| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 6 days | GN2: Provide directory to store sessions in.HEADmain | 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. | |||
| 6 days | 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. | |||
| 2025-01-26 | Specify the character-set for the DB connection. | Frederick Muriuki Muriithi | |
| 2025-01-15 | Replace repo URLs with "/home/git/public" for self-hosted setups. | Munyoki Kilyungi | |
| * genenetwork-development.scm (<genenetwork-configuration>): Replace "https://git.genenetwork.org" with "/home/git/public". * (genenetwork-projects)[gn-libs, gn-auth]{ci-jobs-trigger}: Delete. * (transform-genenetwork-database-project)[repository]: Replace "https://git.genenetwork.org" with "/home/git/public". * (transform-genenetwork-database-project)[repository]: Replace "https://git.genenetwork.org" with "/home/git/public". [ci-jobs-trigger]: Delete. | |||
| 2025-01-06 | Add gn-libs to CI. | Munyoki Kilyungi | |
| 2025-01-06 | Add gn-guile shepherd service genenetwork-service-type. | Munyoki Kilyungi | |
| * genenetwork/services/genenetwork.scm: Import gn-guile, linux-container, git-minimal, shepherd, least-authority, forge utils. (<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields. (gn-guile-gexp): New g-exp for running gn-guile. (gn-guile-shepherd-service): New shepherd service to run gn-guile. (genenetwork-service-type): Add gn-guile-shepherd-service. * production-deploy.sh (container_script): Export gn-docs directory. | |||
| 2025-01-06 | Create a tmpdir for genenetwork2 tests. | Munyoki Kilyungi | |
| 2025-01-06 | Add REQUESTS_CA_BUNDLE to genenetwork2 shepherd service. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-01-06 | Map "/tmp" in gn2/3 and make it writable. | Munyoki Kilyungi | |
| 2025-01-06 | Explicitly set "RSCRIPT" in gn3 g-exp. | Munyoki Kilyungi | |
| 2025-01-06 | Correctly delete virtuoso build directory. | Munyoki Kilyungi | |
| * genenetwork-development.scm (transform-genenetwork-database-gexp): Only delete virtuoso "build" directory. | |||
| 2025-01-06 | Add gn-guile service to genenetwork-shepherd-services. | Munyoki Kilyungi | |
| * genenetwork-development-deploy.sh: share "/export/data/gn-docs/". * genenetwork-development.scm: Import gn-guile. (<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields. (gn-guile-gexp): New g-exp for running gn-guile. (genenetwork-shepherd-services): Add gn-guile service. | |||
| 2025-01-06 | Set gn2 env variables inside the shepherd service. | Munyoki Kilyungi | |
| * genenetwork-development.scm: Import (guix search-paths). (genenetwork2-cd-gexp): Move environment variables ... (genenetwork-shepherd-services)[genenetwork2]: ... here. | |||
| 2025-01-06 | Remove duplicate environment settings. | Munyoki Kilyungi | |
| * genenetwork-development.scm (genenetwork2-cd-gexp): Delete duplicate env settings that are later defined in "gn2.conf". | |||
| 2025-01-03 | Set ownership for `llm-db-path`. | Frederick Muriuki Muriithi | |
| 2024-12-06 | CI/CD: Update database URI - add socket path. | Frederick Muriuki Muriithi | |
| 2024-11-26 | Use forge-nginx-service-type to activate SSL certificates | Frederick Muriuki Muriithi | |
| Use the forge-nginx-service-type rather than the plain nginx-service-type so that we get the SSL certificates setup and maintenance automatically. | |||
| 2024-11-26 | Specify the socket for MariaDB connections. | Frederick Muriuki Muriithi | |
| 2024-11-12 | Add AUTH_SERVER_URL setting to GN3 | Frederick Muriuki Muriithi | |
| 2024-11-12 | Expose the container logs. | Frederick Muriuki Muriithi | |
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