/*
 *                    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.io.mmcif;

import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.biojava.nbio.core.util.InputStreamProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.net.URL;
import java.util.concurrent.atomic.AtomicBoolean;

/**
 * A ChemComp provider that downloads and caches the components.cif file from the wwPDB site. It then loads
 * all chemical components at startup and keeps them in memory. This provider is not used as a default
 * since it is slower at startup and requires more memory than the {@link DownloadChemCompProvider} that is used by default.
 *
 * @author Andreas Prlic
 *
 */
public class AllChemCompProvider implements ChemCompProvider, Runnable{

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

        public static final String COMPONENTS_FILE_LOCATION = "pub/pdb/data/monomers/components.cif.gz";


        private static String path;

        private static String serverName;


        // there will be only one copy of the dictionary across all instances
        // to reduce memory impact
        static ChemicalComponentDictionary dict;

        // flags to make sure there is only one thread running that is loading the dictionary
        static AtomicBoolean loading       = new AtomicBoolean(false);
        static AtomicBoolean isInitialized = new AtomicBoolean(false);

        public AllChemCompProvider(){

                if ( loading.get()) {
                        logger.warn("other thread is already loading all chemcomps, no need to init twice");
                        return;
                }
                if ( isInitialized.get())
                        return;

                loading.set(true);

                Thread t = new Thread(this);
                t.start();

        }


        /** make sure all paths are initialized correctly
         *
         */
        private static void initPath(){

                if (path==null) {
                        UserConfiguration config = new UserConfiguration();
                        path = config.getCacheFilePath();
                }
        }

        private static void initServerName() {

                if (serverName==null) {
                        serverName = LocalPDBDirectory.getServerName();
                }
        }

        private void ensureFileExists() {


                String fileName = getLocalFileName();
                File f = new File(fileName);

                if ( ! f.exists()) {
                        try {
                        downloadFile();
                        } catch (IOException e) {
                                logger.error("Caught IOException",e);
                        }
                }



        }

        /** Downloads the components.cif.gz file from the wwPDB site.
         *
         */
        public static void downloadFile() throws IOException {

                initPath();

                initServerName();

                String localName = getLocalFileName();

                String u = serverName + "/" + COMPONENTS_FILE_LOCATION;

                downloadFileFromRemote(new URL(u), new File(localName));


        }


        private static  void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{
                logger.info("Downloading " + remoteURL + " to: " + localFile);
                FileOutputStream out = new FileOutputStream(localFile);

                InputStream in = remoteURL.openStream();
                byte[] buf = new byte[4 * 1024]; // 4K buffer
                int bytesRead;
                while ((bytesRead = in.read(buf)) != -1) {
                        out.write(buf, 0, bytesRead);
                }
                in.close();
                out.close();


        }


        private static String getLocalFileName(){

                File dir = new File(path, DownloadChemCompProvider.CHEM_COMP_CACHE_DIRECTORY);

                if (! dir.exists()){
                        logger.info("Creating directory {}", dir.toString());
                        dir.mkdir();
                }

                String fileName = new File(dir, "components.cif.gz").toString();

                return fileName;
        }

        /** Load all {@link ChemComp} definitions into memory.
         *
         */
        private void loadAllChemComps() throws IOException {
                String fileName = getLocalFileName();
                logger.debug("Loading " + fileName);
                InputStreamProvider isp = new InputStreamProvider();


                InputStream inStream = isp.getInputStream(fileName);

                MMcifParser parser = new SimpleMMcifParser();

                ChemCompConsumer consumer = new ChemCompConsumer();

                // The Consumer builds up the BioJava - structure object.
                // you could also hook in your own and build up you own data model.
                parser.addMMcifConsumer(consumer);

                parser.parse(new BufferedReader(new InputStreamReader(inStream)));

                dict = consumer.getDictionary();

                inStream.close();

        }


        /** {@inheritDoc}
         *
         */
        @Override
        public ChemComp getChemComp(String recordName) {

                while ( loading.get()) {

                        // another thread is still initializing the definitions
                        try {
                                // wait half a second

                                Thread.sleep(500);
                        } catch (InterruptedException e) {
                                logger.error("Interrepted thread while waiting: "+e.getMessage());
                                //e.printStackTrace();
                        }
                }



                return dict.getChemComp(recordName);
        }


        /** Do the actual loading of the dictionary in a thread.
         *
         */
        @Override
        public void run() {
                long timeS = System.currentTimeMillis();

                initPath();

                ensureFileExists();

                try {
                        loadAllChemComps();

                        long timeE = System.currentTimeMillis();
                        logger.debug("Time to init chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");


                } catch (IOException e) {
                        logger.error("Could not load chemical components definition file {}. Error: {}", getLocalFileName(), e.getMessage());

                } finally {
                        loading.set(false);
                        isInitialized.set(true);
                }
        }

}