[Biojava-l] Java Error:- XML Parsing Error: XML or text declaration not at start of entity
jitesh dundas
jbdundas at gmail.com
Tue Nov 10 14:23:10 UTC 2009
Dear Friends,
Thank you for your help and advise.
The code in the mentioned URL is working fine ->
http://gist.github.com/229248 (this is my code that has been uploaded by a
wise group member. Many thanks to him for doing that)
Hope this helps..
Regards,
JItesh Dundas
On Sun, Nov 8, 2009 at 3:52 PM, jitesh dundas <jbdundas at gmail.com> wrote:
> 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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