Java Error:- XML Parsing Error: XML or text declaration not at start of entity

[jitesh dundas]

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

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http://lists.open-bio.org/mailman/listinfo/biojava-l

[Andreas Prlic-3]

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@...> 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@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

_______________________________________________
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http://lists.open-bio.org/mailman/listinfo/biojava-l

[jitesh dundas]

Dear Dr. *Andreas Prlic,*

 Thank you for the advise. I will do that.

Regards,
Jitesh Dundas



On 11/1/09, Andreas Prlic <andreas@...> 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@...> 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@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>

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[jitesh dundas]

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@...> 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@...> 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@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

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[jitesh dundas]

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@...> 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@...> 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@...>
> 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@...
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>

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[Richard Holland-6]

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 <andreas@...> 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@...> 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@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
> <ImportFromPubmed3.jsp>_______________________________________________
> Biojava-l mailing list  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: [phone] ext 3 | E: holland@...
http://www.eaglegenomics.com/


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[jitesh dundas]

Dear Sir/Madam,

FYI..
Jus trying to contribute to this mailing list and help.

Regards,
Jitesh Dundas

---------- Forwarded message ----------
From: jitesh dundas <jbdundas@...>
Date: Nov 24, 2009 8:17 PM
Subject: Re: [Biojava-l] Java Error:- XML Parsing Error: XML or text
declaration not at start of entity
To: Richard Holland <holland@...>


Dear Sir,

Thank you for your reply. I figured this problem out by sending records in
small sets. e.g. 20 pages per page.

It is like a pagination functionality. For each new page, we need to hit the
URl..

My functionality is working fine.I will be happy to share my code with you
(and anyone) who needs it.

I simply fetch data from the URL and write to an XML file. Next I just read
the XML file and show them in the web page to the user.

Again, I need to know how to fetch records for protein database. Two types
of searches are needed I suspect.

First we use the Esearch utility and then the Efetch utility to get the data
of the specific protein..

I welcome any suggestions on this !

Thank you everyone for your help.

Regards,
Jitesh Dundas

On 11/24/09, Richard Holland <holland@...> wrote:

>
> 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 <andreas@...> 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@...>
> 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@...
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >>
> > <ImportFromPubmed3.jsp>_______________________________________________
> > Biojava-l mailing list  -  Biojava-l@...
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: [phone] ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

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