[DAS] Dalliance: a new genome DAS client

Thomas Down thomas.a.down at gmail.com
Wed Aug 4 19:35:58 UTC 2010


That's great Lincoln.

I don't suppose there's an updated server up somewhere that I could test
against?

Thanks,

             Thomas.


On Wed, Aug 4, 2010 at 8:26 PM, Lincoln Stein <lincoln.stein at gmail.com>wrote:

> Thanks for the pointers. I've added CORS capabilities to the GBrowse DAS
> server.
>
> Lincoln
>
> On Wed, Aug 4, 2010 at 11:03 AM, Leyla Garcia <ljgarcia at ebi.ac.uk> wrote:
>
> > Thanks Andy and Jonathan,
> >
> > The CORS header is already in MyDAS and it will be available for the next
> > release, which will be soon :)
> > I will check the specification about Access-Control-Expose-Headers
> >
> > Jonathan, I am checking the response headers with an add-on in Firefox. I
> > tried the first URL in the dasregistry link you send me, i.e.
> > http://cathdb.info:9000/das/cath_pdb/features?segment=5pti
> > but I do not see the Access-Control-Allow-Origin header there. So I am
> not
> > sure what I missing...
> >
> > Leyla
> >
> >
> >
> > On 04/08/2010 15:54, Jonathan Warren wrote:
> >
> >> resp.setHeader("Access-Control-Allow-Origin", "*");
> >>
> >> On 4 Aug 2010, at 15:51, Jonathan Warren wrote:
> >>
> >>  This url list 150 das sources that implement cors - see traffic light
> on
> >>> the end:
> >>>
> >>>
> >>>
> http://www.dasregistry.org/listServices.jsp?organism=any&CSName=any&CSTypes=any&capabilities=cors&labels=any&spec=any&cmd=find
> <
> >>>
> http://www.dasregistry.org/listServices.jsp?organism=any&CSName=any&CSTypes=any&capabilities=cors&labels=any&spec=any&cmd=find
> >>> >
> >>>
> >>>
> >>> You can check the headers responses for any of their valid responses.
> >>>
> >>> If you  want some java code that adds this functionality to MyDAS I can
> >>> send it to you...
> >>>
> >>> On 4 Aug 2010, at 15:03, Leyla Garcia wrote:
> >>>
> >>>  About CORS,
> >>>>
> >>>> >If you run your own DAS servers and
> >>>> >don't list them in the registry, you'll need to check for CORS
> >>>> compatibility
> >>>> >yourself.  The latest versions of Proserver and Dazzle should both be
> >>>> okay.
> >>>>
> >>>> If I am not mistaken, Proserver already implements CORS headers?
> >>>> Andy, could you please send me a link of a Proserver server that
> >>>> implements this?
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Leyla
> >>>>
> >>>> On 03/08/2010 21:52, Jonathan Warren wrote:
> >>>>
> >>>>> This is very cool - I had a look the other day. Was wondering why
> some
> >>>>> sources could be attached and some can't....
> >>>>> Best browser experience yet by far I'd say.
> >>>>>
> >>>>> No problems about adding CORS support - for the record I'm very happy
> >>>>> to implement new capabilities testing and other suggestions to the
> registry
> >>>>> from anyone who cares to drop me a line. Especially if it's going to
> enhance
> >>>>> and promote the use of the registry :)
> >>>>>
> >>>>>
> >>>>> On 3 Aug 2010, at 20:41, Thomas Down wrote:
> >>>>>
> >>>>>  As some of you already know, I've been experimenting recently with a
> >>>>>> web-based DAS client for genomic data.  It's still in
> >>>>>> a unashamedly prototypical state (in particular, some of the popups
> >>>>>> and
> >>>>>> configuration stuff is outright clunky, and we know it!), but we're
> >>>>>> starting
> >>>>>> to find it quite useful, and would be interested to receive more
> >>>>>> feedback.
> >>>>>> So if you're curious, you can try it here:
> >>>>>>
> >>>>>>            http://www.biodalliance.org/human/ncbi36/
> >>>>>>
> >>>>>> It's a fully-fledged DAS/1.53 client (with a few bits of DAS/1.6,
> and
> >>>>>> hopefully rather more coming soon), but has one major caveat: since
> >>>>>> it's
> >>>>>> pure Javascript code running in your web browser, there are
> >>>>>> limitations to
> >>>>>> which servers it can connect to.  Specifically, it will only work
> with
> >>>>>> DAS
> >>>>>> servers that implement the W3C cross-origin resource sharing model
> >>>>>> (which
> >>>>>> has been discussed on this list before, but drop me a line if you've
> >>>>>> got any
> >>>>>> questions).  What does this mean in practice?  If you're adding
> >>>>>> datasources
> >>>>>> from the registry, things are simple because Dalliance will only
> allow
> >>>>>> you
> >>>>>> to add CORS-enabled sources (a huge thanks to Jonathan Warren for
> >>>>>> adding
> >>>>>> some support for this in the registry).  If you run your own DAS
> >>>>>> servers and
> >>>>>> don't list them in the registry, you'll need to check for CORS
> >>>>>> compatibility
> >>>>>> yourself.  The latest versions of Proserver and Dazzle should both
> be
> >>>>>> okay.
> >>>>>>
> >>>>>> All comments, suggestions, and bug reports are welcome!
> >>>>>>
> >>>>>>                Thomas Down.
> >>>>>> _______________________________________________
> >>>>>> DAS mailing list
> >>>>>> DAS at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/das
> >>>>>>
> >>>>>
> >>>>> Jonathan Warren
> >>>>> Senior Developer and DAS coordinator
> >>>>> blog: http://biodasman.wordpress.com/
> >>>>> jw12 at sanger.ac.uk
> >>>>> Ext: 2314
> >>>>> Telephone: 01223 492314
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>> _______________________________________________
> >>>> DAS mailing list
> >>>> DAS at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/das
> >>>>
> >>>
> >>> Jonathan Warren
> >>> Senior Developer and DAS coordinator
> >>> blog: http://biodasman.wordpress.com/
> >>> jw12 at sanger.ac.uk
> >>> Ext: 2314
> >>> Telephone: 01223 492314
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >> Jonathan Warren
> >> Senior Developer and DAS coordinator
> >> blog: http://biodasman.wordpress.com/
> >> jw12 at sanger.ac.uk <mailto:jw12 at sanger.ac.uk>
> >>
> >> Ext: 2314
> >> Telephone: 01223 492314
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> >> Limited, a charity registered in England with number 1021457 and a
> company
> >> registered in England with number 2742969, whose registered office is
> 215
> >> Euston Road, London, NW1 2BE.
> >>
> >
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
> >
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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>



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