[Iplant-api-dev] loading iRODS data into the browser

[Matthew Vaughn]

This is pretty interesting actually. I just grabbed the header from the IO service, returning that BAM file I linked earlier...

HTTP/1.1 200 OK
Date: Wed, 29 Aug 2012 15:22:48 GMT
Server: Noelios-Restlet-Engine/1.2.m1
Vary: Accept-Charset,Accept-Encoding,Accept-Language,Accept
Accept-Ranges: bytes
Access-Control-Allow-Origin: *
Content-Type: application/octet-stream
Connection: close

It should actually be allowing and handling byte range requests! In fact, IGV is not complaining about errors until it tries to do a seek on the BAM file to display reads. 

On Aug 29, 2012, at 10:00 AM, Cornel Ghiban wrote:

> Hi Matt,
> 
> Thanks for letting us know about user "world" (I was sharing the files to a "dnasubway" user and then have this user stream the files directly to the browser).
> But it still doesn't work since IGV insists on using the "range-byte" requests.
> 
> Thanks,
> Cornel
> 
> On 8/28/2012 6:05 PM, Matthew Vaughn wrote:
>> This is very close, as it presents a publicly available HTTP link for the BAM file, but it doesn't support byte-range fetch.
>> 
>> # Update to your own path, credentials, etc
>> 
>> # Make the BAM and BAI file readable to user 'world'
>> curl -X POST -sku "vaughn" -d "username=world" -d "canRead=true" -d "canWrite:false"  https://foundation.iplantcollaborative.org/io-v1/io/share/vaughn/testbam/bwa_s_6_BC12_sorted.bam
>> 
>> curl -X POST -sku "vaughn" -d "username=world" -d "canRead=true" -d "canWrite:false"  https://foundation.iplantcollaborative.org/io-v1/io/share/vaughn/testbam/bwa_s_6_BC12_sorted.bam.bai
>> 
>> # Access un-authenticated via the /download endpoint
>> curl -X GET -sk https://foundation.iplantc.org/io-v1/io/download/vaughn/testbam/bwa_s_6_BC12_sorted.bam
>> 
>> On Aug 28, 2012, at 4:20 PM, Cornel Ghiban wrote:
>> 
>>> Hi Roger,
>>> 
>>> Well, I was thinking to save some time (and disk space) and stream the bam
>>> files from iRODS to IGV via a perl script, but it looks like IGV requests
>>> use Range headers and it wants slices of the BAM file. I don't think my perl
>>> script will be able to handle this :)
>>> 
>>> Thanks,
>>> Cornel
>>> 
>>> On 8/28/2012 5:15 PM, Barthelson, Roger A - (rogerab) wrote:
>>>> Hi Cornel-
>>>> 
>>>> I assume you mean that you have a running instance of IGV, and you want to
>>>> move BAM files into it. Normally you would want to use icommands or
>>>> similar to move the files into place before you start, but if that is not
>>>> possible for what you are doing, then it seems like maybe you would need
>>>> to have a separate thread run to move the files into place. I doubt there
>>>> is a way of having, for example, IGV address iRods directly. Maybe there
>>>> is somewhere, but I haven't heard of it. So, I think you have to move the
>>>> files into place with a different thread and then open them from IGV. I'm
>>>> not sure how that would work. I found this mysterious perl script
>>>> recently, maybe it could help.
>>>> 
>>>> Roger
>>>> 
>>>> 
>>>> Roger Barthelson Ph.D.
>>>> Bioinformatics Analyst
>>>> iPlant Collaborative
>>>> BIO5 Institute, University of Arizona
>>>> Phone: 520-977-5249
>>>> Email: rogerab at email.arizona.edu
>>>> Web: http://www.iplantcollaborative.org/
>>>>            http://bio-it.arizona.edu/Roger_Barthelson_Home.html
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On 8/28/12 1:42 PM, "Cornel Ghiban" <ghiban at cshl.edu> wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Is there an easy way of sending some data to the user?
>>>>> What I'd like to do is send some BAM files into IGV.
>>>>> 
>>>>> ( I've tried using a proxy web-script, but for some reason IGV fails to
>>>>> load
>>>>> the data. If I save the data to disk and then manually load it into IGV
>>>>> it
>>>>> works fine. )
>>>>> 
>>>>> Thanks,
>>>>> Cornel
>>>>> _______________________________________________
>>>>> Iplant-api-dev mailing list
>>>>> Iplant-api-dev at iplantcollaborative.org
>>>>> http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev
>>>> 
>>> _______________________________________________
>>> Iplant-api-dev mailing list
>>> Iplant-api-dev at iplantcollaborative.org
>>> http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev
>> 
>> --
>> Matthew W. Vaughn, Ph.D.,
>> Manager, Life Sciences Computing Group
>> Texas Advanced Computing Center
>> Austin, TX
>> vaughn at tacc.utexas.edu | (949) 436-6642
>> 
>> 

--
Matthew W. Vaughn, Ph.D.,
Manager, Life Sciences Computing Group
Texas Advanced Computing Center
Austin, TX
vaughn at tacc.utexas.edu | (949) 436-6642