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Get environment variables for data_source_async tools

Open FredericBGA opened this issue 5 years ago • 2 comments

This PR try to make this one useless: https://github.com/galaxyproject/galaxy/pull/9207

It get environment variables from xml in order to send them as parameters in URL for data_source_async tools.

What I've understood: unlike the regular tools there is no command line that is explicitly created here (so I can not use the variables that are exported in ie: database/jobs_directory/000/70/galaxy_70.sh). Instead it creates an URL that is then used as a Request: https://github.com/galaxyproject/galaxy/blob/4dd932290aacaab106a415b1c48a49be6662f79f/lib/galaxy/webapps/galaxy/controllers/tool_runner.py#L138 That's why I need to find way to get these values when the URL is build.

Let me know if it's ok or if it too specific to my needs. If not I can close these two PR. Thank you.

FredericBGA avatar Sep 29 '20 08:09 FredericBGA

Let me know if it's ok or if it too specific to my needs. If not I can close these two PR.

I think it might be okay - I like that you're restricting it to a specific class of tools. I just wish there was a way to test it.

jmchilton avatar Apr 07 '21 13:04 jmchilton

Hi,

tested with an async tool, it works. I will close this one: https://github.com/galaxyproject/galaxy/pull/9207 Could you please help me to add a test for this?

FredericBGA avatar Feb 14 '22 08:02 FredericBGA