/*
 *                    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 java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.URL;
import java.net.URLConnection;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.zip.GZIPOutputStream;

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



/** 
 * This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
 * It is the default way to access these definitions.
 * If this provider is called he first time, it will download and install all chemical
 * component definitions in a local directory.
 * Once the definition files have been installed, it has quick startup time and low memory requirements.
 *
 * An alternative provider, that keeps all definitions in memory is the {@link AllChemCompProvider}. Another provider, that
 * does not require any network access, but only can support a limited set of chemical component definitions, is the {@link ReducedChemCompProvider}.
 *
 *
 * @author Andreas Prlic
 *
 */
public class DownloadChemCompProvider implements ChemCompProvider {

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

        public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";

        public static final String DEFAULT_SERVER_URL = "http://files.rcsb.org/ligands/download/";
        
        public static String serverBaseUrl = DEFAULT_SERVER_URL;
        
        /**
         * Use default RCSB server layout (true) or internal RCSB server layout (false)
         */
        public static boolean useDefaultUrlLayout = true;


        private static File path;
        //private static final String FILE_SEPARATOR = System.getProperty("file.separator");
        private static final String NEWLINE = System.getProperty("line.separator");


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

        static final List<String> protectedIDs = new ArrayList<String> ();
        static {
                protectedIDs.add("CON");
                protectedIDs.add("PRN");
                protectedIDs.add("AUX");
                protectedIDs.add("NUL");
        }

        /** by default we will download only some of the files. User has to request that all files should be downloaded...
         *
         */
        boolean downloadAll = false;

        public DownloadChemCompProvider(){
                logger.debug("Initialising DownloadChemCompProvider");

                // note that path is static, so this is just to make sure that all non-static methods will have path initialised
                initPath();
        }

        public DownloadChemCompProvider(String cacheFilePath){
                logger.debug("Initialising DownloadChemCompProvider");

                // note that path is static, so this is just to make sure that all non-static methods will have path initialised
                path = new File(cacheFilePath);
        }

        private static void initPath(){

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

        /**
         * Checks if the chemical components already have been installed into the PDB directory.
         * If not, will download the chemical components definitions file and split it up into small
         * subfiles.
         */
        public void checkDoFirstInstall(){

                if ( ! downloadAll ) {
                        return;
                }


                // this makes sure there is a file separator between every component,
                // if path has a trailing file separator or not, it will work for both cases
                File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
                File f = new File(dir, "components.cif.gz");

                if ( ! f.exists()) {

                        downloadAllDefinitions();

                } else {
                        // file exists.. did it get extracted?

                        FilenameFilter filter =new FilenameFilter() {

                                @Override
                                public boolean accept(File dir, String file) {
                                        return file.endsWith(".cif.gz");
                                }
                        };
                        String[] files = dir.list(filter);
                        if ( files.length < 500) {
                                // not all did get unpacked
                                try {
                                        split();
                                } catch (IOException e) {
                                        logger.error("Could not split file {} into individual chemical component files. Error: {}",
                                                        f.toString(), e.getMessage());
                                }
                        }
                }
        }

        private void split() throws IOException {

                logger.info("Installing individual chem comp files ...");

                File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
                File f = new File(dir, "components.cif.gz");


                int counter = 0;
                InputStreamProvider prov = new InputStreamProvider();

                try( BufferedReader buf = new BufferedReader (new InputStreamReader (prov.getInputStream(f)));
                                ) {
                        String line = null;
                        line = buf.readLine ();
                        StringWriter writer = new StringWriter();

                        String currentID = null;
                        while (line != null){

                                if ( line.startsWith("data_")) {
                                        // a new record found!

                                        if ( currentID != null) {
                                                writeID(writer.toString(), currentID);
                                                counter++;
                                        }

                                        currentID = line.substring(5);
                                        writer = new StringWriter();
                                }

                                writer.append(line);
                                writer.append(NEWLINE);

                                line = buf.readLine ();
                        }

                        // write the last record...
                        writeID(writer.toString(),currentID);
                        counter++;

                }

                logger.info("Created " + counter + " chemical component files.");
        }

        /**
         * Output chemical contents to a file
         * @param contents File contents
         * @param currentID Chemical ID, used to determine the filename
         * @throws IOException
         */
        private void writeID(String contents, String currentID) throws IOException{

                String localName = DownloadChemCompProvider.getLocalFileName(currentID);

                try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {

                        pw.print(contents);
                        pw.flush();
                }
        }

        /**
         * Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.
         *
         * @param recordName the ID of the {@link ChemComp}
         * @return a new {@link ChemComp} definition.
         */
        @Override
        public  ChemComp getChemComp(String recordName) {

                // make sure we work with upper case records
                recordName = recordName.toUpperCase().trim();

                boolean haveFile = true;
                if ( recordName.equals("?")){
                        return null;
                }

                if ( ! fileExists(recordName)) {
                        // check if we should install all components
                        checkDoFirstInstall();
                }
                if ( ! fileExists(recordName)) {
                        // we previously have installed already the definitions,
                        // just do an incrememntal update
                        haveFile = downloadChemCompRecord(recordName);
                }

                // Added check that download was successful and chemical component is available.
                if (haveFile) {
                        String filename = getLocalFileName(recordName);
                        InputStream inStream = null;
                        try {

                                InputStreamProvider isp = new InputStreamProvider();

                                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)));

