[DAS] DAS1.6: coordinate systems

[Andy Jenkinson]

On 12 Aug 2010, at 16:29, Andreas Prlic wrote:

>> With regards to the alignment command specifically, I wanted to use the URI for both the query and the content as they are more robust, but there was some practical reason for the existing servers that prevented us from doing so. Perhaps Rob or Andreas can comment?
> 
> Do you mean that if you have a URI as part of a URL parameter, you
> need to HTTP escape it?

I'm not sure if you need to escape or not, I don't think so.


But what I meant is that I wanted the XML content to contain the URI instead of the comma separated description, i.e.:
<alignObject dbCoordSys="http://www.dasregistry.org/dasregistry/coordsys/CS_DS123">
instead of:
<alignObject dbCoordSys="name_version,type,species">

I went through the alignment command with Rob when drawing up the 1.6 spec, and this was one of the issues we discussed. The 1.53E documentation does not say what should be used in this field. Rob preferred to use the comma separated version, probably because servers were already doing it that way.

However, the coordinate system can also be specified in the "subjectcoordsys" query parameter (to help when subjects within an alignment have the same name but different coordinate systems):
/das/mysource/alignment?query=alignid&subject=seqid&subjectcoordsys=http://www.dasregistry.org/dasregistry/coordsys/CS_DS123

I remember this being added to 1.53E, but again it is not fully described in the 1.53E documentation. In the 1.6 specification I've written that it should be the URI, but I can't remember why I wrote it this way - it could be a mistake, or there could be servers/clients doing it this way.