[Biojava-l] Java Error:- XML Parsing Error: XML or text declaration not at start of entity

[jitesh dundas]

Hi friends,

I am getting this error on doing a post(using the code below) to this url->
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10

I have written this code in .jsp file. Later I will change it into servlet.

Error:-
XML Parsing Error: XML or text declaration not at start of entity
Location:
http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
    <Id>19877350</Id>        <Id>19877304</Id>        <Id>19877297</Id>
    <Id>19877284</Id>        <Id>19877271</Id>        <Id>19877265</Id>
    <Id>19877250</Id>        <Id>19877245</Id>        <Id>19877226</Id>
    <Id>19877210</Id>        <Id>19877179</Id>        <Id>19877175</Id>
    <Id>19877161</Id>        <Id>19877159</Id>        <Id>19877158</Id>
    <Id>19877123</Id>        <Id>19877122</Id>        <Id>19877120</Id>
    <Id>19877119</Id>        <Id>19877118</Id>
</IdList><TranslationSet><Translation>     <From>cancer</From>
<To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
Fields]</To>    </Translation></TranslationSet><TranslationStack>
<TermSet>    <Term>"neoplasms"[MeSH Terms]</Term>    <Field>MeSH
Terms</Field>    <Count>2082133</Count>    <Explode>Y</Explode>
</TermSet>   <TermSet>    <Term>"neoplasms"[All Fields]</Term>    <Field>All
Fields</Field>    <Count>1634731</Count>    <Explode>Y</Explode>
</TermSet>   <OP>OR</OP>   <TermSet>    <Term>"cancer"[All Fields]</Term>
<Field>All Fields</Field>    <Count>902537</Count>    <Explode>Y</Explode>
</TermSet>   <OP>OR</OP>   <OP>GROUP</OP>   <TermSet>
<Term>2009/10/22[EDAT]</Term>    <Field>EDAT</Field>    <Count>0</Count>
<Explode>Y</Explode>   </TermSet>   <TermSet>
<Term>2009/11/01[EDAT]</Term>    <Field>EDAT</Field>    <Count>0</Count>
<Explode>Y</Explode>   </TermSet>   <OP>RANGE</OP>   <OP>AND</OP>
</TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
"neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
2009/11/01[EDAT]</QueryTranslation></eSearchResult>
^

As you can see, the XML output is coming fine but the above error does not
go..The output via this program should be just like hitting manually the
above URL in the browser..
The browser is Mozilla Firefox.

Code:-

<%@ page language = "java" %>
<%@ page import = "java.sql.*" %>
<%@ page import = "java.util.*" %>
<%@ page import = "java.io.*" %>
<%@ page import="java.lang.*" %>
<%@ page import="java.net.*" %>
<%@ page import="java.nio.*" %>
<%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>


<%

 try
 {
     //String str = "<?xml version='1.0' ?>";
     //out.println("<?xml version='1.0' encoding='utf-8' ?>");

     Properties systemSettings = System.getProperties();
     systemSettings.put("http.proxyHost", "********");
     systemSettings.put("http.proxyPort", "******");
     systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
     systemSettings.put("sun.net.client.defaultReadTimeout", "10000");

      //out.println("Properties Set");
     Authenticator.setDefault(new Authenticator()
     {
           protected PasswordAuthentication getPasswordAuthentication()
           {
                   return new PasswordAuthentication("**",
"******".toCharArray()); // specify ur user name password of iitb login
           }
     });


    System.setProperties(systemSettings);
    //out.println("After Authentication & Properties Settings");

    //create xml file.
    //the input to google api
    //String textAreaContent = request.getParameter("text");
    String textAreaContent = "This si a tst";

    String str = "<?xml version='1.0' encoding='utf-8' ?>";

    //xml file generation ends here..
    //FetchDataFromNCBI_URLString.jsp
    String URLString = request.getParameter("txtURLString").trim();

    //URL url = new URL("
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
");
    URL url = new URL(URLString); //url string taken from user input.
    HttpURLConnection connection = null;

    connection = (HttpURLConnection) url.openConnection();
    System.out.println("After open connection");
    connection.setRequestMethod("POST");
    connection.setDoInput(true);
    connection.setDoOutput(true);

    connection.setUseCaches(false);
    connection.setAllowUserInteraction(false);
    //connection.setFollowRedirects(true);
    //connection.setInstanceFollowRedirects(true);
    //System.out.println("Before-------------------");
    connection.setRequestProperty ("Content-Type","text/xml;
charset=\"utf-8\"");
    //System.out.println("After-------------------");

    //System.out.println(""+ connection.getOutputStream());

    //System.out.println("After dataoutputstream..Line No-65");

    //System.out.println("Response Code="+ connection.getResponseCode);

    OutputStreamWriter dosout = new
OutputStreamWriter(connection.getOutputStream());
    //System.out.println("After dosout object..Line No-63");
    //dosout.write(str);
    dosout.close ();

    BufferedReader in = new BufferedReader( new InputStreamReader(
connection.getInputStream()));

    String decodedString;
    String tempstr = "";


    while ((decodedString = in.readLine()) != null)
    {
        tempstr = tempstr + decodedString;
        //out.println(decodedString);
    }
    out.println(tempstr);
    in.close();
}
catch(Exception ex)
{
  out.println("Exception->"+ex);
  PrintWriter pw = response.getWriter();
  ex.printStackTrace(pw);
}


%>

Thanks in advance..

Regards,
JItesh Dundas