| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2026-03-19 | gn-guile: Setup `HOME` and `USER` envvars. | Frederick Muriuki Muriithi | |
| The `gn-guile' service checks for configurations in the HOME directory and in the current working directory (CWD). If the HOME environment variable is not set, then `(getenv "HOME")' returns `#f' which causes an error to be raised in `guile-config' when it attempts to do `(string-append (getenv "HOME") ...)'. This commit ensures the HOME environment variable is set to prevent the error from occurring. | |||
| 2026-03-19 | gn-guile: Replace envvars configs with CLI-argument configs | Frederick Muriuki Muriithi | |
| Remove the environment variable configs that are no longer used by the service, having moved to use of configuration files and command-line arguments to set up the service configurations. | |||
| 2026-03-19 | gn-guile: Rename config to 'gn-doc-remote-uri' | Frederick Muriuki Muriithi | |
| Rename from 'gn-doc-git-checkout' to 'gn-doc-remote-uri' to make the name better elaborate on what the configuration is about. | |||
| 2026-03-05 | Refactor gn-guile-shepherd-service | Frederick Muriuki Muriithi | |
| * Remove the `ssh-command` and `guile-settings` variables | |||
| 2026-03-05 | gn-guile: Refactor gn-guile-gexp | Frederick Muriuki Muriithi | |
| * Generate the GIT_SSH_COMMAND within the "inner" gexp * Return both the config, and the generated gexp | |||
| 2026-03-05 | gn-guile: Set `GIT_COMMITTER*` envvars. | Frederick Muriuki Muriithi | |
| We need to set the `GIT_COMMITTER_NAME` and `GIT_COMMITTER_EMAIL` envvars to prevent the commit step from failing. | |||
| 2026-03-05 | gn-guile: Disambiguate the working dir from the "remote" repo. | Frederick Muriuki Muriithi | |
| The assumption (before this commit) was that the bare/remote repository from which we'd clone the working repository was exposed to the container as a directory. The parent of that directory doubled as the working directory for the application. This conflation of purposes is wrong, and leads to problems, since the remote repo could be a URL/URI to an external service. This commit explicitly defines the working directory. | |||
| 2026-03-05 | gn-guile: Clone specific branch to use for synchronising with main. | Frederick Muriuki Muriithi | |
| 2026-03-05 | gn-guile: Setup SSH configurations | Frederick Muriuki Muriithi | |
| To enable successful cloning and pushing of repositories, we need to set up the identity file and some known hosts. | |||
| 2026-03-05 | gn-guile: use (gn-machines genenetwork) not (gn packages guile). | Frederick Muriuki Muriithi | |
| 2026-03-05 | gn-uploader: Change ownership of secrets directory and all its files. | Frederick Muriuki Muriithi | |
| 2026-01-27 | gn-uploader: Typo: UPLOAD_DIRECTORY --> UPLOADS_DIRECTORY. | Frederick Muriuki Muriithi | |
| 2026-01-26 | gn-uploader: UPLOAD_FOLDER -> UPLOAD_DIRECTORY | Frederick Muriuki Muriithi | |
| Move the UPLOAD_DIRECTORY under the scratch directory and rename the configuration variable. | |||
| 2026-01-26 | gn-uploader: Rename TEMPORARY_DIRECTORY to SCRATCH_DIRECTORY | Frederick Muriuki Muriithi | |
| Thinking of it as a scratch directory help us disassociate it from the /tmp directory, that we generally want to avoid using in the first place. | |||
| 2026-01-09 | Reduce number of Gunicorn workers. | Frederick Muriuki Muriithi | |
| I reduce the number of workers by 10 to reduce resource usage, and also because we do not need so many workers. | |||
| 2025-12-03 | Expose genotype files directory to uploader | Frederick Muriuki Muriithi | |
| Expose the genotype files directory to the uploader, initially in read-only mode. | |||
| 2025-12-03 | gn-uploader: Specify TMPDIR for gn-uploader. | Frederick Muriuki Muriithi | |
| 2025-12-01 | Use genenetwork package variants from this channel. | Arun Isaac | |
| 2025-10-27 | Share the parent dir for `llm-db-path` with POLA wrapper | Frederick Muriuki Muriithi | |
| Share the parent directory for `llm-db-path` with the POLA wrapper, rather than just the file to ensure that the permissions are set up correctly and prevent SQLite from raising an error. | |||
| 2025-10-27 | Use 'file://' protocol to force git to do shallow local clone. | Frederick Muriuki Muriithi | |
| 2025-10-27 | Pass in the bare repository path to the gexp | Frederick Muriuki Muriithi | |
| Pass in the bare repository path to the gexp and use it instead of fetching the value from the environment. This decouples the gexp from changes in the code, e.g. should the environment variable name be changed, we do not have to change this gexp. | |||
| 2025-10-08 | gn-uploader: Change ownership of and map secrets directory. | Frederick Muriuki Muriithi | |
