Re: [PyWrapper-devel] FW: PyWrapper and Species 2000

[Javier de la T. <ja...@gm...>]

Thanks, got that....

I agree with you, enforce the use of the mailing lists as much as =20
possible!! No private like with Milko, discussions everything public.

Javi.

On 10/11/2006, at 10:58, D=F6ring, Markus wrote:

>
>
> -----Original Message-----
> From: D=F6ring, Markus
> Sent: Freitag, 10. November 2006 10:08
> To: 'Peter Brewer'; Torre de la, Javier
> Subject: RE: PyWrapper and Species 2000
>
>
> Peter,
>
> We are happy to hear that interest from species2000. The current =20
> version of the pywrapper that works with TAPIR and BioMOBY =20
> unfortunately doesn't implement SPICE at all. But I don't hink this =20=

> will be hard to add (I will come back to it later). The previous =20
> version, pywrapper 1.x, that run with biocase supported SPICE. So I =20=

> know pretty well how the specification works.
>
> With TAPIR there are more powerful configurations possible, mainly =20
> through the use of "output models". Using this for SPICE will make =20
> it much easier to implement it. The only thing we would need is an =20
> up to date XML Schema. Then we will have to create a separate =20
> output model for each request-type - we could entirely reuse the =20
> SPICE schema.
>
> Then there would need to be a small and newly developed "protocol" =20
> layer for SPICE in pywrapper. That also shouldn't be too bad. =20
> Overall I would expect something like 2 weeks for the =20
> implementation and another week for testing and configuring a =20
> database like the berlin model.
>
> The only real problem with having a generic and configurable =20
> wrapper is that taxonomic data is build on tree hierarchies. This =20
> is often represented as self-references in databases but not =20
> always. SO inorder to "map" your local database to the SPICE schema =20=

> it usually takes quite some transformation which you often have to =20
> do with views, cause generic wrappers like pywrapper cant handle =20
> this (you cannot simply add some custom SQL). So all I wanted to =20
> say here is that there still remains a bit of the complexity. But =20
> you can be sure the wrappers do understand SPICE correctly and =20
> respond properly - just the data they carry might not be making =20
> sense if they were badly configured.
>
> Anyway. I would be very happy if we can make pywrapper SPICE =20
> compliant again. Unfortunately there is not much manpower left from =20=

> Javier and myself this year, so we could only do little things. But =20=

> we would be very happy to assist someone trying to get into the =20
> python code and do it himself. Its not that hard. Would that be a =20
> possibility?
>
> With thanks,
> Markus
>
>
>
>> -----Original Message-----
>> From: Peter Brewer [mailto:p.w...@re...]
>> Sent: Freitag, 10. November 2006 09:32
>> To: D=F6ring, Markus; Torre de la, Javier
>> Subject: PyWrapper and Species 2000
>>
>>
>> Dear Markus and Javier,
>>
>> I'm currently at a Species 2000 meeting in Amsterdam and one of the
>> issues that has been raised is that of assisting Global
>> Species Database
>> managers to provide wrappers for their databases.  As the new Species
>> 2000 Systems Manager that responsibility apparently falls on
>> my shoulders!
>>
>> It seems clear to me that the best approach is for me to
>> assist with the
>> development of PyWrapper by adding support for the SPICE protocol.
>>
>> I've downloaded your latest development snapshot and I'm very
>> impressed
>> - especially with the excellent level of documentation!  It's such a
>> relief to come across a piece of scientific software with a
>> installation
>> manual more than 3 lines long.  :-)
>>
>> What is the current level of support for SPICE in the PyWrapper?  Has
>> anything been done yet?  I'd be quite surprised if there has
>> because the
>> level of documentation of SPICE is very poor - something I'm
>> also going
>> to work on over the next couple of months.
>>
>> I'll get in touch again next week once I get back to Reading
>> and hope to
>> make progress with this quite quickly.
>>
>> Best wishes
>>
>> Peter Brewer
>>
>>
>>
>>
>>
>
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