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2024-11-04Define 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.
2024-11-04Run script to make non-human data publicFrederick Muriuki Muriithi
2024-11-04Setup public sparql endpoint in container.Frederick Muriuki Muriithi
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.
2024-10-24Add log-level field to genenetwork-configuration.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[log-level]: New field. * genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Pass --log-level to gunicorn. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-24Set REAPER_COMMAND in gn3.conf.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Set REAPER_COMMAND in gn3.conf. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-24Set GENOTYPE_FILES in gn3.conf.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Set GENOTYPE_FILES in gn3.conf. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-18Move directory permissions setting G-exp into separate variable.Arun Isaac
* genenetwork-development.scm (set-build-directory-permissions-gexp): New variable. * genenetwork-development.scm (operating-system)[services]: Use set-build-directory-permissions-gexp.
2024-10-18Provide UTF-8 locale so characters are encoded correctly.Munyoki Kilyungi
* genenetwork-development.scm (gn-gemtext-threads-project)[ci-jobs]: Set LC_ALL environment variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-18Explicitly set AUTH_SERVER_URL in gn3.conf.Munyoki Kilyungi
This fixes an issue where gn3 auth defaults to "auth.genenetwork.org" during query execution. Instead we explicitly set AUTH_SERVER_URL to "auth-cd.genenetwork.org"
2024-10-18Upgrade slurm to 24.05.3.Arun Isaac
* slurm.scm (slurm): Upgrade to 24.05.3. [arguments]: Remove Unix socket disabling.
2024-10-02Update server root for gn-uploader.Frederick Muriuki Muriithi
2024-10-02Update path to genotype files.Frederick Muriuki Muriithi
2024-09-12Enable AI Search in GN2 CD.Munyoki Kilyungi
2024-09-03Configure slurm with --with-yaml.Arun Isaac
* slurm.scm (slurm)[arguments]: Add --with-yaml configure flag.
2024-08-29Install slurmrestd too.Arun Isaac
* slurm-worker-deploy.sh: Install slurmrestd too.
2024-08-29Add slurm deployment scripts for octopus.Arun Isaac
* slurm-deploy.sh: Delete file. * slurm-head-deploy.sh, slurm-worker-deploy.sh: New files. * slurm.scm: Replace tux04 with octopus in comment.
2024-08-29Use http-parser from Guix.Arun Isaac
* slurm.scm: Import http-parser from (gnu packages web). (http-parser): Delete variable.
2024-08-13Forward the scheme to the client to generate correct URIs.Frederick Muriuki Muriithi
2024-08-13Update docsFrederick Muriuki Muriithi
2024-08-13gn-uploader: Configure link to GN2 server.Frederick Muriuki Muriithi
2024-08-07gn-uploader: Add `AUTH_SERVER_URL` to the configurations.Frederick Muriuki Muriithi
2024-08-07gn-uploader: Update ENVVAR nameFrederick Muriuki Muriithi
2024-08-07gn-uploader: Update configuration variable name.Frederick Muriuki Muriithi
2024-08-06Give access to read TTL from the /var/lib/virtuoso directory.Frederick Muriuki Muriithi
2024-07-22gn-uploader: use `gn-uploader-configuration` as default.Frederick Muriuki Muriithi
2024-07-22gn-uploader: make app user owner of upload directory treeFrederick Muriuki Muriithi
Fix the service activation code to make the gn-uploader data directory, and all its children belong to the app user.
2024-07-12Update configurations.Frederick Muriuki Muriithi
2024-07-12Make the container's /var/log directory available on hostFrederick Muriuki Muriithi
Make the container's logs available of the host to help with troubleshooting and some stickiness for the logs.
2024-07-12Indicate environment in container hostnamesFrederick Muriuki Muriithi
While it is a tiny change, it does help to have an explicit indication of what container you are currently working with, especially when you need to do specific tasks inside the container itself with something like `nsenter …` or `guix container exec …`. With this commit, instead of a generic prompt like: `root@genenetwork /#`, you get a more specific prompt such as `root@genenetwork-production /#` which goes some ways in avoiding mistakes.
2024-07-12Add virtuoso to uploader.Frederick Muriuki Muriithi
2024-07-12Extend the genenetwork-service-type with the mcron indexer serviceFrederick Muriuki Muriithi
Add the scheduled indexer service to the genenetwork-service-type. This will run the indexer script every hour.
2024-07-12Make xapian directory writable inside container.Frederick Muriuki Muriithi
2024-07-12Generalise index-genenetwork cron gexpFrederick Muriuki Muriithi
Pass in the configuration to the gexp building function to make the builder function work across environments.
2024-06-28Add tux04 slurm deployment.Arun Isaac
* slurm-deploy.sh, slurm.scm: New files.
2024-06-28Make secrets dirs writable by relevant services.Frederick Muriuki Muriithi
2024-06-28Remove duplicated, and wrong settings.Frederick Muriuki Muriithi
2024-06-28Fix permissions: Only files are read-onlyFrederick Muriuki Muriithi
Directories need the execute bit set to actually be accessible to the owner.