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Expose the genotype files directory to the uploader, initially in
read-only mode.
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Share the parent directory for `llm-db-path` with the POLA wrapper,
rather than just the file to ensure that the permissions are set up
correctly and prevent SQLite from raising an error.
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Pass in the bare repository path to the gexp and use it instead of
fetching the value from the environment. This decouples the gexp from
changes in the code, e.g. should the environment variable name be
changed, we do not have to change this gexp.
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* Change the ownership of the secrets directory and all its children
rather than just the secrets file.
* Expose the secrets directory to the application, rather than just
the secrets file. Make the directory writable.
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Mapping the file only leads to permission issues within the POLA
wrapper since SQLite checks both the file, and the parent
directory; because of this, we have to map the parent directory to the
POLA wrapper too.
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* genenetwork/services/genenetwork.scm (<genenetwork-configuration>):
Add a configuration to track the 'gn-guile' package (version,
build-flags, etc) that is used when setting up the container.
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Redis is being phased out, and part of that is moving the storage of
sessions to the file system, rather than in Redis. This commit allows
configuration of the path to the directory where the session files
will be stored.
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Genenetwork2 changed the way it stores sessions, moving away from
using redis to storing the files in the filesystem. This commit binds
the host directory to use to store the sessions. It also does basic
activation to ensure the directory is writable to the appropriate
user.
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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.
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Pass the directory containing virtuoso's turtle (ttl) files to the
indexer.
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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.
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The `gn-uploader-ca-bundle` variable needs the value from the
`gn-uploader-profile` variable.
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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.
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* 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.
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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.
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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>
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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>
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* 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>
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* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set AI_SEARCH_ENABLED to True in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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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>
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* 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.
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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.
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* genenetwork/services/genenetwork.scm (<genenetwork-configuration>,
<gn-uploader-configuration>, build-xapian-index-cron-gexp): Re-format
and re-indent.
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*
genenetwork/services/genenetwork.scm (<gn-uploader-configuration>)[auth-server-url,
gn2-server-url, log-level]: Regularize getter function names.
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