Re: [PyWrapper-devel] Behold RDF is born unto us!

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Hey Markus,

You know that Elementtreee is already part of PyWrapper distribution =20
no? I am using it in the BioMOBY part.

I think we talked about it some time ago and considered moving =20
everything in pywrapper to use it but discarded because it is quite =20
some work and we were afraid of breaking something...

But I prefer ElementTree than minidom so I am more than happy if you =20
do it :)

Cheers.

Javi.

On 05/01/2007, at 20:08, D=F6ring, Markus wrote:

> I have just tried to use namespaces in attributes. to make it =20
> short: it failed. Its python's minidom implementation that causes =20
> the trouble. When I use the method .setAttributeNS(myNS, =20
> myAttrName, value) it uses xmlns: on the element to define the =20
> namespace. So if the elements NS is different, it actually =20
> overwrites it! So minidom cannot handle mixed namespaces within one =20=

> element.
>
> I've checked ElementTree (which is part of python's standard since =20
> version 2.5) and there it works! It even recognises the RDF =20
> namespace and uses rdf: as the prefix without telling it so.
>
> So I have to update all of pywrapper to use ElementTree instead of =20
> minidom. This is a bit more work so I dont know when there will be =20
> time to update the code - in the worst case I could do this during =20
> the developers meeting.
>
> But at least we know it will work!
> And ElementTree is supposed to be much faster with a much smaller =20
> footprint.
>
> Cheers,
> Markus
>
>
>
>
> -----Original Message-----
> From:	pyw...@li... on behalf of =20
> D=F6ring, Markus
> Sent:	Fri 1/5/2007 5:20 PM
> To:	PyWrapper Developers mailing list
> Cc:	Roger Hyam
> Subject:	Re: [PyWrapper-devel] Behold RDF is born unto us!
>
> well done Roger!
> worked out of the box for me.
>
> I guess you are right that pywrapper ignores attribute namespaces in
> the output. I will take a look into it. Not sure how well the
> frameworks support attribute namespaces, cause I am not aware of how
> to declare namespace prefixes implicitly. The code at least knows the
> namespace of the attribute, so its only a matter of how to get it
> out. Currently I am using DOM to produce the XML but I wanted to
> migrate to Elementree at some point. I will keep you informed.
>
> Creating an alias.txt for the TDWG ontology would be the exact way we
> thought of how to use it. So far pywrapper seemed to work fine with
> multiple CNS files. Simply add a second one in the system configtool
> pane. Just make sure they dont clash - that is defining the same
> namespace or using the same namespace alias. The aliases for the
> concepts don't matter, cause they only form one part of the total
> concept alias. So we only need to keep track of the namespaces and
> their aliases.
>
> cheers,
> markus
>
>
> On Jan 4, 2007, at 5:30 PM, Roger Hyam wrote:
>
>> Happy New Year everyone.
>>
>> If you have a local pywrapper and have connected the training
>> datasource up to a database then you should be able to run this
>> query (long URL) perhaps with minor tweaks to the port etc.
>>
>> http://localhost:8080/pywrapper/pywrapper?
>> dsa=3Dtraining&op=3Dsearch&envelope=3Dfalse&model=3Dhttp://rs.tdwg.org/=

>> ontology/voc/tapir/outputmodel/
>> TaxonName_001.xml&filter=3DUnitID@abcd206+like+"2422"
>>
>> What you will get back is (but for one minor minor thing) valid RDF!
>>
>> After Markus' fix (and after Christmas) I turned to making a real-
>> life output model and it is actually quite simple once you have the
>> framework in place.
>>
>> This is still a fairly trivial example but it shows that it is
>> possible and I'll continue to build on it up to the workshop.
>>
>> **WARNING** I am using the identifications table in the training
>> dsa as if it contained pure nomenclatural data just because I have
>> the TaxonName vocabulary to hand. This is not how the vocabulary
>> should or will be used. It is just a test thing. I'll now try and
>> do some more sensible things.
>>
>> The fun part is that I use the mapped ABCD concepts in my output
>> model. So we are creating RDF from a datasource that was never
>> intended to supply it :) Not sure how possible this will be in real
>> life for retrofitting data suppliers who haven't done the mappings
>> to the central concepts but is a possibility.
>>
>> I have one question about Concept Name Servers. It would make sense
>> to have a CNS for the TDWG ontology. We could then define the RDF
>> generating models and some query templates in it along with their
>> associated concepts. We would need some convention to prevent name
>> clashes with the alias'.
>>
>> Can anyone see a problem with this? Will PyWrapper pick up multiple
>> CNS and load them all? Has this been tested?
>>
>> The mapping is fun here because the TAPIR concepts map to db
>> concepts through the regular mechanisms but are also mapped, via
>> the namespace conventions in the RDF to more general meanings.
>>
>> I also have a request. If you take the result of running the above
>> (it looks like this)
>>
>> <?xml version=3D"1.0" encoding=3D"UTF-8"?>
>>
>>
>> <RDF xmlns=3D'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
>>   <TaxonName xmlns=3D'http://rs.tdwg.org/ontology/voc/TaxonName#'
>> about=3D'2422'>
>>     <title xmlns=3D'http://purl.org/dc/elements/1.1/'>Calicium
>> adspersum Pers. subsp. australe Tibell</title>
>>     <genusPart>Calicium</genusPart>
>>     <specificEpithet>adspersum</specificEpithet>
>>     <infraspecificEpithet>australe</infraspecificEpithet>
>>   </TaxonName>
>> </RDF>
>>
>> and cut and paste it into the W3C RDF validator (http://www.w3.org/
>> RDF/Validator/) you get a single deprecated warning.
>>
>> Error: {W102} unqualified use of rdf:about is deprecated.[Line =3D 5,
>> Column =3D 78]
>>
>> It seems that PyWrapper isn't putting the namespace in for the
>> attribute in the output. I have not looked into it in detail but it
>> is specified in the model and other namespace stuff is followed so
>> I guess it is a bug (this is the minor minor thing that will come
>> to bite us when we need rdf:resource references going).
>>
>> Could someone with their hands on the code (sorry is that you
>> Markus!) look at this one. Then I think we will be really RDF
>> compatible.
>>
>> Many thanks,
>>
>> All the best,
>>
>> Roger
>>
>>
>> ****************************************
>>   Roger Hyam <ro...@td...>
>>   Biodiversity Information Standards
>> ****************************************
>>
>>
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