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

Chris Fields cjfields at illinois.edu
Sun Jan 11 21:16:27 EST 2009

Works for me.  We can work on migrating the (non-working) tests and  
some minimal docs over as well.


On Jan 11, 2009, at 7:44 PM, Jason Stajich wrote:

> 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 available.
> -jason
> 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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