| Age | Commit message (Expand) | Author |
|---|
| 2024-11-12 | Delete %transform-genenetwork-database-export-directory....* genenetwork-development.scm
(%transform-genenetwork-database-export-directory): Delete.
(set-build-directory-permissions-gexp): Remove
%transform-genenetwork-database-export-directory.
| Munyoki Kilyungi |
| 2024-01-05 | Set ownership and permissions on secret files....* genenetwork-development.scm (genenetwork-activation): Set ownership
and permissions on secret files.
* genenetwork-development-deploy.sh: Share /etc/genenetwork/conf
instead of merely exposing it.
| Arun Isaac |
| 2023-10-05 | Mount git repositories read-write....* genenetwork-development-deploy.sh: Mount /home/git/public read-write
into the container.
| Arun Isaac |
| 2023-09-20 | Pass "secrets" configurations to GN2...We need to pass in secrets to the running applications. This commit
does it for GeneNetwork2.
| Frederick Muriuki Muriithi |
| 2023-08-10 | Set up cgit service....* genenetwork-development.scm: Import (forge cgit).
(operating-system)[services]: Add cgit service.
* genenetwork-development-deploy.sh: Expose cgit repository directory.
| Arun Isaac |
| 2023-08-10 | Switch to the forge-nginx and ACME services....* 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.
| Arun Isaac |
| 2023-06-26 | Add virtuoso allowed dirs | Munyoki Kilyungi |
| 2023-05-05 | Run migrations after tests and before restarting genenetwork3....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>
| Frederick Muriuki Muriithi |
| 2023-02-09 | Share the mysqld socket directory into the container....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.
| Arun Isaac |
| 2023-01-18 | Add data directory to genenetwork configuration....*
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.
| Arun Isaac |
| 2023-01-18 | Move xapian directory....* 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.
| Arun Isaac |
| 2023-01-02 | Register containers as garbage collector roots....We don't want the Guix garbage collector accidentally clearing away
store items required by the container. So, register them as garbage
collector roots.
* genenetwork-development-deploy.sh, production-deploy.sh,
public-sparql-deploy.sh, virtuoso-deploy.sh: Register containers as
garbage collector roots.
| Arun Isaac |
| 2022-12-22 | Build and install xapian index nightly....* 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.
| Arun Isaac |
| 2022-12-10 | Move guix container state to /export2....We prefer /export2 to house really large data.
* genenetwork-development-deploy.sh, production-deploy.sh,
public-sparql-deploy.sh, virtuoso-deploy.sh: Move guix container state
to /export2.
| Arun Isaac |
| 2022-09-29 | Expose root of data directory instead of its sub-directories....* genenetwork-development-deploy.sh (container_script): Expose root of
data directory instead of its sub-directories.
| Arun Isaac |
| 2022-09-26 | Set up xapian search index for genenetwork2 CD....* 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.
| Arun Isaac |
| 2022-09-05 | Do not share /srv/http into container..../srv/http is no longer. It was used earlier for the gn-gemtext-threads
website.
* genenetwork-development-deploy.sh: Do not share /srv/http into
container.
| Arun Isaac |
| 2022-08-23 | Expose CD logs to host....* genenetwork-development.scm (genenetwork2-shepherd-service,
genenetwork3-shepherd-service): Move log files into /var/log/cd.
* genenetwork-development-deploy.sh: Share /var/log/cd with host.
| Arun Isaac |
| 2022-07-06 | Switch to tissue service from guix-forge....* 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.
| Arun Isaac |
| 2022-06-24 | Persist virtuoso database....* genenetwork-development-deploy.sh: Persist virtuoso database at
/var/guix-containers/genenetwork-development/var/lib/virtuoso.
| Arun Isaac |
| 2022-04-15 | Initial commit | Arun Isaac |
