//package MobyServices.mips.plant.moby;

import MobyServices.mips.plant.genericparser.GenericMobyOutputwriter;
import MobyServices.mips.plant.genericparser.GetDBname;
import MobyServices.mips.plant.genericparser.GetInputDataForQuery;
import MobyServices.mips.plant.helper.MobyServiceHandler;
import MobyServices.mips.plant.client.RetrieveElementClient;
import sun.jdbc.rowset.CachedRowSet;
import mips.genre.exceptions.GenreException;
import mips.genre.general.DBAccess;

import java.sql.SQLException;
import java.util.Vector;

import org.dom4j.Document;
import org.dom4j.Element;

/**
 * <b>-- Retrieves all details of an element using element name-- .</b>
 * <p>
 * -- Description of Class goes here --
 * </p>
 * (c) <a href="http://mips.gsf.de">MIPS</a> / gsf  * GENome Research 
 Environment (GENRE) <br /> 
 * Apr 30, 2004; 2:09:33 PM
 * @author Vijayalakshmi Janakiraman
 * adapted to new parser by Octave Noubibou
 */

public class RetrieveElementWS extends GetInputDataForQuery{
    private RetrieveElementClient client;
    private GetDBname getDbname;

    public RetrieveElementWS(){
        try {
            client = new RetrieveElementClient();
            getDbname=new GetDBname();
        } catch (GenreException e) {
            e.printStackTrace();  //To change body of catch statement use Options | File Templates.
        }
    }

    public String getElement(String inputXML){
        String mobyobjectresult = null;
        String result = null;

        Vector inner;
        Vector simpletype;

      
        
        GenericMobyOutputwriter gow = new GenericMobyOutputwriter();
        
//      create the document to hold the results
         Document mobyDoc = gow.generateSOAPpayloadDocument("mips.gsf.de");                                                                         
         gow.addServiceNotes(mobyDoc, " Service Provider: mips.gsf.de"); //add some Notes        
        
         /*now, parse alldata you need for a single query and group them in a
         vector see also allparsedData method in the super class
         */
         Vector alldata = allParsedData(inputXML);
        
         for (int i = 0; i < alldata.size(); i++) { //each i is a mobyData node=data for a single query 
            inner = getInnerVector(alldata, i);
            // System.out.println("inner===="+ inner);
            Element mobyDataTag = gow.addMobyDataTagToMobyContentTag(mobyDoc,"");
                               
            Element collection = null;
            if (inner.size() > 1) { //is it a collection? add the collection tag
                collection = gow.addCollectionTagToMobyDataTag(mobyDataTag,
                        "myCollection");

            }

            String queryId = null;
            for (int j = 0; j < inner.size(); j++) {//each j is a simple type Node
                simpletype = getInnerVector(inner, j);
                //System.out.println("simpletype==="+ inner);
                setDataForSingleQuery(simpletype); //initialize the namespace and id
                queryId = getqueryId();
                String locusCode = getId();
                //System.out.println("id==="+ locusCode);
                String namespace = getNamespace();                
                String dbname=getDbname.dbName(namespace);
               
                try{
                    int id=client.getElementIDForElementName(locusCode, dbname);
                    System.out.println("id======"+id);
                    if(id != -1){
//                      use the "plant middleware" to get the result  
                        result = client.getElement(id, dbname);
                    }else{
                        
                        mobyDataTag.attribute("moby:queryID").setValue(queryId);
                        System.out.println("======getElement======= bad ID "+locusCode+" ?");
                        return mobyDoc.asXML(); 
                    }
                    
                }catch (GenreException e) {                  
                    
                    mobyDataTag.attribute("moby:queryID").setValue(queryId);
                    //e.printStackTrace();
                    return mobyDoc.asXML();
                    
                }

                if (inner.size() > 1) {//it is a collection, so add all simple
                                       // tag in the Collection tag
                    Element simpleTag = gow
                            .addSimpleTagToParentElement(collection);
                    gow.addContentToElement(simpleTag, "text-xml", result,
                            namespace, locusCode, null);

                } else { //otherwise add the simple tag directlly to the mobyData tag
                    Element simpleTag = gow
                            .addSimpleTagToParentElement(mobyDataTag);
                    gow.addContentToElement(simpleTag, "text-xml", result,
                            namespace, locusCode, null);
                }

            }
            //gow.setqueryid(mobyDataTag, queryId);
            mobyDataTag.attribute("moby:queryID").setValue(queryId);
        }
        mobyobjectresult = mobyDoc.asXML();// transform the Dom4j document to string
                                    
        return mobyobjectresult;
      
    }

    String con="chr4_pseudomolecule_MAtDB";
    private String con1="mth1-7g13";   
   String ele="At1g01740";
    public String getInputXML(){
        return "<?xml version='1.0' encoding='UTF-8'?> "+
        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>" +
              "<moby:mobyContent>" +
                  "<moby:mobyData moby:articleName='' queryID='1'>"+
                    "<moby:Simple>"+
                        "<Object namespace='MIPS_GE_Arabidopsis' id='"+con+"'/>"+
                    "</moby:Simple></moby:mobyData>"+
               "</moby:mobyContent>"+
        "</moby:MOBY>";
    }
    
    public static void main(String[] args) throws GenreException {
        RetrieveElementWS s = new RetrieveElementWS();
         String str = s.getElement(s.getInputXML());
         System.out.println("str-->"+str);
     }

}