| Age | Commit message (Expand) | Author |
|---|
| 2024-04-12 | gn-uploader: use defined app in wsgi.py to pick up logging configs. | Frederick Muriuki Muriithi |
| 2024-04-12 | Set up log level in gunicornadd-gunicorn-logging | Frederick Muriuki Muriithi |
| 2024-04-10 | gn-uploader: Enable changing of log-level for container....This commit enables us to change the logging level of the gn-uploader
service within the container: this will help in the instances when we
need to debug events in the application that are unexpected.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Change ownership of data-directory...While the share is technically writable from the container, the
service was running as an unprivileged user, and thus could not write
to the data-directory. This commit changes the ownership of the
data-directory to the same user that runs the service.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: share datadir in read-write mode | Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Made datadir writable and set up uploads directory. | Frederick Muriuki Muriithi |
| 2024-04-05 | Document configuration settings | Pjotr Prins |
| 2024-04-05 | README: minor edits | Pjotr Prins |
| 2024-04-04 | fallback: for now use special guix build | Pjotr Prins |
| 2024-04-04 | Remove tmp before creating it | Pjotr Prins |
| 2024-04-03 | Set up SQL_URI for gn-auth. | Frederick Muriuki Muriithi |
| 2024-04-03 | Use gn-uploader from gn-uploader channel...This commit lets us use the bleeding-edge gn-uploader from the
gn-uploader channel.
| Frederick Muriuki Muriithi |
| 2024-04-03 | Use default genenetwork2...The uploader container is for testing that the gn-uploader package
builds and the application is working correctly. It sets up a service
that allows users to upload data.
It does need the other GeneNetwork services, but does not need the
latest and greatest. This commit uses the default genenetwork2
package (which will mostly be stable): thus there are fewer (if any)
issues getting the other services to run.
| Frederick Muriuki Muriithi |
| 2024-04-03 | gendev: special machine for Pjotr | Pjotr Prins |
| 2024-04-02 | fallback: reinstate genenetwork3-stable | Pjotr Prins |
| 2024-04-01 | Share TMPDIR between GN2 and GN3 | Pjotr Prins |
| 2024-04-01 | fallback: have gn2 and gn3 share a source directory so we can update/debug so......topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
| Pjotr Prins |
| 2024-03-28 | gn-uploader: Increment maximum size of uploadable files. | Frederick Muriuki Muriithi |
| 2024-03-25 | Add gn-uploader service....* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>):
New type.
(gn-uploader-activation, gn-uploader-gunicorn-app,
gn-uploader-nginx-server-block): New functions.
(gn-uploader-service-type): New variable.
* uploader.scm, uploader-deploy.sh: New files.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-03-21 | Add timeout for proxies | Pjotr Prins |
| 2024-03-14 | fallback: using genenetwork2-stable package | Pjotr Prins |
| 2024-03-14 | fallback: allow building xapian index inside container | Pjotr Prins |
| 2024-03-11 | Infer profile from guix executable used to build container....Not everyone has GUIX_PROFILE set in their environment. Inferring the
profile from the guix executable is more reliable.
* genenetwork-development.scm (channels-scm-gexp): Infer profile from
guix executable used to build container.
| Arun Isaac |
| 2024-03-06 | Move CI/CD configurations from ENVVARS into a file. | Frederick Muriuki Muriithi |
| 2024-03-05 | Let the gunicorn-gn-auth user own the auth database....gn-auth runs as the gunicorn-gn-auth user, not the genenetwork user.
* genenetwork/services/genenetwork.scm (genenetwork-activation): Let
the gunicorn-gn-auth user own the auth database.
Reported-by: Frederick M. Muriithi <fredmanglis@protonmail.com>
| Arun Isaac |
| 2024-03-05 | Pass on the request scheme to GN2 app...This is useful to enable building URIs with the correct scheme in the
application. These URIs are important when redirection to and from
external services such as the gn-auth service.
| Frederick Muriuki Muriithi |
| 2024-03-04 | Fallback runs base services on host | Pjotr Prins |
| 2024-03-02 | Restore default auth database path on production....*
production.scm (operating-system)[services]{genenetwork-service-type}:
Remove auth-db field.
* production-deploy.sh (container_script): Mount /var/genenetwork.
| Arun Isaac |
| 2024-03-02 | docs: Update process of finding out container PID. | Frederick Muriuki Muriithi |
| 2024-03-01 | Add GeneNetwork service for fallback at spice....* fallback.scm: New file.
| Pjotr Prins |
| 2024-03-01 | Set AUTH_SERVER_URL on production genenetwork2....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set AUTH_SERVER_URL on production genenetwork2.
| Arun Isaac |
| 2024-03-01 | Reverse proxy gn-auth on production....*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth-server-name]:
New field.
