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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-deploy.sh: Persist virtuoso database at
/var/guix-containers/genenetwork-development/var/lib/virtuoso.
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This was missed out in 96fb9608242254a1fc53bbd71168db4245458c8f.
* genenetwork-development.scm (dump-genenetwork-database):
Import (srfi srfi-26).
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The --ignore-errors flag not only avoids printing triples, but also
actually ignores errors. What a surprise! ;-) As a result, rapper does
not stop invalid turtle files, and they end up erroring out when
uploaded to virtuoso.
* genenetwork-development.scm (dump-genenetwork-database): Send rapper
output to /dev/null instead of using --ignore-errors.
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* genenetwork-development.scm (operating-system)[services]: In the
set-dump-genenetwork-database-export-directory-permissions service,
set ownership of directories in
%dump-genenetwork-database-export-directory too, not just the files.
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* genenetwork-development.scm (laminar-reverse-proxy-server-block):
Disable laminar proxy buffering by passing the X-Accel-Buffering HTTP
header through.
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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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* genenetwork-development.scm (laminar-template-gexp): Link to
channels.scm.
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* genenetwork-development.scm: Import (gnu services web) and (guix
channels).
(channels-scm-gexp, laminar-reverse-proxy-server-block): New
functions.
(operating-system)[services]: Bind laminar service to 9089.
Add nginx service on 9090 to reverse proxy laminar.
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* genenetwork-development.scm (laminar-template-gexp): Relabel issue
tracker link as "Issues".
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* genenetwork-development.scm: Import tar from (gnu packages base) and
gzip from (gnu packages compression).
(laminar-template-gexp, install-laminar-template-gexp): New functions.
(operating-system)[services]: Add install-laminar-template service.
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* genenetwork-development.scm (operating-system)[services]: Set title
of Laminar page to "GeneNetwork CI".
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* genenetwork-development.scm (operating-system)[file-systems]: Remove
unnecessary root file system configuration.
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* genenetwork-development.scm (dump-genenetwork-database-tests):
Remove graphviz from manifest.
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* genenetwork-development.scm (dump-genenetwork-database): Add
gnu-make to manifest. Build scheme source files before dumping
database.
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* genenetwork-development.scm: Import virtuoso-ose from (gnu packages
databases). Import guile-hashing from (gnu packages guile-xyz).
(dump-genenetwork-database): Add ccwl, guile-hashing, guile-libyaml,
guile-sparql and virtuoso-ose to manifest. Load dumped RDF into
virtuoso and visualize schema.
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* genenetwork-development.scm: Import raptor2 from (gnu packages rdf).
(dump-genenetwork-database): Validate dumped RDF using rapper.
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*
genenetwork-development.scm (%dump-genenetwork-database-export-directory):
New variable.
(dump-genenetwork-database): New function.
(dump-genenetwork-database-project)[ci-jobs]: Rename
dump-genenetwork-database job to dump-genenetwork-database-tests. Add
new dump-genenetwork-database job.
(operating-system): Add
set-dump-genenetwork-database-export-directory-permissions service.
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* README.org: New file.
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