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2022-12-10Move guix container state to /export2.Arun Isaac
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.
2022-11-10Configure SPARQL endpoint of genenetwork3 server.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[sparql-endpoint]: New field. (genenetwork3-cd-gexp): Set SPARQL_ENDPOINT in gn3.conf. (%virtuoso-sparql-port): New variable. (operating-system)[services]: Configure sparql-endpoint of genenetwork service.
2022-11-07Add public facing SPARQL container.Arun Isaac
* public-sparql-deploy.sh, public-sparql.scm: New files.
2022-11-07Move CD virtuoso ports to 90*.Arun Isaac
In the interest of good organization, we keep all CD ports at 90*. Production and other services can use ports outside this range. * genenetwork-development.scm (operating-system)[services]: Move virtuoso ports from 8891, 8892 to 9081, 9082.
2022-11-04Import GeneRIF by calling the unified dump script.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Import GeneRIF by calling the unified dump script.
2022-10-31Find GeneRIF data in root of export directory.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Find GeneRIF data in root of export directory.
2022-10-31Use guile-zlib in dump-genenetwork-database CI job.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Use guile-zlib.
2022-10-31Ungexp gn2 and gn3 repositories correctly.Arun Isaac
* genenetwork-development.scm (genenetwork2-tests): Ungexp gn2-repository and gn3-repository correctly.
2022-10-31Import (guix build utils) in after scripts of CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Import (guix build utils) in after scripts of CI jobs.
2022-10-30Import GeneRIF into RDF.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database): Import GeneRIF into RDF.
2022-10-30Unite genenetwork2 and genenetwork3 development servers.Arun Isaac
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.
2022-10-28Expose xapian index to genenetwork3 instead of genenetwork2.Arun Isaac
* 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.
2022-10-25Link to gemtext documentation on securing virtuoso.Arun Isaac
* README.org (Virtuoso container for tux01 production): Remove user management commands. (Secure virtuoso authentication): New section.
2022-10-20Use GitHub URI for dump-genenetwork-database repo.Arun Isaac
* genenetwork-development.scm (dump-genenetwork-database-project)[repository]: Use GitHub URI.
2022-10-18Trigger genenetwork2 using laminar, not shepherd.Arun Isaac
This was a typo. * genenetwork-development.scm (genenetwork3-project)[ci-jobs]: Trigger genenetwork2 using laminar, not shepherd.
2022-10-17Use <forge-ip-socket> object to specify webhook port.Arun Isaac
* genenetwork-development.scm: Import (forge socket). (operating-system)[services]: Use <forge-ip-socket> object to specify webhook port.
2022-10-17Use least-authority-wrapper.Arun Isaac
* genenetwork-development.scm: Import (gnu build linux-container), (gnu system file-systems) and (guix least-authority). (genenetwork2-shepherd-service, genenetwork3-shepherd-service): Deprecate make-forkexec-constructor/container in favor of least-authority-wrapper.
2022-10-14Trigger genenetwork2 tests after genenetwork3 tests.Arun Isaac
Since genenetwork2 depends on genenetwork3, updates to genenetwork3 should trigger the genenetwork2 tests. * genenetwork-development.scm (genenetwork3-project): Trigger genenetwork2 tests after genenetwork3 tests.
2022-10-14Comment about triggering of Mechanical Rob.Arun Isaac
* genenetwork-development.scm (genenetwork2-project): Comment about triggering of Mechanical Rob after genenetwork2 tests.
2022-10-14Convert port number to string on host.Arun Isaac
* genenetwork-development.scm (genenetwork2-shepherd-service): Convert port number to string on the host, not on the build side.
2022-10-14Pull in latest genenetwork3 when running genenetwork2 tests.Arun Isaac
So far, whenever genenetwork2 code needed the latest updates from genenetwork3, the guix-bioinformatics channel had to be updated and the development container had to be rebuilt. No more. From now on, the latest genenetwork3 code will be pulled in at all times. The development container need only be rebuilt when the dependencies of genenetwork2 or genenetwork3 change. We may revisit this decision once genenetwork2 and genenetwork3 are better decoupled and we have semantically versioned releases. * genenetwork-development.scm (genenetwork2-tests): Pull in latest genenetwork3 when running genenetwork2 tests.
2022-10-12Add virtuoso container for tux01 production.Arun Isaac
* virtuoso.scm, virtuoso-deploy.sh: New files. * README.org (Virtuoso container for tux01 production): New section.
2022-10-06Enable rust backtrace in genenetwork2 CD.Frederick Muriuki Muriithi
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set RUST_BACKTRACE environment variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-09-29Expose root of data directory instead of its sub-directories.Arun Isaac
* genenetwork-development-deploy.sh (container_script): Expose root of data directory instead of its sub-directories.
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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-20 01:43:31 +0000