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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
2023-11-10Add documentation on connecting to container.Frederick Muriuki Muriithi
2023-11-10Update domain for CD auth service.Frederick Muriuki Muriithi
2023-11-02Secrets: Add instance folder to pola-wrapper.Frederick Muriuki Muriithi
2023-11-02SECRETS: Fix secrets path.Frederick Muriuki Muriithi
2023-11-02Secrets: Setup gn-auth instance path to find the secrets.Frederick Muriuki Muriithi
2023-11-02gn-auth: restart GN2 also after any changes to gn-auth.Frederick Muriuki Muriithi
2023-11-02gn-auth: Remove automated migrations.Frederick Muriuki Muriithi
2023-10-28Do not use upstream Guix in CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Remove default upstream Guix channels.
2023-10-05Fix guix-bioinformatics path in project definition.Arun Isaac
* genenetwork-development.scm (guix-bioinformatics-project)[repository]: Fix path.
2023-10-05Fix typo in comment about cloning the latest gn-auth repository.Arun Isaac
* genenetwork-development.scm (gn-auth-migrations-laminar): Fix typo in comment.
2023-10-05Construct yoyo.ini using guile-ini.Arun Isaac
Constructing INI files from S-expressions instead of using string substitutions is a little nicer. * genenetwork-development.scm (gn-auth-migrations-yoyo-ini-gexp): New function. (gn-auth-migrations): Use gn-auth-migrations-yoyo-ini-gexp.
2023-10-05Mount git repositories read-write.Arun Isaac
* genenetwork-development-deploy.sh: Mount /home/git/public read-write into the container.
2023-10-04Use guix-bioinformatics repository on tux02.Arun Isaac
The guix-bioinformatics repository is now on tux02. There is no webhook to listen for. So, use it directly as a local repository. * genenetwork-development.scm (guix-bioinformatics-project)[repository]: Use local repository on tux02.
2023-10-04Import gn-auth from (gn packages genenetwork).Arun Isaac
* genenetwork-development.scm: Import gn-auth from (gn packages genenetwork) instead of from (gn-auth) or elsewhere.
2023-10-04Import python-mypy from (gnu packages python).Arun Isaac
* genenetwork-development.scm: Import python-mypy from (gnu packages python) instead of (gn packages python).
2023-10-04Use switch-symlinks from (guix build utils).Arun Isaac
switch-symlinks was recently moved from (guix utils) to (guix build utils). It can now be safely used in build-side code. * genenetwork-development.scm (install-laminar-template-gexp): Use switch-symlinks from (guix build utils).
2023-09-28Use upstream mypy.Munyoki Kilyungi
* genenetwork-development.scm: Replace python-mypy-0.981 import with upstream version. (genenetwork3-mypy, genenetwork-projects): Replace python-mypy-0.981 with upstream version. Acked-by: Arun Isaac <arunisaac@systemreboot.net>
2023-09-27Revert "Set the envvar in the gexp"Frederick Muriuki Muriithi
This reverts commit 416bf833737b23e86756b68e0cb162529bbd2665.
2023-09-27Revert "Expose configurations directory to pola-wrapper."Frederick Muriuki Muriithi
This reverts commit 5ec4b45702cba430b8da47949f37317527cf05a6.
2023-09-27Revert "Expose config file to pola-wrapper"Frederick Muriuki Muriithi
This reverts commit d12e7e45883df361ab4f78055c8112ded2e896ca.
2023-09-20Expose config file to pola-wrapperFrederick Muriuki Muriithi
2023-09-20Expose configurations directory to pola-wrapper.Frederick Muriuki Muriithi
2023-09-20Set the envvar in the gexpFrederick Muriuki Muriithi
2023-09-20Pass "secrets" configurations to GN2Frederick Muriuki Muriithi
We need to pass in secrets to the running applications. This commit does it for GeneNetwork2.
2023-09-19Use appropriate mypy for Python3.10Frederick Muriuki Muriithi
2023-09-19Add missing `gn-auth-repository` configurationFrederick Muriuki Muriithi
2023-09-16Add CI/CD definitions for gn-authFrederick Muriuki Muriithi
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-19 23:58:02 +0000