X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=9b58e58cd341d3154e47959862ce38fc807043ab;hb=7d602d0e4b439e56af3e4551ed71f181a8025534;hp=6a4f369def30e72345fc5fe2a77e86ec7fedfeb0;hpb=a9f0472fe6fd4737b47d7955d198e76923e6aabc;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 6a4f369..9b58e58 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -1,29 +1,70 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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;
 
-public class EnsemblXref extends EnsemblRestClient
+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
+ * 
+ * @author gmcarstairs
+ * @see http://rest.ensembl.org/documentation/info/xref_id
+ */
+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, String dbSource, String version)
+  {
+    super(d);
+    dbName = dbSource;
+    xrefVersion = dbSource + ":" + version;
+
+  }
+
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (xref)";
+    return dbName;
   }
 
   @Override
@@ -35,8 +76,7 @@ public class EnsemblXref extends EnsemblRestClient
   @Override
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getUrl(ids.get(0));
   }
 
   @Override
@@ -45,114 +85,88 @@ public 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
-   * name. The "dbname" returned by Ensembl is canonicalised to Jalview's
-   * standard version, and a DBRefEntry constructed.
+   * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
+   * standard version, and a DBRefEntry constructed. Currently takes all
+   * identifiers apart from GO terms and synonyms.
    * 
    * @param identifier
-   * @param database
+   *          an Ensembl stable identifier
    * @return
    */
-  public List<DBRefEntry> getCrossReferences(String identifier,
-          String... database)
+  @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
     {
-      for (String db : database)
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
+      while (rvals.hasNext())
       {
-        URL url = getUrl(identifier, db);
-        if (url != null)
-        {
-          br = getHttpResponse(url, ids);
-        }
-        for (DBRefEntry xref : parseResponse(br))
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        String db = val.get("dbname").toString();
+        String id = val.get("primary_id").toString();
+        if (db != null && id != null
+                && !GO_GENE_ONTOLOGY.equals(db))
         {
-          if (!result.contains(xref))
-          {
-            result.add(xref);
-          }
+          db = DBRefUtils.getCanonicalName(db);
+          DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
+          result.add(dbref);
         }
-        br.close();
       }
-    } catch (IOException e)
+    } catch (ParseException | 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
+//   */
+//  @SuppressWarnings("unchecked")
+//protected List<DBRefEntry> parseResponse(BufferedReader br)
+//          throws IOException
+//  {
+//    return result;
+//  }
+//
+  private String xrefVersion = "ENSEMBL:0";
+
   /**
-   * Parses "primary_id" and "dbname" values from the JSON response and returns
-   * a list of DBRefEntry constructed.
+   * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
    * 
-   * @param br
    * @return
-   * @throws IOException
    */
-  protected List<DBRefEntry> parseResponse(BufferedReader br)
-          throws IOException
+  public String getXRefVersion()
   {
-    JSONParser jp = new JSONParser();
-    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
-    try
-    {
-      JSONArray responses = (JSONArray) jp.parse(br);
-      Iterator rvals = responses.iterator();
-      while (rvals.hasNext())
-      {
-        JSONObject val = (JSONObject) rvals.next();
-        String dbName = val.get("dbname").toString();
-        String id = val.get("primary_id").toString();
-        if (dbName != null && id != null)
-        {
-          dbName = DBRefUtils.getCanonicalName(dbName);
-          DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
-          result.add(dbref);
-        }
-      }
-    } catch (ParseException e)
-    {
-      // ignore
-    }
-    return result;
+    return xrefVersion;
   }
 
-  protected URL getUrl(String identifier, String db)
+  /**
+   * Returns the URL for the REST endpoint to fetch all cross-references for an
+   * identifier. Note this may return protein cross-references for nucleotide.
+   * Filter the returned list as required.
+   * 
+   * @param identifier
+   * @return
+   */
+  protected URL getUrl(String identifier)
   {
-    String url = ENSEMBL_REST + "/xrefs/id/" + identifier
-            + "?content-type=application/json&external_db=" + db;
+    String url = getDomain() + "/xrefs/id/" + identifier
+            + CONTENT_TYPE_JSON + "&all_levels=1";
     try
     {
       return new URL(url);