X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=714a5c011120801f85cd571dab9af79be73fff13;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=c0b00b182f8fc528974dff004831e33607c82f4d;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index c0b00b1..714a5c0 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -20,23 +20,20 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.util.DBRefUtils;
-
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.util.DBRefUtils;
+
 /**
  * A class to fetch cross-references from Ensembl by calling the /xrefs REST
  * service
@@ -88,18 +85,6 @@ class EnsemblXref extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
   /**
    * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
    * ("primary_id") for the given identifier (Ensembl accession id) and database
@@ -111,83 +96,54 @@ class EnsemblXref extends EnsemblRestClient
    *          an Ensembl stable identifier
    * @return
    */
+  @SuppressWarnings("unchecked")
   public List<DBRefEntry> getCrossReferences(String identifier)
   {
-    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
-    List<String> ids = new ArrayList<String>();
+    List<DBRefEntry> result = new ArrayList<>();
+    List<String> ids = new ArrayList<>();
     ids.add(identifier);
 
-    BufferedReader br = null;
-    try
-    {
-      URL url = getUrl(identifier);
-      if (url != null)
-      {
-        br = getHttpResponse(url, ids);
-      }
-      return (parseResponse(br));
-    } catch (IOException e)
-    {
-      // ignore
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
-
-    return result;
-  }
-
-  /**
-   * Parses "primary_id" and "dbname" values from the JSON response and
-   * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
-   * don't parse "synonyms" as they appear to be either redirected or obsolete
-   * in Uniprot.
-   * 
-   * @param br
-   * @return
-   * @throws IOException
-   */
-  protected List<DBRefEntry> parseResponse(BufferedReader br)
-          throws IOException
-  {
-    JSONParser jp = new JSONParser();
-    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
     try
     {
-      JSONArray responses = (JSONArray) jp.parse(br);
-      Iterator rvals = responses.iterator();
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(
+              getUrl(identifier), ids, -1, MODE_ITERATOR, null);
       while (rvals.hasNext())
       {
-        JSONObject val = (JSONObject) rvals.next();
-        String dbName = val.get("dbname").toString();
-        if (dbName.equals(GO_GENE_ONTOLOGY))
-        {
-          continue;
-        }
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        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);
         }
       }
-    } catch (ParseException e)
+    } catch (ParseException | IOException e)
     {
       // ignore
     }
     return result;
   }
 
+  // /**
+  // * Parses "primary_id" and "dbname" values from the JSON response and
+  // * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note
+  // we
+  // * don't parse "synonyms" as they appear to be either redirected or obsolete
+  // * in Uniprot.
+  // *
+  // * @param br
+  // * @return
+  // * @throws IOException
+  // */
+  // @SuppressWarnings("unchecked")
+  // protected List<DBRefEntry> parseResponse(BufferedReader br)
+  // throws IOException
+  // {
+  // return result;
+  // }
+  //
   private String xrefVersion = "ENSEMBL:0";
 
   /**
@@ -210,8 +166,8 @@ class EnsemblXref extends EnsemblRestClient
    */
   protected URL getUrl(String identifier)
   {
-    String url = getDomain() + "/xrefs/id/" + identifier
-            + "?content-type=application/json&all_levels=1";
+    String url = getDomain() + "/xrefs/id/" + identifier + CONTENT_TYPE_JSON
+            + "&all_levels=1";
     try
     {
       return new URL(url);