| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 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 |
| 2022-12-10 | Move guix container state to /export2....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.
| Arun Isaac |
| 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 | Add public facing SPARQL container....* public-sparql-deploy.sh, public-sparql.scm: New files.
| 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 |
| 2022-10-25 | Link to gemtext documentation on securing virtuoso....* README.org (Virtuoso container for tux01 production): Remove
user management commands.
(Secure virtuoso authentication): New section.
| 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 |
| 2022-10-14 | Comment about triggering of Mechanical Rob....* genenetwork-development.scm (genenetwork2-project): Comment about
triggering of Mechanical Rob after genenetwork2 tests.
| Arun Isaac |
| 2022-10-14 | Convert port number to string on host....* genenetwork-development.scm (genenetwork2-shepherd-service): Convert
port number to string on the host, not on the build side.
| Arun Isaac |
| 2022-10-14 | Pull in latest genenetwork3 when running genenetwork2 tests....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.
| Arun Isaac |
| 2022-10-12 | Add virtuoso container for tux01 production....* virtuoso.scm, virtuoso-deploy.sh: New files.
* README.org (Virtuoso container for tux01 production): New section.
| Arun Isaac |
| 2022-10-06 | Enable rust backtrace in genenetwork2 CD....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
RUST_BACKTRACE environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2022-09-29 | Expose root of data directory instead of its sub-directories....* genenetwork-development-deploy.sh (container_script): Expose root of
data directory instead of its sub-directories.
| Arun Isaac |
| 2022-09-29 | Run genenetwork2 CD on gunicorn....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Run
genenetwork2 CD on gunicorn.
| Arun Isaac |
| 2022-09-26 | Set up xapian search index for genenetwork2 CD....* 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.
| Arun Isaac |
| 2022-09-21 | Use pytest, rather than unittest, to run tests....* genenetwork-development.scm (genenetwork2-project)[ci-jobs]: Use
pytest instead of unittest.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2022-09-15 | Copy laminar HTML template from git source....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.
| Arun Isaac |
| 2022-09-15 | Link to CD from the navigation menu....* genenetwork-development.scm (laminar-template-gexp): Link to
continuous deployment from the navigation menu.
| Arun Isaac |
| 2022-09-08 | Set genenetwork3 API endpoint used by genenetwork2 to /api3....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL to /api3.
| Arun Isaac |
| 2022-09-08 | Expose continuously deployed genenetwork at cd.genenetwork.org....* 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.
| Arun Isaac |
| 2022-09-08 | Use %genenetwork3-port in genenetwork2 tests....* genenetwork-development.scm (genenetwork2-tests): Use
%genenetwork3-port.
| Arun Isaac |
| 2022-09-06 | Expose webhook at ci.genenetwork.org....* genenetwork-development.scm (%webhook-port): New variable.
(laminar-server-reverse-proxy-server-block): Expose webhook under
/hooks/.
(operating-system)[services]: Use %webhook-port.
| Arun Isaac |
| 2022-09-05 | Set host name of the laminar nginx server....* genenetwork-development.scm (laminar-reverse-proxy-server-block):
Set host name of the laminar nginx server.
| Arun Isaac |
| 2022-09-05 | Do not list guix channel in CI published channels.scm....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.
| Arun Isaac |
| 2022-09-05 | Do not share /srv/http into container..../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.
| Arun Isaac |
| 2022-09-05 | Remove website directory of gn-gemtext-threads forge project....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.
| Arun Isaac |
| 2022-08-29 | Run mysql server in production....* production.scm: Import (gnu services databases).
(operating-system)[services]: Add mysql-service-type.
* production-deploy.sh: Share mysql directory with container.
| Arun Isaac |
| 2022-08-29 | Run production in separate network namespace....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.
| Arun Isaac |
| 2022-08-25 | Run genenetwork services as genenetwork user and group....* 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.
| Arun Isaac |
