[DAS2] DAS/2 writeback

Allen Day allenday at ucla.edu
Tue Jun 27 06:54:52 UTC 2006

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


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-
> > 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
> >

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