aboutsummaryrefslogtreecommitdiff
path: root/genenetwork-development.scm
AgeCommit message (Collapse)Author
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>
2023-09-05Use 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>
2023-08-10Set 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.
2023-07-19Use 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.
2023-07-11Revert "Disable tests"Munyoki Kilyungi
This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
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>
2023-06-26Add 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>
2023-06-08Share 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>
2023-05-05Run 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.
2023-01-18Add 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.
2023-01-05Create custom 502 error page for CD.Arun Isaac
This 502 error page is more informative than a generic "Bad Gateway" error message. It tells the user that the CD is down but not the entire container itself. * genenetwork-development.scm: Import guile-lib from (gnu packages guile-xyz). (%ci-domain): New variable. (cd-error-pages-gexp): New function. (development-server-reverse-proxy-server-block): Use (cd-error-pages-gexp) to construct error pages. (laminar-reverse-proxy-server-block): Use %ci-domain.
2022-12-22Build and install xapian index nightly.Arun Isaac
* genenetwork-development.scm: Import (gnu services mcron). (%xapian-directory): New variable. (build-xapian-index-gexp): New function. (genenetwork-projects): Add genenetwork3-build-xapian-index CI job to genenetwork3 project. (operating-system)[sudoers-file]: Allow laminar user to start and stop genenetwork3. [services]: Add mcron service to trigger nightly xapian build. Use %xapian-directory instead of its literal value. chown %xapian-directory to the laminar user.
2022-12-22Separate out sudo into a variable.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Separate out "/run/setuid-programs/sudo" into ... (sudo): ... new variable.
2022-12-22gn3: tests: Update the tests invocationFrederick Muriuki Muriithi
* genenetwork-development.scm: use pytest rather than unittest to run the tests.
2022-11-10Configure SPARQL endpoint of genenetwork3 server.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[sparql-endpoint]: New field. (genenetwork3-cd-gexp): Set SPARQL_ENDPOINT in gn3.conf. (%virtuoso-sparql-port): New variable. (operating-system)[services]: Configure sparql-endpoint of genenetwork service.
2022-11-07Move CD virtuoso ports to 90*.Arun Isaac
In the interest of good organization, we keep all CD ports at 90*. Production and other services can use ports outside this range. * genenetwork-development.scm (operating-system)[services]: Move virtuoso ports from 8891, 8892 to 9081, 9082.
2022-11-04Import GeneRIF by calling the unified dump script.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Import GeneRIF by calling the unified dump script.
2022-10-31Find GeneRIF data in root of export directory.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Find GeneRIF data in root of export directory.
2022-10-31Use guile-zlib in dump-genenetwork-database CI job.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Use guile-zlib.
2022-10-31Ungexp gn2 and gn3 repositories correctly.Arun Isaac
* genenetwork-development.scm (genenetwork2-tests): Ungexp gn2-repository and gn3-repository correctly.
2022-10-31Import (guix build utils) in after scripts of CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Import (guix build utils) in after scripts of CI jobs.
2022-10-30Import GeneRIF into RDF.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Import GeneRIF into RDF.
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.
2022-10-20Use GitHub URI for dump-genenetwork-database repo.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database-project)[repository]: Use GitHub URI.
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-19 16:48:18 +0000