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2022-09-29Run genenetwork2 CD on gunicorn.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Run genenetwork2 CD on gunicorn.
2022-09-26Set up xapian search index for genenetwork2 CD.Arun Isaac
* 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.
2022-09-21Use pytest, rather than unittest, to run tests.Frederick Muriuki Muriithi
* genenetwork-development.scm (genenetwork2-project)[ci-jobs]: Use pytest instead of unittest. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-09-15Copy laminar HTML template from git source.Arun Isaac
The upstream laminar package now uses git-fetch instead of url-fetch. Hence, we must adapt our laminar template G-expression. * genenetwork-development.scm (laminar-template-gexp): Copy /src/resources/index.html from git source instead of extracting it from a tarball.
2022-09-15Link to CD from the navigation menu.Arun Isaac
* genenetwork-development.scm (laminar-template-gexp): Link to continuous deployment from the navigation menu.
2022-09-08Set genenetwork3 API endpoint used by genenetwork2 to /api3.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set GN_SERVER_URL to /api3.
2022-09-08Expose continuously deployed genenetwork at cd.genenetwork.org.Arun Isaac
* genenetwork-development.scm (%genenetwork2-port): New variable. (genenetwork2-project): Use %genenetwork2-port. (development-server-reverse-proxy-server-block): New function. (operating-system)[services]: Use %genenetwork2-port. Add reverse proxy block for cd.genenetwork.org.
2022-09-08Use %genenetwork3-port in genenetwork2 tests.Arun Isaac
* genenetwork-development.scm (genenetwork2-tests): Use %genenetwork3-port.
2022-09-06Expose webhook at ci.genenetwork.org.Arun Isaac
* genenetwork-development.scm (%webhook-port): New variable. (laminar-server-reverse-proxy-server-block): Expose webhook under /hooks/. (operating-system)[services]: Use %webhook-port.
2022-09-05Set host name of the laminar nginx server.Arun Isaac
* genenetwork-development.scm (laminar-reverse-proxy-server-block): Set host name of the laminar nginx server.
2022-09-05Do not list guix channel in CI published channels.scm.Arun Isaac
The guix channel is a dependency of the gn-bioinformatics channel. Therefore, it is always implicitly present. * genenetwork-development.scm (operating-system)[services]: Do not list guix channel in CI published channels.scm.
2022-09-05Do not share /srv/http into container.Arun Isaac
/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.
2022-09-05Remove website directory of gn-gemtext-threads forge project.Arun Isaac
The gn-gemtext-threads forge project does not need a website directory. Its website is completely managed by the tissue service. * genenetwork-development.scm (gn-gemtext-threads-project)[website-directory]: Remove.
2022-08-29Run mysql server in production.Arun Isaac
* production.scm: Import (gnu services databases). (operating-system)[services]: Add mysql-service-type. * production-deploy.sh: Share mysql directory with container.
2022-08-29Run production in separate network namespace.Arun Isaac
The production container need interact with the outside world only through a single Unix socket file on which the GeneNetwork web server listens. Hide all other interfaces to it. * production-deploy.sh (container_script): Remove --network flag.
2022-08-25Run genenetwork services as genenetwork user and group.Arun Isaac
* genenetwork-development.scm (%genenetwork-accounts): New variable. (genenetwork2-shepherd-service, genenetwork3-shepherd-service): Run as genenetwork user and group. (genenetwork2-service-type, genenetwork3-service-type): Create genenetwork user and group.
2022-08-25Add production container.Arun Isaac
* production-deploy.sh, production.scm: New files.
2022-08-25Document the required channels.Arun Isaac
* README.org (GeneNetwork development container): Document the required channels.
2022-08-25Credit Frederick for 5cd33ed762f6fe1301f6e5bb615eb9101012af23.Arun Isaac
* genenetwork-development.scm: Add copyright line for Frederick Muriuki Muriithi.
2022-08-23Expose CD logs to host.Arun Isaac
* 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.
2022-08-16Add trailing slash to GN_PROXY_URL.Arun Isaac
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.scm (genenetwork2-tests): Add trailing slash to GN_PROXY_URL.
