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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ccd9ab0..1851be7 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2547,63 +2547,61 @@ public class Jalview2XML
   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
           SequenceI parentseq, SequenceI jds, boolean recurse)
   {
-    Mapping mp = null;
-    if (jmp.getMap() != null)
+    if (jmp.getMap() == null)
     {
-      mp = new Mapping();
+      return null;
+    }
+    Mapping mp = new Mapping();
+
+    if (jmp.getMappedFromId() != null)
+    {
+      mp.setMappingType(jmp.getMappedFromId());
+    }
+    
+    jalview.util.MapList mlst = jmp.getMap();
+    List<int[]> r = mlst.getFromRanges();
+    for (int[] range : r)
+    {
+      MapListFrom mfrom = new MapListFrom();
+      mfrom.setStart(range[0]);
+      mfrom.setEnd(range[1]);
+      mp.getMapListFrom().add(mfrom);
+    }
+    r = mlst.getToRanges();
+    for (int[] range : r)
+    {
+      MapListTo mto = new MapListTo();
+      mto.setStart(range[0]);
+      mto.setEnd(range[1]);
+      mp.getMapListTo().add(mto);
+    }
+    mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+    mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+    if (jmp.getTo() != null)
+    {
+      // check/create ID for the sequence referenced by getTo()
 
-      jalview.util.MapList mlst = jmp.getMap();
-      List<int[]> r = mlst.getFromRanges();
-      for (int[] range : r)
+      String jmpid = "";
+      SequenceI ps = null;
+      if (parentseq != jmp.getTo()
+              && parentseq.getDatasetSequence() != jmp.getTo())
       {
-        MapListFrom mfrom = new MapListFrom();
-        mfrom.setStart(range[0]);
-        mfrom.setEnd(range[1]);
-        // mp.addMapListFrom(mfrom);
-        mp.getMapListFrom().add(mfrom);
+        // chaining dbref rather than a handshaking one
+        jmpid = seqHash(ps = jmp.getTo());
       }
-      r = mlst.getToRanges();
-      for (int[] range : r)
+      else
       {
-        MapListTo mto = new MapListTo();
-        mto.setStart(range[0]);
-        mto.setEnd(range[1]);
-        // mp.addMapListTo(mto);
-        mp.getMapListTo().add(mto);
+        jmpid = seqHash(ps = parentseq);
       }
-      mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
-      mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
-      if (jmp.getTo() != null)
+      mp.setDseqFor(jmpid);
+      if (!seqRefIds.containsKey(jmpid))
       {
-        // MappingChoice mpc = new MappingChoice();
-
-        // check/create ID for the sequence referenced by getTo()
-
-        String jmpid = "";
-        SequenceI ps = null;
-        if (parentseq != jmp.getTo()
-                && parentseq.getDatasetSequence() != jmp.getTo())
-        {
-          // chaining dbref rather than a handshaking one
-          jmpid = seqHash(ps = jmp.getTo());
-        }
-        else
-        {
-          jmpid = seqHash(ps = parentseq);
-        }
-        // mpc.setDseqFor(jmpid);
-        mp.setDseqFor(jmpid);
-        if (!seqRefIds.containsKey(jmpid))
-        {
-          jalview.bin.Cache.log.debug("creatign new DseqFor ID");
-          seqRefIds.put(jmpid, ps);
-        }
-        else
-        {
-          jalview.bin.Cache.log.debug("reusing DseqFor ID");
-        }
-
-        // mp.setMappingChoice(mpc);
+        jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+        seqRefIds.put(jmpid, ps);
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("reusing DseqFor ID");
       }
     }
     return mp;
@@ -5637,6 +5635,8 @@ public class Jalview2XML
             fto, m.getMapFromUnit().intValue(),
             m.getMapToUnit().intValue());
 
+    jmap.setMappedFromId(m.getMappingType());
+    
     /*
      * (optional) choice of dseqFor or Sequence
      */

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);
+  }
 }