Dear Dr. *Andreas Prlic,* Thank you for the advise. I will do that.
Regards, Jitesh Dundas On 11/1/09, Andreas Prlic <[email protected]> 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 <[email protected]> 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 - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
