Biomart client java help

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Biomart client java help

Francesco Fazzini

Dear all,

my name is Francesco, I premise i don't have a deep knowledge of Biomart.

I am trying to query Biomart via Java code using HTTP/REST and SOAP ways and I have problems with both:
 
SOAP: i have problem to generate the stub and binding classes with Axis(that's really strange) from Eclipse and Intellj.
The Axis version is 1.4.
  
REST: i am using Apache Http Client library to query Biomart(martview). I get an HTTP 301(Redirect, Moved permanently),so my client doesn't get in the Http response the desired value.
Service used: http://www.ebi.ac.uk/interpro/biomart/martview
 
The same client works fine for "martservice", in fact invoking this http://www.biomart.org/biomart/martservice?type=registry  i get back thecorrect result in the response.
 
I hope to have been clear, basically for SOAP i have problem to generate the client from the WSDL and for REST i have that problem with the redirect.
Do you have some suggestions? Have you already got this kind of problem? Thanks in advance.
 
Kind regards,
Francesco

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Re: Biomart client java help

Syed Haider
Dear Francesco,



On 17/01/2011 22:29, Francesco Fazzini wrote:
> Dear all,
>
> my name is Francesco, I premise i don't have a deep knowledge of Biomart.
>
> I am trying to query Biomart via Java code using HTTP/REST and SOAP ways and I have problems with both:
>
> SOAP: i have problem to generate the stub and binding classes with Axis(that's really strange) from Eclipse and Intellj.
> The Axis version is 1.4.
> Services used: http://www.ebi.ac.uk/interpro/biomart/martwsdl

Unfortunately the auto wsdl to class generators donot work great, and
axis is one of those who does not work biomart wsdl. Its not a huge
wsdl, it only has ~5 service endpoints, so you can parse it directly if
you prefer.

>
> REST: i am using Apache Http Client library to query Biomart(martview). I get an HTTP 301(Redirect, Moved permanently),so my client doesn't get in the Http response the desired value.
> Service used: http://www.ebi.ac.uk/interpro/biomart/martview

I see that your URL is not point to the service end-point, it should be
pointing to martservice e.g:
http://www.ebi.ac.uk/interpro/biomart/martservice?type=registry

MartView is not a webservice end-point.


Best,
Syed

>
> The same client works fine for "martservice", in fact invoking this http://www.biomart.org/biomart/martservice?type=registry  i get back thecorrect result in the response.
>
> I hope to have been clear, basically for SOAP i have problem to generate the client from the WSDL and for REST i have that problem with the redirect.
> Do you have some suggestions? Have you already got this kind of problem? Thanks in advance.
>
> Kind regards,
> Francesco
>
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Re: Biomart client java help

Francesco Fazzini
Dear Syed,
 
i switched to Rest Api, now using the url you provided me yesterday it works fine. Thanks.
 
Regards,
Francesco

2011/1/17 Syed Haider <[hidden email]>
Dear Francesco,




On 17/01/2011 22:29, Francesco Fazzini wrote:
Dear all,

my name is Francesco, I premise i don't have a deep knowledge of Biomart.

I am trying to query Biomart via Java code using HTTP/REST and SOAP ways and I have problems with both:

SOAP: i have problem to generate the stub and binding classes with Axis(that's really strange) from Eclipse and Intellj.
The Axis version is 1.4.
Services used: http://www.ebi.ac.uk/interpro/biomart/martwsdl

Unfortunately the auto wsdl to class generators donot work great, and axis is one of those who does not work biomart wsdl. Its not a huge wsdl, it only has ~5 service endpoints, so you can parse it directly if you prefer.



REST: i am using Apache Http Client library to query Biomart(martview). I get an HTTP 301(Redirect, Moved permanently),so my client doesn't get in the Http response the desired value.
Service used: http://www.ebi.ac.uk/interpro/biomart/martview

I see that your URL is not point to the service end-point, it should be pointing to martservice e.g:
http://www.ebi.ac.uk/interpro/biomart/martservice?type=registry

MartView is not a webservice end-point.


Best,
Syed



The same client works fine for "martservice", in fact invoking this http://www.biomart.org/biomart/martservice?type=registry  i get back thecorrect result in the response.

I hope to have been clear, basically for SOAP i have problem to generate the client from the WSDL and for REST i have that problem with the redirect.
Do you have some suggestions? Have you already got this kind of problem? Thanks in advance.

Kind regards,
Francesco



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