Job execution notification emails do not generate accurate URLs for jobs.

[lparsons]

Describe the bug
When an email is sent to notify the user that a job has completed, the link to the job uses the galaxy_infrastructure_url, which is not always appropriate. Instead, it should use url_for.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 21.05 (expect it to exist on 24.1 and up as well)

Browser and Operating System
Operating System: Windows, Linux, macOS (all)
Browser: Firefox, Chrome, Chrome-based, Safari (all)

To Reproduce
Steps to reproduce the behavior:

1. Run a job and select email notification when complete
2. The URLs in the email will be to localhost or whatever galaxy_infrastructure_url is set to.

Expected behavior
The URL should use the appropriate server address. The galaxy_infrastructure_url is only intended to be used by internal services.

Additional context
The post execution job action uses galaxy_infrastructure_url.

galaxy/lib/galaxy/job_execution/actions/post.py

Lines 58 to 61 in fb4d5be

	link_invocation = (
	f"{app.config.galaxy_infrastructure_url}/workflows/invocations/report?id={invocation_id_encoded}"
	)
	link = f"{app.config.galaxy_infrastructure_url}/histories/view?id={history_id_encoded}"

Instead, it should use url_for which is done in the error reporting emails.

galaxy/lib/galaxy/tools/errors.py

Lines 164 to 166 in fb4d5be

	history_view_link = self.app.url_for("/histories/view", id=history_id_encoded, qualified=True)
	hda_id_encoded = self.app.security.encode_id(hda.id)
	hda_show_params_link = self.app.url_for(

[mvdbeek]

Hey @lparsons, that is not possible unfortunately, url_for only works in a web context that is not available in the job and workflow handlers where these are used. The error report emails are handled within the web context, that's why they can use url_for. This is the relevant work to add another variable for this purpose #18576.

Realistically there's only a problem with galaxy_infrastructure_url if it is set to a truly internal URL for ITs or pulsar that is distinct from the public fqdn.

[lparsons]

Thanks @mvdbeek. I didn't realize the issue with using url_for, that's too bad. We never had galaxy_infrastrucutre_url set since it didn't seem necessary, and the default is technically correct (localhost), however, it caused the links to be broken. I guess going forward we'll just make sure to set it to the public URL instead.