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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>
2023-09-11Update the repo-url for transforming genenetwork databases.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use correct name for python-mypyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Update arguments to pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use mypy defined in guix-bioinformaticsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-04Use self-hosted git repoMunyoki Kilyungi
2023-09-04Use self-hosted GN repositoryMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-12Add link to git repoPjotr Prins
2023-08-10Set up cgit service.Arun Isaac
* genenetwork-development.scm: Import (forge cgit). (operating-system)[services]: Add cgit service. * genenetwork-development-deploy.sh: Expose cgit repository directory.
2023-08-10Switch to the forge-nginx and ACME services.Arun Isaac
* genenetwork-development.scm: Import only nginx-server-configuration and nginx-location-configuration from (gnu services web). Import (forge acme) and (forge nginx). (development-server-reverse-proxy-server-block, laminar-reverse-proxy-server-block, tissue-reverse-proxy-server-block): Remove listen argument. (operating-system)[sudoers-file]: Permit the acme user to restart nginx. [services]: Replace nginx service with a forge-nginx service. Add ACME service. * genenetwork-development-deploy.sh: Share /var/lib/acme.
2023-08-10Add nginx package with the ssl_preread module.Arun Isaac
* nginx-preread.scm, nginx-preread-deploy.sh: New files.
2023-07-27README: Remove references to penguin2.Arun Isaac
penguin2 is no more. We now use tux02 for development. * README.org: Change references to penguin2 to tux02.
2023-07-27Revert "README: host names"Arun Isaac
This reverts commit fc65c2a2c056ee9f313631da6e5f93adec277dd5.
2023-07-19Use tissue from guix-forge.Arun Isaac
The libgit2 patch is now in guix-forge. So, we don't have to repeat it here. * genenetwork-development.scm (libgit2-1.3, guile-git-for-tissue, tissue): Delete variables. (operating-system)[services]: Do not specify package for tissue service.
2023-07-19Disable verbose build logs for guix-bioinformatics job.Arun Isaac
* genenetwork-development.scm (guix-bioinformatics-project): Disable verbose build logs.
2023-07-19Use guix-channel-job-gexp for genenetwork3 tests.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Use guix-channel-job-gexp for genenetwork3 tests.
2023-07-19Add guix-bioinformatics CI job.Arun Isaac
* genenetwork-development.scm (guix-channel-job-gexp): New function. (guix-bioinformatics-project): New variable. (operating-system)[services]: Add guix-bioinformatics-project to forge-service-type.
2023-07-11README: host namesPjotr Prins
2023-07-11Revert "Disable tests"Munyoki Kilyungi
This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
2023-07-10Add a troubleshooting subsection to READMEMunyoki Kilyungi
2023-07-10Revert "Fix genotype file path"Munyoki Kilyungi
This reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.
2023-07-10Fix genotype file pathMunyoki Kilyungi
2023-07-10Disable testsMunyoki Kilyungi
Rob is giving a demo, so disable tests and fix them later. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-10Basic mail/opensmtpd service addedPjotr Prins
2023-06-26Add virtuoso allowed dirsMunyoki Kilyungi
2023-06-15Increase threshold for number-of-buffers and maximum-dirty-buffers.Munyoki Kilyungi
* genenetwork-development.scm, public-sparql.scm (operating-system)[services]<virtuoso-service>: Set number-of-buffers and maximum-dirty-buffers. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-15Add links to README.Munyoki Kilyungi
* README.org (GeneNetwork development container): Link to guix-bioinformatics and guix-forge channels. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-08Share auth-db-path with genenetwork3-pola-wrapper.Frederick Muriuki Muriithi
* genenetwork-development.scm (genenetwork-shepherd-services): Share auth-db-path with genenetwork3-pola-wrapper. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-06Set AUTH_DB, not AUTH_DB_PATH.Frederick Muriuki Muriithi
genenetwork3 expects AUTH_DB, not AUTH_DB_PATH. * genenetwork-development.scm (genenetwork3-cd-gexp): Set AUTH_DB, not AUTH_DB_PATH. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-31Do not create xapian build directory.Arun Isaac
* genenetwork-development.scm (build-xapian-index-gexp): Do not create xapian build directory.
