[DAS2] [DAS] [Fwd: Re: Writeback implementation]

[Gregg Helt]

Sorry for being imprecise about URIs, what I meant to say was that every
feature in DAS/2.0 has a unique _absolute_ URI.  Most IDs can be treated as
relative URIs but not absolute URIs, and referring to relative URIs is not
particularly useful outside their context.

Furthermore technically not all arbitrary ID strings can actually be
relative URIs either.  I thought this was mostly a theoretical issue until
my Trellis/Ivy DAS1-->DAS2 proxy choked on such a case on only the third
DAS1 data source I was testing,
http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_CD4.  It returns features
that derive their IDs from their genomic location, like
"21:26029715,26029814".  Which can't be any form of URI, because according
to the URI syntax spec <http://tools.ietf.org/html/rfc3986> the appearance
of the colon before any forward slash means the "21" should be treated as
the URI scheme, but the scheme can't have a digit as the first character.
This isn't just a rare instance either -- I count at least sixteen data
sources like this (probably more) on ProServer servers for the latest human
genome assembly alone.  On a side note, I'm not sure if these IDs are legal
DAS1.53 feature IDs either, since many of them will not be unique within
their DAS server, and depeding on how you interpret the 1.53 spec the colon
may not be a legal ID character.

The Trellis/Ivy proxy now deals with these cases, but checking each ID to
see if it's a legal URI, and figuring out what to do if it's not, is
definitely adding some performance overhead to the proxy.

This also points to the need for better validation of server responses,
preferably as enhancements to the validation that the DAS1 registry already
does.  I doubt if the current DAS2 validator would catch these kinds of
things either.

I'll chime in with my opinion on the other issues you raise in another
email...

     Gregg

On Wed, Oct 29, 2008 at 12:04 PM, Andy Jenkinson
<andy.jenkinson at ebi.ac.uk>wrote:

> The difference between an ID and a URI is not so great, any ID can be a URI
> if we refer to the URN definition.