| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-01-02 | Change path to default genenetwork2 settings file....The default settings file in the genenetwork2 code base has been moved
from etc/default_settings.py to gn2/default_settings.py. Adapt.
* genenetwork-development.scm (genenetwork-projects,
genenetwork2-cd-gexp): Change path to default genenetwork2 settings
file.
| Arun Isaac |
| 2023-12-30 | Delete unused qc-tests and qc-project....Somehow this code, that was deleted in
aaf6750858e061e5f5740fb1edbc49b68b3c4717, was added back in
93ff9ed6fd9f2ca15cf6a8930eae26c9f5c65450.
* genenetwork-development.scm (qc-tests, qc-project): Delete
variables.
| Arun Isaac |
| 2023-12-30 | Separate out guix-bioinformatics job that builds all packages....We split guix-bioinformatics into two jobs—one that only does a `guix
pull' and another that does a `guix pull' and builds all
packages. This allows us to catch failures in `guix pull'
separately. The job that builds all packages is practically always
bound to fail.
* genenetwork-development.scm (guix-bioinformatics-project): Split
guix-bioinformatics job into guix-bioinformatics and
guix-bioinformatics-all-packages jobs.
| Arun Isaac |
| 2023-12-30 | Do not auto-upgrade mysql databases in production....* production.scm (operating-system)[services]{mysql-service-type}: Set
auto-upgrade? to #f.
| Arun Isaac |
| 2023-12-21 | Simple gn-guile system container builds | Pjotr Prins |
| 2023-12-20 | Use local gn-transform-databases git repository....*
genenetwork-development.scm (transform-genenetwork-database-project)[repository]:
Set to local gn-transform-databases git repository.
[ci-jobs-trigger]: Do not use webhook. Reset to default.
| Arun Isaac |
| 2023-12-20 | Use guix-channel-job-gexp for gn-transform-databases CI job....* genenetwork-development.scm: Import (guix ci).
(transform-genenetwork-database-tests): Delete variable.
(%default-guix-channel-with-substitutes): New variable.
(transform-genenetwork-database-project): Use guix-channel-job-gexp
for transform-genenetwork-database-tests CI job.
* genenetwork/development-helper.scm: Delete file.
| Arun Isaac |
| 2023-12-19 | Delete unused qc-tests variable....* genenetwork-development.scm (qc-tests): Delete variable.
* genenetwork/development-helper.scm (asdf-test-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for gn-auth pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-tests): Delete function.
(gn-auth-pylint): Delete variable.
(genenetwork-projects): Build only the gn-auth variable in the gn-auth
CI job. Combine gn-auth-mypy and gn-auth-pylint CI jobs into a
gn-auth-all-tests job that uses guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for genenetwork3 pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-mypy,
genenetwork3-pylint): Delete variables.
(genenetwork-projects): Build only genenetwork3 variable in
genenetwork3 CI job. Combine genenetwork3-mypy and genenetwork3-pylint
CI jobs into a genenetwork3-all-tests job that uses
guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork3-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Delete unused genenetwork3-unit-tests variable....* genenetwork-development.scm (genenetwork3-unit-tests): Delete
variable.
| Arun Isaac |
| 2023-12-19 | Remove qc-project....* genenetwork-development.scm (qc-project): Delete variable.
(operating-system)[services]{forge-service-type}: Unlist qc-project.
| Arun Isaac |
| 2023-12-19 | Rebuild xapian index every hour....The xapian index rebuild cron job runs every hour, but doesn't
actually rebuild the index unless the MySQL database has changed since
the previous index rebuild.
* genenetwork-development.scm (operating-system): Run xapian index
rebuild job every hour.
| Arun Isaac |
| 2023-12-19 | Trigger xapian index rebuild conditionally....* genenetwork-development.scm: Import mariadb from (gnu packages
databases). Import guile-dsv and guile-xapian from (gnu packages
guile-xyz).
(build-xapian-index-cron-gexp): New variable.
(operating-system)[services]: Use build-xapian-index-cron-gexp.
| Arun Isaac |
