/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.io;

import java.io.*;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.StringTokenizer;

import org.apache.axis.client.*;
import org.apache.axis.encoding.XMLType;

import javax.xml.namespace.QName;
import javax.xml.rpc.ParameterMode;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class EBIFetchClient
{
    Call call;
    String format = "default";
    String style = "raw";

    /**
     * Creates a new EBIFetchClient object.
     */
    public EBIFetchClient()
    {
        try
        {
            call = (Call) new Service().createCall();
            call.setTargetEndpointAddress(new java.net.URL(
                    "http://www.ebi.ac.uk/ws/services/Dbfetch"));
        }
        catch (Exception ex)
        {
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String[] getSupportedDBs()
    {
        try
        {
            call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
            call.setReturnType(XMLType.SOAP_ARRAY);

            return (String[]) call.invoke(new Object[] {  });
        }
        catch (Exception ex)
        {
            return null;
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String[] getSupportedFormats()
    {
        try
        {
            call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
            call.setReturnType(XMLType.SOAP_ARRAY);

            return (String[]) call.invoke(new Object[] {  });
        }
        catch (Exception ex)
        {
            return null;
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String[] getSupportedStyles()
    {
        try
        {
            call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
            call.setReturnType(XMLType.SOAP_ARRAY);

            return (String[]) call.invoke(new Object[] {  });
        }
        catch (Exception ex)
        {
            return null;
        }
    }

    public static void main (String [] args)
    {
      EBIFetchClient ebi = new EBIFetchClient();
      String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
                           "xml", null);

     try{
       java.io.PrintWriter out = new java.io.PrintWriter(
      new java.io.FileWriter("out.xml"));


       for(int i=0; i<result.length; i++)
       {
         out.println(result[i]);
       }
       out.close();
     }catch(Exception ex){ex.printStackTrace();}

    }


    public File fetchDataAsFile(String ids, String f, String s)
    {
      String [] data = fetchData(ids, f, s);
      File outFile = null;
      try{
        outFile = File.createTempFile("jalview", ".xml");
        outFile.deleteOnExit();
        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
        int index=0;
        while( index < data.length )
        {
          out.println(data[index]);
          index++;
        }
        out.close();
      }catch(Exception ex){}
      return outFile;
    }

    /**
     * Single DB multiple record retrieval
     *
     * @param ids db:query1;query2;query3
     * @param f raw/xml
     * @param s ?
     *
     * @return Raw string array result of query set
     */
    public String[] fetchData(String ids, String f, String s)
    {
        // Need to split
        // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
        
        StringTokenizer queries=new StringTokenizer(ids,";");
        String db=null;
        StringBuffer querystring=null;
        while (queries.hasMoreTokens()) {
            String query=queries.nextToken();
            int p;
            if ((p=query.indexOf(':'))>-1 && (p+3<query.length())) {
                db = query.substring(0,p);
                query = query.substring(p+1);
            }
            if (querystring==null) {
                querystring = new StringBuffer(query);
            } else {
                querystring.append(","+query);
            }
        }
        if (db==null) {
            System.err.println("Invalid Query string : '"+ids+"'\nShould be of form 'dbname:q1;q2;q3;q4'");
        }
        return fetchBatch(querystring.toString(), db, f, s);
    }
    public String[] fetchBatch(String ids, String db, String f, String s) {
        // max 50 ids can be added at one time
        try
        {
            //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
            call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
            call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
            call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
            call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
            call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
            call.setReturnType(XMLType.SOAP_ARRAY);

            if (f != null)
            {
                format = f;
            }

            if (s != null)
            {
                style = s;
            }

            try{
              return (String[]) call.invoke(new Object[]
                                            {ids.toLowerCase(), db.toLowerCase(), format, style});
            }catch(OutOfMemoryError er)
            {
              System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM "+db+":\n"+ids);
            }
            return null;
        }
        catch (Exception ex)
        {
            if (ex.getMessage().startsWith("uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
                return null;
            System.err.println("Unexpected exception when retrieving from "+db+"\nQuery was : '"+ids+"'");
            ex.printStackTrace(System.err);
            return null;
        }
    }
}