Source common_startup script vs running it so the activated venv appl…

[afgane]

…ies to the parent script's shell. Fixes #1847.

My testing resulted in the venv getting and staying activated when starting reports app.

[dannon]

This is an alternate fix to #1890.

I don't know the background of why the common startup scripts were executed and not sourced, maybe someone who has tinkered with this can chime in?

(on the face of it, this seems to be a better approach to me)

[nsoranzo]

Ping @natefoo, he expressed some reservations on IRC when we spoke about this option.

[davebx]

@galaxybot test this

[jmchilton]

👍 - we really need to merge one of these fixes - I don't care which.

[natefoo]

We just need to take care that nothing in common_startup.sh would affect anything in the calling environment. Previously this level of care was not necessary. Things like $CREATE_VENV and $RMFILES will now override anything already set in the environment (but I don't know of anything that this would affect). However, $GALAXY_CONFIG_FILE will always be set now. This probably won't break anything, but it does change the way Galaxy starts. Note that run.sh also attempts to set $GALAXY_CONFIG_FILE in a slightly different way, and none of that code will be entered anymore. And actually - common_startup.sh does not export it but run.sh does if it was not already set, meaning it will not be set for Galaxy's child processes.

Ideally, the venv creation code should probably be placed in a function and the variables it uses should be set local. Any variable that can be made function-local probably should be.

It should also remain possible to call common_startup.sh on its own without sourcing.

[jmchilton]

Ping @afgane - can you close this or adapt it based on @natefoo's comments?

[afgane]

Closing this as I'm not really in tune with @natefoo's comments - it seems to me those changes would complicate this significantly yet the solution from #1890 has been working fine for months now so I don't see a reason to intertwine the startup procedure even more.