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

[Peter B. <p.w...@re...>]

Sure... I'll make sure all discussion is on list - it's just handy to 
have a 'hotline' text chat to solve some ID10T errors that I'd rather 
not publicise! ;-)

Cheers

Pete


Javier de la Torre wrote:
> jaja,
>
> Sorry, I thought that was Markus sending me a private email :D
>
> By the way... we have 5 days left if we wanna ask the TDWG TIP  
> project to fund a developers meeting... and probably IPGRI would also  
> be happy to collaborate on the organization of the meeting. What  
> about a meeting in IPGRI, Rome?
>
> Javi.
>
> On 10/11/2006, at 10:58, Döring, Markus wrote:
>
>   
>> -----Original Message-----
>> From: Döring, 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  
>> 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: Döring, 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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>
>
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