*/
package jalview.ext.paradise;
+import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
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;
}
+ /**
+ * @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 RvalsIterator rvals = new RvalsIterator(responses);
- return rvals;
+ @SuppressWarnings("unchecked")
+ final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+ return new Iterator<>()
+ {
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Reader next()
+ {
+ Map<String, Object> val = (Map<String, Object>) 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.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())
+ {
+ rvals.next();
+ }
+ super.finalize();
+ }
+ };
} catch (Exception foo)
{
throw new Exception(MessageManager.getString(
"exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
-
}
public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
}
}
-
-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();
- }
- }
-}