Re: [Treebase-devel] [eX-purgate bulk]: Re: PhyloWS, CQL, NeXML on TreeBASE2

[Rutger V. <rut...@gm...>]

Hi Bill,

glad you like it. I think I will use this on one of the days in Lisbon
to have students download data and process it.

On Fri, Jul 3, 2009 at 9:13 AM, William Piel<wil...@ya...> wrote:
> cool stuff.
> I notice that this departs a bit from the phylows that is proposed here.
>  For example, the proposed phylows puts "/find/" before "/tree/", whereas
> you have it the other way. And the other major difference is that the
> proposed phylows suggest that to search on trees you do something like:
> /phylows/find/tree/?name=Primates
> whereas you are implementing:
> /phylows/taxon/find/?name=Primates&recordSchema=tree

The former, "standard" way to me seems very ambiguous. I would
interpret it to mean the name of the tree, not of a taxon in the tree.

> Your method is probably better and clearer -- in that it makes more sense
> that we're doing a find on a taxon with the result being a tree (only the
> taxon label is inherently part of the tree object), but perhaps we should
> get the other PhyloWS developers in agreement (i.e. Ryan Scherle), and then
> modify the wiki accordingly.
> I notice that while the following produces a hit of one record:
> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo
> ...yet I'm unable to get any results via rss:
> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&format=rss1
> Is my syntax incorrect?

I don't know - I *am* getting an rss feed with a single item returned.
Maybe you should "view source" to see it?

> Also, I believe that this should give me a list of trees:
> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&recordSchema=tree
> but instead it gives me a list of taxa. Perhaps my syntax is wrong?

The recordSchema switch is only used in combination with format=rss1,
the thinking being that the web interface behaviour should stay the
same (we can switch tabs anyway to project a result set into a
different context) but for programmatic access we do need recordSchema
(because - no tabs).

Cheers,

Rutger

> On Jul 2, 2009, at 9:40 PM, Rutger Vos wrote:
>
> erm, please substitute 8ball.sdsc.edu:6666 for localhost:8080 in the
> examples below.
>
> On Thu, Jul 2, 2009 at 4:10 PM, Rutger Vos<rut...@gm...> wrote:
>
> Hi,
>
> I've implemented nexml export on treebase2, and made the serializer
>
> attach predicates from this list
>
> (http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw) in
>
> the indicated locations. The predicates with asterisks can be used as
>
> search predicates through the PhyloWS architecture as described here:
>
> http://localhost:8080/treebase-web/help/urlAPI.jsp
>
> In addition, CQL searches can be tried out on the main search tabs by
>
> clicking the "Advanced search..." links, e.g. see:
>
> http://localhost:8080/treebase-web/search/studySearch.html
>
> Rutger
>
> --
>
> Dr. Rutger A. Vos
>
> Department of zoology
>
> University of British Columbia
>
> http://www.nexml.org
>
> http://rutgervos.blogspot.com
>
>
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com