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# 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="XXXX"
FAHAMU_AUTH_TOKEN="XXXX"
```
### 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.
|
