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

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

I've checked ElementTree (which is part of python's standard since =
version 2.5) and there it works! It even recognises the RDF namespace =
and uses rdf: as the prefix without telling it so.

So I have to update all of pywrapper to use ElementTree instead of =
minidom. This is a bit more work so I dont know when there will be time =
to update the code - in the worst case I could do this during the =
developers meeting.

But at least we know it will work!
And ElementTree is supposed to be much faster with a much smaller =
footprint.

Cheers,
Markus

-----Original Message-----
From:	pyw...@li... on behalf of =
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 =20
the output. I will take a look into it. Not sure how well the =20
frameworks support attribute namespaces, cause I am not aware of how =20
to declare namespace prefixes implicitly. The code at least knows the =20
namespace of the attribute, so its only a matter of how to get it =20
out. Currently I am using DOM to produce the XML but I wanted to =20
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 =20
thought of how to use it. So far pywrapper seemed to work fine with =20
multiple CNS files. Simply add a second one in the system configtool =20
pane. Just make sure they dont clash - that is defining the same =20
namespace or using the same namespace alias. The aliases for the =20
concepts don't matter, cause they only form one part of the total =20
concept alias. So we only need to keep track of the namespaces and =20
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 =20
> datasource up to a database then you should be able to run this =20
> query (long URL) perhaps with minor tweaks to the port etc.
>
> http://localhost:8080/pywrapper/pywrapper?=20
> =
dsa=3Dtraining&op=3Dsearch&envelope=3Dfalse&model=3Dhttp://rs.tdwg.org/=20
> ontology/voc/tapir/outputmodel/=20
> 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-=20
> life output model and it is actually quite simple once you have the =20
> framework in place.
>
> This is still a fairly trivial example but it shows that it is =20
> possible and I'll continue to build on it up to the workshop.
>
> **WARNING** I am using the identifications table in the training =20
> dsa as if it contained pure nomenclatural data just because I have =20
> the TaxonName vocabulary to hand. This is not how the vocabulary =20
> should or will be used. It is just a test thing. I'll now try and =20
> do some more sensible things.
>
> The fun part is that I use the mapped ABCD concepts in my output =20
> model. So we are creating RDF from a datasource that was never =20
> intended to supply it :) Not sure how possible this will be in real =20
> life for retrofitting data suppliers who haven't done the mappings =20
> to the central concepts but is a possibility.
>
> I have one question about Concept Name Servers. It would make sense =20
> to have a CNS for the TDWG ontology. We could then define the RDF =20
> generating models and some query templates in it along with their =20
> associated concepts. We would need some convention to prevent name =20
> clashes with the alias'.
>
> Can anyone see a problem with this? Will PyWrapper pick up multiple =20
> CNS and load them all? Has this been tested?
>
> The mapping is fun here because the TAPIR concepts map to db =20
> concepts through the regular mechanisms but are also mapped, via =20
> the namespace conventions in the RDF to more general meanings.
>
> I also have a request. If you take the result of running the above =20
> (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#' =20
> about=3D'2422'>
>     <title xmlns=3D'http://purl.org/dc/elements/1.1/'>Calicium =20
> 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/=20
> 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 =20
> attribute in the output. I have not looked into it in detail but it =20
> is specified in the model and other namespace stuff is followed so =20
> I guess it is a bug (this is the minor minor thing that will come =20
> to bite us when we need rdf:resource references going).
>
> Could someone with their hands on the code (sorry is that you =20
> Markus!) look at this one. Then I think we will be really RDF =20
> compatible.
>
> Many thanks,
>
> All the best,
>
> Roger
>
>
> ****************************************
>   Roger Hyam <ro...@td...>
>   Biodiversity Information Standards
> ****************************************
>
>
> ---------------------------------------------------------------------- =

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