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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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Not everyone has GUIX_PROFILE set in their environment. Inferring the
profile from the guix executable is more reliable.
* genenetwork-development.scm (channels-scm-gexp): Infer profile from
guix executable used to build container.
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gn-auth runs as the gunicorn-gn-auth user, not the genenetwork user.
* genenetwork/services/genenetwork.scm (genenetwork-activation): Let
the gunicorn-gn-auth user own the auth database.
Reported-by: Frederick M. Muriithi <fredmanglis@protonmail.com>
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This is useful to enable building URIs with the correct scheme in the
application. These URIs are important when redirection to and from
external services such as the gn-auth service.
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*
production.scm (operating-system)[services]{genenetwork-service-type}:
Remove auth-db field.
* production-deploy.sh (container_script): Mount /var/genenetwork.
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* fallback.scm: New file.
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* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set AUTH_SERVER_URL on production genenetwork2.
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*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth-server-name]:
New field.
*
genenetwork/services/genenetwork.scm (genenetwork-nginx-server-block):
Rename to ...
(genenetwork-nginx-server-blocks): ... this. Return list of reverse
proxy blocks including one for gn-auth.
* genenetwork/services/genenetwork.scm (genenetwork-service-type): Use
genenetwork-nginx-server-blocks instead of
genenetwork-nginx-server-block.
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production.scm (operating-system)[services]{genenetwork-service-type}:
Add gn-auth-server-name.
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* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
owner-only permissions on secrets files.
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* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
ownership of secrets files.
* production-deploy.sh: Mount secrets files read-write.
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* genenetwork/services/genenetwork.scm: Import gn-auth from (gn
packages genenetwork).
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genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth,
gn-auth-port, gn-auth-secrets]: New fields.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add gn-auth gunicorn app.
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* genenetwork-development.scm: Bump copyright year for Fred.
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genenetwork-development.scm (<genenetwork-configuration>)[gn-auth-secrets]:
New field.
* genenetwork-development.scm (gn-auth-cd-gexp): Set GN_AUTH_SECRTS
from gn-auth-secrets of <genenetwork-configuration> object.
(operating-system)[services]{genenetwork-service-type}: Set
gn-auth-secrets.
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* genenetwork-development.scm (gn-auth-cd-gexp): Run with 8 workers.
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