Problems downloading files via bioblend

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Problems downloading files via bioblend

Brad Zeitner
I have a python script that I use to download the qc data generated in one of the steps in a workflow.
It used to work on a previous install of galaxy – but we’ve gone through and updated our Galaxy install so that it’s now running on a new file system - and when I try and use the bioblend api to download the dataset the request for the file gets redirected to the login page.

The call to download it is - 
dm = gi.datasets.download_dataset(qcf.get("id"), outfile, False )
Where qcf is the history step
This calls the following url:/datasets/4fa2da3cf0e735a4/display?to_ext=html

If I visit the url in a browser that’s not in a session, it behaves the same way – but works correctly when I am logged in.
How can I access this using the api key?  When I add the parameters key=${myKey}  it still fails.

Thanks,
-Brad Zeitner


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Re: Problems downloading files via bioblend

John Chilton-4
Yes sorry about this - Eric reported this same problem this week.
bioblend is not using API endpoints to download datasets and this is a
problem for proxies with REMOTE_USER configured since most such
proxies are only configured to allow through requests on /api and this
is definitely not the route bioblend is using. I fixed a problem
earlier this week and know at least bioblend is consistently using the
wrong URL.

https://github.com/afgane/bioblend/commit/01c20b18df68f00c016ef28e9d8bac20435dbe31

I added an API endpoint for downloading datasets from Galaxy in
https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equivalent-of-dataset-display/diff
and I used it for some stuff - but it seems it has never made it into
bioblend. I will try to find some time to update bioblend to use this
- very sorry.

-John

On Thu, Aug 21, 2014 at 5:55 PM, Brad Zeitner
<[hidden email]> wrote:

> I have a python script that I use to download the qc data generated in one
> of the steps in a workflow.
> It used to work on a previous install of galaxy – but we’ve gone through and
> updated our Galaxy install so that it’s now running on a new file system -
> and when I try and use the bioblend api to download the dataset the request
> for the file gets redirected to the login page.
>
> The call to download it is -
> dm = gi.datasets.download_dataset(qcf.get("id"), outfile, False )
> Where qcf is the history step
> This calls the following url:/datasets/4fa2da3cf0e735a4/display?to_ext=html
>
> If I visit the url in a browser that’s not in a session, it behaves the same
> way – but works correctly when I am logged in.
> How can I access this using the api key?  When I add the parameters
> key=${myKey}  it still fails.
>
> Thanks,
> -Brad Zeitner
>
> ________________________________
> --CONFIDENTIALITY NOTICE--: The information contained in this email is
> intended for the exclusive use of the addressee and may contain confidential
> information. If you are not the intended recipient, you are hereby notified
> that any form of dissemination of this communication is strictly prohibited.
> www.benaroyaresearch.org
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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