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2023-07-11Revert "Disable tests"Munyoki Kilyungi
This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
2023-07-10Add a troubleshooting subsection to READMEMunyoki Kilyungi
2023-07-10Revert "Fix genotype file path"Munyoki Kilyungi
This reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.
2023-07-10Fix genotype file pathMunyoki Kilyungi
2023-07-10Disable testsMunyoki Kilyungi
Rob is giving a demo, so disable tests and fix them later. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-10Basic mail/opensmtpd service addedPjotr Prins
2023-06-26Add virtuoso allowed dirsMunyoki Kilyungi
2023-06-15Increase threshold for number-of-buffers and maximum-dirty-buffers.Munyoki Kilyungi
* genenetwork-development.scm, public-sparql.scm (operating-system)[services]<virtuoso-service>: Set number-of-buffers and maximum-dirty-buffers. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-15Add links to README.Munyoki Kilyungi
* README.org (GeneNetwork development container): Link to guix-bioinformatics and guix-forge channels. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-08Share auth-db-path with genenetwork3-pola-wrapper.Frederick Muriuki Muriithi
* genenetwork-development.scm (genenetwork-shepherd-services): Share auth-db-path with genenetwork3-pola-wrapper. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-06Set AUTH_DB, not AUTH_DB_PATH.Frederick Muriuki Muriithi
genenetwork3 expects AUTH_DB, not AUTH_DB_PATH. * genenetwork-development.scm (genenetwork3-cd-gexp): Set AUTH_DB, not AUTH_DB_PATH. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-31Do not create xapian build directory.Arun Isaac
* genenetwork-development.scm (build-xapian-index-gexp): Do not create xapian build directory.
2023-05-31Use an absolute GN_SERVER_URL.Frederick Muriuki Muriithi
A relative GN_SERVER_URL sometimes leads to issues when code (in libraries e.g. requests and the like) cannot expand the URI since it does not have context about the running server. * genenetwork-development.scm (genenetwork2-cd-gexp): Use an absolute GN_SERVER_URL. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-31Add trailing slash to GN_SERVER_URL.Frederick Muriuki Muriithi
Without the trailing slash, the urllib.parse.urljoin function produces the wrong endpoint. * genenetwork-development.scm (genenetwork2-cd-gexp): Add trailing slash to GN_SERVER_URL. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-05-22Document getting a shell into containerFrederick Muriuki Muriithi
For some tasks (e.g. debugging the xapian index build), we need to manually queue the job, which means we need a shell into the container. Getting a shell using the default command displayed actually fails with: nsenter: failed to execute /bin/bash: No such file or directory so we need to provide the correct path to bash, and optionally, initialise the shell to setup the correct paths.
2023-05-05Run migrations after tests and before restarting genenetwork3.Frederick Muriuki Muriithi
Add a CI job that applies the auth database migrations. This job is run after the genenetwork3 tests have passed but before genenetwork3 is restarted. * genenetwork-development-deploy.sh: Share /export/data/genenetwork-sqlite. * genenetwork-development.scm: Import yoyo-migrations from (gnu packages databases). (<genenetwork-configuration>)[auth-db-path]: New field. (genenetwork3-auth-migrations-genenetwork, genenetwork3-auth-migrations-laminar, genenetwork-activation): New functions. (genenetwork-projects): Add genenetwork3-auth-migrations CI job. Trigger this job after genenetwork3 tests. (genenetwork3-cd-gexp): Configure AUTH_DB_PATH in gn3.conf. (genenetwork-service-type): Extend activation-service-type with genenetwork-activation. (operating-system)[sudoers-file]: Permit the laminar user to run auth database migrations as the genenetwork user. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-04-12Run tissue on an IP socket.Arun Isaac
tissue fails to clean up its Unix socket when deployed with shepherd. So, when tissue crashes, it fails to restart. Until this issue is resolved, run tissue on an IP socket. * genenetwork-development.scm (%tissue-port): New variable. (tissue-reverse-proxy-server-block): Forward tissue requests to IP socket. (operating-system)[services]: Run tissue on an IP socket.
2023-04-12Disable libgit2 repository ownership validation.Arun Isaac
* genenetwork-development.scm: Import guile-git from (gnu packages guile), libgit2-1.3 from (gnu packages version-control), and (guix utils). Prefix tissue import from (gnu packages web) with guix:. (libgit2-1.3, guile-git-for-tissue, tissue): New variables. (operating-system)[services]: Use local variant of tissue package.
2023-04-11Use tissue package from Guix upstream.Arun Isaac
The tissue package is now in Guix upstream and longer in the guix-forge channel. * genenetwork-development.scm: Import tissue from (gnu packages web).
2023-04-11Provide MySQL URI to the xapian indexing script.Frederick Muriuki Muriithi
* genenetwork-development.scm (build-xapian-index-gexp): Provide MySQL URI to the xapian indexing script.
2023-02-09Share the mysqld socket directory into the container.Arun Isaac
We ought to share the mysqld socket directory into the container, not the socket itself. If we only shared the socket, when the mysql server is restarted and a new socket is created, the bind mounting into the container would break and the container would need to be restarted. * genenetwork-development-deploy.sh: Share /var/run/mysqld, not /var/run/mysqld/mysqld.sock. * genenetwork-development.scm (genenetwork-shepherd-services): Share /run/mysqld, not /run/mysqld/mysqld.sock.
2023-01-21GN3: pylint - Check more files and directoriesFrederick Muriuki Muriithi
2023-01-18Add data directory to genenetwork configuration.Arun Isaac
* genenetwork-development.scm (<genenetwork-configuration>)[data-directory]: New field. (genenetwork3-cd-gexp): Set DATA_DIR in settings file. (genenetwork-shepherd-services): Map data directory into container. (operating-system)[services]: Set data-directory of genenetwork service to /export/data/genenetwork. * genenetwork-development-deploy.sh: Expose entire data directory /export/data/genenetwork instead of the contained genotype files directory.
2023-01-18Move xapian directory.Arun Isaac
* genenetwork-development.scm (%xapian-directory): Move from /export/data/genenetwork/xapian to /export/data/genenetwork-xapian. * genenetwork-development-deploy.sh (container_script): Share /export/data/genenetwork-xapian instead of /export/data/genenetwork/xapian.
2023-01-08Clean up xapian build directory if previous build failed to.Arun Isaac
* genenetwork-development.scm (build-xapian-index-gexp): Clean up xapian build directory if previous build failed to.
2023-01-05Create custom 502 error page for CD.Arun Isaac
This 502 error page is more informative than a generic "Bad Gateway" error message. It tells the user that the CD is down but not the entire container itself. * genenetwork-development.scm: Import guile-lib from (gnu packages guile-xyz). (%ci-domain): New variable. (cd-error-pages-gexp): New function. (development-server-reverse-proxy-server-block): Use (cd-error-pages-gexp) to construct error pages. (laminar-reverse-proxy-server-block): Use %ci-domain.
2023-01-02Register containers as garbage collector roots.Arun Isaac
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.
2022-12-22Build and install xapian index nightly.Arun Isaac
* 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.
2022-12-22Separate out sudo into a variable.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Separate out "/run/setuid-programs/sudo" into ... (sudo): ... new variable.
2022-12-22gn3: tests: Update the tests invocationFrederick Muriuki Muriithi
* genenetwork-development.scm: use pytest rather than unittest to run the tests.
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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-20 02:47:12 +0000