| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-10-18 | Explicitly set AUTH_SERVER_URL in gn3.conf. | Munyoki Kilyungi | |
| This fixes an issue where gn3 auth defaults to "auth.genenetwork.org" during query execution. Instead we explicitly set AUTH_SERVER_URL to "auth-cd.genenetwork.org" | |||
| 2024-10-18 | Upgrade slurm to 24.05.3. | Arun Isaac | |
| * slurm.scm (slurm): Upgrade to 24.05.3. [arguments]: Remove Unix socket disabling. | |||
| 2024-10-02 | Update server root for gn-uploader. | Frederick Muriuki Muriithi | |
| 2024-10-02 | Update path to genotype files. | Frederick Muriuki Muriithi | |
| 2024-09-12 | Enable AI Search in GN2 CD. | Munyoki Kilyungi | |
| 2024-09-03 | Configure slurm with --with-yaml. | Arun Isaac | |
| * slurm.scm (slurm)[arguments]: Add --with-yaml configure flag. | |||
| 2024-08-29 | Install slurmrestd too. | Arun Isaac | |
| * slurm-worker-deploy.sh: Install slurmrestd too. | |||
| 2024-08-29 | Add slurm deployment scripts for octopus. | Arun Isaac | |
| * slurm-deploy.sh: Delete file. * slurm-head-deploy.sh, slurm-worker-deploy.sh: New files. * slurm.scm: Replace tux04 with octopus in comment. | |||
| 2024-08-29 | Use http-parser from Guix. | Arun Isaac | |
| * slurm.scm: Import http-parser from (gnu packages web). (http-parser): Delete variable. | |||
| 2024-08-13 | Forward the scheme to the client to generate correct URIs. | Frederick Muriuki Muriithi | |
| 2024-08-13 | Update docs | Frederick Muriuki Muriithi | |
| 2024-08-13 | gn-uploader: Configure link to GN2 server. | Frederick Muriuki Muriithi | |
| 2024-08-07 | gn-uploader: Add `AUTH_SERVER_URL` to the configurations. | Frederick Muriuki Muriithi | |
| 2024-08-07 | gn-uploader: Update ENVVAR name | Frederick Muriuki Muriithi | |
| 2024-08-07 | gn-uploader: Update configuration variable name. | Frederick Muriuki Muriithi | |
| 2024-08-06 | Give access to read TTL from the /var/lib/virtuoso directory. | Frederick Muriuki Muriithi | |
| 2024-07-22 | gn-uploader: use `gn-uploader-configuration` as default. | Frederick Muriuki Muriithi | |
| 2024-07-22 | gn-uploader: make app user owner of upload directory tree | Frederick Muriuki Muriithi | |
| Fix the service activation code to make the gn-uploader data directory, and all its children belong to the app user. | |||
| 2024-07-12 | Update configurations. | Frederick Muriuki Muriithi | |
| 2024-07-12 | Make the container's /var/log directory available on host | Frederick Muriuki Muriithi | |
| Make the container's logs available of the host to help with troubleshooting and some stickiness for the logs. | |||
| 2024-07-12 | Indicate environment in container hostnames | Frederick Muriuki Muriithi | |
| While it is a tiny change, it does help to have an explicit indication of what container you are currently working with, especially when you need to do specific tasks inside the container itself with something like `nsenter …` or `guix container exec …`. With this commit, instead of a generic prompt like: `root@genenetwork /#`, you get a more specific prompt such as `root@genenetwork-production /#` which goes some ways in avoiding mistakes. | |||
| 2024-07-12 | Add virtuoso to uploader. | Frederick Muriuki Muriithi | |
| 2024-07-12 | Extend the genenetwork-service-type with the mcron indexer service | Frederick Muriuki Muriithi | |
| Add the scheduled indexer service to the genenetwork-service-type. This will run the indexer script every hour. | |||
| 2024-07-12 | Make xapian directory writable inside container. | Frederick Muriuki Muriithi | |
| 2024-07-12 | Generalise index-genenetwork cron gexp | Frederick Muriuki Muriithi | |
| Pass in the configuration to the gexp building function to make the builder function work across environments. | |||
| 2024-06-28 | Add tux04 slurm deployment. | Arun Isaac | |
| * slurm-deploy.sh, slurm.scm: New files. | |||
| 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 | Frederick Muriuki Muriithi | |
| Directories need the execute bit set to actually be accessible to the owner. | |||
| 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 | Frederick Muriuki Muriithi | |
| Put the secrets for the different services in service-specific directories, all of them sharing the same parent directory. | |||
| 2024-06-19 | Replace tabs with white spaces. | Munyoki Kilyungi | |
| * genenetwork-development.scm: Run "M-x untabify". | |||
| 2024-06-19 | Move xapian re-indexing checks into the indexing script. | Munyoki Kilyungi | |
| 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> | |||
| 2024-06-17 | Configure CI for guile-lapack. | Arun Isaac | |
| * genenetwork-development.scm (guile-lapack-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-lapack-project. | |||
| 2024-06-17 | Configure CI for guile-gsl. | Arun Isaac | |
| * genenetwork-development.scm (guile-gsl-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-gsl-project. | |||
| 2024-06-12 | gn-uploader: Setup profile path | Frederick Muriuki Muriithi | |
| The profile path is necessary for use retrieving the included bootstrap content. | |||
| 2024-05-07 | gn-uploader: Serve static files via nginx. | Frederick Muriuki Muriithi | |
| * 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> | |||
| 2024-05-02 | Mount llm-db-path into genenetwork3 container. | Arun Isaac | |
| * genenetwork-development.scm (genenetwork-shepherd-services): Mount llm-db-path into genenetwork3 container. | |||
| 2024-04-28 | Add llm-db-path for CD. | Alexander_Kabui | |
| 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> | |||
| 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. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-04-09 | gn-uploader: Change ownership of data-directory | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-04-09 | gn-uploader: share datadir in read-write mode | Frederick Muriuki Muriithi | |
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