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We don't want the Guix garbage collector accidentally clearing away
store items required by the container. So, register them as garbage
collector roots.
* genenetwork-development-deploy.sh, production-deploy.sh,
public-sparql-deploy.sh, virtuoso-deploy.sh: Register containers as
garbage collector roots.
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* genenetwork-development.scm: Import (gnu services mcron).
(%xapian-directory): New variable.
(build-xapian-index-gexp): New function.
(genenetwork-projects): Add genenetwork3-build-xapian-index CI job to
genenetwork3 project.
(operating-system)[sudoers-file]: Allow laminar user to start and stop
genenetwork3.
[services]: Add mcron service to trigger nightly xapian build. Use
%xapian-directory instead of its literal value. chown
%xapian-directory to the laminar user.
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We prefer /export2 to house really large data.
* genenetwork-development-deploy.sh, production-deploy.sh,
public-sparql-deploy.sh, virtuoso-deploy.sh: Move guix container state
to /export2.
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* genenetwork-development-deploy.sh (container_script): Expose root of
data directory instead of its sub-directories.
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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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/srv/http is no longer. It was used earlier for the gn-gemtext-threads
website.
* genenetwork-development-deploy.sh: Do not share /srv/http into
container.
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* genenetwork-development.scm (genenetwork2-shepherd-service,
genenetwork3-shepherd-service): Move log files into /var/log/cd.
* genenetwork-development-deploy.sh: Share /var/log/cd with host.
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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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* genenetwork-development-deploy.sh: Persist virtuoso database at
/var/guix-containers/genenetwork-development/var/lib/virtuoso.
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