aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2024-06-28Fix permissions: Only files are read-onlyFrederick Muriuki Muriithi
Directories need the execute bit set to actually be accessible to the owner.
2024-06-28Make relevant services available to each service.Frederick Muriuki Muriithi
2024-06-28Set secrets as directories for services with multiple secrets.Frederick Muriuki Muriithi
2024-06-28Add JWT SSL keys configurations.Frederick Muriuki Muriithi
2024-06-28Split the secrets directoriesFrederick Muriuki Muriithi
Put the secrets for the different services in service-specific directories, all of them sharing the same parent directory.
2024-06-19Replace tabs with white spaces.Munyoki Kilyungi
* genenetwork-development.scm: Run "M-x untabify".
2024-06-19Move xapian re-indexing checks into the indexing script.Munyoki Kilyungi
Let the python xapian indexing script check the checksums, instead of using a G-expression. This approach is simpler and more understandable; it is also more versatile and allows easier modification. * genenetwork-development.scm (build-xapian-index-cron-gexp): Use the indexing script to compare checksums. If the checksums changed, queue the genenetwork3-build-xapian-index laminar job. Co-authored-by: John Nduli <rookie101@jnduli.co.ke>
2024-06-17Configure CI for guile-lapack.Arun Isaac
* genenetwork-development.scm (guile-lapack-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-lapack-project.
2024-06-17Configure CI for guile-gsl.Arun Isaac
* genenetwork-development.scm (guile-gsl-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-gsl-project.
2024-06-12gn-uploader: Setup profile pathFrederick Muriuki Muriithi
The profile path is necessary for use retrieving the included bootstrap content.
2024-05-07gn-uploader: Serve static files via nginx.Frederick Muriuki Muriithi
* genenetwork/services/genenetwork.scm: Import nginx from (gnu packages web), python from (gnu packages python), (guix build python-build-system) and (guix packages). (gn-uploader-nginx-server-block): Serve static files via nginx. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-05-02Mount llm-db-path into genenetwork3 container.Arun Isaac
* genenetwork-development.scm (genenetwork-shepherd-services): Mount llm-db-path into genenetwork3 container.
2024-04-28Add llm-db-path for CD.Alexander_Kabui
genenetwork-development.scm (<genenetwork-configuration>)[llm-db-path]: New field. (genenetwork3-cd-gexp): Configure LLM_DB_PATH in gn3.conf. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-04-26gn-auth: Use new entry-point script.Frederick Muriuki Muriithi
2024-04-26Set up SSL keys for CI/CD for gn2 and gn-authFrederick Muriuki Muriithi
2024-04-26gn-auth: Update repository URLFrederick Muriuki Muriithi
2024-04-12gn-uploader: use installed entry-point.Frederick Muriuki Muriithi
2024-04-12gn-uploader: use defined app in wsgi.py to pick up logging configs.Frederick Muriuki Muriithi
2024-04-12Set up log level in gunicornadd-gunicorn-loggingFrederick Muriuki Muriithi
2024-04-10gn-uploader: Enable changing of log-level for container.Frederick Muriuki Muriithi
This commit enables us to change the logging level of the gn-uploader service within the container: this will help in the instances when we need to debug events in the application that are unexpected.
2024-04-09gn-uploader: Change ownership of data-directoryFrederick Muriuki Muriithi
While the share is technically writable from the container, the service was running as an unprivileged user, and thus could not write to the data-directory. This commit changes the ownership of the data-directory to the same user that runs the service.
2024-04-09gn-uploader: share datadir in read-write modeFrederick Muriuki Muriithi
2024-04-09gn-uploader: Made datadir writable and set up uploads directory.Frederick Muriuki Muriithi
2024-04-05Document configuration settingsPjotr Prins
2024-04-05README: minor editsPjotr Prins
2024-04-04fallback: for now use special guix buildPjotr Prins
2024-04-04Remove tmp before creating itPjotr Prins
2024-04-03Set up SQL_URI for gn-auth.Frederick Muriuki Muriithi
2024-04-03Use gn-uploader from gn-uploader channelFrederick Muriuki Muriithi
This commit lets us use the bleeding-edge gn-uploader from the gn-uploader channel.
2024-04-03Use default genenetwork2Frederick Muriuki Muriithi
The uploader container is for testing that the gn-uploader package builds and the application is working correctly. It sets up a service that allows users to upload data. It does need the other GeneNetwork services, but does not need the latest and greatest. This commit uses the default genenetwork2 package (which will mostly be stable): thus there are fewer (if any) issues getting the other services to run.
2024-04-03gendev: special machine for PjotrPjotr Prins
2024-04-02fallback: reinstate genenetwork3-stablePjotr Prins
2024-04-01Share TMPDIR between GN2 and GN3Pjotr Prins
2024-04-01fallback: have gn2 and gn3 share a source directory so we can update/debug ↵Pjotr Prins
source code for development. See topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
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.