2022-08-16Add trailing slash to GN_PROXY_URL.Frederick Muriuki Muriithi
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>
2022-07-08Map mysqld socket into the genenetwork3 container.Arun Isaac
* genenetwork-development.scm (genenetwork3-shepherd-service): Map mysqld socket into the container.
2022-07-08Set GN_SERVER_URL when running genenetwork2.Arun Isaac
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set GN_SERVER_URL.
2022-07-08Support tissue URIs without the html extension.Arun Isaac
* genenetwork-development.scm (tissue-reverse-proxy-server-block): Support URIs without the html extension.
2022-07-06Switch to tissue service from guix-forge.Arun Isaac
* 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.
2022-07-01Switch to new tissue configuration file.Arun Isaac
* genenetwork-development.scm (<tissue-configuration>)[address, port, indexed-repository]: Delete fields. [listen, hosts]: New fields. * genenetwork-development.scm (<tissue-host>): New type. (tissue-conf-gexp): New function. (tissue-shepherd-service): Remove --address and --port arguments. Compute and pass tissue.conf configuration file. Create file system mappings for all hosts. (operating-system)[services]: Use new tissue-configuration fields.
2022-06-29Build tissue static website in temporary writable directory.Arun Isaac
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.
2022-06-29Add tissue search interface.Arun Isaac
* 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.
2022-06-29Remove tissue's dependence on the git CLI tool.Arun Isaac
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.
2022-06-24Persist virtuoso database.Arun Isaac
* genenetwork-development-deploy.sh: Persist virtuoso database at /var/guix-containers/genenetwork-development/var/lib/virtuoso.
2022-06-24Import missing SRFI-26 in dump-genenetwork-database G-exp.Arun Isaac
This was missed out in 96fb9608242254a1fc53bbd71168db4245458c8f. * genenetwork-development.scm (dump-genenetwork-database): Import (srfi srfi-26).
2022-06-24Send rapper output to /dev/null instead of using --ignore-errors.Arun Isaac
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.
2022-06-24Set ownership of database dump directories too, not just files.Arun Isaac
* 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.
2022-06-14Disable laminar proxy buffering by passing X-Accel-Buffering.Arun Isaac
* genenetwork-development.scm (laminar-reverse-proxy-server-block): Disable laminar proxy buffering by passing the X-Accel-Buffering HTTP header through.
2022-06-14Reassure git that the gn-gemtext-threads source directory is safe.Arun Isaac
* 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.
2022-06-10Link to channels.scm from laminar page.Arun Isaac
* genenetwork-development.scm (laminar-template-gexp): Link to channels.scm.
2022-06-10Publish channels.scm for laminar.Arun Isaac
* 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.
2022-06-10Relabel issue tracker link as "Issues".Arun Isaac
* genenetwork-development.scm (laminar-template-gexp): Relabel issue tracker link as "Issues".
2022-06-09Link to issue tracker from Laminar page.Arun Isaac
* 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.
2022-06-09Brand Laminar page with a title of "GeneNetwork CI".Arun Isaac
* genenetwork-development.scm (operating-system)[services]: Set title of Laminar page to "GeneNetwork CI".
2022-06-09Remove unnecessary root file system configuration.Arun Isaac
* genenetwork-development.scm (operating-system)[file-systems]: Remove unnecessary root file system configuration.
2022-05-05Remove graphviz from dump-genenetwork-database-test manifest.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database-tests): Remove graphviz from manifest.
2022-05-05Build dump-genenetwork-database before dumping database.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Add gnu-make to manifest. Build scheme source files before dumping database.
2022-05-04Load dumped RDF into virtuoso and visualize schema.Arun Isaac
* 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.
2022-05-04Validate dumped RDF using rapper.Arun Isaac
* genenetwork-development.scm: Import raptor2 from (gnu packages rdf). (dump-genenetwork-database): Validate dumped RDF using rapper.
2022-04-20Add dump-genenetwork-database CI job.Arun Isaac
* 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.
2022-04-15Add README.Arun Isaac
* README.org: New file.
2022-04-15Initial commitArun Isaac
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 05:09:54 +0000