[DAS2] DAS/2 writeback

[Helt,Gregg]

I'm pretty familiar with a few annotated regions in human, which should
help for testing, so I'd vote for human.
 
            thanks!
            gregg
 
-----Original Message-----
From: allenday at gmail.com [mailto:allenday at gmail.com] On Behalf Of Allen
Day
Sent: Monday, June 26, 2006 11:55 PM
To: Helt,Gregg
Cc: DAS/2
Subject: Re: [DAS2] DAS/2 writeback
 
Hi Gregg,

Sounds like it was a bad idea for me to make a chimeric data source -- I
don't want to debug bugs related to this, as it is really a
misapplication of the vsource in the first place.

Which would you prefer to have -- human or yeast?  I will zap the
segments and features for the one you don't want, and remove the vsource
from das.biopackages.net

-Allen


On 6/26/06, Helt,Gregg <Gregg_Helt at affymetrix.com> wrote:
Things are getting stranger.  I'm trying to writeback annotations on
chr21, and they seem to succeed, returning me an id mapping document.
But once I've sent the annotations to the server, then try to retrieve
them, I can't always see them from the human source.  But I can see them

from the yeast source.  This is easiest to see with a simple query to
get all features.  A query to the yeast writeback source to get all
features:
http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature

currently returns 30 features (top-level and children), including the
ones I've added on chr21.

However a query to the human writeback source for all features: 
http://das.biopackages.net/das/genome/human/writeback/feature

currently returns only 9 features (top-level and children), all on chrI.


Furthermore, if I restrict my human query with a region filter:
http://das.biopackages.net/das/genome/human/writeback/feature?overlaps=c

hr21/0:46944323

I _do_ get back the 5 top-level "centromere" annotations I've added to
chr21, and their children.  But if I then add a type filter:
http://das.biopackages.net/das/genome/human/writeback/feature?overlaps=c
hr21/0:46944323;type=SO:centromere

I only get back 1 top-level "centromere" feature and it's children.

I'm not sure what it all means, but I'm hoping the results above may 
help diagnose the problem.

        Thanks,
        Gregg

> -----Original Message-----
> From: das2-bounces at lists.open-bio.org [mailto: das2-bounces at lists.open
<mailto:das2-bounces at lists.open> -
> bio.org] On Behalf Of Helt,Gregg
> Sent: Monday, June 26, 2006 3:43 PM
> To: allenday at ucla.edu
> Cc: DAS/2 
> Subject: Re: [DAS2] DAS/2 writeback
>
> Thanks, that helped, the problem was on my end.  Looks like I was
> POSTing but not making sure the data buffer was flushed out to the
> server before I tried to read the server response.  I fixed that, now 
I
> get a mapping document back.  I'm not sure how much effort to put into
> parsing the mapping doc though - the next update of the spec is
supposed
> to change so that rather than a new mapping document type, the server 
> responds with the full feature XML of the created/updated features.
>
> More progress - if I stick to the human genome (chr21), after the
> writeback I'm able to retrieve the features via DAS/2 and visualize in

> IGB.
>
>             thanks again,
>             Gregg
>