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guix-forge has introduced a breaking change in tissue configuration.
Update configuration.
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genenetwork-development.scm (operating-system)[services]{tissue-service-type}:
Update tissue configuration.
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*
genenetwork-development.scm (operating-system)[services]{virtuoso-service-type}:
Make dirs-allowed a list of directories.
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Redis is being phased out, and part of that is moving the storage of
sessions to the file system, rather than in Redis. This commit allows
configuration of the path to the directory where the session files
will be stored.
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The disk mounted on /export2 was full, so we move the
uploader-container to the disk on /export which has more space.
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Break the implicit connection between the paths on the host system
with the paths inside the container. This allows the operating-system
definition to define its own paths, regardless of what is on the host.
The builder script will explicitly do the mapping between host
directories and container paths.
We also collect all uploader-related directories under the host path
`/export2/guix-containers/uploader` to make maintenance easier.
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The changes to the way the various applications work lead to a need
for extra shares from the host to the container — this commit provides
the bindings for these shares.
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Genenetwork2 changed the way it stores sessions, moving away from
using redis to storing the files in the filesystem. This commit binds
the host directory to use to store the sessions. It also does basic
activation to ensure the directory is writable to the appropriate
user.
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The disk mounted on `/export2` is failing, so we move our data over to
the enterprise disk mounted on `/export` instead.
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We connect to a MariaDB database outside the container, therefore, the
container does not need to run a database server. This commit removes
the service from the container.
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Bind the original host path that was previously bound to the
container's /tmp directory to instead be bound to genenetwork's TMPDIR
directory.
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Add the `gn-tmpdir` configuration setting to help with providing a way
to configure a separate temporary directory for the genenetwork
services that is separate from the container's `/tmp` directory.
This might also help in resolving some issue with `/etc/resolv.conf`
not being found in `/tmp` for some reason.
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Attempting to invoke the container build with the comments in place
was leading to the error:
```
guix system: error: wrong number of arguments for action
'container'
```
This commit removes the comments to fix that.
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Pass the directory containing virtuoso's turtle (ttl) files to the
indexer.
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The directory containing the turtle (ttl) files for virtuoso is used
by the xapian indexer to determine whether or not to run. We provide
it as one of the settings we can configure.
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The uploader container will not concern it with editing the gn-docs
repository, but might still need it present to allow the system to
run. This ensures it is present.
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The uploader container uses a separate database from that used by
CI/CD, since the uploader does (potentially) destructive changes to
the data in the database.
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The `gn-uploader-ca-bundle` variable needs the value from the
`gn-uploader-profile` variable.
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Update the log-level value to use a symbol rather than text, since
that's what's expected by the newer system.
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Some request (e.g. for mapping) from GN2 can get big, depending on the
trait(s) in use. This commit increases the maximum allowed size for
the client body to allow bigger requests.
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* genenetwork-development.scm (<genenetwork-configuration>): Replace
"https://git.genenetwork.org" with "/home/git/public".
* (genenetwork-projects)[gn-libs, gn-auth]{ci-jobs-trigger}: Delete.
* (transform-genenetwork-database-project)[repository]: Replace
"https://git.genenetwork.org" with "/home/git/public".
* (transform-genenetwork-database-project)[repository]: Replace
"https://git.genenetwork.org" with "/home/git/public".
[ci-jobs-trigger]: Delete.
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* genenetwork/services/genenetwork.scm: Import gn-guile, linux-container,
git-minimal, shepherd, least-authority, forge utils.
(<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields.
(gn-guile-gexp): New g-exp for running gn-guile.
(gn-guile-shepherd-service): New shepherd service to run gn-guile.
(genenetwork-service-type): Add gn-guile-shepherd-service.
* production-deploy.sh (container_script): Export gn-docs directory.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* genenetwork-development.scm (transform-genenetwork-database-gexp): Only
delete virtuoso "build" directory.
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* genenetwork-development-deploy.sh: share "/export/data/gn-docs/".
* genenetwork-development.scm: Import gn-guile.
(<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields.
(gn-guile-gexp): New g-exp for running gn-guile.
(genenetwork-shepherd-services): Add gn-guile service.
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