[Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests

Jason Stajich jason at bioperl.org
Mon Jan 12 01:44:07 UTC 2009

One thought is we could do is package them up in bioperl-pise in the  
event that anyone else had setup a pise server and wanted to use it -  
that was sort of what iNquiry provided I thought.  Since in this  
instance they are all related it could be best to keep them in the  
same package and helps separate them from the core.

I had hoped that eventually parameters & methodnames & validation for  
the webservices would to be autogenerated from the same XML/Grammar  
files that were used to generate the front ends rather than having to  
code method names explicitly in all the modules.  But I guess there  
will always be bridging code that converts the Bio::Seq object into  
the sequence data stream the webservice needs.

At any rate - I agree pull them out of bioperl-run for 1.6, but maybe  
migrate them to a new package for any future development.  bioperl- 
mobyle could eventually be launched if the devs want to see it  

On Jan 11, 2009, at 1:13 PM, Chris Fields wrote:

> All,
> We'll probably deprecate the Pise modules (according to Catherine's  
> response below) unless someone wants to take them over (the service  
> has been discontinued).  This will (in effect) remove 285 modules  
> from bioperl-run.
> They won't be included in the 1.6 release since the tests won't  
> pass, but it's possible the module may come in useful for setting up  
> a bioperl API for mobyle.  Should we leave them in the bioperl-run  
> main trunk or remove them?
> chris
> Begin forwarded message:
>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote:
>>> Hi,
>>> Le 10 janv. 09 à 23:01, Chris Fields a écrit :
>>>> All,
>>>> I have been updating bioperl-run tests in subversion to use  
>>>> Bio::Root::Test.  I need devs and anyone interested to check out  
>>>> the latest bioperl-run and run tests checking for failures.  I'll  
>>>> start tracking errors.
>>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests  
>>>> are failing.  I have updated the tests so they run to completion,  
>>>> but (if possible) I need some indication whether these web  
>>>> services are still available and should be incldued in a BioPerl- 
>>>> run 1.6 release.
>>> No, they are no longer available - Pise server has been replaced  
>>> by mobyle.pasteur.fr, which does not yet offer a bioperl API.  I  
>>> had sent a message to the bioperl mailing-list a few monthes ago  
>>> about this service being discontinued, but the message had been  
>>> rejected. It is possible to change the default Pise server address  
>>> - provided someone else is willing to offer these services. If  
>>> not, you can either remove the test or better, remove the Pise  
>>> modules.
>>> Best,
>>> 	Catherine Letondal
>> Thanks for letting us know Catherine.  I'll forward your response  
>> to the mail list to get everyone's response.
>> I'll remove the Pise modules from the 1.6 branch when it's ready  
>> (should be the next day or two).  We'll likely also remove it from  
>> main trunk if no one wants to take it over.  The effort into  
>> maintaining it would probably be better spent towards developing a  
>> mobyle API if anyone's interested.
>> chris
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Jason Stajich
jason at bioperl.org

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