X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=b8ba8475ff1d9eff05d5ba8958e622c95cd18dc8;hb=c45250cbe36b278beded735cbfad39cd073f48af;hp=b0adb45eca276af14549c58fc7b344b7ec40565a;hpb=ccd574c354cee52f67ab73d28381f44ffe3e5a7c;p=jalview.git

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index b0adb45..b8ba847 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -1,34 +1,262 @@
+/*
+ * 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.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.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.parser.ContentHandler;
+import org.json.simple.parser.ParseException;
 
+/**
+ * simple methods for calling the various paradise RNA tools
+ * 
+ * @author jimp
+ * 
+ * @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
 {
+  // 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";
 
-  public static Reader getRNAMLForPDBFileAsString(String pdbfile)
+  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;
+      }
+
+      @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>();
+    List<NameValuePair> vals = new ArrayList<>();
+    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));
+    ArrayList<Reader> readers = new ArrayList<>();
+    final BufferedReader postResponse = HttpClientUtils
+            .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+    readers.add(postResponse);
+    return readers.iterator();
+
+  }
+
+  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 RvalsIterator rvals = new RvalsIterator(responses);
+      return rvals;
+    } catch (Exception foo)
+    {
+      throw new Exception(MessageManager.getString(
+              "exception.couldnt_parse_responde_from_annotated3d_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>();
+    List<NameValuePair> vals = new ArrayList<>();
+    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("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<>();
+    readers.add(new InputStreamReader(geturl.openStream()));
+    return readers.iterator();
+  }
+
+}
+
+class RvalsIterator implements Iterator, AutoCloseable
+{
+  private Iterator rvals;
+
+  protected RvalsIterator(JSONArray responses)
+  {
+    this.rvals = responses.iterator();
+  }
+
+  @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(
+            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
+  public void close()
+  {
+    while (rvals.hasNext())
+    {
+      rvals.next();
+    }
+  }
 }