/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.quaternary.io;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.client.JFatCatClient;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;

public class RemoteBioUnitDataProvider implements BioUnitDataProvider {


        private static final Logger logger = LoggerFactory.getLogger(RemoteBioUnitDataProvider.class);

        public static final String DEFAULT_SERVERNAME = "http://pepper.rcsb.org:8080/pdb/rest/biolassembly/";

        public static final String NR_BIOL_APPEND = "nrBiolAssemblies?structureId=%s";

        public static final String BIO_ASSEMBLY = "bioAssembly?structureId=%s&nr=%s";

        private static final int DEFAULT_TIMEOUT = 5000;

        private String serverName;

        private int timeout;

        public RemoteBioUnitDataProvider(){
                serverName = DEFAULT_SERVERNAME;
                timeout = DEFAULT_TIMEOUT;
        }

        @Override
        public List<BiologicalAssemblyTransformation> getBioUnitTransformationList(
                        String pdbId, int biolAssemblyNr) {

                String serverURL = serverName + BIO_ASSEMBLY;

                String u = String.format(serverURL,pdbId, biolAssemblyNr) ;
                List<BiologicalAssemblyTransformation> transformations = new ArrayList<BiologicalAssemblyTransformation>();

                try {
                        URL url = new URL(u);
                        System.out.println("requesting biol assemblies from server..."  + url);
                        // have a short timeout for this...
                        // 5 sec
                        InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);

                        String xml = null;


                        xml = JFatCatClient.convertStreamToString(stream);

                        if ( stream != null) {

                                System.out.println(xml);
                                transformations = BiologicalAssemblyTransformation.fromMultiXML(xml);
                        }
                } catch (IOException e){
                        logger.error("Exception caught while getting biological assemblies",e);
                } catch (SAXException e) {
                        logger.error("Exception caught while getting biological assemblies",e);
                } catch (ParserConfigurationException e) {
                        logger.error("Exception caught while getting biological assemblies",e);
                }

                return transformations;

        }

        @Override
        public int getNrBiolAssemblies(String pdbId) {
                String serverURL = serverName + NR_BIOL_APPEND;
                int nrBiolAssemblies = -1;
                try {
                        String u = String.format(serverURL,pdbId) ;


                        URL url = new URL(u);
                        System.out.println("requesting nr biol assemblies from server..."  + url);
                        // have a short timeout for this...
                        // 5 sec
                        InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);

                        String xml = null;

                        if ( stream != null) {

                                xml = JFatCatClient.convertStreamToString(stream);
                                System.out.println("got XML from server: " + xml);

                                nrBiolAssemblies = extractNrBiolAssemblies(xml);
                        }
                } catch (IOException e){
                        logger.error("Exception caught while getting number of biological assemblies",e);
                }
                return nrBiolAssemblies;
        }

        @Override
        public boolean hasBiolAssembly(String pdbId) {
                int nrBiolAssemblies =  getNrBiolAssemblies(pdbId);
                if ( nrBiolAssemblies > 0)
                        return true;
                return false;
        }

        private static int extractNrBiolAssemblies(String xml) {
                int nrBiolAssemblies = -1;

                try {
                        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
                        DocumentBuilder db = factory.newDocumentBuilder();
                        InputSource inStream = new InputSource();
                        inStream.setCharacterStream(new StringReader(xml));
                        Document doc = db.parse(inStream);

                        // normalize text representation
                        doc.getDocumentElement().normalize();


                        //Element rootElement = doc.getDocumentElement();

                        NodeList listOfPairs = doc.getElementsByTagName("nrBiolAssemblies");
                        //int numArrays = listOfArrays.getLength();

                        // go over the blocks
                        for(int i=0; i<listOfPairs.getLength() ; i++)
                        {
                                Node pair       = listOfPairs.item(i);
                                //NodeList valList = pair.getChildNodes();
                                //int numChildren  = valList.getLength();

                                NamedNodeMap map = pair.getAttributes();

                                String count =  map.getNamedItem("count").getTextContent();
                                nrBiolAssemblies = Integer.parseInt(count);
                        }

                } catch (IOException e){
                        logger.error("Exception caught while getting number of biological assemblies",e);
                } catch (SAXException e) {
                        logger.error("Exception caught while getting number of biological assemblies",e);
                } catch (ParserConfigurationException e) {
                        logger.error("Exception caught while getting number of biological assemblies",e);
                }
                return nrBiolAssemblies;
        }

        @Override
        public Structure getAsymUnit(String pdbId) {
                logger.error("RemoteBioUnitDataProvider getAsymUnit Not implemented yet!");
                return null;


        }

        @Override
        public void setAsymUnit(Structure s){
                // nothing to be done here so far..
        }

        @Override
        public void setAtomCache(AtomCache cache) {
                // TODO Auto-generated method stub

        }

        @Override
        public AtomCache getAtomCache() {
                // TODO Auto-generated method stub
                return null;
        }

}