[Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests
jason at bioperl.org
Sun Jan 11 20:44:07 EST 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:
> 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?
> Begin forwarded message:
>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote:
>>> Le 10 janv. 09 à 23:01, Chris Fields a écrit :
>>>> 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
>>> 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.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
jason at bioperl.org
More information about the Bioperl-l