X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblInfo.java;h=71730def48935a4fe249068f7cdccb62c14da5b5;hb=61484f9c89a866cc5c9a22499653a1c17b938ffb;hp=de55a536430b7a62e8b809b1c37e24999a0c0fca;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index de55a53..71730de 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -3,7 +3,6 @@ package jalview.ext.ensembl;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -13,25 +12,25 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.json.simple.JSONArray;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 public class EnsemblInfo extends EnsemblRestClient
 {
 
-  /*
+  /**
    * cached results of REST /info/divisions service, currently
+   * 
    * <pre>
    * { 
-   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBL", "http://rest.ensembl.org" }
+   *  "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBL", "http://rest.ensembl.org"
    *  }
    * </pre>
+   * 
    * The values for EnsemblGenomes are retrieved by a REST call, that for
    * Ensembl is added programmatically for convenience of lookup
    */
@@ -61,18 +60,6 @@ public class EnsemblInfo extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
   /**
    * Answers the domain (http://rest.ensembl.org or
    * http://rest.ensemblgenomes.org) for the given division, or null if not
@@ -101,54 +88,21 @@ public class EnsemblInfo extends EnsemblRestClient
     /*
      * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
      */
-    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST);
-
-    BufferedReader br = null;
+    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
     try
     {
-      URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST);
-      if (url != null)
+      @SuppressWarnings("unchecked")
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(
+              getDivisionsUrl(ensemblGenomesDomain), null, -1,
+              MODE_ITERATOR, null);
+      if (rvals == null)
       {
-        br = getHttpResponse(url, null);
+        return;
       }
-      parseResponse(br, ENSEMBL_GENOMES_REST);
-    } catch (IOException e)
-    {
-      // ignore
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
-  }
-
-  /**
-   * Parses the JSON response to /info/divisions, and add each to the lookup map
-   * 
-   * @param br
-   * @param domain
-   */
-  void parseResponse(BufferedReader br, String domain)
-  {
-    JSONParser jp = new JSONParser();
-
-    try
-    {
-      JSONArray parsed = (JSONArray) jp.parse(br);
-
-      Iterator rvals = parsed.iterator();
       while (rvals.hasNext())
       {
         String division = rvals.next().toString();
-        divisions.put(division.toUpperCase(), domain);
+        divisions.put(division.toUpperCase(), ensemblGenomesDomain);
       }
     } catch (IOException | ParseException | NumberFormatException e)
     {
@@ -174,7 +128,8 @@ public class EnsemblInfo extends EnsemblRestClient
    * 
    * @return
    */
-  public Set<String> getDivisions() {
+  public Set<String> getDivisions()
+  {
     if (divisions == null)
     {
       fetchDivisions();