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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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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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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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* 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.
*
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).
*
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/services/genenetwork.scm (genenetwork-gunicorn-apps):
Increase gunicorn timeout for genenetwork3 to 1200 seconds.
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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/services/genenetwork.scm: New file.
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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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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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We unite the genenetwork2 and genenetwork3 development servers into
a single Guix service. This unifies many of the configuration
settings and simplifies the configuration. Changes to the genenetwork3
repository also immediately reflect in the genenetwork2 continuous
deployment without guix-bioinformatics having to be updated.
* genenetwork-development.scm (<development-server-configuration>):
Delete type.
(<genenetwork-configuration>): New type.
(development-server-redeploy, development-server-activation,
genenetwork2-project, genenetwork2-shepherd-service,
genenetwork3-project, genenetwork3-shepherd-service): Delete
functions.
(genenetwork2-tests): Accept <genenetwork-configuration> object
instead of <forge-project> object.
(%genotype-files, %xapian-db-path,
%default-genenetwork2-configuration, genenetwork2-service-type,
%default-genenetwork3-configuration, genenetwork3-service-type):
Delete variables.
(genenetwork-projects, genenetwork2-cd-gexp, genenetwork3-cd-gexp,
genenetwork-shepherd-services): New functions.
(operating-system)[services]: Replace genenetwork2 and genenetwork3
services with the unified genenetwork service.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp,
genenetwork3-runner-gexp): Delete functions.
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* genenetwork-development.scm (genenetwork2-shepherd-service): Do not
expose xapian index.
(genenetwork3-shepherd-service): Expose xapian index.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Do
not accept xapian index argument.
(genenetwork3-runner-gexp): Accept config file argument.
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* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
RUST_BACKTRACE environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Run
genenetwork2 CD on gunicorn.
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* genenetwork-development.scm (%xapian-db-path): New variable.
(genenetwork2-shepherd-service)[start]: Share %xapian-db-path with the
container.
(%default-genenetwork2-configuration)[runner]: Pass %xapian-db-path to
CD runner.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp):
Accept xapian-db-path argument and set XAPIAN_DB_PATH environment
variable.
* genenetwork-development-deploy.sh: Expose
/export/data/genenetwork/xapian in the container.
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* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL to /api3.
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The urljoin function reduces a URL without a trailing slash to just
the base, e.g. "http://genenetwork.org/gn3-proxy" is reduced to
"http://genenetwork.org", which is not what we want.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Add
trailing slash to GN_PROXY_URL environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL.
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* genenetwork-development-deploy.sh: Share tissue state directory with
container.
* genenetwork-development.scm: Do not import tissue from (gn packages
gemini). Import (forge tissue).
(<tissue-configuration>, <tissue-host>): Delete types.
(%tissue-accounts, tissue-service-type): Delete variables.
(gn-gemtext-threads-website, gn-gemtext-threads-index,
tissue-conf-gexp, tissue-shepherd-service): Delete functions.
(gn-gemtext-threads-project)[ci-jobs]: Use tissue pull in
gn-gemtext-threads job.
(tissue-reverse-proxy-server-block): Use default tissue state
directory and unix socket paths. Do not accept them as arguments.
(operating-system)[services]: Use new tissue-service-type
parameters. Update invocation of tissue-reverse-proxy-server-block.
* genenetwork/development-helper.scm (tissue-website-gexp,
tissue-index-gexp): Delete functions.
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tissue now builds a xapian index and this requires a writable
directory.
* genenetwork/development-helper.scm (tissue-website-gexp): Build
static website in temporary writable directory.
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* genenetwork-development.scm: Import shadow from (gnu packages
admin).
(gn-gemtext-threads-index): New function.
(gn-gemtext-threads-project)[ci-jobs]: Add gn-gemtext-threads-index.
(<tissue-configuration>): New type.
(tissue-shepherd-service, tissue-reverse-proxy-server-block): New
function.
(%tissue-accounts, tissue-service-type): New variables.
(operating-system)[services]: Add tissue tissue service and reverse
proxy it.
* genenetwork/development-helper.scm (tissue-index-gexp): New
function.
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tissue now uses libgit2 through guile-git and does not use the git CLI
tool.
* genenetwork-development.scm (gn-gemtext-threads-website): Remove
git-minimal from manifest.
* genenetwork/development-helper.scm (tissue-website-gexp): Remove
reassurance to git.
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* genenetwork/development-helper.scm (tissue-website-gexp): Reassure
git that the gn-gemtext-threads source directory is safe.
* genenetwork-development.scm (gn-gemtext-threads-website): Add
git-minimal to manifest.
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