/* * Created on Jul 6, 2006
*
* TODO To change the template for this generated file go to
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*/

/**
 * @author Betsy Rolland
 *
 * TODO To change the template for this generated type comment go to
 * Window - Preferences - Java - Code Style - Code Templates
 */

package org.biomediator.wrappers;

import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.*;
import java.net.URL;
import java.util.HashMap;
import java.util.Iterator;
import java.util.TreeSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.biomediator.util.AttribOption;
import org.biomediator.util.StringUtility;

import com.oroinc.text.regex.Perl5StreamInput;

import java.io.FileReader;


import java.util.*;

import org.biomediator.util.AttribOption;
import org.biomediator.util.StringUtility;
import org.biomediator.xml.XMLParser;
import org.biomediator.xml.XMLAttributeParser;

import org.xml.sax.XMLReader;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.helpers.XMLReaderFactory;
import org.xml.sax.helpers.DefaultHandler;


public class InterProSequenceWrapper extends AbstractWrapper {

	public static final String IP_HELP_TEXT =
		"        Description:\n" +
        "                Provides an interface for searching the InterPro database by sequence.\n" +
        "\n" +
        "        Usage:\n" +
        "        Servlet examples:\n" +
	   "				 ?term=term[tvalue=MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIAAGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ]" ;
	
	public static final String IP_SOURCE_TAG = "interpro_source";
	public static final String IP_CMD_TERM = "term";
	public static final String IP_OPTION_MAP_TVALUE = "tvalue";
    public static final String IP_OPTION_MAP_HEXENCODED = "hexencoded";
	public static final int MAX_DOCSIZE = 1024 * 10000;
	public static final int REFRESH_LIMIT 				= 40;
	public static final int REFRESH_RATE 				= 8000;
	private static String ENDLINE = "\n";
	
	public static final String ipsHitResultPattern		= "<interpro_matches>";
	   
    public String proxyUrl = null;
	private Pattern pattern = null;
	private Matcher matcher = null;
	private HashMap queryMap = null;
    private String sequence = "";

	
    public static void main(String[] args) {

    	InterProSequenceWrapper ip = new InterProSequenceWrapper();    			//invoking the constructor
        ip.out = new PrintWriter(System.out, true);
        if (args.length > 0) {
            ip.processRequest(args[0]);
        }
        else {
            ip.processRequest("");
        }
    }
    
    public void processRequest(String query) {
        
        // Make sure the servlet is initialized.
        initializeServlet(IP_HELP_TEXT, IP_SOURCE_TAG, getWrapperProperties("interprosequence"));
        		
        // Parse the query string and process commands.
        if (query == null || query.equals("")) {
            query = CMD_HELP;
        }
        AttribOption ao = new AttribOption(query);
        processCommands(ao, getWrapperProperties("interprosequence"));
        
        // Check to see if we should exit immeditely.
        if (isExitCmd) {
            return;
        }
        
        String proxy = wrapperProperties.getProperty(WrapperProperties.PROP_PROXY_URL);
        if (proxy == null) {
            proxyUrl = "";
        }
        else {
            proxyUrl = proxy + "?";
        }
    	
        String convertedQuery = null;
        TreeSet termTypeSet = ao.getAttribMapSet(IP_CMD_TERM);
        if (termTypeSet != null) {
        	convertedQuery = constructIPQuery(termTypeSet.iterator());
        }
        
        String urlBase = "http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&cmd=submit&crc=1&goterms=1&sequence=";

       
        
        try {
            // Download XML page.
        	
