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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.
2025-01-06Set 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.
2025-01-06Remove duplicate environment settings.Munyoki Kilyungi
* genenetwork-development.scm (genenetwork2-cd-gexp): Delete duplicate env settings that are later defined in "gn2.conf".
2025-01-03Set ownership for `llm-db-path`.Frederick Muriuki Muriithi
2024-12-06CI/CD: Update database URI - add socket path.Frederick Muriuki Muriithi
2024-11-26Use forge-nginx-service-type to activate SSL certificatesFrederick 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.
2024-11-26Specify the socket for MariaDB connections.Frederick Muriuki Muriithi
2024-11-12Add AUTH_SERVER_URL setting to GN3Frederick Muriuki Muriithi
2024-11-12Expose the container logs.Frederick Muriuki Muriithi
2024-11-12Bind a host directory to container's /tmpFrederick Muriuki Muriithi
Bind a host directory to container's /tmp to provide more space for the /tmp and prevent the container from running out of space.
2024-11-12Unbind mysql director(y/ies)Frederick Muriuki Muriithi
Not needed for the virtuoso daemon.
2024-11-12Use virtuoso's state directory as its data directoryFrederick Muriuki Muriithi
This helps avoid having a long list of directories to track and manage.
2024-11-12Explicitly set Virtuoso's Database and Transaction files.Frederick Muriuki Muriithi
Explicitly name the public virtuoso's Database and transaction files to prevent any possible conflicts with other virtuoso instances.
2024-11-12Pass log-level to gn-auth applicationFrederick Muriuki Muriithi
2024-11-12Define REQUESTS_CA_BUNDLE envvar for python-requestsFrederick Muriuki Muriithi
Define the `REQUESTS_CA_BUNDLE` for all applications that make use of python's requests library. The library needs to know the location of valid CA certificates in order to work as expected. Expose the CA certificates bundles by adding them to the applications' environments using the mappings objects.
2024-11-12Add cron job for running transform-genenetwork-database-gexp.Munyoki Kilyungi
2024-11-12Delete %transform-genenetwork-database-export-directory.Munyoki Kilyungi
* genenetwork-development.scm (%transform-genenetwork-database-export-directory): Delete. (set-build-directory-permissions-gexp): Remove %transform-genenetwork-database-export-directory.
2024-11-12Rename transform-genenetwork-database.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database): Rename this to... (transform-genenetwork-database-project): ... this. (transform-genenetwork-database-project): Ditto.
2024-11-12Make %virtuoso-data-dir writeable by laminar.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-11-12Refactor ttl and data-loading into Virtuoso in ci job.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database): Use a script to generate and validate ttl files. (%connection-settings): New variable. Contains the sparql and mysql login credentials. (%virtuoso-data-dir): New variable. (transform-genenetwork-database-project): Update how the transform-genenetwork-database gexp is called. Add web hook.
2024-11-05Bind host directory to the container's /tmp directoryFrederick Muriuki Muriithi
Since the /tmp directory is used for a lot of things in the code, we bind a host directory to it, so as to allow easier cleanup, and also ensure the container does not run out of disk space.
2024-10-30Explicitly name virtuoso's database files.Frederick Muriuki Muriithi
2024-10-29Do not share auth-db with genenetwork3 gunicorn app.Frederick Muriuki Muriithi
GeneNetwork3 should not have direct access to the authorisation database file. * genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Do not mount auth-db into genenetwork3 gunicorn app container. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-29Specify path to LLM database in production.Frederick Muriuki Muriithi
* production.scm (operating-system)[services]{genenetwork-service-type}: Add llm-db-path. * production-deploy.sh: Share /export2/guix-containers/genenetwork/var/lib/genenetwork-gnqa with container. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-29Add llm-db-path field to genenetwork configuration..Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[llm-db-path]: New field. (genenetwork-gunicorn-apps): Set LLM_DB_PATH in gn3.conf. Mount LLM database into the container. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-29Remove obsolete SSL key configuration.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Remove SSL_PRIVATE_KEY and AUTH_SERVER_SSL_PUBLIC_KEY. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-29Enable AI search in genenetwork service.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Set AI_SEARCH_ENABLED to True in gn3.conf. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-29Add additional virtuso configuration.Frederick Muriuki Muriithi
* production.scm (operating-system)[services]{virtuoso-service-type}: Add dirs-allowed, number-of-buffers and maximum-dirty-buffers. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-24Move production to tux04.Frederick Muriuki Muriithi
* production-deploy.sh: Update paths for mysql, xapian and genenetwork-sqlite directories. Share path to redis state directory. * production.scm (operating-system)[services]{virtuoso-service-type}: Update server-port and http-server-port. {forge-nginx-service-type}: Update http and https ports. {redis-service-type}: New service. {genenetwork-service-type}: Update server-name, gn-auth-server-name, gn2-port, gn3-port, gn-auth-port, xapian-db, sparql-endpoint and gn3-data-directory. Add auth-db, log-level and gn3-alias-server-port. Remove genotype-files. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-24Add GN3 alias server to genenetwork service.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn3-alias-server-port]: New field. (genenetwork-nginx-server-blocks): Rewrite URLs for the GN3 alias server. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-24Add sanitizer for log-level configuration field.Arun Isaac
* genenetwork/services/genenetwork.scm: Import (guix diagnostics) and (guix i18n). (sanitize-log-level): New function. (<genenetwork-configuration>)[log-level]: Use sanitize-log-level as the sanitizer. (<gn-uploader-configuration>)[log-level]: Use sanitize-log-level as the sanitizer.
2024-10-24Make <gn-uploader-configuration> log-level a symbol.Arun Isaac
* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>)[log-level]: Change default to the symbol 'warning. * genenetwork/services/genenetwork.scm (gn-uploader-gunicorn-app): Pass --log-level to gunicorn.
2024-10-24Re-format and improve indentation.Arun Isaac
* genenetwork/services/genenetwork.scm (<genenetwork-configuration>, <gn-uploader-configuration>, build-xapian-index-cron-gexp): Re-format and re-indent.
2024-10-24Regularize <gn-uploader-configuration> getter functions.Arun Isaac
* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>)[auth-server-url, gn2-server-url, log-level]: Regularize getter function names.
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-16 00:42:08 +0000