upgrade to latest paradise services model using JSon response.

[jalview.git] / src / jalview / ext / paradise / Annotate3D.java

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index b0adb45..114de42 100644 (file)
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -2,33 +2,186 @@ package jalview.ext.paradise;
 
 import jalview.ws.HttpClientUtils;
 
+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 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;
 
+/**
+ * simple methods for calling the various paradise RNA tools
+ * 
+ * @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
+ */
 public class Annotate3D
 {
+  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+  private static ContentHandler createContentHandler()
+  {
+    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
+      public boolean startObject() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean endObject() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean startObjectEntry(String key) throws ParseException,
+              IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
 
-  public static Reader getRNAMLForPDBFileAsString(String pdbfile)
+      @Override
+      public boolean endObjectEntry() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean startArray() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean endArray() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      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
   {
     List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
-    return HttpClientUtils.doHttpUrlPost(
-            "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
-            vals);
+    vals.add(new BasicNameValuePair("output", "rnaml"));
+    return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+  }
+  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>() 
+        {
+          @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()
+          {
+            throw new Error("Remove: Not implemented");
+            
+          }@Override
+          protected Object clone() throws CloneNotSupportedException
+          {
+            throw new CloneNotSupportedException("Clone: Not implemented");
+          }@Override
+          public boolean equals(Object obj)
+          {
+            return super.equals(obj);
+          }@Override
+          protected void finalize() throws Throwable
+          {
+            while (rvals.hasNext())
+            {
+              rvals.next();
+            }
+            super.finalize();
+          }
+        };
+    } catch (Exception foo)
+    {
+      throw new Exception("Couldn't parse response from Annotate3d server.",foo);
+    }
+    
+    
   }
 
-  public static 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));
-    return HttpClientUtils.doHttpUrlPost(
-            "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
-            vals);
+    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()));
   }
 
 }