[DAS] Dalliance: a new genome DAS client

Wed Aug 4 20:14:08 UTC 2010

No, it will be a while before this version is up on a live site.

Lincoln

On Wed, Aug 4, 2010 at 3:35 PM, Thomas Down <thomas.a.down at gmail.com> wrote:

> 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>
>> _______________________________________________
>> 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>