X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=caff3bbab03e648d36d0eb35e137afc4d89303e1;hb=4dcde5117f9bcd025e52fe137fff7bb11ee35f46;hp=55c3c1dd4cf9342e75f38dad3af4d2158cef5f80;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 55c3c1d..caff3bb 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.paradise;
 
+import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
 import jalview.ws.HttpClientUtils;
 
@@ -32,11 +33,10 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import org.apache.http.NameValuePair;
 import org.apache.http.message.BasicNameValuePair;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
 import org.json.simple.parser.ContentHandler;
 import org.json.simple.parser.ParseException;
 
@@ -45,13 +45,20 @@ import org.json.simple.parser.ParseException;
  * 
  * @author jimp
  * 
- *         History: v1.0 revised from original due to refactoring of
- *         paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
- *         http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ * @version v1.0 revised from original due to refactoring of
+ *          paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ *          http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/>
+ *          See also testing URL from fjossinet:<br/>
+ *          http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/>
+ *          If in doubt, check against the REST client at:
+ *          https://github.com/fjossinet/RNA-Science
+ *          -Toolbox/blob/master/pyrna/restclient.py
  */
 public class Annotate3D
 {
-  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+  // also test with
+  // "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d";
+  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview";
 
   private static ContentHandler createContentHandler()
   {
@@ -87,8 +94,8 @@ public class Annotate3D
       }
 
       @Override
-      public boolean startObjectEntry(String key) throws ParseException,
-              IOException
+      public boolean startObjectEntry(String key)
+              throws ParseException, IOException
       {
         // TODO Auto-generated method stub
         return false;
@@ -116,8 +123,8 @@ public class Annotate3D
       }
 
       @Override
-      public boolean primitive(Object value) throws ParseException,
-              IOException
+      public boolean primitive(Object value)
+              throws ParseException, IOException
       {
         // TODO Auto-generated method stub
         return false;
@@ -130,28 +137,34 @@ public class Annotate3D
   public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
           throws Exception
   {
-    List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    List<NameValuePair> vals = new ArrayList<>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
     vals.add(new BasicNameValuePair("output", "rnaml"));
     // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
     // vals));
-    ArrayList<Reader> readers = new ArrayList<Reader>();
-    final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+    ArrayList<Reader> readers = new ArrayList<>();
+    final BufferedReader postResponse = HttpClientUtils
+            .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
     readers.add(postResponse);
     return readers.iterator();
 
   }
 
+  /**
+   * @param respons
+   * @return
+   * @throws Exception
+   */
   public static Iterator<Reader> processJsonResponseFor(Reader respons)
           throws Exception
   {
-    org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+	  // BH 2019 never called?
     try
     {
-      final JSONArray responses = (JSONArray) jp.parse(respons);
-      final Iterator rvals = responses.iterator();
-      return new Iterator<Reader>()
+      @SuppressWarnings("unchecked")
+	final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+      return new Iterator<>()
       {
         @Override
         public boolean hasNext()
@@ -159,10 +172,11 @@ public class Annotate3D
           return rvals.hasNext();
         }
 
-        @Override
+        @SuppressWarnings("unchecked")
+		@Override
         public Reader next()
         {
-          JSONObject val = (JSONObject) rvals.next();
+          Map<String, Object> val = (Map<String, Object>) rvals.next();
 
           Object sval = null;
           try
@@ -172,32 +186,31 @@ public class Annotate3D
           {
             x.printStackTrace();
           }
-          ;
           if (sval == null)
           {
-            System.err
-                    .println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+            System.err.println(
+                    "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
                             + val.toString());
 
             sval = "";
           }
-          return new StringReader(
-                  (sval instanceof JSONObject) ? ((JSONObject) sval)
-                          .toString() : sval.toString());
+          return new StringReader(sval.toString());
 
         }
 
         @Override
         public void remove()
         {
-          throw new Error(MessageManager.getString("error.not_implemented_remove"));
+          throw new Error(
+                  MessageManager.getString("error.not_implemented_remove"));
 
         }
 
         @Override
         protected Object clone() throws CloneNotSupportedException
         {
-          throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
+          throw new CloneNotSupportedException(
+                  MessageManager.getString("error.not_implemented_clone"));
         }
 
         @Override
@@ -218,15 +231,16 @@ public class Annotate3D
       };
     } catch (Exception foo)
     {
-      throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
+      throw new Exception(MessageManager.getString(
+              "exception.couldnt_parse_responde_from_annotated3d_server"),
+              foo);
     }
-
   }
 
   public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
           throws Exception
   {
-    List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    List<NameValuePair> vals = new ArrayList<>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("pdbid", pdbid));
     vals.add(new BasicNameValuePair("output", "rnaml"));
@@ -234,7 +248,7 @@ public class Annotate3D
             + pdbid + "&output=rnaml");
     // return processJsonResponseFor(new
     // InputStreamReader(geturl.openStream()));
-    ArrayList<Reader> readers = new ArrayList<Reader>();
+    ArrayList<Reader> readers = new ArrayList<>();
     readers.add(new InputStreamReader(geturl.openStream()));
     return readers.iterator();
   }