[DAS2] DAS/2 writeback

[Allen Day]

Great.  Why the full das2xml feature doc instead of the mapping doc as
response?

-Allen

On 6/26/06, Helt,Gregg <Gregg_Helt at affymetrix.com> wrote:
>
>  Thanks, that helped, the problem was on my end.  Looks like I was POSTingbut 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
>
>
>
> -----Original Message-----
> *From:* allenday at gmail.com [mailto:allenday at gmail.com] *On Behalf Of *Allen
> Day
> *Sent:* Monday, June 26, 2006 3:04 PM
> *To:* Helt,Gregg
> *Subject:* Re: DAS/2 writeback
>
>
>
> The content-type shouldn't matter.  I think I was submitting with
> application/x-form-encoded, or something like that.
>
> The CGI just reads whatever you sent it directly from STDIN though.  From
> the error log it looks like you are not POSTing the document.  There is no
> web page there, you need to issue a POST request, XML doc as the body,
> directly to that CGI.
>
> -Allen
>
>  On 6/26/06, *Helt,Gregg* <Gregg_Helt at affymetrix.com> wrote:
>
> That's my guess.
>
>
>
> Also, I'm attempting to post variations of your XML example to http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/das2xml-parser/stable1.pl
>
> <http://genomics.ctrl.ucla.edu/%7Eallenday/cgi-bin/das2xml-parser/stable1.pl>,
>
>
> but so far I've only gotten "500 Internal Server Error" responses back.
> Can you tell what's happening?  Do I need to set the content-type for the
> POST or some other header?
>
>
>
>             gregg
>
>
>
> -----Original Message-----
> *From:* allenday at gmail.com [mailto:allenday at gmail.com] *On Behalf Of *Allen
> Day
>
> *Sent:* Monday, June 26, 2006 2:40 PM
> *To:* Helt,Gregg
> *Subject:* Re: DAS/2 writeback
>
>
>
> Ok, i will check into it.  Only showing human segments, is it?
>
> -Allen
>
> On 6/26/06, *Helt,Gregg* <Gregg_Helt at affymetrix.com> wrote:
>
> But there's no entry in the segment query for chrI, which is the
> chromosome you used in the the example XML you posted.  So I can't find
> those annotations via IGB.
>
>
>
>             gregg
>
>
>
> -----Original Message-----
> *From:* allenday at gmail.com [mailto:allenday at gmail.com] *On Behalf Of *Allen
> Day
> *Sent:* Monday, June 26, 2006 2:11 PM
> *To:* Helt,Gregg
> *Cc:* DAS/2
>
> *Subject:* Re: DAS/2 writeback
>
>
>
> This datasource contains both yeast and human segments.  I set it up this
> way so features can be written for either human or yeast, then viewed at
> one  of:
>
> http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature
> http://das.biopackages.net/das/genome/human/17-writeback/feature
>
> I thought this would be more useful so you can test viewing writeback
> features alongside both "real" human and yeast features.
>
> So you can just ignore the irrelevant segments, or if you'd prefer I can
> delete one set of segments or the other.
>
> -Allen
>
> On 6/26/06, *Helt,Gregg* <Gregg_Helt at affymetrix.com> wrote:
>
> Allen, thanks for getting the start of a writeback server up and
> running!
>
> I'm hoping to try writing back annotations later today.  However, I'm
> having problems looking at the annotations in the writeback server via
> IGB.  It looks to me like the main issue is that
> http://das.biopackages.net/das/genome/yeast/S228C-writeback/segment
> returns human chromosome ids in the uri attribute of the SEGMENT
> element, instead of yeast ids.  When IGB uses this to compose a query
> like
>
> http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature?over
> laps=chr1/10:15000;type=SO:centromere
>
> it gets back an empty feature list.  But if I manually edit this to
> replace "chr1" with "chrI",
>
> http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature?over
> laps=chrI/10:15000;type=SO:centromere
>
> I get back a list of feature that satisfies the query filters.
>
> Any ideas?
>
>         Thanks,
>         Gregg
>
> > -----Original Message-----
> > From: das2-bounces at lists.open-bio.org [mailto:das2-bounces at lists.open -
> > bio.org] On Behalf Of Allen Day
> > Sent: Saturday, June 24, 2006 2:24 AM
> > To: Chervitz, Steve
> > Cc: DAS/2
> > Subject: Re: [DAS2] Notes from the weekly DAS/2 teleconference, 19 Jun
> > 2006
> >
> > You can see the features that are posted here:
> >
> > http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature
> >
> > It is fully compatible with the usual yeast source:
> >
> > http://das.biopackages.net/das/genome/yeast/S228C/feature
> >
> > All the usual feature filters apply.  The response at this URL is not
> > cached
> > to keep the content fresh, at the expense of ever-slower load times as
> > written features accumulate.
> >
> > -Allen
> >
> >
> >
> > On 6/24/06, Allen Day <allenday at ucla.edu> wrote:
> > >
> > > I have a temporary CGI set up to accept WRITEBACK documents:
> > >
> > > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/das2xml-<http://genomics.ctrl.ucla.edu/%7Eallenday/cgi-bin/das2xml->
> > parser/stable1.pl< http://genomics.ctrl.ucla.edu/%7Eallenday/cgi-
> > bin/das2xml-parser/stable1.pl>
> > >
> > > I have attached a das2xml document that POSTs cleanly for me using
> the
> > > lwp-request that is part of libwww-perl.  Please modify this
> document,
> > post,
> > > and let me know if anything breaks.
> > >
> > > This implementation accepts only new records.  It supports neither
> > updates
> > > nor deletes.  Furthermore, it only accepts new feature records.  It
> does
> > not
> > > support new type records, new region records, or any other type of
> > record.
> > >
> > > Feature records may have 0 or more locations, 0 or more parents, 0
> or
> > more
> > > children, and 0 or more properties.  All parts/parents must be
> present
> > in
> > > the document (no refering to existing features by URI), or it will
> throw
> > a
> > > HTTP 500 error.
> > >
> > > Next I will implement the update and delete support.  This should be
> > > fairly straightforward, and may be doable over the weekend.
> > >
> > > -Allen
> > >
>
>
>
>
>
>
>