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
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/01c20b18df68f00c016ef28e9d8bac2043...
I added an API endpoint for downloading datasets from Galaxy in https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equiv... 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 BZeitner@benaroyaresearch.org 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/
galaxy-dev@lists.galaxyproject.org
-
Brad Zeitner -
John Chilton