2023-05-31Use an absolute GN_SERVER_URL.Frederick Muriuki Muriithi
A relative GN_SERVER_URL sometimes leads to issues when code (in libraries e.g. requests and the like) cannot expand the URI since it does not have context about the running server. * genenetwork-development.scm (genenetwork2-cd-gexp): Use an absolute GN_SERVER_URL. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-31Add trailing slash to GN_SERVER_URL.Frederick Muriuki Muriithi
Without the trailing slash, the urllib.parse.urljoin function produces the wrong endpoint. * genenetwork-development.scm (genenetwork2-cd-gexp): Add trailing slash to GN_SERVER_URL. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-22Document getting a shell into containerFrederick Muriuki Muriithi
For some tasks (e.g. debugging the xapian index build), we need to manually queue the job, which means we need a shell into the container. Getting a shell using the default command displayed actually fails with: nsenter: failed to execute /bin/bash: No such file or directory so we need to provide the correct path to bash, and optionally, initialise the shell to setup the correct paths.
2023-05-05Run migrations after tests and before restarting genenetwork3.Frederick Muriuki Muriithi
Add a CI job that applies the auth database migrations. This job is run after the genenetwork3 tests have passed but before genenetwork3 is restarted. * genenetwork-development-deploy.sh: Share /export/data/genenetwork-sqlite. * genenetwork-development.scm: Import yoyo-migrations from (gnu packages databases). (<genenetwork-configuration>)[auth-db-path]: New field. (genenetwork3-auth-migrations-genenetwork, genenetwork3-auth-migrations-laminar, genenetwork-activation): New functions. (genenetwork-projects): Add genenetwork3-auth-migrations CI job. Trigger this job after genenetwork3 tests. (genenetwork3-cd-gexp): Configure AUTH_DB_PATH in gn3.conf. (genenetwork-service-type): Extend activation-service-type with genenetwork-activation. (operating-system)[sudoers-file]: Permit the laminar user to run auth database migrations as the genenetwork user. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-04-12Run tissue on an IP socket.Arun Isaac
tissue fails to clean up its Unix socket when deployed with shepherd. So, when tissue crashes, it fails to restart. Until this issue is resolved, run tissue on an IP socket. * genenetwork-development.scm (%tissue-port): New variable. (tissue-reverse-proxy-server-block): Forward tissue requests to IP socket. (operating-system)[services]: Run tissue on an IP socket.
2023-04-12Disable libgit2 repository ownership validation.Arun Isaac
* genenetwork-development.scm: Import guile-git from (gnu packages guile), libgit2-1.3 from (gnu packages version-control), and (guix utils). Prefix tissue import from (gnu packages web) with guix:. (libgit2-1.3, guile-git-for-tissue, tissue): New variables. (operating-system)[services]: Use local variant of tissue package.
2023-04-11Use tissue package from Guix upstream.Arun Isaac
The tissue package is now in Guix upstream and longer in the guix-forge channel. * genenetwork-development.scm: Import tissue from (gnu packages web).
2023-04-11Provide MySQL URI to the xapian indexing script.Frederick Muriuki Muriithi
* genenetwork-development.scm (build-xapian-index-gexp): Provide MySQL URI to the xapian indexing script.
2023-02-09Share the mysqld socket directory into the container.Arun Isaac
We ought to share the mysqld socket directory into the container, not the socket itself. If we only shared the socket, when the mysql server is restarted and a new socket is created, the bind mounting into the container would break and the container would need to be restarted. * genenetwork-development-deploy.sh: Share /var/run/mysqld, not /var/run/mysqld/mysqld.sock. * genenetwork-development.scm (genenetwork-shepherd-services): Share /run/mysqld, not /run/mysqld/mysqld.sock.
2023-01-21GN3: pylint - Check more files and directoriesFrederick Muriuki Muriithi
2023-01-18Add data directory to genenetwork configuration.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[data-directory]: New field. (genenetwork3-cd-gexp): Set DATA_DIR in settings file. (genenetwork-shepherd-services): Map data directory into container. (operating-system)[services]: Set data-directory of genenetwork service to /export/data/genenetwork. * genenetwork-development-deploy.sh: Expose entire data directory /export/data/genenetwork instead of the contained genotype files directory.
2023-01-18Move xapian directory.Arun Isaac
* genenetwork-development.scm (%xapian-directory): Move from /export/data/genenetwork/xapian to /export/data/genenetwork-xapian. * genenetwork-development-deploy.sh (container_script): Share /export/data/genenetwork-xapian instead of /export/data/genenetwork/xapian.
2023-01-08Clean up xapian build directory if previous build failed to.Arun Isaac
* genenetwork-development.scm (build-xapian-index-gexp): Clean up xapian build directory if previous build failed to.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-07 20:53:00 +0000