| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-10-24 | Move production to tux04....* production-deploy.sh: Update paths for mysql, xapian and
genenetwork-sqlite directories. Share path to redis state directory.
* production.scm (operating-system)[services]{virtuoso-service-type}:
Update server-port and http-server-port.
{forge-nginx-service-type}: Update http and https ports.
{redis-service-type}: New service.
{genenetwork-service-type}: Update server-name, gn-auth-server-name,
gn2-port, gn3-port, gn-auth-port, xapian-db, sparql-endpoint and
gn3-data-directory. Add auth-db, log-level and gn3-alias-server-port.
Remove genotype-files.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-24 | Add GN3 alias server to genenetwork service....*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn3-alias-server-port]:
New field.
(genenetwork-nginx-server-blocks): Rewrite URLs for the GN3 alias
server.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-24 | Add sanitizer for log-level configuration field....* genenetwork/services/genenetwork.scm: Import (guix diagnostics)
and (guix i18n).
(sanitize-log-level): New function.
(<genenetwork-configuration>)[log-level]: Use sanitize-log-level as
the sanitizer.
(<gn-uploader-configuration>)[log-level]: Use sanitize-log-level as
the sanitizer.
| Arun Isaac |
| 2024-10-24 | Make <gn-uploader-configuration> log-level a symbol....*
genenetwork/services/genenetwork.scm (<gn-uploader-configuration>)[log-level]:
Change default to the symbol 'warning.
* genenetwork/services/genenetwork.scm (gn-uploader-gunicorn-app):
Pass --log-level to gunicorn.
| Arun Isaac |
| 2024-10-24 | Re-format and improve indentation....* genenetwork/services/genenetwork.scm (<genenetwork-configuration>,
<gn-uploader-configuration>, build-xapian-index-cron-gexp): Re-format
and re-indent.
| Arun Isaac |
| 2024-10-24 | Regularize <gn-uploader-configuration> getter functions....*
genenetwork/services/genenetwork.scm (<gn-uploader-configuration>)[auth-server-url,
gn2-server-url, log-level]: Regularize getter function names.
| Arun Isaac |
| 2024-10-24 | Add log-level field to genenetwork-configuration....*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[log-level]:
New field.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Pass --log-level to gunicorn.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-24 | Set REAPER_COMMAND in gn3.conf....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set REAPER_COMMAND in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-24 | Set GENOTYPE_FILES in gn3.conf....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set GENOTYPE_FILES in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-10-18 | Move directory permissions setting G-exp into separate variable....* genenetwork-development.scm (set-build-directory-permissions-gexp):
New variable.
* genenetwork-development.scm (operating-system)[services]: Use
set-build-directory-permissions-gexp.
| Arun Isaac |
| 2024-10-18 | Provide UTF-8 locale so characters are encoded correctly....* genenetwork-development.scm (gn-gemtext-threads-project)[ci-jobs]:
Set LC_ALL environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 2024-10-18 | Explicitly set AUTH_SERVER_URL in gn3.conf....This fixes an issue where gn3 auth defaults to "auth.genenetwork.org" during
query execution. Instead we explicitly set AUTH_SERVER_URL to
"auth-cd.genenetwork.org"
| Munyoki Kilyungi |
| 2024-10-18 | Upgrade slurm to 24.05.3....* slurm.scm (slurm): Upgrade to 24.05.3.
[arguments]: Remove Unix socket disabling.
| Arun Isaac |
| 2024-10-02 | Update server root for gn-uploader. | Frederick Muriuki Muriithi |
| 2024-10-02 | Update path to genotype files. | Frederick Muriuki Muriithi |
| 2024-09-12 | Enable AI Search in GN2 CD. | Munyoki Kilyungi |
| 2024-09-03 | Configure slurm with --with-yaml....* slurm.scm (slurm)[arguments]: Add --with-yaml configure flag.
| Arun Isaac |
| 2024-08-29 | Install slurmrestd too....* slurm-worker-deploy.sh: Install slurmrestd too.
| Arun Isaac |
| 2024-08-29 | Add slurm deployment scripts for octopus....* slurm-deploy.sh: Delete file.
* slurm-head-deploy.sh, slurm-worker-deploy.sh: New files.
* slurm.scm: Replace tux04 with octopus in comment.
| Arun Isaac |
| 2024-08-29 | Use http-parser from Guix....* slurm.scm: Import http-parser from (gnu packages web).
(http-parser): Delete variable.
| Arun Isaac |
| 2024-08-13 | Forward the scheme to the client to generate correct URIs. | Frederick Muriuki Muriithi |
| 2024-08-13 | Update docs | Frederick Muriuki Muriithi |
| 2024-08-13 | gn-uploader: Configure link to GN2 server. | Frederick Muriuki Muriithi |
| 2024-08-07 | gn-uploader: Add `AUTH_SERVER_URL` to the configurations. | Frederick Muriuki Muriithi |
| 2024-08-07 | gn-uploader: Update ENVVAR name | Frederick Muriuki Muriithi |
| 2024-08-07 | gn-uploader: Update configuration variable name. | Frederick Muriuki Muriithi |
| 2024-08-06 | Give access to read TTL from the /var/lib/virtuoso directory. | Frederick Muriuki Muriithi |
| 2024-07-22 | gn-uploader: use `gn-uploader-configuration` as default. | Frederick Muriuki Muriithi |
| 2024-07-22 | gn-uploader: make app user owner of upload directory tree...Fix the service activation code to make the gn-uploader data
directory, and all its children belong to the app user.
| Frederick Muriuki Muriithi |
| 2024-07-12 | Update configurations. | Frederick Muriuki Muriithi |
| 2024-07-12 | Make the container's /var/log directory available on host...Make the container's logs available of the host to help with
troubleshooting and some stickiness for the logs.
| Frederick Muriuki Muriithi |
| 2024-07-12 | Indicate environment in container hostnames...While it is a tiny change, it does help to have an explicit indication
of what container you are currently working with, especially when you
need to do specific tasks inside the container itself with something
like `nsenter …` or `guix container exec …`.
With this commit, instead of a generic prompt like:
`root@genenetwork /#`,
you get a more specific prompt such as
`root@genenetwork-production /#`
which goes some ways in avoiding mistakes.
| Frederick Muriuki Muriithi |
| 2024-07-12 | Add virtuoso to uploader. | Frederick Muriuki Muriithi |
| 2024-07-12 | Extend the genenetwork-service-type with the mcron indexer service...Add the scheduled indexer service to the
genenetwork-service-type. This will run the indexer script every hour.
| Frederick Muriuki Muriithi |
| 2024-07-12 | Make xapian directory writable inside container. | Frederick Muriuki Muriithi |
| 2024-07-12 | Generalise index-genenetwork cron gexp...Pass in the configuration to the gexp building function to make the
builder function work across environments.
| Frederick Muriuki Muriithi |
