X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=de1d90cbdae01ac5aa4a4a7b8fbba73a4266d145;hb=290d1c0638e869b08d5f2729472197873fa06af0;hp=114de42ee4afa4b35a8fe864a956e91ac352fdcb;hpb=9d75efeeb9a6e51bd328f56e376dca4e007b635c;p=jalview.git
diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 114de42..de1d90c 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -1,53 +1,82 @@
+/*
+ * 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 .
+ * 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
+ * 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()
{
- 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
@@ -65,8 +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;
@@ -94,94 +123,153 @@ 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;
}
-
+
};
return ch;
}
+
public static Iterator getRNAMLForPDBFileAsString(String pdbfile)
throws Exception
{
- List vals = new ArrayList();
+ List 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));
+ // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
+ // vals));
+ ArrayList readers = new ArrayList<>();
+ final BufferedReader postResponse = HttpClientUtils
+ .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+ readers.add(postResponse);
+ return readers.iterator();
+
}
- public static Iterator processJsonResponseFor(Reader respons) throws Exception
+
+ public static Iterator 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()
- {
- @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 getRNAMLForPDBId(String pdbid) throws Exception
+ public static Iterator getRNAMLForPDBId(String pdbid)
+ throws Exception
{
- List vals = new ArrayList();
+ List vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("pdbid", pdbid));
- vals.add(new BasicNameValuePair("format", "rnaml"));
- java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&output=rnaml&pdbid="+pdbid);
- return processJsonResponseFor(new InputStreamReader(geturl.openStream()));
+ 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 readers = new ArrayList<>();
+ readers.add(new InputStreamReader(geturl.openStream()));
+ return readers.iterator();
+ }
+
+}
+
+class RvalsIterator implements Iterator, AutoCloseable
+{
+ private Iterator