[Biojava-l] Java Error:- XML Parsing Error: XML or text declaration not at start of entity
jitesh dundas
jbdundas at gmail.com
Sun Nov 8 10:22:59 UTC 2009
Dear Sir,
My program is working fine and can send me an xml file with 20
records. However, it does not allow me to send large amounts of
records.
For e.g. if I enter "cancer" it will return only 20 records.
Can you please tell me what I should do next to get all those records.
Thank you in advance
Regards,
Jitesh Dundas
On Sun, Nov 1, 2009 at 9:36 PM, 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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