String, File> savedProjects = new HashMap<>();
+    Map<String, File> savedProjects = new HashMap<>();
 
 //    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
 //    {
@@ -201,15 +253,16 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
             if (pass2 == 0)
             { // retrieve and show cross-refs in this thread
-              cra = new CrossRefAction(af, seqs, dna, db);
+              cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
               cra.run();
-              if (cra.getXrefViews().size() == 0)
+              cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+                      "xrefViews");
+              if (cra_views.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
                               + " -> " + db);
@@ -301,16 +354,18 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
                   if (pass3 == 0)
                   {
-
                     SequenceI[] xrseqs = avp.getAlignment()
                             .getSequencesArray();
                     AlignFrame nextaf = Desktop.getAlignFrameFor(avp
                             .getAlignViewport());
 
-                    cra = new CrossRefAction(nextaf, xrseqs, avp
-                            .getAlignViewport().isNucleotide(), xrefdb);
+                    cra = CrossRefAction.getHandlerFor(xrseqs, avp
+                            .getAlignViewport().isNucleotide(), xrefdb,
+                            nextaf);
                     cra.run();
-                    if (cra.getXrefViews().size() == 0)
+                    cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
+                            cra, "xrefViews");
+                    if (cra_views2.size() == 0)
                     {
                       failedXrefMenuItems
                               .add("No crossrefs retrieved for '"
@@ -318,7 +373,6 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                                       + " via '" + nextaf.getTitle() + "'");
                       continue;
                     }
-                    cra_views2 = cra.getXrefViews();
                     assertNucleotide(cra_views2.get(0),
                             "Nucleotide panel included proteins for '"
                                     + nextxref + "' to " + xrefdb
@@ -556,8 +610,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
    *          viewpanel needs to be called with a distinct xrefpath to ensure
    *          each one's strings are compared)
    */
-  private void stringify(HashMap<String, String> dbtoviewBit,
-          HashMap<String, File> savedProjects, String xrefpath,
+  private void stringify(Map<String, String> dbtoviewBit,
+          Map<String, File> savedProjects, String xrefpath,
           AlignmentViewPanel avp)
   {
     if (savedProjects != null)