[DAS] GBrowse as a DAS client
Jonathan Warren
jw12 at sanger.ac.uk
Thu Aug 5 08:47:20 UTC 2010
Hi Lincoln
I noticed for the GBrowse clients that I've seen online that the
option of a user adding a DAS track is not available, only the GBrowse
provider can do so in the config?
For the new GBrowse is there a plan/chance that it will use the
registry and/or allow people to specify a url directly?
There is some registry code available now that is written purely in
javascript that would make interacting with the registry very easy to
add.
On 4 Aug 2010, at 21:14, Lincoln Stein wrote:
> 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>
> _______________________________________________
> 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
--
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.
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