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Diffstat (limited to 'topics')
| -rw-r--r-- | topics/systems/gn-qa-system.gmi | 164 |
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diff --git a/topics/systems/gn-qa-system.gmi b/topics/systems/gn-qa-system.gmi new file mode 100644 index 0000000..629f261 --- /dev/null +++ b/topics/systems/gn-qa-system.gmi @@ -0,0 +1,164 @@ +# Fire up system container for GN-QA System + +# Tags + +* assigned: bonfacem, alexm + + +The current code is a WIP. Patches will be sent after a working container is set-up. Most recent code can be found at /home/bonfacem/gn-machines and the current confs that were copied to the respective paths can be found at: /home/bonfacem/qa-set-up-files/. Important files that were changed/introduced are: /home/bonfacem/gn-machines/{qa-gn.scm, qa-gn-deploy.sh, genenetwork/services/genenetwork.scm}. + +### Setting up SSL Keys + +Generated RS256 key-pairs by following: + +=> Generating How to generate Key-Pairs + +Currently, on tux02, you can find the key-pairs: + +``` +ls /home/bonfacem/qa-set-up-files/*pem +``` + +These have been saved in + +``` +/export2/guix-containers/genenetwork/gn-qa/var/ssl +``` + +The client key pairs have been saved in: + +``` +/export2/guix-containers/genenetwork/gn-qa/var/ssl/clients-public-keys/ +``` + +If the above directory is empty, gn-auth will crap out. + +In the container, we have that mounted as: + +``` +--share=/export2/guix-containers/genenetwork/gn-qa/var/ssl=/var/ssl +``` + +Because of permission issues, this is a lazy work-around---when setting up the container---to get things up and running: + +``` +(for-each (lambda (file) + (chmod file #o777)) + (find-files #$ssl-path #:directories? #t)) +``` + +and for the gunicorn app, for similar issues around permissions: + +``` +(gunicorn-app + (name "gn-auth") + (package gn-auth) + (sockets (list (forge-ip-socket + (port gn-auth-port)))) + (wsgi-app-module "gn_auth:create_app()") + (workers 20) + (environment-variables + (list (environment-variable + (name "GN_AUTH_CONF") + (value gn-auth-conf)) + (environment-variable + (name "HOME") + (value "/tmp")) + (environment-variable + (name "AUTHLIB_INSECURE_TRANSPORT") + (value "true")))) + (mappings (list database-mapping + [...] + (file-system-mapping + (source ssl-path) + (target source) + (writable? #t))))) +``` + +### GN2 Set-up + + +Had the following tangled to /export2/guix-containers/genenetwork/gn-qa/etc/genenetwork/gn2-secrets.py: + +``` +SECRET_KEY="XXXX" +OAUTH2_CLIENT_ID="XXXX" +OAUTH2_CLIENT_SECRET="XXXX" +``` + +### GN3 Set-up + +Had the following tangled to /export2/guix-containers/genenetwork/gn-qa/etc/genenetwork/gn3-secrets.py: + +``` +SECRET_KEY="f@D{ra4uZfAU?9GfV!Y}" +FAHAMU_AUTH_TOKEN="SFMyNTY.g2gDYQJuBgDhZbMejgFiAAFRgA.Qj7KGv9WmDxcHzjQo8IExMtIbZt8lDZ4h14rcjYl_Q8" +``` + +### gn-auth Set-up + +Had the following tangled to /export2/guix-containers/genenetwork/gn-qa/etc/genenetwork/gn3-secrets.py: + +``` +SECRET_KEY="XXXX" +FAHAMU_AUTH_TOKEN="XXXXX" +``` + +For the db, I manually inserted entries for Bonfacem and AlexM using scripts from gn-auth in SQLITE and saved that to /export/data/gn-qa/genenetwork-sqlite/auth-qa.db + +### Nginx configuration / Building the container + +Added this block to /etc/nginx/nginx.conf: + + +``` +stream { + [...] + + upstream qa-gn-genenetwork { + server 127.0.0.1:10908; + } + + [...] + + map $ssl_preread_server_name $upstream { + qa.genenetwork.org qa-gn-genenetwork; + qa-auth.genenetwork.org qa-gn-genenetwork; + [...] + } +``` + +Reload nginx gracefully: + +``` +sudo systemctl reload nginx +``` + +### AI Set-up and Systemd service set-up + + +XXX: TODO with Alexm + +### Troubleshooting + +In the container SSL issues were resolved by running: + +``` +/usr/bin/acme renew +``` + +Error related to a missing key in GN2 when trying to sign a new user in wqflask/oauth2/toplevel.py: + +``` +[...] +"sub": request.args["user_id"] +[...] +````` + +was fixed by using the latest gn-auth code. The one in guix-bioinformatics is stale. + +There was an error when displaying the error page. Fixed upstream in guix-bioinformatics: + +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=7f9908d03acd6d2c44733188122313036dc63b64 + +Whenever our git instance fails, CD---in particular auth---will fail. This needs further investigation. Restarting the CD container will fix things. |