Hi Thomas and Andy
Thanks for posting this to the list.
I don't think from our brief discussions at the Sanger/EBI that people
here would object to moving to the DAS2 way for parents/parts. My
impression of the DAS2 spec was that it was thought about and
discussed in great detail and thus there would be very good reasons
for doing it this way? Also an advantage of moving to this way is that
it has been tested by people implementing DAS2 extensively already?
As the DAS 1.6 spec is in pretty much every other respect (apart from
minor things like cvIds) a consolidation of the way DAS "IS" being
used in the community surely it has been tested already?
The main principles of the 1.6 spec have been largely unchanged for
over a year and were agreed by everyone at the 3rd day of the workshop
in 2009- most changes say over the last 6 months I believe have
largely been clarifications. The last year or so the DAS1.6 spec was
supposed to be in a testing phase - but I agree that maybe not many
clients have tested it yet. There has been much work at the EBI on
clients and servers for proteins with 1.6.
I would like the spec to be set in stone, but I don't think it needs
to be that way and I don't see that it can't be tweaked if needs be
shortly after initial release. I think by releasing the spec we are
saying "this is how the DAS community think the system should work
and we have provided servers that conform to that spec, code that will
help clients process the xml and a registry that can validate and hold
1.6 data sources". Given the lack of testing buy clients so far, I'm
not sure how we can move DAS forward any other way?
The current situation is that Andy has kindly agreed to postpone the
release for another week or so for developers to look at the spec and
preferably do some testing with it.
It would be really great to get some more feedback from client
developers and some more 1.6 clients out there using 1.6 - thanks for
your wise words Thomas.
On 2 Sep 2010, at 17:35, Thomas Down wrote:
On Tue, Aug 31, 2010 at 5:28 PM, Andy Jenkinson <[email protected]
>wrote:
Hi all,
As many of you know, DAS version 1.6 has been in development for a
while
now, and we would really like to get it out of the door and
"official". To
this end, we aim to do the following:
1. resolve the remaining questions over the current draft
(principally,
alignments and categorize) *
2. ensure core Java and Perl software libraries support the
specification
**
3. officially switch over ***
4. developers of solid client and server implementations will
announce
dates for 1.6 support
I agree that it'll be nice to get this out, although I'm still kind-of
nervous about setting changes in stone when there aren't already
implementations out there (client-side, in particular). Are there any
client developers who've had a good poke around and can reassure me?
The other concern (which I've only just noticed, and had some
discussions
off-list with Andy) is that -- in the new PART/PARENT system -- it is
explicitly stated that you'll only get features overlapping the query
region. Features outside the query region will be excluded even if
they're
PARTs of something that is included (e.g., you'll only get a subset
of exons
for a gene).
To my mind, the biggest advantage of a feature hierarchy system over
the
GROUP system it replaces is that you can guarantee that you'll get the
complete dataset for a complex feature in a single fetch. I note
that the
DAS/2 spec (which has a very similar PART/PARENT system) takes the
opposite
approach and states that you'll always get complete graphs of
features back.
Given that this is a new (to DAS/1) system, is there any reason not
to do
things the DAS/2 way?
Thomas.
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
[email protected]
Ext: 2314
Telephone: 01223 492314
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