/*
 *                    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.biojavax.bio.alignment.blast;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.HashMap;

import org.biojava.bio.BioException;
import org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties;
import org.biojavax.bio.alignment.RemotePairwiseAlignmentService;
import org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties;
import org.biojavax.bio.seq.RichSequence;

/**
 * RemoteQBlastService - A simple way of submitting BLAST request to the QBlast
 * service at NCBI.
 * 
 * <p>
 * NCBI provides a Blast server through a CGI-BIN interface. RemoteQBlastService
 * simply encapsulates an access to it by giving users access to get/set methods
 * to fix sequence, program and database as well as advanced options.
 * </p>
 * 
 * <p>
 * The philosophy behind RemoteQBlastService is to disconnect submission of
 * Blast requests from collection of Blast results. This is done so to allow a
 * user to submit multiple Blast requests while allowing recovery of the reports
 * at a later time.
 * </p>
 * 
 * <p>
 * Presently, only blastall programs are accessible. blastpgp and megablast are
 * high-priorities.
 * </p>
 * 
 * @author Sylvain Foisy, Diploide BioIT
 * @since 1.8
 * 
 */
public class RemoteQBlastService implements RemotePairwiseAlignmentService {

        private static String baseurl = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
        private URL aUrl;
        private URLConnection uConn;
        private OutputStreamWriter fromQBlast;
        private BufferedReader rd;
        
        private String email = "anonymous@biojava.org";
        private String tool = "biojavax";
         

        private String seq = null;
        private String prog = null;
        private String db = null;
//      private String advanced = null;

        private String rid;
        private long step;
        private long start;
        private HashMap<String, Long> holder = new HashMap<String, Long>();

        /**
         * The constructor for a QBlast service request.
         * 
         * @throws BioException
         *             if the NCBI URL is unresponsive
         * 
         */
        public RemoteQBlastService() throws BioException {
                try {
                        aUrl = new URL(baseurl);
                        uConn = setQBlastServiceProperties(aUrl.openConnection());
                }
                /*
                 * Needed but should never be thrown since the URL is static and known
                 * to exist
                 */
                catch (MalformedURLException e) {
                        throw new BioException(
                                        "It looks like the URL for NCBI QBlast service is wrong.\n");
                }
                /*
                 * Intercept if the program can't connect to QBlast service
                 */
                catch (IOException e) {
                        throw new BioException(
                                        "Impossible to connect to QBlast service at this time. Check your network connection.\n");
                }
        }

        /**
         * This class is the actual worker doing all the dirty stuff related to
         * sending the Blast request to the CGI_BIN interface. It should never be
         * used as is but any method wanting to send a Blast request should manage
         * to use it by feeding it the right parameters.
         * 
         * @param str : a <code>String</code> representation of a sequence from either of the
         *              three wrapper methods
         * @param rpa :a <code>RemotePairwiseAlignmentProperties</code> object
         * @return rid : the ID of this request on the NCBI QBlast server
         * @throws BioException if unable to connect to the NCBI QBlast service
         */
        private String sendActualAlignementRequest(String str,
                        RemotePairwiseAlignmentProperties rpa) throws BioException {

                seq = "QUERY=" + str;
                prog = "PROGRAM=" + rpa.getAlignmentOption("PROGRAM");
                db = "DATABASE=" + rpa.getAlignmentOption("DATABASE");

                if (prog == null || db == null || str == null || str.length() == 0) {
                        throw new BioException(
                                        "Impossible to execute QBlast request. One or more of sequence|database|program has not been set correctly.\n");
                }

                String cmd = "CMD=Put&SERVICE=plain" + "&" + seq + "&" + prog + "&"
                                + db + "&" + "FORMAT_TYPE=HTML"+"&TOOL="+getTool()+"&EMAIL="+getEmail();

                // This is a not so good hack to be fix by forcing key 
                // checking in RemoteQBlastAlignmentProperties
                if (rpa.getAlignmentOption("OTHER_ADVANCED") != null) {
                        cmd += cmd + "&" + rpa.getAlignmentOption("OTHER_ADVANCED");
                }

                try {

                        uConn = setQBlastServiceProperties(aUrl.openConnection());

                        fromQBlast = new OutputStreamWriter(uConn.getOutputStream());

                        fromQBlast.write(cmd);
                        fromQBlast.flush();

                        // Get the response
                        rd = new BufferedReader(new InputStreamReader(uConn
                                        .getInputStream()));

                        String line = "";