        	String queryURL = proxyUrl + urlBase + convertedQuery;
            //out.println("queryURL is " + queryURL);
            BufferedReader br = new BufferedReader(new InputStreamReader(new URL(queryURL).openStream()));
            StringBuffer lineBuf = new StringBuffer();
            String line = null;
            
            while ((line = br.readLine()) != null) {
                lineBuf.append(line + "\n");
                if (lineBuf.length() > MAX_DOCSIZE) {
                    break;
                }
            }
            br.close();

            // Isolate and process the portion of the page that contains data. 
            String data = lineBuf.toString();
            //find this string and get the job number -- var bookmarktitle="iprscan?tool=iprscan&jobid=iprscan-20060809-20001592"
            String jobNumberRegEx = "iprscan?tool=iprscan&jobid=iprscan-";
            int jobNumberStringStart = data.indexOf(jobNumberRegEx); 
            int jobNumberStartIndex = jobNumberStringStart + 35;
            String jobNumber = data.substring(jobNumberStartIndex, jobNumberStartIndex + 17);
            
            //out.println("jobNumber is " + jobNumber);
            String baseURL = "http://www.ebi.ac.uk/jobresults/iprscan/iprscan-";
            String xmlURL = ".xml?";
            String resultsURL = baseURL + jobNumber + xmlURL;
            out.println("resultsURL is " + resultsURL);
            
            boolean ready = false;
            while (!ready){
            	ready = refreshIPSLink(resultsURL);
            }            

            //BufferedReader br2 = new BufferedReader(new InputStreamReader(new URL(resultsURL).openStream()));
            InputStream inStream = new BufferedInputStream(new URL(resultsURL).openStream());
            StringBuffer lineBuf2 = new StringBuffer();
            lineBuf2.append(HEADER_XML + "\n");
            

            XMLAttributeParser xap = new XMLAttributeParser(inStream, lineBuf2);
            lineBuf2 = xap.parseData();

            // Isolate and process the portion of the page that contains data. 
            String data2 = lineBuf2.toString();

            // Convert retrieved document to valid XML (order of replacements is important).
            data2 = data2.replaceAll("<\\?xml version=\"1\\.0\"[^>]*>", HEADER_XML);
            data2 = data2.replaceAll("<!DOCTYPE[^>]*>", "");
            data2 = data2.replaceAll("interpro_matches",IP_SOURCE_TAG);
            data2 = data2.replaceAll("/interpro_matches",IP_SOURCE_TAG);
          
            
 
            // Print XML output to the client.
            out.print((data2 != null) ? data2 : "");
            out.flush();
    
            
        } //end of try
        	catch (Exception e) {
            System.err.println(e);
        }
    } //end of processRequest
    
    
    public String constructIPQuery(Iterator queryIterator) {

        StringBuffer termBuf = new StringBuffer("");
        HashMap groupMap = new HashMap();
        String ttype = null;
        String tvalue = null;
     
        String hexencoded = null;
        
        if (queryIterator.hasNext()) {
            while (queryIterator.hasNext()) {
                // Retrieve the term values that were parsed from the query URL.
                HashMap queryMap = (HashMap) queryIterator.next();
                ttype = (String) queryMap.get(AttribOption.OPTION_PARAM_NAME);
                tvalue = (String) queryMap.get(IP_OPTION_MAP_TVALUE);
                            
                hexencoded = (String) queryMap.get(IP_OPTION_MAP_HEXENCODED);
       

                // Convert term values from hex to ascii if necessary.
                if (hexencoded != null && hexencoded.equals("true")) {
                	tvalue = StringUtility.convertHexToASCII(tvalue);
                }
           }
        }

        //out.println("tvalue is "+ tvalue);
        return tvalue;
    }
    
    public boolean refreshIPSLink(String ipsLink) {
		URL ipsSocket;
		BufferedReader br;
		int refreshToken = 0;		
		try {
			ipsSocket = new URL(ipsLink);
			br = new BufferedReader(new InputStreamReader(ipsSocket.openStream()));
			
			String ln;
			StringBuffer lines = new StringBuffer();
			while ((ln = br.readLine()) != null)
				lines.append(ln + ENDLINE);
			
			pattern = Pattern.compile(ipsHitResultPattern); //what should this be?
			matcher = pattern.matcher(lines);
			
			if(matcher.find()) {	// results are complete
			    		//out.println("found a match!");
			    		return true;
			}
		}
		catch (Exception e) {
		    e.printStackTrace();
		}
		return false;
    }
        
    public void terminate() {
        // TODO Auto-generated method stub

    }

}