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2024-03-28gn-uploader: Increment maximum size of uploadable files.Frederick Muriuki Muriithi
2024-03-25Add gn-uploader service.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>): New type. (gn-uploader-activation, gn-uploader-gunicorn-app, gn-uploader-nginx-server-block): New functions. (gn-uploader-service-type): New variable. * uploader.scm, uploader-deploy.sh: New files. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-03-21Add timeout for proxiesPjotr Prins
2024-03-14fallback: using genenetwork2-stable packagePjotr Prins
2024-03-14fallback: allow building xapian index inside containerPjotr Prins
2024-03-11Infer profile from guix executable used to build container.Arun Isaac
Not everyone has GUIX_PROFILE set in their environment. Inferring the profile from the guix executable is more reliable. * genenetwork-development.scm (channels-scm-gexp): Infer profile from guix executable used to build container.
2024-03-06Move CI/CD configurations from ENVVARS into a file.Frederick Muriuki Muriithi
2024-03-05Let the gunicorn-gn-auth user own the auth database.Arun Isaac
gn-auth runs as the gunicorn-gn-auth user, not the genenetwork user. * genenetwork/services/genenetwork.scm (genenetwork-activation): Let the gunicorn-gn-auth user own the auth database. Reported-by: Frederick M. Muriithi <fredmanglis@protonmail.com>
2024-03-05Pass on the request scheme to GN2 appFrederick Muriuki Muriithi
This is useful to enable building URIs with the correct scheme in the application. These URIs are important when redirection to and from external services such as the gn-auth service.
2024-03-04Fallback runs base services on hostPjotr Prins
2024-03-02Restore default auth database path on production.Arun Isaac
* production.scm (operating-system)[services]{genenetwork-service-type}: Remove auth-db field. * production-deploy.sh (container_script): Mount /var/genenetwork.
2024-03-02docs: Update process of finding out container PID.Frederick Muriuki Muriithi
2024-03-01Add GeneNetwork service for fallback at spice.Pjotr Prins
* fallback.scm: New file.
2024-03-01Set AUTH_SERVER_URL on production genenetwork2.Arun Isaac
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Set AUTH_SERVER_URL on production genenetwork2.
2024-03-01Reverse proxy gn-auth on production.Arun Isaac
* genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth-server-name]: New field. * genenetwork/services/genenetwork.scm (genenetwork-nginx-server-block): Rename to ... (genenetwork-nginx-server-blocks): ... this. Return list of reverse proxy blocks including one for gn-auth. * genenetwork/services/genenetwork.scm (genenetwork-service-type): Use genenetwork-nginx-server-blocks instead of genenetwork-nginx-server-block. * production.scm (operating-system)[services]{genenetwork-service-type}: Add gn-auth-server-name.
2024-03-01Set owner-only permissions on secrets files.Arun Isaac
* genenetwork/services/genenetwork.scm (genenetwork-activation): Set owner-only permissions on secrets files.
2024-03-01Set ownership of secrets files.Arun Isaac
* genenetwork/services/genenetwork.scm (genenetwork-activation): Set ownership of secrets files. * production-deploy.sh: Mount secrets files read-write.
2024-03-01Add gn-auth to production genenetwork service.Arun Isaac
* genenetwork/services/genenetwork.scm: Import gn-auth from (gn packages genenetwork). * genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth, gn-auth-port, gn-auth-secrets]: New fields. * genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Add gn-auth gunicorn app.
2024-02-29Bump copyright year for Fred.Arun Isaac
* genenetwork-development.scm: Bump copyright year for Fred.
2024-02-29Do not hard-code GN_AUTH_SECRETS.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[gn-auth-secrets]: New field. * genenetwork-development.scm (gn-auth-cd-gexp): Set GN_AUTH_SECRTS from gn-auth-secrets of <genenetwork-configuration> object. (operating-system)[services]{genenetwork-service-type}: Set gn-auth-secrets.
2024-02-28Set up correct secrets file for gn-authFrederick Muriuki Muriithi
2024-02-16Run genenetwork auth CD with 8 workers.Arun Isaac
* genenetwork-development.scm (gn-auth-cd-gexp): Run with 8 workers.
2024-02-16Run genenetwork3 CD with 8 workers.Arun Isaac
* genenetwork-development.scm (genenetwork3-cd-gexp): Run with 8 workers.
2024-01-29Update module path in launch of mechanical-rob.Frederick Muriuki Muriithi
With the reorganisation of the modules, and a change in the startup of genenetwork2, the way mechanical-rob is launched has also changed. This commit updates the launch command. * genenetwork-development.scm (genenetwork-projects): Update module path in launch of mechanical-rob CI job. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-01-18Configure CI for guile-lmdb.Arun Isaac
* genenetwork-development.scm (guile-lmdb-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-lmdb-project.
2024-01-18Fix channel name on transform-genenetwork-database channel.Arun Isaac
* genenetwork-development.scm (transform-genenetwork-database-project): Fix channel name.
2024-01-09Add "=" before --load-path argument value.Arun Isaac
guix requires "=" between argument names and values. * production-deploy.sh: Add "=" before --load-path argument value.
2024-01-09genenetwork: Increase gunicorn timeout for genenetwork3.Arun Isaac
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Increase gunicorn timeout for genenetwork3 to 1200 seconds.
2024-01-08Increase gunicorn timeout for genenetwork3.Arun Isaac
* genenetwork-development.scm (genenetwork3-cd-gexp): Increase gunicorn timeout to 1200 seconds. * genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps): Add TODO note to increase gunicorn timeout to 1200 seconds.
