JAL-3705 unit test and "fix" borrowing unused schema attribute

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

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 3ca6ed8..a336d6d 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -24,20 +24,6 @@ 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;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentTest;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.CrossRefAction;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.SequenceFetcher;
-import jalview.project.Jalview2XML;
-import jalview.util.DBRefUtils;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -51,6 +37,20 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
 import junit.extensions.PA;
 
 @Test(singleThreaded = true)
@@ -678,4 +678,66 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               "stringify mismatch for " + xrefpath);
     }
   }
+
+  /**
+   * Test for JAL-3705, that verifies fetching an EMBL entry, saving to project,
+   * reloading, and showing cross-references
+   */
+  @Test(groups = { "Operational" }, enabled = true)
+  public void testRestoreGeneXrefsFromProject() throws Exception
+  {
+    /*
+     * fetch EMBL:J03321 and verify a couple of its UNIPROT xrefs, which should
+     * have the EMBL proteinId as Mapping.mappedFromId
+     */
+    SequenceFetcher sf = new SequenceFetcher(Desktop.instance, "EMBL",
+            "J03321");
+    sf.run();
+    AlignFrame[] afs = Desktop.getAlignFrames();
+    assertEquals(afs.length, 1);
+    SequenceI seq = afs[0].getViewport().getAlignment().getSequenceAt(0);
+    assertEquals(seq.getName(), "EMBL|J03321");
+    int found = 0;
+    for (DBRefEntry dbref : seq.getDBRefs())
+    {
+      if ("UNIPROT".equals(dbref.getSource()))
+      {
+        found++;
+        if ("P10559".equals(dbref.getAccessionId()))
+        {
+          assertEquals(dbref.getMap().getMappedFromId(), "AAA91573.1");
+        }
+        else if ("P10560".equals(dbref.getAccessionId()))
+        {
+          assertEquals(dbref.getMap().getMappedFromId(), "AAA91574.1");
+        }
+      }
+    }
+    final int expectedUniprotXrefs = 8; // this might change in future!
+    assertEquals(found, expectedUniprotXrefs);
+
+    /*
+     * save to project, close all, reload project, Get Cross-References | UNIPROT
+     * - should use the restored mappedFromId for the CDS sequence ids
+     */
+    File tfile = File.createTempFile("testRestoreGeneXrefsFromProject",
+            ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+    new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    afs = Desktop.getAlignFrames();
+    assertEquals(afs.length, 1);
+    seq = afs[0].getViewport().getAlignment().getSequenceAt(0);
+    assertEquals(seq.getName(), "EMBL|J03321");
+    CrossRefAction.getHandlerFor(new SequenceI[] {seq}, true, "UNIPROT", afs[0]).run();
+    AlignFrame[] afs2 = Desktop.getAlignFrames();
+    assertEquals(afs2.length, 3); // gene sequence, plus split frame
+    List<SequenceI> cds = afs2[1].getViewport().getAlignment().getSequences();
+    assertEquals(cds.size(), expectedUniprotXrefs);
+    assertEquals(cds.get(0).getName(), "CDS|AAA91567.1");
+    assertEquals(cds.get(7).getName(), "CDS|AAA91574.1");
+
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
 }