GAT2021 Followup Overhaul #2371
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topics/admin/tutorials/ansible-galaxy/group_vars/galaxyservers.yml
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| enable_quotas: true | ||
| allow_user_deletion: true | ||
| show_welcome_with_login: true | ||
| expose_user_name: true |
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I wouldn't add this, since it probably violates the GDPR (not that I'm advocating to add enable_beta_gdpr: true here).
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Yeah. I really wish we had a lawyer to comment on that but in retrospect it is a "Public User Name" (per the registration form), there should be a strong expectation that it's public. I was too conservative in the original implementation and I regret that.
topics/admin/tutorials/ansible-galaxy/group_vars/galaxyservers.yml
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but I did something dumb with the galaxy systemd, it doesn't behave nicely if you just want to e.g. set the env, rather than also setting that it should be mules. That's what I get for using dictionaries instead of just a bazillion variables. |
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@natefoo @Slugger70 that's all I have energy for, hope y'all can get the ball across the line on this one.
(or any other mixture of people recording but yeah.) |
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@hexylena I'll be rerecording the ephemeris stuff |
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@cat-bro amazing, thank you!
Weird about the cache update. I had to switch the machines to the Ubuntu
repos in NZ again, the Aussie ones didn't work for me again and I don't
know why.
Weird to see that error. Galaxy-wait worked after I added the updated LE
fake root certs, I would have expected bioblend to, too.
Op vr 4 jun. 2021 06:51 schreef cat-bro ***@***.***>:
… @hexylena <https://github.com/hexylena> I'll be rerecording the ephemeris
stuff
A note on git-gat: I'm currently running it on one of the gat machines and
I needed to update the cache before it was able to install packages. I'm
not sure if this belongs in the playbook or the bootstrap.
A note on the ephemeris tutorial: I'm currently failing to install things
on my gat machine with bioblend.ConnectionError:
HTTPSConnectionPool(host='gat-2.oz.training.galaxyproject.eu', port=443):
Max retries exceeded with url:
/api/tools?in_panel=True&key=45fc909559337090b1969c4abcb80e9c (Caused by
SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: unable to get local issuer certificate
(_ssl.c:1123)'))), 0 attempts left:. I don't think this came up in
January. I'll have a go at troubleshooting this later on today.
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Looking through the scrollback I can see that galaxy-wait did work perfectly during the run of .scripts/1-ansible-galaxy-run.sh but no longer does. Galaxy is running and logs look fine |
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@cat-bro fixed, something was wrong with the certificates but can't tell what. The LE fake roots x1 and x2 were there (one had an unexpected filename, .pem.crt, both should have been .crt) so I'm suspicious that they didn't get deployed properly. I re-ran that task from bootstrapping and it works now. |
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I cannot explain it working initially, that's,, interesting. |
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@hexylena thanks for fixing! scripts/1 was run, followed by scripts/2, followed by my installing ephemeris in a virtual environment. Whatever went wrong happened sometime after the end of scripts/1. That .pem.crt file is a fake one that I added to try to fix it. |
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The problem seems to arise from installing ephemeris in a virtual environment when it is already installed globally. This time it's only broken within the virtual environment. The first time it broke globally as well, no idea why. |
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Ahhhh that could make sense. It was installed globally as part of the testing process. Should we just install it globally? skip the venv step then? |
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Would it be safer if git-gat had a venv for its requirements? If it's installed globally there's a chance that a student would create the ephemeris_venv and break it. The ephemeris_venv is also part of the data libraries tutorial [updated] The machines already have global ephemeris because they have planemo installed as part of the bootstrap process, so it must have been there last time too but the venv was ok. I'll add a step to check whether ephemeris is already installed in the tut and skip the venv step. |
Hey @hexylena - I will re-record singularity and pulsar as soon as this PR is merged. |
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@Slugger70 approved so I'm going to merge this. We'll put everything else in a new PR(s) but should be easier to contribute once this huge chunk is merged. |
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Nice job @hexylena 🥇 |
GAT 2021 Followup
This PR contains a large number of bugfixes targeted at issues discovered during #2274
Fixes #2274
Admin Training: Automated
This branch includes numerous fixes for the admin training topic, collected from GAT2021:Online, but it also starts the project of automating GAT.
There is alpha quality code for building the completely automated videos (slides to video, but instead tutorial to videos). This needs more testing before it's productive, we're aiming for GAT 2022 for that.