| Age | Commit message (Expand) | Author |
|---|
| 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 | 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 |
| 2023-08-10 | 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 |
| 2023-07-19 | 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 | Revert "Disable tests"...This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
| 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 |
| 2023-06-26 | 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 |
| 2023-06-08 | 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 |
| 2023-05-05 | 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 |
| 2023-01-18 | 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 |
| 2022-12-22 | Build and install xapian index nightly....* 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.
| Arun Isaac |
| 2022-12-22 | Separate out sudo into a variable....* genenetwork-development.scm (genenetwork-projects): Separate out
"/run/setuid-programs/sudo" into ...
(sudo): ... new variable.
| Arun Isaac |
| 2022-12-22 | gn3: tests: Update the tests invocation...* genenetwork-development.scm: use pytest rather than unittest to run
the tests.
| Frederick Muriuki Muriithi |
| 2022-11-10 | Configure SPARQL endpoint of genenetwork3 server....*
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.
| Arun Isaac |
| 2022-11-07 | Move CD virtuoso ports to 90*....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.
| Arun Isaac |
| 2022-11-04 | Import GeneRIF by calling the unified dump script....* genenetwork-development.scm (dump-genenetwork-database): Import
GeneRIF by calling the unified dump script.
| Arun Isaac |
| 2022-10-31 | Find GeneRIF data in root of export directory....* genenetwork-development.scm (dump-genenetwork-database): Find
GeneRIF data in root of export directory.
| Arun Isaac |
| 2022-10-31 | Use guile-zlib in dump-genenetwork-database CI job....* genenetwork-development.scm (dump-genenetwork-database): Use
guile-zlib.
| Arun Isaac |
| 2022-10-31 | Ungexp gn2 and gn3 repositories correctly....* genenetwork-development.scm (genenetwork2-tests): Ungexp
gn2-repository and gn3-repository correctly.
| Arun Isaac |
| 2022-10-31 | Import (guix build utils) in after scripts of CI jobs....* genenetwork-development.scm (genenetwork-projects): Import (guix
build utils) in after scripts of CI jobs.
| Arun Isaac |
| 2022-10-30 | Import GeneRIF into RDF....* genenetwork-development.scm (dump-genenetwork-database): Import
GeneRIF into RDF.
| Arun Isaac |
| 2022-10-30 | Unite genenetwork2 and genenetwork3 development servers....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.
| Arun Isaac |
| 2022-10-28 | Expose xapian index to genenetwork3 instead of genenetwork2....* 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.
| Arun Isaac |
| 2022-10-20 | Use GitHub URI for dump-genenetwork-database repo....*
genenetwork-development.scm (dump-genenetwork-database-project)[repository]:
Use GitHub URI.
| Arun Isaac |
| 2022-10-18 | Trigger genenetwork2 using laminar, not shepherd....This was a typo.
* genenetwork-development.scm (genenetwork3-project)[ci-jobs]: Trigger
genenetwork2 using laminar, not shepherd.
| Arun Isaac |
| 2022-10-17 | Use <forge-ip-socket> object to specify webhook port....* genenetwork-development.scm: Import (forge socket).
(operating-system)[services]: Use <forge-ip-socket> object to specify
webhook port.
| Arun Isaac |
| 2022-10-17 | Use least-authority-wrapper....* 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.
| Arun Isaac |
| 2022-10-14 | Trigger genenetwork2 tests after genenetwork3 tests....Since genenetwork2 depends on genenetwork3, updates to genenetwork3
should trigger the genenetwork2 tests.
* genenetwork-development.scm (genenetwork3-project): Trigger
genenetwork2 tests after genenetwork3 tests.
| Arun Isaac |
