X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=3b7044bb18fa5a1c8d14af9fadc60d04f119f925;hb=8e7cf85a7f61f425e808cac53ead7bc27e402242;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..3b7044b 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
+ * See also testing URL from fjossinet:
+ * http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d
+ * 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;
@@ -137,20 +144,26 @@ public class Annotate3D
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList readers = new ArrayList();
- final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+ final BufferedReader postResponse = HttpClientUtils
+ .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
return readers.iterator();
}
+ /**
+ * @param respons
+ * @return
+ * @throws Exception
+ */
public static Iterator 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();
+ @SuppressWarnings("unchecked")
+ final Iterator