Easy linkage to user dataset files
Dear Galactic Overlords, I'd like to be able to provide external access via HTTP GET-able URL to individual data files that are generated in the course of Galaxy analysis. For example, say a user wanted to import her data in Galaxy, do some basic manipulation and then download the resulting data file into another environment using curl or wget... If the user is not authenticated into the Galaxy server (ie is a guest), and she copies the link from a data set in her history by right clicking on the 'Save' icon, she gets something like this: http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval and this URL is retrievable via curl -O "http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval" resulting in a file. However, if the user is coming from an authenticated environment, the link will fail with a Permissions Error from Galaxy. Presumably, this is because the server is checking for presence of a cookie that is set during user authentication. Short of sniffing the authentication token and passing it using curl/wget along with the request (and this will fail when the token expires), is there any way to accomplish what I am asking? Is there a way to provide user credentials via the URL string perhaps? Thanks, Matt == Matthew W. Vaughn, Ph.D. Scientific Lead, iPlant Collaborative Research Assistant Professor Cold Spring Harbor Laboratory 1 Bungtown Road Williams #5 Cold Spring Harbor, NY 11724 USA web: http://hispaniola.cshl.edu/ web: http://www.iplantcollaborative.org/ tel: (516) 367-8808 cell: (516) 353-7055 google-talk: matt.vaughn@gmail.com
Matthew Vaughn wrote:
Dear Galactic Overlords,
I'd like to be able to provide external access via HTTP GET-able URL to individual data files that are generated in the course of Galaxy analysis. For example, say a user wanted to import her data in Galaxy, do some basic manipulation and then download the resulting data file into another environment using curl or wget...
If the user is not authenticated into the Galaxy server (ie is a guest), and she copies the link from a data set in her history by right clicking on the 'Save' icon, she gets something like this:
http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval
and this URL is retrievable via curl -O "http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval" resulting in a file.
However, if the user is coming from an authenticated environment, the link will fail with a Permissions Error from Galaxy. Presumably, this is because the server is checking for presence of a cookie that is set during user authentication.
Short of sniffing the authentication token and passing it using curl/wget along with the request (and this will fail when the token expires), is there any way to accomplish what I am asking? Is there a way to provide user credentials via the URL string perhaps?
Hi Matt, The answer right now is no, there's not a way. We're hoping to have a RESTful interface to Galaxy in the coming months that would solve this problem. --nate
Thanks,
Matt
== Matthew W. Vaughn, Ph.D. Scientific Lead, iPlant Collaborative Research Assistant Professor Cold Spring Harbor Laboratory 1 Bungtown Road Williams #5 Cold Spring Harbor, NY 11724 USA
web: http://hispaniola.cshl.edu/ web: http://www.iplantcollaborative.org/
tel: (516) 367-8808 cell: (516) 353-7055 google-talk: matt.vaughn@gmail.com
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