| Age | Commit message (Expand) | Author |
|---|
| 2 days | Split the tempdirs for various applications.HEADmain | Frederick Muriuki Muriithi |
| 3 days | Remove 'mysql-service-type' service from 'production' container....We connect to a MariaDB database outside the container, therefore, the
container does not need to run a database server. This commit removes
the service from the container.
| Frederick Muriuki Muriithi |
| 3 days | Don't allow GN3 user write permissions to 'TMPDIR'. | Frederick Muriuki Muriithi |
| 3 days | Assign ownership of 'TMPDIR' and its contents to GN2 user. | Frederick Muriuki Muriithi |
| 4 days | Don't share MariaDB data directory with the production container. | Frederick Muriuki Muriithi |
| 6 days | Grant ownership of genotype-files to GN2 user. | Frederick Muriuki Muriithi |
| 12 days | Bind the chosen host directory to genenetwork's TMPDIR path....Bind the original host path that was previously bound to the
container's /tmp directory to instead be bound to genenetwork's TMPDIR
directory.
| Frederick Muriuki Muriithi |
| 12 days | Add `gn-tmpdir` configuration setting to <genenetwork-configuration>...Add the `gn-tmpdir` configuration setting to help with providing a way
to configure a separate temporary directory for the genenetwork
services that is separate from the container's `/tmp` directory.
This might also help in resolving some issue with `/etc/resolv.conf`
not being found in `/tmp` for some reason.
| Frederick Muriuki Muriithi |
| 12 days | Remove comments: The comments were causing a build invocation error....Attempting to invoke the container build with the comments in place
was leading to the error:
```
guix system: error: wrong number of arguments for action
'container'
```
This commit removes the comments to fix that.
| Frederick Muriuki Muriithi |
| 12 days | Update `dirs-allowed` for gn2-container virtuoso. | Frederick Muriuki Muriithi |
| 2025-02-03 | Pass ttl directory in list of allowed directories for virtuoso. | Frederick Muriuki Muriithi |
| 2025-02-03 | 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 |
| 2025-02-03 | Bind virtuoso's TTL directory (readonly) to genenetwork container. | Frederick Muriuki Muriithi |
| 2025-02-03 | Bind virtuoso's ttl directory (read/write) to virtuoso container. | Frederick Muriuki Muriithi |
| 2025-02-03 | 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 |
| 2025-01-29 | Update SQL URI for uploader application. | Frederick Muriuki Muriithi |
| 2025-01-29 | Update the SQL URI for the uploader container. | Frederick Muriuki Muriithi |
| 2025-01-28 | Update config to point to llm.db binding. | Frederick Muriuki Muriithi |
| 2025-01-28 | 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 |
| 2025-01-28 | 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 |
| 2025-01-28 | Link to the GNQnA SQLite database. | Frederick Muriuki Muriithi |
| 2025-01-28 | Move uploader directories out of another container's directories. | Frederick Muriuki Muriithi |
| 2025-01-28 | 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 |
| 2025-01-28 | 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 |
| 2025-01-28 | 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 |
| 2025-01-26 | 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 |
