+/*
+ * 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.JSONUtils;
+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 java.util.Map;
import org.apache.http.NameValuePair;
import org.apache.http.message.BasicNameValuePair;
+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 Reader getRNAMLForPDBId(String pdbid) throws Exception
+ /**
+ * @param respons
+ * @return
+ * @throws Exception
+ */
+ public static Iterator<Reader> processJsonResponseFor(Reader respons)
+ throws Exception
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ try
+ {
+ @SuppressWarnings("unchecked")
+ List<Object> responses = (List<Object>) JSONUtils.parse(respons);
+ return new RvalsIterator(responses);
+ } catch (Exception foo)
+ {
+ throw new Exception(MessageManager.getString(
+ "exception.couldnt_parse_responde_from_annotated3d_server"),
+ foo);
+ }
+ }
+
+ public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
+ throws Exception
+ {
+ 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<Reader>, AutoCloseable
+{
+ private Iterator<Object> rvals;
+
+ protected RvalsIterator(List<Object> responses)
+ {
+ this.rvals = responses.iterator();
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @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 UnsupportedOperationException();
}
+ @Override
+ protected Object clone() throws CloneNotSupportedException
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public void close()
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff