JAL-2253 safer simpler resolution of identifiers using lookup endpoint;

[jalview.git] / src / jalview / ext / ensembl / EnsemblXref.java

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index c0b00b1..9634ad3 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -125,7 +125,10 @@ class EnsemblXref extends EnsemblRestClient
       {
         br = getHttpResponse(url, ids);
       }
-      return (parseResponse(br));
+      if (br != null)
+      {
+        result = parseResponse(br);
+      }
     } catch (IOException e)
     {
       // ignore
@@ -168,16 +171,13 @@ class EnsemblXref extends EnsemblRestClient
       while (rvals.hasNext())
       {
         JSONObject val = (JSONObject) rvals.next();
-        String dbName = val.get("dbname").toString();
-        if (dbName.equals(GO_GENE_ONTOLOGY))
-        {
-          continue;
-        }
+        String db = val.get("dbname").toString();
         String id = val.get("primary_id").toString();
-        if (dbName != null && id != null)
+        if (db != null && id != null
+                && !GO_GENE_ONTOLOGY.equals(db))
         {
-          dbName = DBRefUtils.getCanonicalName(dbName);
-          DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
+          db = DBRefUtils.getCanonicalName(db);
+          DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
           result.add(dbref);
         }
       }