[PyWrapper-devel] FW: PyWrapper and Species 2000

[<m.d...@BG...>]

-----Original Message-----
From: D=F6ring, Markus=20
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 version =
of the pywrapper that works with TAPIR and BioMOBY unfortunately doesn't =
implement SPICE at all. But I don't hink this will be hard to add (I =
will come back to it later). The previous version, pywrapper 1.x, that =
run with biocase supported SPICE. So I know pretty well how the =
specification works.

With TAPIR there are more powerful configurations possible, mainly =
through the use of "output models". Using this for SPICE will make it =
much easier to implement it. The only thing we would need is an up to =
date XML Schema. Then we will have to create a separate output model for =
each request-type - we could entirely reuse the SPICE schema.

Then there would need to be a small and newly developed "protocol" layer =
for SPICE in pywrapper. That also shouldn't be too bad. Overall I would =
expect something like 2 weeks for the implementation and another week =
for testing and configuring a database like the berlin model.

The only real problem with having a generic and configurable wrapper is =
that taxonomic data is build on tree hierarchies. This is often =
represented as self-references in databases but not always. SO inorder =
to "map" your local database to the SPICE schema it usually takes quite =
some transformation which you often have to do with views, cause generic =
wrappers like pywrapper cant handle this (you cannot simply add some =
custom SQL). So all I wanted to say here is that there still remains a =
bit of the complexity. But you can be sure the wrappers do understand =
SPICE correctly and respond properly - just the data they carry might =
not be making sense if they were badly configured.

Anyway. I would be very happy if we can make pywrapper SPICE compliant =
again. Unfortunately there is not much manpower left from Javier and =
myself this year, so we could only do little things. But we would be =
very happy to assist someone trying to get into the python code and do =
it himself. Its not that hard. Would that be a 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
>=20
>=20
> Dear Markus and Javier,
>=20
> I'm currently at a Species 2000 meeting in Amsterdam and one of the
> issues that has been raised is that of assisting Global=20
> Species Database=20
> managers to provide wrappers for their databases.  As the new Species=20
> 2000 Systems Manager that responsibility apparently falls on=20
> my shoulders!
>=20
> It seems clear to me that the best approach is for me to
> assist with the=20
> development of PyWrapper by adding support for the SPICE protocol.
>=20
> I've downloaded your latest development snapshot and I'm very
> impressed=20
> - especially with the excellent level of documentation!  It's such a=20
> relief to come across a piece of scientific software with a=20
> installation=20
> manual more than 3 lines long.  :-)
>=20
> 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=20
> because the=20
> level of documentation of SPICE is very poor - something I'm=20
> also going=20
> to work on over the next couple of months.
>=20
> I'll get in touch again next week once I get back to Reading
> and hope to=20
> make progress with this quite quickly.
>=20
> Best wishes
>=20
> Peter Brewer
>=20
>  =20
>=20
>=20
>=20