Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalvi...

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

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index fa24f1e..85f421d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,9 +1,25 @@
+/*
+ * 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.DBRefSource;
-
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -13,10 +29,11 @@ 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;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
 public class EnsemblInfo extends EnsemblRestClient
 {
 
@@ -90,53 +107,16 @@ public class EnsemblInfo extends EnsemblRestClient
      * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
      */
     divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
-
-    BufferedReader br = null;
     try
     {
-      URL url = getDivisionsUrl(ensemblGenomesDomain);
-      if (url != null)
-      {
-        br = getHttpResponse(url, null);
-      }
-      parseResponse(br, ensemblGenomesDomain);
-    } 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();
+      @SuppressWarnings("unchecked")
+         Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
+      if (rvals == null)
+         return;
       while (rvals.hasNext())
       {
         String division = rvals.next().toString();
-        divisions.put(division.toUpperCase(), domain);
+        divisions.put(division.toUpperCase(), ensemblGenomesDomain);
       }
     } catch (IOException | ParseException | NumberFormatException e)
     {