| Age | Commit message (Expand) | Author |
|---|
| 34 hours | Pass ttl directory in list of allowed directories for virtuoso.pass-virtuoso-ttl-dir-to-xapian-indexer | Frederick Muriuki Muriithi |
| 34 hours | Pass virtuoso's ttl directory to the xapian indexer script....Pass the directory containing virtuoso's turtle (ttl) files to the
indexer.
| Frederick Muriuki Muriithi |
| 34 hours | Bind virtuoso's TTL directory (readonly) to genenetwork container. | Frederick Muriuki Muriithi |
| 34 hours | Bind virtuoso's ttl directory (read/write) to virtuoso container. | Frederick Muriuki Muriithi |
| 34 hours | Add 'gn-virtuoso-ttl-directory' setting to genenetwork-configuration...The directory containing the turtle (ttl) files for virtuoso is used
by the xapian indexer to determine whether or not to run. We provide
it as one of the settings we can configure.
| Frederick Muriuki Muriithi |
| 38 hours | Update config to point to llm.db binding. | Frederick Muriuki Muriithi |
| 38 hours | Link to existing gn-docs....The uploader container will not concern it with editing the gn-docs
repository, but might still need it present to allow the system to
run. This ensures it is present.
| Frederick Muriuki Muriithi |
| 38 hours | Link to the appropriate mysqld socket...The uploader container uses a separate database from that used by
CI/CD, since the uploader does (potentially) destructive changes to
the data in the database.
| Frederick Muriuki Muriithi |
| 38 hours | Link to the GNQnA SQLite database. | Frederick Muriuki Muriithi |
| 39 hours | Move uploader directories out of another container's directories. | Frederick Muriuki Muriithi |
| 39 hours | gn-uploader: gn-uploader-gunicorn-app: Switch from `let` to `let*`...The `gn-uploader-ca-bundle` variable needs the value from the
`gn-uploader-profile` variable.
| Frederick Muriuki Muriithi |
| 39 hours | uploader log-level: use symbol rather than text....Update the log-level value to use a symbol rather than text, since
that's what's expected by the newer system.
| Frederick Muriuki Muriithi |
| 41 hours | Increase the allowed size of the client request body....Some request (e.g. for mapping) from GN2 can get big, depending on the
trait(s) in use. This commit increases the maximum allowed size for
the client body to allow bigger requests.
| Frederick Muriuki Muriithi |
| 4 days | Specify the character-set for the DB connection. | Frederick Muriuki Muriithi |
| 2025-01-15 | Replace repo URLs with "/home/git/public" for self-hosted setups....* genenetwork-development.scm (<genenetwork-configuration>): Replace
"https://git.genenetwork.org" with "/home/git/public".
* (genenetwork-projects)[gn-libs, gn-auth]{ci-jobs-trigger}: Delete.
* (transform-genenetwork-database-project)[repository]: Replace
"https://git.genenetwork.org" with "/home/git/public".
* (transform-genenetwork-database-project)[repository]: Replace
"https://git.genenetwork.org" with "/home/git/public".
[ci-jobs-trigger]: Delete.
| Munyoki Kilyungi |
| 2025-01-06 | Add gn-libs to CI. | Munyoki Kilyungi |
| 2025-01-06 | Add gn-guile shepherd service genenetwork-service-type....* genenetwork/services/genenetwork.scm: Import gn-guile, linux-container,
git-minimal, shepherd, least-authority, forge utils.
(<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields.
(gn-guile-gexp): New g-exp for running gn-guile.
(gn-guile-shepherd-service): New shepherd service to run gn-guile.
(genenetwork-service-type): Add gn-guile-shepherd-service.
* production-deploy.sh (container_script): Export gn-docs directory.
| Munyoki Kilyungi |
| 2025-01-06 | Create a tmpdir for genenetwork2 tests. | Munyoki Kilyungi |
| 2025-01-06 | Add REQUESTS_CA_BUNDLE to genenetwork2 shepherd service....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2025-01-06 | Map "/tmp" in gn2/3 and make it writable. | Munyoki Kilyungi |
| 2025-01-06 | Explicitly set "RSCRIPT" in gn3 g-exp. | Munyoki Kilyungi |
| 2025-01-06 | Correctly delete virtuoso build directory....* genenetwork-development.scm (transform-genenetwork-database-gexp): Only
delete virtuoso "build" directory.
| Munyoki Kilyungi |
| 2025-01-06 | Add gn-guile service to genenetwork-shepherd-services....* genenetwork-development-deploy.sh: share "/export/data/gn-docs/".
* genenetwork-development.scm: Import gn-guile.
(<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields.
(gn-guile-gexp): New g-exp for running gn-guile.
(genenetwork-shepherd-services): Add gn-guile service.
| Munyoki Kilyungi |
| 2025-01-06 | Set gn2 env variables inside the shepherd service....* genenetwork-development.scm: Import (guix search-paths).