2024-01-05Set ownership and permissions on secret files.Arun Isaac
* genenetwork-development.scm (genenetwork-activation): Set ownership and permissions on secret files. * genenetwork-development-deploy.sh: Share /etc/genenetwork/conf instead of merely exposing it.
2024-01-05Abstract out gn2/gn3 secrets as configuration fields.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[gn2-secrets, gn3-secrets]: New fields. * genenetwork-development.scm (genenetwork2-cd-gexp): Use gn2-secrets configuration field. (genenetwork3-cd-gexp): Use gn3-secrets configuration field. (operating-system)[services]: Set gn2-secrets and gn3-secrets fields in genenetwork configuration.
2024-01-03Add GeneNetwork service to production container.Arun Isaac
* production.scm: Import (genenetwork services genenetwork), (forge acme), (forge nginx) and (forge socket). Import shepherd from (gnu packages admin). (operating-system)[sudoers-file]: Allow acme user to restart nginx. (services): Add forge-nginx, acme and genenetwork services.
2024-01-03Add GeneNetwork service.Arun Isaac
* genenetwork/services/genenetwork.scm: New file.
2024-01-02Change path to default genenetwork2 settings file.Arun Isaac
The default settings file in the genenetwork2 code base has been moved from etc/default_settings.py to gn2/default_settings.py. Adapt. * genenetwork-development.scm (genenetwork-projects, genenetwork2-cd-gexp): Change path to default genenetwork2 settings file.
2023-12-30Delete unused qc-tests and qc-project.Arun Isaac
Somehow this code, that was deleted in aaf6750858e061e5f5740fb1edbc49b68b3c4717, was added back in 93ff9ed6fd9f2ca15cf6a8930eae26c9f5c65450. * genenetwork-development.scm (qc-tests, qc-project): Delete variables.
2023-12-30Separate out guix-bioinformatics job that builds all packages.Arun Isaac
We split guix-bioinformatics into two jobs—one that only does a `guix pull' and another that does a `guix pull' and builds all packages. This allows us to catch failures in `guix pull' separately. The job that builds all packages is practically always bound to fail. * genenetwork-development.scm (guix-bioinformatics-project): Split guix-bioinformatics job into guix-bioinformatics and guix-bioinformatics-all-packages jobs.
2023-12-30Do not auto-upgrade mysql databases in production.Arun Isaac
* production.scm (operating-system)[services]{mysql-service-type}: Set auto-upgrade? to #f.
2023-12-21Simple gn-guile system container buildsPjotr Prins
2023-12-20Use local gn-transform-databases git repository.Arun Isaac
* genenetwork-development.scm (transform-genenetwork-database-project)[repository]: Set to local gn-transform-databases git repository. [ci-jobs-trigger]: Do not use webhook. Reset to default.
2023-12-20Use guix-channel-job-gexp for gn-transform-databases CI job.Arun Isaac
* genenetwork-development.scm: Import (guix ci). (transform-genenetwork-database-tests): Delete variable. (%default-guix-channel-with-substitutes): New variable. (transform-genenetwork-database-project): Use guix-channel-job-gexp for transform-genenetwork-database-tests CI job. * genenetwork/development-helper.scm: Delete file.
2023-12-19Delete unused qc-tests variable.Arun Isaac
* genenetwork-development.scm (qc-tests): Delete variable. * genenetwork/development-helper.scm (asdf-test-gexp): Delete function.
2023-12-19Use guix-channel-job-gexp for gn-auth pylint and mypy CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork3-tests): Delete function. (gn-auth-pylint): Delete variable. (genenetwork-projects): Build only the gn-auth variable in the gn-auth CI job. Combine gn-auth-mypy and gn-auth-pylint CI jobs into a gn-auth-all-tests job that uses guix-channel-job-gexp. * genenetwork/development-helper.scm (genenetwork-lint-gexp): Delete function.
2023-12-19Use guix-channel-job-gexp for genenetwork3 pylint and mypy CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork3-mypy, genenetwork3-pylint): Delete variables. (genenetwork-projects): Build only genenetwork3 variable in genenetwork3 CI job. Combine genenetwork3-mypy and genenetwork3-pylint CI jobs into a genenetwork3-all-tests job that uses guix-channel-job-gexp. * genenetwork/development-helper.scm (genenetwork3-lint-gexp): Delete function.
2023-12-19Delete unused genenetwork3-unit-tests variable.Arun Isaac
* genenetwork-development.scm (genenetwork3-unit-tests): Delete variable.
2023-12-19Remove qc-project.Arun Isaac
* genenetwork-development.scm (qc-project): Delete variable. (operating-system)[services]{forge-service-type}: Unlist qc-project.
2023-12-19Rebuild xapian index every hour.Arun Isaac
The xapian index rebuild cron job runs every hour, but doesn't actually rebuild the index unless the MySQL database has changed since the previous index rebuild. * genenetwork-development.scm (operating-system): Run xapian index rebuild job every hour.
2023-12-19Trigger xapian index rebuild conditionally.Arun Isaac
* genenetwork-development.scm: Import mariadb from (gnu packages databases). Import guile-dsv and guile-xapian from (gnu packages guile-xyz). (build-xapian-index-cron-gexp): New variable. (operating-system)[services]: Use build-xapian-index-cron-gexp.
2023-11-13Allow http transport for proxied appFrederick Muriuki Muriithi
The application is behind a proxy and is running as http, therefore, to allow the redirects within the application and responses to work, we need to enable the http transport for the application.
2023-11-13GN Secrets: Set up secrets files for GN2 and GN3Frederick Muriuki Muriithi
2023-11-10auth: define setting for CI/CD auth.Frederick Muriuki Muriithi
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-09 23:10:02 +0000