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Fix the service activation code to make the gn-uploader data
directory, and all its children belong to the app user.
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Make the container's logs available of the host to help with
troubleshooting and some stickiness for the logs.
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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.
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Add the scheduled indexer service to the
genenetwork-service-type. This will run the indexer script every hour.
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Pass in the configuration to the gexp building function to make the
builder function work across environments.
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* slurm-deploy.sh, slurm.scm: New files.
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Directories need the execute bit set to actually be accessible to the
owner.
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Put the secrets for the different services in service-specific
directories, all of them sharing the same parent directory.
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* genenetwork-development.scm: Run "M-x untabify".
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Let the python xapian indexing script check the checksums, instead of using a
G-expression. This approach is simpler and more understandable; it is also
more versatile and allows easier modification.
* genenetwork-development.scm (build-xapian-index-cron-gexp): Use the indexing
script to compare checksums. If the checksums changed, queue the
genenetwork3-build-xapian-index laminar job.
Co-authored-by: John Nduli <rookie101@jnduli.co.ke>
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* genenetwork-development.scm (guile-lapack-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lapack-project.
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* genenetwork-development.scm (guile-gsl-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-gsl-project.
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The profile path is necessary for use retrieving the included
bootstrap content.
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* 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>
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* genenetwork-development.scm (genenetwork-shepherd-services): Mount
llm-db-path into genenetwork3 container.
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genenetwork-development.scm (<genenetwork-configuration>)[llm-db-path]:
New field.
(genenetwork3-cd-gexp): Configure LLM_DB_PATH in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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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.
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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.
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This commit lets us use the bleeding-edge gn-uploader from the
gn-uploader channel.
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The uploader container is for testing that the gn-uploader package
builds and the application is working correctly. It sets up a service
that allows users to upload data.
It does need the other GeneNetwork services, but does not need the
latest and greatest. This commit uses the default genenetwork2
package (which will mostly be stable): thus there are fewer (if any)
issues getting the other services to run.
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source code for development. See
topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
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* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>):
New type.
(gn-uploader-activation, gn-uploader-gunicorn-app,
gn-uploader-nginx-server-block): New functions.
(gn-uploader-service-type): New variable.
* uploader.scm, uploader-deploy.sh: New files.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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