From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 25 Aug 2016 19:55:19 +0000 (+0100)
Subject: JAL-2106 JAL-2154 cross-refs from Ensembl should verify as cross refs only
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=76de4fc452184b56e01960d05cb2235b1807e836;p=jalview.git

JAL-2106 JAL-2154 cross-refs from Ensembl should verify as cross refs only
---

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index b4d2783..50e1032 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -174,7 +174,8 @@ public class EnsemblGene extends EnsemblSeqProxy
        */
       else
       {
-        List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+        List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+                getDbVersion()).getIds(acc);
         for (String geneId : ids)
         {
           if (!geneIds.contains(geneId))
@@ -196,7 +197,8 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getGeneIdentifiersForName(String query)
   {
-    List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
+    List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+            getDbVersion()).getIds(query);
     if (ids != null)
     {
       for (String id : ids)
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index e44b610..5a32736 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -308,7 +308,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq = seq.getDatasetSequence();
     }
 
-    EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
+    EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
+            getEnsemblDataVersion());
     List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
     for (DBRefEntry xref : xrefs)
     {
diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 1c47f11..b8c8c54 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -25,11 +25,13 @@ public class EnsemblSymbol extends EnsemblXref
   /**
    * Constructor given the target domain to fetch data from
    * 
-   * @param d
+   * @param domain
+   * @param dbName
+   * @param dbVersion
    */
-  public EnsemblSymbol(String d)
+  public EnsemblSymbol(String domain, String dbName, String dbVersion)
   {
-    super(d);
+    super(domain, dbName, dbVersion);
   }
 
   /**
diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index fa86865..313572f 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -29,20 +29,25 @@ class EnsemblXref extends EnsemblRestClient
 
   private static final String GO_GENE_ONTOLOGY = "GO";
 
+  private String dbName = "ENSEMBL (xref)";
+
   /**
    * Constructor given the target domain to fetch data from
    * 
    * @param d
    */
-  public EnsemblXref(String d)
+  public EnsemblXref(String d, String dbSource, String version)
   {
     super(d);
+    dbName = dbSource;
+    xrefVersion = dbSource + ":" + version;
+    
   }
 
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (xref)";
+    return dbName;
   }
 
   @Override
@@ -152,7 +157,7 @@ class EnsemblXref extends EnsemblRestClient
         if (dbName != null && id != null)
         {
           dbName = DBRefUtils.getCanonicalName(dbName);
-          DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+          DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
           result.add(dbref);
         }
       }
@@ -163,6 +168,18 @@ class EnsemblXref extends EnsemblRestClient
     return result;
   }
 
+  private String xrefVersion = "ENSEMBL:0";
+
+  /**
+   * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
+   * 
+   * @return
+   */
+  public String getXRefVersion()
+  {
+    return xrefVersion;
+  }
+
   /**
    * Returns the URL for the REST endpoint to fetch all cross-references for an
    * identifier. Note this may return protein cross-references for nucleotide.
diff --git a/test/jalview/ext/ensembl/EnsemblXrefTest.java b/test/jalview/ext/ensembl/EnsemblXrefTest.java
index 1dc9b8d..4dc8ab2 100644
--- a/test/jalview/ext/ensembl/EnsemblXrefTest.java
+++ b/test/jalview/ext/ensembl/EnsemblXrefTest.java
@@ -1,6 +1,7 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 
 import jalview.datamodel.DBRefEntry;
 
@@ -24,8 +25,11 @@ public class EnsemblXrefTest
   @Test(groups = "Functional")
   public void testGetCrossReferences()
   {
+    String dbName = "ENSEMBL";
+    String dbVers = "0.6.2b1";
     System.out.println(JSON);
-    EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org")
+    EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
+            dbVers)
     {
       @Override
       protected BufferedReader getHttpResponse(URL url, List<String> ids)
@@ -40,8 +44,12 @@ public class EnsemblXrefTest
     assertEquals(2, dbrefs.size());
     assertEquals("CCDS", dbrefs.get(0).getSource());
     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
+    assertFalse(dbrefs.get(0).isPrimary());
+    assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
     // Uniprot name should get converted to Jalview canonical form
     assertEquals("UNIPROT", dbrefs.get(1).getSource());
     assertEquals("P15056", dbrefs.get(1).getAccessionId());
+    assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
+    assertFalse(dbrefs.get(1).isPrimary());
   }
 }