| Age | Commit message (Expand) | Author |
|---|
| 2 days | 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 |
| 2 days | 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 |
| 2 days | 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 |
| 3 days | 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 |
| 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 |
| 2025-01-03 | Set ownership for `llm-db-path`. | Frederick Muriuki Muriithi |
| 2024-11-12 | Add AUTH_SERVER_URL setting to GN3 | 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 |
| 2024-10-29 | 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 | 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 |
| 2024-10-24 | 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 |
| 2024-10-02 | Update server root for gn-uploader. | Frederick Muriuki Muriithi |
| 2024-08-13 | Forward the scheme to the client to generate correct URIs. | 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 |
| 2024-07-22 | 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 | 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 | 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 |
| 2024-06-28 | Make secrets dirs writable by relevant services. | Frederick Muriuki Muriithi |
| 2024-06-28 | Remove duplicated, and wrong settings. | Frederick Muriuki Muriithi |
| 2024-06-28 | Fix permissions: Only files are read-only...Directories need the execute bit set to actually be accessible to the
owner.
| Frederick Muriuki Muriithi |
| 2024-06-28 | Make relevant services available to each service. | Frederick Muriuki Muriithi |
| 2024-06-28 | Set secrets as directories for services with multiple secrets. | Frederick Muriuki Muriithi |
| 2024-06-28 | Add JWT SSL keys configurations. | Frederick Muriuki Muriithi |
| 2024-06-12 | gn-uploader: Setup profile path...The profile path is necessary for use retrieving the included
bootstrap content.
| Frederick Muriuki Muriithi |
| 2024-05-07 | gn-uploader: Serve static files via nginx....* genenetwork/services/genenetwork.scm: Import nginx from (gnu
packages web), python from (gnu packages python), (guix build
python-build-system) and (guix packages).
(gn-uploader-nginx-server-block): Serve static files via nginx.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-04-12 | gn-uploader: use installed entry-point. | Frederick Muriuki Muriithi |
| 2024-04-12 | gn-uploader: use defined app in wsgi.py to pick up logging configs. | Frederick Muriuki Muriithi |
| 2024-04-12 | Set up log level in gunicornadd-gunicorn-logging | Frederick Muriuki Muriithi |
| 2024-04-10 | gn-uploader: Enable changing of log-level for container....This commit enables us to change the logging level of the gn-uploader
service within the container: this will help in the instances when we
need to debug events in the application that are unexpected.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Change ownership of data-directory...While the share is technically writable from the container, the
service was running as an unprivileged user, and thus could not write
to the data-directory. This commit changes the ownership of the
data-directory to the same user that runs the service.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Made datadir writable and set up uploads directory. | Frederick Muriuki Muriithi |
| 2024-04-05 | Document configuration settings | Pjotr Prins |
| 2024-04-03 | Set up SQL_URI for gn-auth. | Frederick Muriuki Muriithi |
| 2024-04-03 | gendev: special machine for Pjotr | Pjotr Prins |
| 2024-04-01 | Share TMPDIR between GN2 and GN3 | Pjotr Prins |
| 2024-04-01 | fallback: have gn2 and gn3 share a source directory so we can update/debug so......topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
| Pjotr Prins |
