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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.
2022-06-29Remove tissue's dependence on the git CLI tool.Arun Isaac
tissue now uses libgit2 through guile-git and does not use the git CLI tool. * genenetwork-development.scm (gn-gemtext-threads-website): Remove git-minimal from manifest. * genenetwork/development-helper.scm (tissue-website-gexp): Remove reassurance to git.
2022-06-14Reassure git that the gn-gemtext-threads source directory is safe.Arun Isaac
* genenetwork/development-helper.scm (tissue-website-gexp): Reassure git that the gn-gemtext-threads source directory is safe. * genenetwork-development.scm (gn-gemtext-threads-website): Add git-minimal to manifest.
2022-04-15Initial commitArun Isaac