| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Production: Reorganise filesystem paths for sqlite databases. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Provide common host directory for sqlite databases. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Production: bind the gn-docs repository to the container. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Production: Update filesystem paths from `/export2/*` to `/export/*` | Frederick Muriuki Muriithi | |
| 2025-07-02 | Update filesystem shares for "public-sparql" container. | Frederick Muriuki Muriithi | |
| 2025-04-03 | ACME: Allow acme service to restart nginx with no sudo password | Frederick Muriuki Muriithi | |
| 2025-04-03 | public-sparql: use the /export2 disk. | Frederick Muriuki Muriithi | |
| 2025-04-03 | public-sparql: Separate instance dir from data directories | Frederick Muriuki Muriithi | |
| The "allowed" directories are directories other than the instance directory, which virtuoso can access to load data. | |||
| 2025-03-28 | Update tissue configuration in line with guix-forge update. | Arun Isaac | |
| guix-forge has introduced a breaking change in tissue configuration. Update configuration. * genenetwork-development.scm (operating-system)[services]{tissue-service-type}: Update tissue configuration. | |||
| 2025-03-28 | Make dirs-allowed a list of directories. | Arun Isaac | |
| * genenetwork-development.scm (operating-system)[services]{virtuoso-service-type}: Make dirs-allowed a list of directories. | |||
| 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. | |||
| 2025-03-21 | uploader-container: /export2 is full, move files to /export | Frederick Muriuki Muriithi | |
| The disk mounted on /export2 was full, so we move the uploader-container to the disk on /export which has more space. | |||
| 2025-03-21 | uploader-container: Abstract away paths in the container. | Frederick Muriuki Muriithi | |
| Break the implicit connection between the paths on the host system with the paths inside the container. This allows the operating-system definition to define its own paths, regardless of what is on the host. The builder script will explicitly do the mapping between host directories and container paths. We also collect all uploader-related directories under the host path `/export2/guix-containers/uploader` to make maintenance easier. | |||
| 2025-03-21 | uploader-container: Bind missing directories to the container. | Frederick Muriuki Muriithi | |
| The changes to the way the various applications work lead to a need for extra shares from the host to the container — this commit provides the bindings for these shares. | |||
| 2025-03-21 | uploader-container: Remove unnecessary `virtuoso-service-type` | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-03-07 | Change paths for use with tux02. | Frederick Muriuki Muriithi | |
| 2025-02-24 | gn-guile: Set up correct ownership for gn-docs. | Frederick Muriuki Muriithi | |
| 2025-02-24 | Provide bare checkout of 'gn-docs' for production 'gn-guile'. | Frederick Muriuki Muriithi | |
| 2025-02-24 | public-sparql: Fix configuration — Expects list, use list. | Frederick Muriuki Muriithi | |
| 2025-02-24 | Use enterprise disk for container data storage. | Frederick Muriuki Muriithi | |
| The disk mounted on `/export2` is failing, so we move our data over to the enterprise disk mounted on `/export` instead. | |||
| 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 | Remove 'mysql-service-type' service from 'production' container. | Frederick Muriuki Muriithi | |
| We connect to a MariaDB database outside the container, therefore, the container does not need to run a database server. This commit removes the service from the container. | |||
| 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 | |
| 2025-02-19 | Don't share MariaDB data directory with the production container. | Frederick Muriuki Muriithi | |
| 2025-02-17 | Grant ownership of genotype-files to GN2 user. | Frederick Muriuki Muriithi | |
| 2025-02-11 | Bind the chosen host directory to genenetwork's TMPDIR path. | Frederick Muriuki Muriithi | |
| Bind the original host path that was previously bound to the container's /tmp directory to instead be bound to genenetwork's TMPDIR directory. | |||
| 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. | |||
| 2025-02-11 | Remove comments: The comments were causing a build invocation error. | Frederick Muriuki Muriithi | |
| Attempting to invoke the container build with the comments in place was leading to the error: ``` guix system: error: wrong number of arguments for action 'container' ``` This commit removes the comments to fix that. | |||
| 2025-02-11 | Update `dirs-allowed` for gn2-container virtuoso. | Frederick Muriuki Muriithi | |
| 2025-02-03 | Pass ttl directory in list of allowed directories for virtuoso. | Frederick Muriuki Muriithi | |
| 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 | Bind virtuoso's TTL directory (readonly) to genenetwork container. | Frederick Muriuki Muriithi | |
| 2025-02-03 | Bind virtuoso's ttl directory (read/write) to virtuoso container. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-01-29 | Update SQL URI for uploader application. | Frederick Muriuki Muriithi | |
| 2025-01-29 | Update the SQL URI for the uploader container. | Frederick Muriuki Muriithi | |
| 2025-01-28 | Update config to point to llm.db binding. | Frederick Muriuki Muriithi | |
| 2025-01-28 | Link to existing gn-docs. | Frederick Muriuki Muriithi | |
| The uploader container will not concern it with editing the gn-docs repository, but might still need it present to allow the system to run. This ensures it is present. | |||
| 2025-01-28 | Link to the appropriate mysqld socket | Frederick Muriuki Muriithi | |
| The uploader container uses a separate database from that used by CI/CD, since the uploader does (potentially) destructive changes to the data in the database. | |||
| 2025-01-28 | Link to the GNQnA SQLite database. | Frederick Muriuki Muriithi | |
| 2025-01-28 | Move uploader directories out of another container's directories. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-01-28 | uploader log-level: use symbol rather than text. | Frederick Muriuki Muriithi | |
| Update the log-level value to use a symbol rather than text, since that's what's expected by the newer system. | |||
| 2025-01-28 | Increase the allowed size of the client request body. | Frederick Muriuki Muriithi | |
| Some request (e.g. for mapping) from GN2 can get big, depending on the trait(s) in use. This commit increases the maximum allowed size for the client body to allow bigger requests. | |||
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