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* genenetwork-development.scm
(%transform-genenetwork-database-export-directory): Delete.
(set-build-directory-permissions-gexp): Remove
%transform-genenetwork-database-export-directory.
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* genenetwork-development.scm (transform-genenetwork-database): Rename this to...
(transform-genenetwork-database-project): ... this.
(transform-genenetwork-database-project): Ditto.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* genenetwork-development.scm (transform-genenetwork-database): Use a script
to generate and validate ttl files.
(%connection-settings): New variable. Contains the sparql and mysql
login credentials.
(%virtuoso-data-dir): New variable.
(transform-genenetwork-database-project): Update how the
transform-genenetwork-database gexp is called. Add web hook.
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* genenetwork-development.scm (set-build-directory-permissions-gexp):
New variable.
* genenetwork-development.scm (operating-system)[services]: Use
set-build-directory-permissions-gexp.
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* genenetwork-development.scm (gn-gemtext-threads-project)[ci-jobs]:
Set LC_ALL environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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This fixes an issue where gn3 auth defaults to "auth.genenetwork.org" during
query execution. Instead we explicitly set AUTH_SERVER_URL to
"auth-cd.genenetwork.org"
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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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* 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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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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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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* 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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* genenetwork-development.scm (genenetwork3-cd-gexp): Run with 8
workers.
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With the reorganisation of the modules, and a change in the startup of
genenetwork2, the way mechanical-rob is launched has also
changed. This commit updates the launch command.
* genenetwork-development.scm (genenetwork-projects): Update module
path in launch of mechanical-rob CI job.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork-development.scm (guile-lmdb-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lmdb-project.
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genenetwork-development.scm (transform-genenetwork-database-project):
Fix channel name.
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* genenetwork-development.scm (genenetwork3-cd-gexp): Increase
gunicorn timeout to 1200 seconds.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add TODO note to increase gunicorn timeout to 1200 seconds.
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* genenetwork-development.scm (genenetwork-activation): Set ownership
and permissions on secret files.
* genenetwork-development-deploy.sh: Share /etc/genenetwork/conf
instead of merely exposing it.
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*
genenetwork-development.scm (<genenetwork-configuration>)[gn2-secrets,
gn3-secrets]: New fields.
* genenetwork-development.scm (genenetwork2-cd-gexp): Use gn2-secrets
configuration field.
(genenetwork3-cd-gexp): Use gn3-secrets configuration field.
(operating-system)[services]: Set gn2-secrets and gn3-secrets fields
in genenetwork configuration.
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The default settings file in the genenetwork2 code base has been moved
from etc/default_settings.py to gn2/default_settings.py. Adapt.
* genenetwork-development.scm (genenetwork-projects,
genenetwork2-cd-gexp): Change path to default genenetwork2 settings
file.
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Somehow this code, that was deleted in
aaf6750858e061e5f5740fb1edbc49b68b3c4717, was added back in
93ff9ed6fd9f2ca15cf6a8930eae26c9f5c65450.
* genenetwork-development.scm (qc-tests, qc-project): Delete
variables.
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We split guix-bioinformatics into two jobs—one that only does a `guix
pull' and another that does a `guix pull' and builds all
packages. This allows us to catch failures in `guix pull'
separately. The job that builds all packages is practically always
bound to fail.
* genenetwork-development.scm (guix-bioinformatics-project): Split
guix-bioinformatics job into guix-bioinformatics and
guix-bioinformatics-all-packages jobs.
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*
genenetwork-development.scm (transform-genenetwork-database-project)[repository]:
Set to local gn-transform-databases git repository.
[ci-jobs-trigger]: Do not use webhook. Reset to default.
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* genenetwork-development.scm: Import (guix ci).
(transform-genenetwork-database-tests): Delete variable.
(%default-guix-channel-with-substitutes): New variable.
(transform-genenetwork-database-project): Use guix-channel-job-gexp
for transform-genenetwork-database-tests CI job.
* genenetwork/development-helper.scm: Delete file.
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* genenetwork-development.scm (qc-tests): Delete variable.
* genenetwork/development-helper.scm (asdf-test-gexp): Delete
function.
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* genenetwork-development.scm (genenetwork3-tests): Delete function.
(gn-auth-pylint): Delete variable.
(genenetwork-projects): Build only the gn-auth variable in the gn-auth
CI job. Combine gn-auth-mypy and gn-auth-pylint CI jobs into a
gn-auth-all-tests job that uses guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork-lint-gexp): Delete
function.
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* genenetwork-development.scm (genenetwork3-mypy,
genenetwork3-pylint): Delete variables.
(genenetwork-projects): Build only genenetwork3 variable in
genenetwork3 CI job. Combine genenetwork3-mypy and genenetwork3-pylint
CI jobs into a genenetwork3-all-tests job that uses
guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork3-lint-gexp): Delete
function.
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* genenetwork-development.scm (genenetwork3-unit-tests): Delete
variable.
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* genenetwork-development.scm (qc-project): Delete variable.
(operating-system)[services]{forge-service-type}: Unlist qc-project.
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The xapian index rebuild cron job runs every hour, but doesn't
actually rebuild the index unless the MySQL database has changed since
the previous index rebuild.
* genenetwork-development.scm (operating-system): Run xapian index
rebuild job every hour.
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* genenetwork-development.scm: Import mariadb from (gnu packages
databases). Import guile-dsv and guile-xapian from (gnu packages
guile-xyz).
(build-xapian-index-cron-gexp): New variable.
(operating-system)[services]: Use build-xapian-index-cron-gexp.
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The application is behind a proxy and is running as http, therefore,
to allow the redirects within the application and responses to work,
we need to enable the http transport for the application.
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