| Age | Commit message (Expand) | Author |
|---|
| 2024-07-12 | Make xapian directory writable inside container. | Frederick Muriuki Muriithi |
| 2024-07-12 | Generalise index-genenetwork cron gexp...Pass in the configuration to the gexp building function to make the
builder function work across environments.
| Frederick Muriuki Muriithi |
| 2024-06-28 | Add tux04 slurm deployment....* slurm-deploy.sh, slurm.scm: New files.
| Arun Isaac |
| 2024-06-28 | Make secrets dirs writable by relevant services. | Frederick Muriuki Muriithi |
| 2024-06-28 | Remove duplicated, and wrong settings. | Frederick Muriuki Muriithi |
| 2024-06-28 | Fix permissions: Only files are read-only...Directories need the execute bit set to actually be accessible to the
owner.
| Frederick Muriuki Muriithi |
| 2024-06-28 | Make relevant services available to each service. | Frederick Muriuki Muriithi |
| 2024-06-28 | Set secrets as directories for services with multiple secrets. | Frederick Muriuki Muriithi |
| 2024-06-28 | Add JWT SSL keys configurations. | Frederick Muriuki Muriithi |
| 2024-06-28 | Split the secrets directories...Put the secrets for the different services in service-specific
directories, all of them sharing the same parent directory.
| Frederick Muriuki Muriithi |
| 2024-06-19 | Replace tabs with white spaces....* genenetwork-development.scm: Run "M-x untabify".
| Munyoki Kilyungi |
| 2024-06-19 | Move xapian re-indexing checks into the indexing script....Let the python xapian indexing script check the checksums, instead of using a
G-expression. This approach is simpler and more understandable; it is also
more versatile and allows easier modification.
* genenetwork-development.scm (build-xapian-index-cron-gexp): Use the indexing
script to compare checksums. If the checksums changed, queue the
genenetwork3-build-xapian-index laminar job.
Co-authored-by: John Nduli <rookie101@jnduli.co.ke>
| Munyoki Kilyungi |
| 2024-06-17 | Configure CI for guile-lapack....* genenetwork-development.scm (guile-lapack-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lapack-project.
| Arun Isaac |
| 2024-06-17 | Configure CI for guile-gsl....* genenetwork-development.scm (guile-gsl-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-gsl-project.
| Arun Isaac |
| 2024-06-12 | gn-uploader: Setup profile path...The profile path is necessary for use retrieving the included
bootstrap content.
| Frederick Muriuki Muriithi |
| 2024-05-07 | gn-uploader: Serve static files via nginx....* genenetwork/services/genenetwork.scm: Import nginx from (gnu
packages web), python from (gnu packages python), (guix build
python-build-system) and (guix packages).
(gn-uploader-nginx-server-block): Serve static files via nginx.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-05-02 | Mount llm-db-path into genenetwork3 container....* genenetwork-development.scm (genenetwork-shepherd-services): Mount
llm-db-path into genenetwork3 container.
| Arun Isaac |
| 2024-04-28 | Add llm-db-path for CD....genenetwork-development.scm (<genenetwork-configuration>)[llm-db-path]:
New field.
(genenetwork3-cd-gexp): Configure LLM_DB_PATH in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Alexander_Kabui |
| 2024-04-26 | gn-auth: Use new entry-point script. | Frederick Muriuki Muriithi |
| 2024-04-26 | Set up SSL keys for CI/CD for gn2 and gn-auth | Frederick Muriuki Muriithi |
| 2024-04-26 | gn-auth: Update repository URL | Frederick Muriuki Muriithi |
| 2024-04-12 | gn-uploader: use installed entry-point. | Frederick Muriuki Muriithi |
| 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 |
