[jdom-interest] Problem getting my XML in

[Edd Dawson]

Hi

I am developing some code in Java to access to a publicly accessible
gene database via simple URL's and import the XML into a parser all
using Jdom..

the code is as follows :

=============================================================

package PJB;
/**
* <p>Title: PjbImportCentre </p>
* <p>Description: Class for importing data from Entrez gene</p>
* <p>Copyright: Copyright MitchellConnerSearson Ltd(c) 2004</p>
* <p>Company: MitchellConnerSearson </p>
* @author Edd Dawson
* @version 1.0
*/

import java.net.*;
import java.util.*;
import java.io.*;
import org.jdom.Element;
import org.jdom.Document;
import org.jdom.output.XMLOutputter;
import org.jdom.input.SAXBuilder;



public class PjbImportCentre {

private URL urlObj;

//URL of the webservice which provides data
private final static String EG_URL =
"http://www.ncbi.nlm.gov/entrez/query.fcgi?cmd=text&";


 /**
  * Constructor for McsCheckerCentre  Objects.
  *
  * Creates new instance of McsCheckerCentre
  *
  *
  */

 public PjbImportCentre()
 {
 }



 /**
 *Gets the xml file for a specific gene uid
 *
 *@param uid String = the uid of the gene you wish to get
 *
 *@return
 **/

 public String getGene(String uid) {


    String xml = "db=gene&dopt=xml&uid=" + uid;



   try {
       //--------open connection to the xml gateway

       URL urlObj = new URL(EG_URL + xml);

       SAXBuilder builder = new SAXBuilder();
       Document doc = null;
       try {
           doc = builder.build(urlObj);
       }
       catch(Exception ex) {
           return "Error on making xml returned SAXable" +
ex.getMessage();
       }


       String geneTrackGeneId =
doc.getRootElement().getChild("Entrezgene_track-info").getChild("Gene-track").getChild("Gene-track_geneid").getTextTrim();;

       return geneTrackGeneId;




   }
   catch(Exception ex) {
       return "error on POST : " + ex.getMessage();
   }
}


}

================================================================================

I have a little bit of code to run the class as follows ;

================================================================================

import PJB.*;


class Pjb {


    private void doExample(String search)  {



            PjbImportCentre xmlExample = new PjbImportCentre();
            System.out.println(xmlExample.getGene(search));
    }


    public static void main(String[] args) {

        Pjb test = new Pjb();

        test.doExample(args[0]);
           }
}

========================================================================

when i run the code as follows :

c:\PJB\java Pjb 4537

i get the following result

"Error on making xml returned SAXable null"


If i pull back the XML from a browser it starts like this :

<?xml version="1.0"?>
<!DOCTYPE Entrezgene PUBLIC "-//NCBI//NCBI Entrezgene/EN"
"NCBI_Entrezgene.dtd">
<Entrezgene>
  <Entrezgene_track-info>
    <Gene-track>
      <Gene-track_geneid>4537</Gene-track_geneid>
      <Gene-track_create-date>
        <Date>


(for the full document just go to
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=gene&dopt=xml&uid=4537)


I am wondering why this is happening, it would appear to be that there
is a problem with the XML being returned if the parser is rejecting it.
Does anyone have any experience of this happening before?

thanks

Edd Dawson