                        while ((line = rd.readLine()) != null) {
                                if (line.contains("RID")) {
                                        String[] arr = line.split("=");
                                        rid = arr[1].trim();
                                } else if (line.contains("RTOE")) {
                                        String[] arr = line.split("=");
                                        step = Long.parseLong(arr[1].trim()) * 1000;
                                        start = System.currentTimeMillis() + step;
                                }
                                holder.put(rid, start);
                        }
                } catch (IOException e) {
                        throw new BioException(
                                        "Can't submit sequence to BLAST server at this time.\n");
                }

                return rid;
        }

        /**
         * This method is a wrapper that executes the Blast request via the Put
         * command of the CGI-BIN interface with the specified parameters and a
         * string representing the sequence. It gets the estimated time of
         * completion by capturing the value of the RTOE variable and sets a loop
         * that will check for completion of analysis at intervals specified by
         * RTOE.
         * 
         * <p>
         * It also capture the value for the RID variable, necessary for fetching
         * the actual results after completion.
         * </p>
         * 
         * @param str : a <code>String</code> with a sequence
         * @param rpa : a <code>RemotePairwiseAlignmentProperties</code> object
         * @return rid : a <code>String</code> with the request ID for this sequence
         * @throws BioException if it is not possible to sent the BLAST command
         */
        public String sendAlignmentRequest(String str,
                        RemotePairwiseAlignmentProperties rpa) throws BioException {

                /*
                 * sending the command to execute the Blast analysis
                 */
                return rid = sendActualAlignementRequest(seq, rpa);
        }

        /**
         * This method is a wrapper that executes the Blast request via the Put
         * command of the CGI-BIN interface with the specified parameters and a
         * RichSequence. It gets the estimated time of completion by capturing the
         * value of the RTOE variable and sets a loop that will check for completion
         * of analysis at intervals specified by RTOE.
         * 
         * <p>
         * It also capture the value for the RID variable, necessary for fetching
         * the actual results after completion.
         * </p>
         * 
         * @param rs :a <code>RichSequence</code> object
         * @param rpa :a <code>RemotePairwiseAlignmentProperties</code> object
         * @return rid : a <code>String</code> with the request ID for this sequence
         * 
         * @throws BioException if it is not possible to sent the BLAST command
         */
        public String sendAlignmentRequest(RichSequence rs,
                        RemotePairwiseAlignmentProperties rpa) throws BioException {

                seq = rs.seqString();

                return rid = sendActualAlignementRequest(seq, rpa);
        }

        /**
         * This method is a wrapper that executes the Blast request via the Put
         * command of the CGI-BIN interface with the specified parameters and a
         * GenBank GID. It gets the estimated time of completion by capturing the
         * value of the RTOE variable and sets a loop that will check for completion
         * of analysis at intervals specified by RTOE.
         * 
         * <p>
         * It also capture the value for the RID variable, necessary for fetching
         * the actual results after completion.
         * </p>
         * 
         * @param gid :an integer with a Genbank GID
         * @param rpa :a <code>RemotePairwiseAlignmentProperties</code> object
         * @return rid : a String with the request ID for this sequence
         * @throws BioException if it is not possible to sent the BLAST command
         */
        public String sendAlignmentRequest(int gid,
                        RemotePairwiseAlignmentProperties rpa) throws BioException {

                seq = Integer.toString(gid);
                return rid = sendActualAlignementRequest(seq, rpa);
        }

        /**
         * <p>
         * This method is used only for the executeBlastSearch method to check for
         * completion of request using the NCBI specified RTOE variable
         * </p>
         * 
         * @param id : a valid request ID
         * @param present : a representation of "now" using System.currentTimeMillis().
         * @return a boolean value telling if the request has been completed or not.
         */
        public boolean isReady(String id, long present) throws BioException {
                boolean ready = false;
                String check = "CMD=Get&RID=" + id;

                if (holder.containsKey(id)) {
                        /*
                         * If present time is less than the start of the search added to
                         * step obtained from NCBI, just do nothing ;-)
                         * 
                         * This is done so that we do not send zillions of requests to the
                         * server. We do the waiting internally first.
                         */
                        if (present < start) {
                                ready = false;
                        }
                        /*
                         * If we are at least step seconds in the future from the actual
                         * call sendAlignementRequest()
                         */
                        else {
                                try {
                                        uConn = setQBlastServiceProperties(aUrl.openConnection());

                                        fromQBlast = new OutputStreamWriter(uConn.getOutputStream());
                                        fromQBlast.write(check);
                                        fromQBlast.flush();