(genenetwork2-cd-gexp): Move environment variables ...
(genenetwork-shepherd-services)[genenetwork2]: ... here.
| Munyoki Kilyungi |
| 2025-01-06 | Remove duplicate environment settings....* genenetwork-development.scm (genenetwork2-cd-gexp): Delete duplicate env
settings that are later defined in "gn2.conf".
| Munyoki Kilyungi |
| 2025-01-03 | Set ownership for `llm-db-path`. | Frederick Muriuki Muriithi |
| 2024-12-06 | CI/CD: Update database URI - add socket path. | Frederick Muriuki Muriithi |
| 2024-11-26 | Use forge-nginx-service-type to activate SSL certificates...Use the forge-nginx-service-type rather than the plain
nginx-service-type so that we get the SSL certificates setup and
maintenance automatically.
| Frederick Muriuki Muriithi |
| 2024-11-26 | Specify the socket for MariaDB connections. | Frederick Muriuki Muriithi |
| 2024-11-12 | Add AUTH_SERVER_URL setting to GN3 | Frederick Muriuki Muriithi |
| 2024-11-12 | Expose the container logs. | Frederick Muriuki Muriithi |
| 2024-11-12 | Bind a host directory to container's /tmp...Bind a host directory to container's /tmp to provide more space for
the /tmp and prevent the container from running out of space.
| Frederick Muriuki Muriithi |
| 2024-11-12 | Unbind mysql director(y/ies)...Not needed for the virtuoso daemon.
| Frederick Muriuki Muriithi |
| 2024-11-12 | Use virtuoso's state directory as its data directory...This helps avoid having a long list of directories to track and manage.
| Frederick Muriuki Muriithi |
| 2024-11-12 | Explicitly set Virtuoso's Database and Transaction files....Explicitly name the public virtuoso's Database and transaction files
to prevent any possible conflicts with other virtuoso instances.
| Frederick Muriuki Muriithi |
| 2024-11-12 | Pass log-level to gn-auth application | Frederick Muriuki Muriithi |
| 2024-11-12 | Define REQUESTS_CA_BUNDLE envvar for python-requests...Define the `REQUESTS_CA_BUNDLE` for all applications that make use of
python's requests library. The library needs to know the location of
valid CA certificates in order to work as expected.
Expose the CA certificates bundles by adding them to the applications'
environments using the mappings objects.
| Frederick Muriuki Muriithi |
| 2024-11-12 | Add cron job for running transform-genenetwork-database-gexp. | Munyoki Kilyungi |
| 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 |
| 2024-11-12 | Rename transform-genenetwork-database....* genenetwork-development.scm (transform-genenetwork-database): Rename this to...
(transform-genenetwork-database-project): ... this.
(transform-genenetwork-database-project): Ditto.
| Munyoki Kilyungi |
| 2024-11-12 | Make %virtuoso-data-dir writeable by laminar....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-11-12 | Refactor ttl and data-loading into Virtuoso in ci job....* genenetwork-development.scm (transform-genenetwork-database): Use a script
to generate and validate ttl files.
(%connection-settings): New variable. Contains the sparql and mysql
login credentials.
(%virtuoso-data-dir): New variable.
(transform-genenetwork-database-project): Update how the
transform-genenetwork-database gexp is called. Add web hook.
| Munyoki Kilyungi |
| 2024-11-05 | Bind host directory to the container's /tmp directory...Since the /tmp directory is used for a lot of things in the code, we
bind a host directory to it, so as to allow easier cleanup, and also
ensure the container does not run out of disk space.
| Frederick Muriuki Muriithi |
| 2024-10-30 | Explicitly name virtuoso's database files. | Frederick Muriuki Muriithi |
| 2024-10-29 | Do not share auth-db with genenetwork3 gunicorn app....GeneNetwork3 should not have direct access to the authorisation
database file.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Do not mount auth-db into genenetwork3 gunicorn app container.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-29 | Specify path to LLM database in production....*
production.scm (operating-system)[services]{genenetwork-service-type}:
Add llm-db-path.
* production-deploy.sh: Share
/export2/guix-containers/genenetwork/var/lib/genenetwork-gnqa with
container.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-29 | Add llm-db-path field to genenetwork configuration.....*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[llm-db-path]:
New field.
(genenetwork-gunicorn-apps): Set LLM_DB_PATH in gn3.conf. Mount LLM
database into the container.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-29 | Remove obsolete SSL key configuration....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Remove SSL_PRIVATE_KEY and AUTH_SERVER_SSL_PUBLIC_KEY.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-29 | Enable AI search in genenetwork service....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set AI_SEARCH_ENABLED to True in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-29 | Add additional virtuso configuration....* production.scm (operating-system)[services]{virtuoso-service-type}:
Add dirs-allowed, number-of-buffers and maximum-dirty-buffers.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
