Dear Sir, Thank you for uploading the code. That definitely helps..
Regards, Jitesh Dundas On Sun, Nov 8, 2009 at 6:20 PM, Henrique de Miranda Gontijo < [email protected]> wrote: > Hi, > > I think here is better to read the code. > http://gist.github.com/229248 > > There is a parameter to tell the max registries you want to retrieve > retMax=x > where x is the max regs to retrieve > > This will give 100 or less regs > > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10&retmax=100 > > More info about params > > http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/esearch_help.html#URLparameters > > Best regards, > Henrique. > > On Sun, Nov 8, 2009 at 8:24 AM, jitesh dundas <[email protected]> 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 >> >> File attached with this email. >> >> 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 >> > >> > >> >> >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "The Java Posse" group. 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