| * Change the ownership of the secrets directory and all its children rather than just the secrets file. * Expose the secrets directory to the application, rather than just the secrets file. Make the directory writable. | |||
| 2025-10-08 | Define and schedule "samples counts" script to run. | Frederick Muriuki Muriithi | |
| 2025-10-08 | Map the auth db parent directory rather than just the file. | Frederick Muriuki Muriithi | |
| Mapping the file only leads to permission issues within the POLA wrapper since SQLite checks both the file, and the parent directory; because of this, we have to map the parent directory to the POLA wrapper too. | |||
| 2025-10-04 | Add mouse-longevity service | Pjotr Prins | |
| 2025-10-04 | Add mouse-longevity service | jgart | |
| 2025-10-04 | Add genecup container service. | jgart | |
| 2025-08-18 | gn-guile: Setup envvars for X.509 certificates. | Frederick Muriuki Muriithi | |
| 2025-08-18 | <genenetwork-configuration>: Track package of 'gn-guile' that's used | Frederick Muriuki Muriithi | |
| * genenetwork/services/genenetwork.scm (<genenetwork-configuration>): Add a configuration to track the 'gn-guile' package (version, build-flags, etc) that is used when setting up the container. | |||
| 2025-08-18 | Set runtime directory for gn-guile to writable dir. | Frederick Muriuki Muriithi | |
| 2025-08-18 | filesystem mappings: Expose gn-docs checkout parent to pola-wrapper. | Frederick Muriuki Muriithi | |
| 2025-08-18 | Activations: Make the parent dir of gn-docs repo checkout writable. | Frederick Muriuki Muriithi | |
| 2025-08-11 | gn-guile-port: provide missing config variable. | Frederick Muriuki Muriithi | |
| 2025-07-21 | Set GN_GUILE_SERVER_URL for dev container (aka GN4) | Pjotr Prins | |
| 2025-07-02 | Increase timeout value for gn-auth and gn-uploader. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Define setting for the asynchronous/background jobs sqlite db. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Provide common host directory for sqlite databases. | Frederick Muriuki Muriithi | |
| 2025-03-21 | uploader-container: Define directory to store sessions in. | Frederick Muriuki Muriithi | |
| Redis is being phased out, and part of that is moving the storage of sessions to the file system, rather than in Redis. This commit allows configuration of the path to the directory where the session files will be stored. | |||
| 2025-03-20 | GN2: Allow form size up to 50MB in size. | Frederick Muriuki Muriithi | |
| 2025-03-07 | GN2: Provide directory to store sessions in. | Frederick Muriuki Muriithi | |
| Genenetwork2 changed the way it stores sessions, moving away from using redis to storing the files in the filesystem. This commit binds the host directory to use to store the sessions. It also does basic activation to ensure the directory is writable to the appropriate user. | |||
| 2025-02-24 | gn-guile: Set up correct ownership for gn-docs. | Frederick Muriuki Muriithi | |
| 2025-02-24 | gn-auth: Remove obsolete configuration variables. | Frederick Muriuki Muriithi | |
| 2025-02-21 | Split the tempdirs for various applications. | Frederick Muriuki Muriithi | |
| 2025-02-20 | Don't allow GN3 user write permissions to 'TMPDIR'. | Frederick Muriuki Muriithi | |
| 2025-02-20 | Assign ownership of 'TMPDIR' and its contents to GN2 user. | Frederick Muriuki Muriithi | |
| 2025-02-17 | Grant ownership of genotype-files to GN2 user. | Frederick Muriuki Muriithi | |
| 2025-02-11 | Add `gn-tmpdir` configuration setting to <genenetwork-configuration> | Frederick Muriuki Muriithi | |
| Add the `gn-tmpdir` configuration setting to help with providing a way to configure a separate temporary directory for the genenetwork services that is separate from the container's `/tmp` directory. This might also help in resolving some issue with `/etc/resolv.conf` not being found in `/tmp` for some reason. | |||
| 2025-02-03 | Pass virtuoso's ttl directory to the xapian indexer script. | Frederick Muriuki Muriithi | |
| Pass the directory containing virtuoso's turtle (ttl) files to the indexer. | |||
| 2025-02-03 | Add 'gn-virtuoso-ttl-directory' setting to genenetwork-configuration | Frederick Muriuki Muriithi | |
| The directory containing the turtle (ttl) files for virtuoso is used by the xapian indexer to determine whether or not to run. We provide it as one of the settings we can configure. | |||
| 2025-01-28 | gn-uploader: gn-uploader-gunicorn-app: Switch from `let` to `let*` | Frederick Muriuki Muriithi | |
| The `gn-uploader-ca-bundle` variable needs the value from the `gn-uploader-profile` variable. | |||
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