[Biojava-l] Java Error:- XML Parsing Error: XML or text declaration not at start of entity
jitesh dundas
jbdundas at gmail.com
Mon Nov 2 08:19:19 UTC 2009
Dear Dr. *Andreas Prlic,*
Thank you for the advise. I will do that.
Regards,
Jitesh Dundas
On 11/1/09, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> Hi Jitesh,
>
> It is hard to read your code with all the formatting off probably due to
> email and many commented lines that don;t seem to get used. Can you provide
> the stacktrace, so we can see what part of biojava is affected?
>
> Probably a good strategy to write and debug this is to simply the problem
> into smaller steps. Try to first download the files you want to parse and
> write the code to parse them from the local file. That will avoid any
> issues you might encounter with networking and server/client communication.
> Once the parsing is working you could take it to the next step and add the
> server communication...
>
> Andreas
>
>
>
>
> On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas at gmail.com> wrote:
>
>> 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
>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
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