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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
2024-06-12gn-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>
2024-04-12gn-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: Made datadir writable and set up uploads directory.Frederick Muriuki Muriithi
2024-04-05Document configuration settingsPjotr Prins
2024-04-03Set up SQL_URI for gn-auth.Frederick Muriuki Muriithi
2024-04-03gendev: special machine for PjotrPjotr 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
2024-03-05Let 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.
2024-03-01Set 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.
2024-01-09genenetwork: 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.
2024-01-03Add GeneNetwork service.Arun Isaac
* genenetwork/services/genenetwork.scm: New file.
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.
2023-09-16Add CI/CD definitions for gn-authFrederick Muriuki Muriithi
2023-09-05Update arguments to pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-01-21GN3: pylint - Check more files and directoriesFrederick Muriuki Muriithi
2022-10-30Unite genenetwork2 and genenetwork3 development servers.Arun Isaac
We unite the genenetwork2 and genenetwork3 development servers into a single Guix service. This unifies many of the configuration settings and simplifies the configuration. Changes to the genenetwork3 repository also immediately reflect in the genenetwork2 continuous deployment without guix-bioinformatics having to be updated. * genenetwork-development.scm (<development-server-configuration>): Delete type. (<genenetwork-configuration>): New type. (development-server-redeploy, development-server-activation, genenetwork2-project, genenetwork2-shepherd-service, genenetwork3-project, genenetwork3-shepherd-service): Delete functions. (genenetwork2-tests): Accept <genenetwork-configuration> object instead of <forge-project> object. (%genotype-files, %xapian-db-path, %default-genenetwork2-configuration, genenetwork2-service-type, %default-genenetwork3-configuration, genenetwork3-service-type): Delete variables. (genenetwork-projects, genenetwork2-cd-gexp, genenetwork3-cd-gexp, genenetwork-shepherd-services): New functions. (operating-system)[services]: Replace genenetwork2 and genenetwork3 services with the unified genenetwork service. * genenetwork/development-helper.scm (genenetwork2-runner-gexp, genenetwork3-runner-gexp): Delete functions.
2022-10-28Expose xapian index to genenetwork3 instead of genenetwork2.Arun Isaac
* genenetwork-development.scm (genenetwork2-shepherd-service): Do not expose xapian index. (genenetwork3-shepherd-service): Expose xapian index. * genenetwork/development-helper.scm (genenetwork2-runner-gexp): Do not accept xapian index argument. (genenetwork3-runner-gexp): Accept config file argument.
2022-10-06Enable rust backtrace in genenetwork2 CD.Frederick Muriuki Muriithi
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set RUST_BACKTRACE environment variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-09-29Run genenetwork2 CD on gunicorn.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Run genenetwork2 CD on gunicorn.
2022-09-26Set up xapian search index for genenetwork2 CD.Arun Isaac
* genenetwork-development.scm (%xapian-db-path): New variable. (genenetwork2-shepherd-service)[start]: Share %xapian-db-path with the container. (%default-genenetwork2-configuration)[runner]: Pass %xapian-db-path to CD runner. * genenetwork/development-helper.scm (genenetwork2-runner-gexp): Accept xapian-db-path argument and set XAPIAN_DB_PATH environment variable. * genenetwork-development-deploy.sh: Expose /export/data/genenetwork/xapian in the container.
2022-09-08Set genenetwork3 API endpoint used by genenetwork2 to /api3.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set GN_SERVER_URL to /api3.
2022-08-16Add trailing slash to GN_PROXY_URL.Frederick Muriuki Muriithi
The urljoin function reduces a URL without a trailing slash to just the base, e.g. "http://genenetwork.org/gn3-proxy" is reduced to "http://genenetwork.org", which is not what we want. * genenetwork/development-helper.scm (genenetwork2-runner-gexp): Add trailing slash to GN_PROXY_URL environment variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-07-08Set GN_SERVER_URL when running genenetwork2.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set GN_SERVER_URL.
2022-07-06Switch to tissue service from guix-forge.Arun Isaac
* genenetwork-development-deploy.sh: Share tissue state directory with container. * genenetwork-development.scm: Do not import tissue from (gn packages gemini). Import (forge tissue). (<tissue-configuration>, <tissue-host>): Delete types. (%tissue-accounts, tissue-service-type): Delete variables. (gn-gemtext-threads-website, gn-gemtext-threads-index, tissue-conf-gexp, tissue-shepherd-service): Delete functions. (gn-gemtext-threads-project)[ci-jobs]: Use tissue pull in gn-gemtext-threads job. (tissue-reverse-proxy-server-block): Use default tissue state directory and unix socket paths. Do not accept them as arguments. (operating-system)[services]: Use new tissue-service-type parameters. Update invocation of tissue-reverse-proxy-server-block. * genenetwork/development-helper.scm (tissue-website-gexp, tissue-index-gexp): Delete functions.
2022-06-29Build tissue static website in temporary writable directory.Arun Isaac
tissue now builds a xapian index and this requires a writable directory. * genenetwork/development-helper.scm (tissue-website-gexp): Build static website in temporary writable directory.
2022-06-29Add tissue search interface.Arun Isaac
* genenetwork-development.scm: Import shadow from (gnu packages admin). (gn-gemtext-threads-index): New function. (gn-gemtext-threads-project)[ci-jobs]: Add gn-gemtext-threads-index. (<tissue-configuration>): New type. (tissue-shepherd-service, tissue-reverse-proxy-server-block): New function. (%tissue-accounts, tissue-service-type): New variables. (operating-system)[services]: Add tissue tissue service and reverse proxy it. * genenetwork/development-helper.scm (tissue-index-gexp): New function.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 10:12:42 +0000