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12 hoursUpdate tissue configuration in line with guix-forge update.HEADmainArun 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.
12 hoursMake dirs-allowed a list of directories.Arun Isaac
* genenetwork-development.scm (operating-system)[services]{virtuoso-service-type}: Make dirs-allowed a list of directories.
7 daysuploader-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.
7 daysuploader-container: /export2 is full, move files to /exportFrederick Muriuki Muriithi
The disk mounted on /export2 was full, so we move the uploader-container to the disk on /export which has more space.
7 daysuploader-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.
7 daysuploader-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.
7 daysuploader-container: Remove unnecessary `virtuoso-service-type`Frederick Muriuki Muriithi
8 daysGN2: Allow form size up to 50MB in size.Frederick Muriuki Muriithi
2025-03-07GN2: 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.
2025-03-07Change paths for use with tux02.Frederick Muriuki Muriithi
2025-02-24gn-guile: Set up correct ownership for gn-docs.Frederick Muriuki Muriithi
2025-02-24Provide bare checkout of 'gn-docs' for production 'gn-guile'.Frederick Muriuki Muriithi
2025-02-24public-sparql: Fix configuration — Expects list, use list.Frederick Muriuki Muriithi
2025-02-24Use 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.
2025-02-24gn-auth: Remove obsolete configuration variables.Frederick Muriuki Muriithi
2025-02-21Split the tempdirs for various applications.Frederick Muriuki Muriithi
2025-02-20Remove '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.
2025-02-20Don't allow GN3 user write permissions to 'TMPDIR'.Frederick Muriuki Muriithi
2025-02-20Assign ownership of 'TMPDIR' and its contents to GN2 user.Frederick Muriuki Muriithi
2025-02-19Don't share MariaDB data directory with the production container.Frederick Muriuki Muriithi
2025-02-17Grant ownership of genotype-files to GN2 user.Frederick Muriuki Muriithi
2025-02-11Bind 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.
2025-02-11Add `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.
2025-02-11Remove 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.
2025-02-11Update `dirs-allowed` for gn2-container virtuoso.Frederick Muriuki Muriithi
2025-02-03Pass ttl directory in list of allowed directories for virtuoso.Frederick Muriuki Muriithi
2025-02-03Pass virtuoso's ttl directory to the xapian indexer script.Frederick Muriuki Muriithi
Pass the directory containing virtuoso's turtle (ttl) files to the indexer.
2025-02-03Bind virtuoso's TTL directory (readonly) to genenetwork container.Frederick Muriuki Muriithi
2025-02-03Bind virtuoso's ttl directory (read/write) to virtuoso container.Frederick Muriuki Muriithi
2025-02-03Add 'gn-virtuoso-ttl-directory' setting to genenetwork-configurationFrederick 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.
2025-01-29Update SQL URI for uploader application.Frederick Muriuki Muriithi
2025-01-29Update the SQL URI for the uploader container.Frederick Muriuki Muriithi
2025-01-28Update config to point to llm.db binding.Frederick Muriuki Muriithi
2025-01-28Link 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.
2025-01-28Link to the appropriate mysqld socketFrederick 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.
2025-01-28Link to the GNQnA SQLite database.Frederick Muriuki Muriithi
2025-01-28Move uploader directories out of another container's directories.Frederick Muriuki Muriithi
2025-01-28gn-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.
2025-01-28uploader 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.
2025-01-28Increase 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.
2025-01-26Specify the character-set for the DB connection.Frederick Muriuki Muriithi
2025-01-15Replace 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.
2025-01-06Add gn-libs to CI.Munyoki Kilyungi
2025-01-06Add 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.
2025-01-06Create a tmpdir for genenetwork2 tests.Munyoki Kilyungi
2025-01-06Add REQUESTS_CA_BUNDLE to genenetwork2 shepherd service.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-01-06Map "/tmp" in gn2/3 and make it writable.Munyoki Kilyungi
2025-01-06Explicitly set "RSCRIPT" in gn3 g-exp.Munyoki Kilyungi
2025-01-06Correctly delete virtuoso build directory.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database-gexp): Only delete virtuoso "build" directory.
2025-01-06Add 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.