| Age | Commit message (Expand) | Author |
|---|
| 2023-09-20 | Pass "secrets" configurations to GN2...We need to pass in secrets to the running applications. This commit
does it for GeneNetwork2.
| Frederick Muriuki Muriithi |
| 2023-09-19 | Use appropriate mypy for Python3.10 | Frederick Muriuki Muriithi |
| 2023-09-19 | Add missing `gn-auth-repository` configuration | Frederick Muriuki Muriithi |
| 2023-09-16 | Add CI/CD definitions for gn-auth | Frederick Muriuki Muriithi |
| 2023-09-11 | sed /s/dump-genenetwork/transform-genenetwork/g....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | sed /s/dump-genenetwork/transform-genenetwork/g....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | Update the repo-url for transforming genenetwork databases....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Use correct name for python-mypy...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Update arguments to pylint...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Use mypy defined in guix-bioinformatics...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-04 | Use self-hosted git repo | Munyoki Kilyungi |
| 2023-09-04 | Use self-hosted GN repository...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-12 | Add link to git repo | Pjotr Prins |
| 2023-08-10 | Set up cgit service....* genenetwork-development.scm: Import (forge cgit).
(operating-system)[services]: Add cgit service.
* genenetwork-development-deploy.sh: Expose cgit repository directory.
| Arun Isaac |
| 2023-08-10 | Switch to the forge-nginx and ACME services....* genenetwork-development.scm: Import only nginx-server-configuration
and nginx-location-configuration from (gnu services
web). Import (forge acme) and (forge nginx).
(development-server-reverse-proxy-server-block,
laminar-reverse-proxy-server-block,
tissue-reverse-proxy-server-block): Remove listen argument.
(operating-system)[sudoers-file]: Permit the acme user to restart
nginx.
[services]: Replace nginx service with a forge-nginx service. Add ACME
service.
* genenetwork-development-deploy.sh: Share /var/lib/acme.
| Arun Isaac |
| 2023-08-10 | Add nginx package with the ssl_preread module....* nginx-preread.scm, nginx-preread-deploy.sh: New files.
| Arun Isaac |
| 2023-07-27 | README: Remove references to penguin2....penguin2 is no more. We now use tux02 for development.
* README.org: Change references to penguin2 to tux02.
| Arun Isaac |
| 2023-07-27 | Revert "README: host names"...This reverts commit fc65c2a2c056ee9f313631da6e5f93adec277dd5.
| Arun Isaac |
| 2023-07-19 | Use tissue from guix-forge....The libgit2 patch is now in guix-forge. So, we don't have to repeat it
here.
* genenetwork-development.scm (libgit2-1.3, guile-git-for-tissue,
tissue): Delete variables.
(operating-system)[services]: Do not specify package for tissue
service.
| Arun Isaac |
| 2023-07-19 | Disable verbose build logs for guix-bioinformatics job....* genenetwork-development.scm (guix-bioinformatics-project): Disable
verbose build logs.
| Arun Isaac |
| 2023-07-19 | Use guix-channel-job-gexp for genenetwork3 tests....* genenetwork-development.scm (genenetwork-projects): Use
guix-channel-job-gexp for genenetwork3 tests.
| Arun Isaac |
| 2023-07-19 | Add guix-bioinformatics CI job....* genenetwork-development.scm (guix-channel-job-gexp): New function.
(guix-bioinformatics-project): New variable.
(operating-system)[services]: Add guix-bioinformatics-project to
forge-service-type.
| Arun Isaac |
| 2023-07-11 | README: host names | Pjotr Prins |
| 2023-07-11 | Revert "Disable tests"...This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
| Munyoki Kilyungi |
| 2023-07-10 | Add a troubleshooting subsection to README | Munyoki Kilyungi |
| 2023-07-10 | Revert "Fix genotype file path"...This reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.
| Munyoki Kilyungi |
| 2023-07-10 | Fix genotype file path | Munyoki Kilyungi |
| 2023-07-10 | Disable tests...Rob is giving a demo, so disable tests and fix them later.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-10 | Basic mail/opensmtpd service added | Pjotr Prins |
| 2023-06-26 | Add virtuoso allowed dirs | Munyoki Kilyungi |
| 2023-06-15 | Increase threshold for number-of-buffers and maximum-dirty-buffers....* 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>
| Munyoki Kilyungi |
| 2023-06-15 | Add links to README....* README.org (GeneNetwork development container): Link to
guix-bioinformatics and guix-forge channels.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 2023-06-08 | Share auth-db-path with genenetwork3-pola-wrapper....* genenetwork-development.scm (genenetwork-shepherd-services): Share
auth-db-path with genenetwork3-pola-wrapper.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2023-06-06 | Set AUTH_DB, not AUTH_DB_PATH....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>
| Frederick Muriuki Muriithi |
| 2023-05-31 | Do not create xapian build directory....* genenetwork-development.scm (build-xapian-index-gexp): Do not create
xapian build directory.
| Arun Isaac |
| 2023-05-31 | Use an absolute GN_SERVER_URL....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>
| Frederick Muriuki Muriithi |
| 2023-05-31 | Add trailing slash to GN_SERVER_URL....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>
| Frederick Muriuki Muriithi |
| 2023-05-22 | Document getting a shell into container...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.
| Frederick Muriuki Muriithi |
| 2023-05-05 | Run migrations after tests and before restarting genenetwork3....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>
| Frederick Muriuki Muriithi |
| 2023-04-12 | Run tissue on an IP socket....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.
| Arun Isaac |
| 2023-04-12 | Disable libgit2 repository ownership validation....* 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.
| Arun Isaac |
| 2023-04-11 | Use tissue package from Guix upstream....The tissue package is now in Guix upstream and longer in the
guix-forge channel.
* genenetwork-development.scm: Import tissue from (gnu packages web).
| Arun Isaac |
| 2023-04-11 | Provide MySQL URI to the xapian indexing script....* genenetwork-development.scm (build-xapian-index-gexp): Provide MySQL
URI to the xapian indexing script.
| Frederick Muriuki Muriithi |
| 2023-02-09 | Share the mysqld socket directory into the container....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.
| Arun Isaac |
| 2023-01-21 | GN3: pylint - Check more files and directories | Frederick Muriuki Muriithi |
| 2023-01-18 | Add data directory to genenetwork configuration....*
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.
| Arun Isaac |
| 2023-01-18 | Move xapian directory....* 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.
| Arun Isaac |
| 2023-01-08 | Clean up xapian build directory if previous build failed to....* genenetwork-development.scm (build-xapian-index-gexp): Clean up
xapian build directory if previous build failed to.
| Arun Isaac |
| 2023-01-05 | Create custom 502 error page for CD....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.
| Arun Isaac |
| 2023-01-02 | Register containers as garbage collector roots....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.
| Arun Isaac |