*
genenetwork/services/genenetwork.scm (genenetwork-nginx-server-block):
Rename to ...
(genenetwork-nginx-server-blocks): ... this. Return list of reverse
proxy blocks including one for gn-auth.
* genenetwork/services/genenetwork.scm (genenetwork-service-type): Use
genenetwork-nginx-server-blocks instead of
genenetwork-nginx-server-block.
*
production.scm (operating-system)[services]{genenetwork-service-type}:
Add gn-auth-server-name.
| Arun Isaac |
| 2024-03-01 | Set owner-only permissions on secrets files....* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
owner-only permissions on secrets files.
| Arun Isaac |
| 2024-03-01 | Set ownership of secrets files....* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
ownership of secrets files.
* production-deploy.sh: Mount secrets files read-write.
| Arun Isaac |
| 2024-03-01 | Add gn-auth to production genenetwork service....* genenetwork/services/genenetwork.scm: Import gn-auth from (gn
packages genenetwork).
*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth,
gn-auth-port, gn-auth-secrets]: New fields.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add gn-auth gunicorn app.
| Arun Isaac |
| 2024-02-29 | Bump copyright year for Fred....* genenetwork-development.scm: Bump copyright year for Fred.
| Arun Isaac |
| 2024-02-29 | Do not hard-code GN_AUTH_SECRETS....*
genenetwork-development.scm (<genenetwork-configuration>)[gn-auth-secrets]:
New field.
* genenetwork-development.scm (gn-auth-cd-gexp): Set GN_AUTH_SECRTS
from gn-auth-secrets of <genenetwork-configuration> object.
(operating-system)[services]{genenetwork-service-type}: Set
gn-auth-secrets.
| Arun Isaac |
| 2024-02-28 | Set up correct secrets file for gn-auth | Frederick Muriuki Muriithi |
| 2024-02-16 | Run genenetwork auth CD with 8 workers....* genenetwork-development.scm (gn-auth-cd-gexp): Run with 8 workers.
| Arun Isaac |
| 2024-02-16 | Run genenetwork3 CD with 8 workers....* genenetwork-development.scm (genenetwork3-cd-gexp): Run with 8
workers.
| Arun Isaac |
| 2024-01-29 | Update module path in launch of mechanical-rob....With the reorganisation of the modules, and a change in the startup of
genenetwork2, the way mechanical-rob is launched has also
changed. This commit updates the launch command.
* genenetwork-development.scm (genenetwork-projects): Update module
path in launch of mechanical-rob CI job.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-01-18 | Configure CI for guile-lmdb....* genenetwork-development.scm (guile-lmdb-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lmdb-project.
| Arun Isaac |
| 2024-01-18 | Fix channel name on transform-genenetwork-database channel....*
genenetwork-development.scm (transform-genenetwork-database-project):
Fix channel name.
| Arun Isaac |
| 2024-01-09 | Add "=" before --load-path argument value....guix requires "=" between argument names and values.
* production-deploy.sh: Add "=" before --load-path argument value.
| Arun Isaac |
| 2024-01-09 | genenetwork: Increase gunicorn timeout for genenetwork3....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Increase gunicorn timeout for genenetwork3 to 1200 seconds.
| Arun Isaac |
| 2024-01-08 | Increase gunicorn timeout for genenetwork3....* genenetwork-development.scm (genenetwork3-cd-gexp): Increase
gunicorn timeout to 1200 seconds.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add TODO note to increase gunicorn timeout to 1200 seconds.
| Arun Isaac |
| 2024-01-05 | Set ownership and permissions on secret files....* genenetwork-development.scm (genenetwork-activation): Set ownership
and permissions on secret files.
* genenetwork-development-deploy.sh: Share /etc/genenetwork/conf
instead of merely exposing it.
| Arun Isaac |
| 2024-01-05 | Abstract out gn2/gn3 secrets as configuration fields....*
genenetwork-development.scm (<genenetwork-configuration>)[gn2-secrets,
gn3-secrets]: New fields.
* genenetwork-development.scm (genenetwork2-cd-gexp): Use gn2-secrets
configuration field.
(genenetwork3-cd-gexp): Use gn3-secrets configuration field.
(operating-system)[services]: Set gn2-secrets and gn3-secrets fields
in genenetwork configuration.
| Arun Isaac |
| 2024-01-03 | Add GeneNetwork service to production container....* production.scm: Import (genenetwork services genenetwork), (forge
acme), (forge nginx) and (forge socket). Import shepherd from (gnu
packages admin).
(operating-system)[sudoers-file]: Allow acme user to restart nginx.
(services): Add forge-nginx, acme and genenetwork services.
| Arun Isaac |
| 2024-01-03 | Add GeneNetwork service....* genenetwork/services/genenetwork.scm: New file.
| Arun Isaac |
