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

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Well done Markus. That is brilliant news.

I am not sure when I will get to try it out. I may get a chance =20
tomorrow but then I am off for with the family for a long weekend and =20=

then in meetings in London early next week so it might be a week till =20=

I get a go at it.

I'll continue working on the output models and vocabularies so we can =20=

put some more meaningful demos together.

I'm also thinking about the kind of stuff would need to add to =20
PyWrapper to make it an LSID Authority. Perhaps we could talk a =20
little about that at the workshop. I don't think it would take much =20
at all. Documentation/education would probably be the hardest part.

All the best,

Roger

On 8 Jan 2007, at 08:41, Markus D=F6ring wrote:

> And basically its done now:)
> The latest trunk gives back correct RDF, Roger!
> I haven't been able to test this version a lot, so I am nearly =20
> positive that I must have introduced some new bugs, but at least =20
> Rogers example and the queryform requests work fine!
>
> Gonna try to find some time today to do some cleanup and finally =20
> stream records and not keep the entire result in memory. we'll see.
> Markus
>
>
>
> On Jan 8, 2007, at 5:07 AM, Javier de la Torre wrote:
>
>> Hey Markus,
>>
>> You know that Elementtreee is already part of PyWrapper distribution
>> no? I am using it in the BioMOBY part.
>>
>> I think we talked about it some time ago and considered moving
>> everything in pywrapper to use it but discarded because it is quite
>> some work and we were afraid of breaking something...
>>
>> But I prefer ElementTree than minidom so I am more than happy if you
>> 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
>>> 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
>>> 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 =20=

>>> 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 =20
>>> 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.or=
g/
>>>> 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 =20
>>>> 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
>>>> ****************************************
>>>>
>>>>
>>>> -------------------------------------------------------------------=20=

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