                                ChemicalComponentDictionary dict = consumer.getDictionary();

                                ChemComp chemComp = dict.getChemComp(recordName);

                                return chemComp;

                        } catch (IOException e) {

                                logger.error("Could not parse chemical component file {}. Error: {}. "
                                                + "There will be no chemical component info available for {}", filename, e.getMessage(), recordName);

                        }
                        finally{
                                // Now close it
                                if(inStream!=null){
                                        try {
                                                inStream.close();
                                        } catch (IOException e) {
                                                // This would be weird...
                                                logger.error("Could not close chemical component file {}. A resource leak could occur!!", filename);
                                        }
                                }

                        }
                }

                // see https://github.com/biojava/biojava/issues/315
                // probably a network error happened. Try to use the ReducedChemCOmpProvider
                ReducedChemCompProvider reduced = new ReducedChemCompProvider();

                return reduced.getChemComp(recordName);

        }

        /** 
         * Returns the file name that contains the definition for this {@link ChemComp}
         *
         * @param recordName the ID of the {@link ChemComp}
         * @return full path to the file
         */
        public static String getLocalFileName(String recordName){

                if ( protectedIDs.contains(recordName)){
                        recordName = "_" + recordName;
                }

                initPath();

                File f = new File(path, CHEM_COMP_CACHE_DIRECTORY);
                if (! f.exists()){
                        logger.info("Creating directory " + f);

                        boolean success = f.mkdir();
                        // we've checked in initPath that path is writable, so there's no need to check if it succeeds
                        // in the unlikely case that in the meantime it isn't writable at least we log an error
                        if (!success) logger.error("Directory {} could not be created",f);

                }

                File theFile = new File(f,recordName + ".cif.gz");

                return theFile.toString();
        }

        private static  boolean fileExists(String recordName){

                String fileName = getLocalFileName(recordName);

                File f = new File(fileName);

                return f.exists();

        }

        /**
         * @param recordName : three-letter name
         * @return true if successful download
         */
        private static boolean downloadChemCompRecord(String recordName) {

                String localName = getLocalFileName(recordName);
                File newFile;
                try{
                        newFile = File.createTempFile("chemcomp"+recordName, "cif");
                        logger.debug("Will write chem comp file to temp file {}", newFile.toString());
                }
                catch(IOException e){
                        logger.error("Could not write to temp directory {} to create the chemical component download temp file", System.getProperty("java.io.tmpdir"));
                        return false;
                }
                String u;
                if(useDefaultUrlLayout){
                        u = serverBaseUrl + recordName + ".cif";
                }
                else{
                        u = serverBaseUrl + recordName.charAt(0) + "/"  + recordName +"/" + recordName + ".cif";
                }

                logger.debug("downloading " + u);

                URL url = null;


                try {
                        url = new URL(u);
                        URLConnection uconn = URLConnectionTools.openURLConnection(url);

                        try( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(newFile)));
                                        BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()));
                                        ) {

                                String line;

                                while ((line = fileBuffer.readLine()) != null) {
                                        pw.println(line);
                                }

                                pw.flush();
                        }
                        // Now we move this across to where it actually wants to be
                        Files.move(newFile.toPath(), Paths.get(localName), StandardCopyOption.REPLACE_EXISTING);

                        return true;
                }  catch (IOException e){
                        logger.error("Could not download "+url.toString()+" OR store locally to "+localName+" Error ="+e.getMessage());
                        newFile.delete();
                }
                return false;
        }

        private void downloadAllDefinitions() {

                if ( loading.get()){
                        logger.info("Waiting for other thread to install chemical components...");
                }

                while ( loading.get() ) {

                        // another thread is already downloading the components definitions
                        // wait for the other thread to finish...

                        try {
                                // wait half a second

                                Thread.sleep(500);
                        } catch (InterruptedException e) {
                                //e.printStackTrace();
                                logger.error("Thread interrupted "+e.getMessage());
                        }

                        logger.info("Another thread installed the chemical components.");
                        return;

                }

                loading.set(true);
                long timeS = System.currentTimeMillis();

                logger.info("Performing first installation of chemical components.");
                logger.info("Downloading components.cif.gz ...");


                try {
                        AllChemCompProvider.downloadFile();
                } catch (IOException e){
                        logger.error("Could not download the all chemical components file. Error: {}. "
                                        + "Chemical components information won't be available", e.getMessage());
                        // no point in trying to split if the file could not be downloaded
                        loading.set(false);
                        return;
                }
                try {
                        split();
                } catch (IOException e) {
                        logger.error("Could not split all chem comp file into individual chemical component files. Error: {}",
                                        e.getMessage());
                        // no point in reporting time
                        loading.set(false);
                        return;
                }
                long timeE = System.currentTimeMillis();
                logger.info("time to install chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");
                loading.set(false);

        }

        /** By default this provider will download only some of the {@link ChemComp} files.
         * The user has to request that all files should be downloaded by setting this parameter to true.
         *
         *  @return flag if the all components should be downloaded and installed at startup. (default: false)
         */
        public boolean isDownloadAll() {
                return downloadAll;
        }

        /** By default this provider will download only some of the {@link ChemComp} files.
         * The user has to request that all files should be downloaded by setting this parameter to true.
         *
         * @param  flag if the all components should be downloaded and installed at startup. (default: false)
         */
        public void setDownloadAll(boolean downloadAll) {
                this.downloadAll = downloadAll;
        }





}