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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.
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