                                        rd = new BufferedReader(new InputStreamReader(uConn
                                                        .getInputStream()));

                                        String line = "";

                                        while ((line = rd.readLine()) != null) {
                                                if (line.contains("READY")) {
                                                        ready = true;
                                                } else if (line.contains("WAITING")) {
                                                        /*
                                                         * Else, move start forward in time... for the next
                                                         * iteration
                                                         */
                                                        start = present + step;
                                                        holder.put(id, start);
                                                }
                                        }
                                } catch (IOException e) {
                                        e.printStackTrace();
                                }
                        }
                } else {
                        throw new BioException("Impossible to check for request ID named "
                                        + id + " because it does not exists!\n");
                }
                return ready;
        }

        /**
         * <p>
         * This method extracts the actual Blast report for this request ID. It uses
         * an object implementing the RemotePairwiseAlignmentOutputProperties
         * interface which will specify output formatting options.
         * </p>
         * 
         * @param id :a valid request ID
         * @param rb : a <code>RemotePairwiseAlignmentOutputProperties</code> that
         *             will specify specific output formatting commands
         * @return an <code>InputStream</code> that can be use any way one might
         *         desire
         * @throws BioException if it is not possible to recover the results.
         */
        public InputStream getAlignmentResults(String id,
                        RemotePairwiseAlignmentOutputProperties rb) throws BioException {
                if (holder.containsKey(id)) {
                        String srid = "CMD=Get&RID=" + id + "&"
                                        + rb.getOutputOption("FORMAT_TYPE") + "&"
                                        + rb.getOutputOption("ALIGNMENT_VIEW") + "&"
                                        + rb.getOutputOption("DESCRIPTIONS") + "&"
                                        + rb.getOutputOption("ALIGNMENTS")
                                        + "&TOOL="+getTool()+"&EMAIL="+getEmail();

                        try {
                                uConn = setQBlastServiceProperties(aUrl.openConnection());

                                fromQBlast = new OutputStreamWriter(uConn.getOutputStream());
                                fromQBlast.write(srid);
                                fromQBlast.flush();

                                return uConn.getInputStream();

                        } catch (IOException ioe) {
                                throw new BioException(
                                                "It is not possible to fetch Blast report from NCBI at this time.\n");
                        }
                } else {
                        throw new BioException(
                                        "Impossible to get output for request ID named " + id
                                                        + " because it does not exists!\n");
                }
        }

        /**
         * A simple method to check the availability of the QBlast service
         * 
         * @throws BioException if unable to connect to the NCBI QBlast service
         */
        public void printRemoteBlastInfo() throws BioException {
                try {
                        OutputStreamWriter out = new OutputStreamWriter(uConn
                                        .getOutputStream());

                        out.write("CMD=Info");
                        out.flush();

                        // Get the response
                        BufferedReader rd = new BufferedReader(new InputStreamReader(uConn
                                        .getInputStream()));

                        String line = "";

                        while ((line = rd.readLine()) != null) {
                                System.out.println(line);
                        }

                        out.close();
                        rd.close();
                } catch (IOException e) {
                        throw new BioException(
                                        "Impossible to get info from QBlast service at this time. Check your network connection.\n");
                }
        }

        private URLConnection setQBlastServiceProperties(URLConnection conn) {

                URLConnection tmp = conn;

                conn.setDoOutput(true);
                conn.setUseCaches(false);

                tmp.setRequestProperty("User-Agent", "Biojava/RemoteQBlastService");
                tmp.setRequestProperty("Connection", "Keep-Alive");
                tmp.setRequestProperty("Content-type",
                                "application/x-www-form-urlencoded");
                tmp.setRequestProperty("Content-length", "200");

                return tmp;
        }
    /** 
     * Set the tool identifier for QBlast. Defaults to 'biojavax'.
     * @param tool the new identifier.
     */
    public void setTool(String tool) {
        this.tool = tool;
    }

    /** 
     * Get the tool identifier for QBlast. Defaults to 'biojavax'.
     * @return the identifier.
     */
    public String getTool() {
        return this.tool;
    }

    /** 
     * Set the email for QBlast. Defaults to 'anonymous@biojava.org'.
     * @param email the new email.
     */
    public void setEmail(String email) {
        this.email = email;
    }

    /** 
     * Get the email for QBlast. Defaults to 'anonymous@biojava.org'.
     * @return the email.
     */
    public String getEmail() {
        return this.email;
    }   
}