On 12 Aug 2010, at 15:35, Andy Jenkinson wrote:
On 12 Aug 2010, at 12:16, Thomas Down wrote:
A few other questions (don't really have "preferred" answers to any
of these, just trying to test the boundaries):
1. What do you expect a server to do if it sees a CS URI
that it hasn't seen before?
I assume you mean an alignment server receiving such a URI as a
parameter? If so I think there is only one realistic thing it can do
right now, which is return nothing (i.e. no alignments). It is not
an authority on which coordinate systems are real and which aren't,
it just knows about the ones it is using. In essence it simply has
no data for the requested subject because it doesn't recognise the
subject. We could invent error situations for things like this, but
that would make DAS more complex for little gain IMO..
2. If my organization has sequenced a new genome and is
running some internal DAS stuff on that while we finish annotating,
etc., what URI do we use for the coordinate system?
3. If my organization is running an internal mirror of the
central DAS registry, would I mirror the CS URIs ("http://das.bigpharma.com/dasregistry/coordsys/CS_DS40/
"). Still point to dasregistry.org? Something else?
As Jon says, I think it's easier just to create the coordinate
system in the registry. At the moment you need admin privileges to
do that via the interface, but I implemented a programmatic version
of this wherein the registry accepts POSTed coordinate system XML
(sans URI) and replies with the same (with URI included). It is
restricted to allow you to create new authority/versions, but not
new "segment types": so you can create "GRCh_38,Chromosome,Homo
sapiens" but not "GRCh_37,wibble,Homo sapiens". We were a bit wary
of opening up the ability to do the latter in fear of ending up with
different spellings of the same thing, or other similar issues.
I suppose the same thing could be made available to registered users
in the interface (possibly at the same time reworking it to use the
web services underneath).
This functionality is currently available in the interface for admin
users.
Thomas.
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Jonathan Warren
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blog: http://biodasman.wordpress.com/
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