X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=3b7044bb18fa5a1c8d14af9fadc60d04f119f925;hb=b3d9eaf8829a3aeb2bbc522315207a7940b0844e;hp=114de42ee4afa4b35a8fe864a956e91ac352fdcb;hpb=9d75efeeb9a6e51bd328f56e376dca4e007b635c;p=jalview.git

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 114de42..3b7044b 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -1,22 +1,42 @@
+/*
+ * 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.paradise;
 
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
 import jalview.ws.HttpClientUtils;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.io.StringReader;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 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.JSONStreamAware;
 import org.json.simple.parser.ContentHandler;
 import org.json.simple.parser.ParseException;
 
@@ -25,29 +45,38 @@ 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()
   {
-    ContentHandler ch = new ContentHandler() {
+    ContentHandler ch = new ContentHandler()
+    {
 
       @Override
       public void startJSON() throws ParseException, IOException
       {
         // TODO Auto-generated method stub
-        
+
       }
 
       @Override
       public void endJSON() throws ParseException, IOException
       {
         // TODO Auto-generated method stub
-        
+
       }
 
       @Override
@@ -65,8 +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;
@@ -94,16 +123,17 @@ 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;
       }
-      
+
     };
     return ch;
   }
+
   public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
           throws Exception
   {
@@ -111,77 +141,118 @@ public class Annotate3D
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
     vals.add(new BasicNameValuePair("output", "rnaml"));
-    return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
+    // vals));
+    ArrayList<Reader> readers = new ArrayList<Reader>();
+    final BufferedReader postResponse = HttpClientUtils
+            .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+    readers.add(postResponse);
+    return readers.iterator();
+
   }
-  public static Iterator<Reader> processJsonResponseFor(Reader respons) throws Exception
+
+  /**
+   * @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();
-    try {
-      final JSONArray responses = (JSONArray) jp.parse(respons);
-      final Iterator rvals = responses.iterator();
-      return new Iterator<Reader>() 
+	  // BH 2019 never called?
+    try
+    {
+      @SuppressWarnings("unchecked")
+	final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+      return new Iterator<Reader>()
+      {
+        @Override
+        public boolean hasNext()
         {
-          @Override
-          public boolean hasNext()
-          {
-            return rvals.hasNext();
-          }
-          @Override
-          public Reader next()
-          {
-            JSONObject val=(JSONObject) rvals.next();
-            
-            Object sval = null;
-            try {
-              sval = val.get("2D");
-            } catch (Exception x) {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 :"+val.toString());
-              
-              sval = "";
-            }
-            return new StringReader((sval instanceof JSONObject) ? ((JSONObject)sval).toString():sval.toString());
-            
-          }@Override
-          public void remove()
+          return rvals.hasNext();
+        }
+
+        @SuppressWarnings("unchecked")
+		@Override
+        public Reader next()
+        {
+          Map<String, Object> val = (Map<String, Object>) rvals.next();
+
+          Object sval = null;
+          try
           {
-            throw new Error("Remove: Not implemented");
-            
-          }@Override
-          protected Object clone() throws CloneNotSupportedException
+            sval = val.get("2D");
+          } catch (Exception x)
           {
-            throw new CloneNotSupportedException("Clone: Not implemented");
-          }@Override
-          public boolean equals(Object obj)
+            x.printStackTrace();
+          }
+          ;
+          if (sval == null)
           {
-            return super.equals(obj);
-          }@Override
-          protected void finalize() throws Throwable
+            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.toString());
+
+        }
+
+        @Override
+        public void 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"));
+        }
+
+        @Override
+        public boolean equals(Object obj)
+        {
+          return super.equals(obj);
+        }
+
+        @Override
+        protected void finalize() throws Throwable
+        {
+          while (rvals.hasNext())
           {
-            while (rvals.hasNext())
-            {
-              rvals.next();
-            }
-            super.finalize();
+            rvals.next();
           }
-        };
+          super.finalize();
+        }
+      };
     } catch (Exception foo)
     {
-      throw new Exception("Couldn't parse response from Annotate3d server.",foo);
+      throw new Exception(MessageManager.getString(
+              "exception.couldnt_parse_responde_from_annotated3d_server"),
+              foo);
     }
-    
-    
+
   }
 
-  public static Iterator<Reader> getRNAMLForPDBId(String pdbid) throws Exception
+  public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
+          throws Exception
   {
     List<NameValuePair> vals = new ArrayList<NameValuePair>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("pdbid", pdbid));
-    vals.add(new BasicNameValuePair("format", "rnaml"));
-    java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&output=rnaml&pdbid="+pdbid);
-    return processJsonResponseFor(new InputStreamReader(geturl.openStream()));
+    vals.add(new BasicNameValuePair("output", "rnaml"));
+    java.net.URL geturl = new URL(twoDtoolsURL + "?tool=rnaview&pdbid="
+            + pdbid + "&output=rnaml");
+    // return processJsonResponseFor(new
+    // InputStreamReader(geturl.openStream()));
+    ArrayList<Reader> readers = new ArrayList<Reader>();
+    readers.add(new InputStreamReader(geturl.openStream()));
+    return readers.iterator();
   }
 
 }