Your program takes an input 'txtURLString' - could you give an example of the value that this usually contains? I suspect that this URL is where your problem lies but without seeing an example value I couldn't say for sure.
thanks, Richard On 8 Nov 2009, at 10:22, jitesh dundas 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 <[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 >> >> > <ImportFromPubmed3.jsp>_______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
