[Biojava-dev] Biojava Interface to BLAST web/remote services

[Sylvain Foisy]

Hi Scooter,

That is one way of doing it ;-) I was thinking of creating an object that
the user would either:

- Feed into the BJ Blast parser
- Do something else entirely.

Best regards

Sylvain

On 04/06/09 09:28, "[NAME]" <[ADDRESS]> wrote:

> Sylvain
> 
> Given that BioJava already has a BLAST file parser that returns results
> the goal should be to have a remote/web call return the same set of
> classes as if you had parsed the file locally. That is going to be my
> approach. Once we get a couple services working we can integrate into a
> common factory/interface approach.
> 
> Thanks
> 
> Scooter
> 
> 
> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org
> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Sylvain
> Foisy
> Sent: Thursday, June 04, 2009 9:07 AM
> To: Scooter Willis; Andreas Prlic
> Cc: biojava-dev at lists.open-bio.org
> Subject: Re: [Biojava-dev] Biojava Interface to BLAST web/remote
> services
> 
> Hi Scooter,
> 
> On 04/06/09 07:38, "[NAME]" <[ADDRESS]> wrote:
> 
>> Looks like the rolled their own URL interface and did not do a WSDL.
> Not a big
>> deal but does appear they have some sort of submit get a "ticket" and
> then
>> check back with the "ticket" identifier for the results. The BioJava
> API would
>> hide the transport layer so you could use a custom URL approach or web
>> services. 
> 
> That is basically the way it works. I am working on a RemoteBlastWrapper
> class that would do exactly what you are writing.
> 
>   
>> Not sure how the other WSDL interfaces handle long running tasks but I
> assume
>> the Web Services can handle a call that takes say 5 minutes to respond
> without
>> timing out. Some process would need to distinguish between a long
> running
>> server task and a server that is no longer responding.
> 
> We'll have to try ;-)
> 
> Best regards
> 
> Sylvain
> 
> 
> ===================================================================
> 
>  Sylvain Foisy, Ph. D.
>  Consultant Bio-informatique / Bioinformatics
>  Diploide.net - TI pour la vie / IT for Life
> 
>  Courriel: sylvain.foisy at diploide.net
>  Web: http://www.diploide.net
>  Tel: (514) 893-4363
> ===================================================================
> 
> 
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