+/*
+ * 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.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;
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
+import jalview.ws.HttpClientUtils;
+
/**
* 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
+ * @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
}
@Override
- public boolean startObjectEntry(String key) throws ParseException,
- IOException
+ public boolean startObjectEntry(String key)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
}
@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
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("data", pdbfile));
vals.add(new BasicNameValuePair("output", "rnaml"));
- // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
- ArrayList<Reader> readers = new ArrayList<Reader>();
- readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ // 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
+
+ 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();
- }
- };
+ try
+ {
+ final RvalsIterator rvals = new RvalsIterator(respons);
+ return rvals;
} 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>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("pdbid", pdbid));
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>();
+ 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<Object> rvals;
+
+ @SuppressWarnings("unchecked")
+ protected RvalsIterator(Reader respons) throws IOException, ParseException
+ {
+ /*
+ * as in 2.11.1 (pre-JalviewJS)
+ */
+ // final JSONArray responses = (JSONArray) jp.parse(respons);
+ // this.rvals = responses.iterator();
+
+ /*
+ * as in JalviewJS (with comment that this code is never called)
+ */
+ this.rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @Override
+ public Reader next()
+ {
+ // JSONObject val = (JSONObject) rvals.next(); // 2.11.1
+ @SuppressWarnings("unchecked")
+ 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 = "";
+ }
+ // 2.11.1:
+ // return new StringReader(
+ // (sval instanceof JSONObject) ? ((JSONObject) sval).toString()
+ // : sval.toString());
+ 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
+ public void close()
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff