| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-08-25 | Add production container....* production-deploy.sh, production.scm: New files.
| Arun Isaac |
| 2022-08-25 | Document the required channels....* README.org (GeneNetwork development container): Document the
required channels.
| Arun Isaac |
| 2022-08-25 | Credit Frederick for 5cd33ed762f6fe1301f6e5bb615eb9101012af23....* genenetwork-development.scm: Add copyright line for Frederick
Muriuki Muriithi.
| Arun Isaac |
| 2022-08-23 | Expose CD logs to host....* 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.
| Arun Isaac |
| 2022-08-16 | Add trailing slash to GN_PROXY_URL....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.
| Arun Isaac |
| 2022-08-16 | Add trailing slash to GN_PROXY_URL....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>
| Frederick Muriuki Muriithi |
| 2022-07-08 | Map mysqld socket into the genenetwork3 container....* genenetwork-development.scm (genenetwork3-shepherd-service): Map
mysqld socket into the container.
| Arun Isaac |
| 2022-07-08 | Set GN_SERVER_URL when running genenetwork2....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL.
| Arun Isaac |
| 2022-07-08 | Support tissue URIs without the html extension....* genenetwork-development.scm (tissue-reverse-proxy-server-block):
Support URIs without the html extension.
| Arun Isaac |
| 2022-07-06 | Switch to tissue service from guix-forge....* 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.
| Arun Isaac |
| 2022-07-01 | Switch to new tissue configuration file....* genenetwork-development.scm (<tissue-configuration>)[address, port,
indexed-repository]: Delete fields.
[listen, hosts]: New fields.
* genenetwork-development.scm (<tissue-host>): New type.
(tissue-conf-gexp): New function.
(tissue-shepherd-service): Remove --address and --port
arguments. Compute and pass tissue.conf configuration file. Create
file system mappings for all hosts.
(operating-system)[services]: Use new tissue-configuration fields.
| Arun Isaac |
| 2022-06-29 | Build tissue static website in temporary writable directory....tissue now builds a xapian index and this requires a writable
directory.
* genenetwork/development-helper.scm (tissue-website-gexp): Build
static website in temporary writable directory.
| Arun Isaac |
| 2022-06-29 | Add tissue search interface....* genenetwork-development.scm: Import shadow from (gnu packages
admin).
(gn-gemtext-threads-index): New function.
(gn-gemtext-threads-project)[ci-jobs]: Add gn-gemtext-threads-index.
(<tissue-configuration>): New type.
(tissue-shepherd-service, tissue-reverse-proxy-server-block): New
function.
(%tissue-accounts, tissue-service-type): New variables.
(operating-system)[services]: Add tissue tissue service and reverse
proxy it.
* genenetwork/development-helper.scm (tissue-index-gexp): New
function.
| Arun Isaac |
| 2022-06-29 | Remove tissue's dependence on the git CLI tool....tissue now uses libgit2 through guile-git and does not use the git CLI
tool.
* genenetwork-development.scm (gn-gemtext-threads-website): Remove
git-minimal from manifest.
* genenetwork/development-helper.scm (tissue-website-gexp): Remove
reassurance to git.
| Arun Isaac |
| 2022-06-24 | Persist virtuoso database....* genenetwork-development-deploy.sh: Persist virtuoso database at
/var/guix-containers/genenetwork-development/var/lib/virtuoso.
| Arun Isaac |
| 2022-06-24 | Import missing SRFI-26 in dump-genenetwork-database G-exp....This was missed out in 96fb9608242254a1fc53bbd71168db4245458c8f.
* genenetwork-development.scm (dump-genenetwork-database):
Import (srfi srfi-26).
| Arun Isaac |
| 2022-06-24 | Send rapper output to /dev/null instead of using --ignore-errors....The --ignore-errors flag not only avoids printing triples, but also
actually ignores errors. What a surprise! ;-) As a result, rapper does
not stop invalid turtle files, and they end up erroring out when
uploaded to virtuoso.
* genenetwork-development.scm (dump-genenetwork-database): Send rapper
output to /dev/null instead of using --ignore-errors.
| Arun Isaac |
| 2022-06-24 | Set ownership of database dump directories too, not just files....* genenetwork-development.scm (operating-system)[services]: In the
set-dump-genenetwork-database-export-directory-permissions service,
set ownership of directories in
%dump-genenetwork-database-export-directory too, not just the files.
| Arun Isaac |
| 2022-06-14 | Disable laminar proxy buffering by passing X-Accel-Buffering....* genenetwork-development.scm (laminar-reverse-proxy-server-block):
Disable laminar proxy buffering by passing the X-Accel-Buffering HTTP
header through.
| Arun Isaac |
| 2022-06-14 | Reassure git that the gn-gemtext-threads source directory is safe....* genenetwork/development-helper.scm (tissue-website-gexp): Reassure
git that the gn-gemtext-threads source directory is safe.
* genenetwork-development.scm (gn-gemtext-threads-website): Add
git-minimal to manifest.
| Arun Isaac |
| 2022-06-10 | Link to channels.scm from laminar page....* genenetwork-development.scm (laminar-template-gexp): Link to
channels.scm.
| Arun Isaac |
| 2022-06-10 | Publish channels.scm for laminar....* genenetwork-development.scm: Import (gnu services web) and (guix
channels).
(channels-scm-gexp, laminar-reverse-proxy-server-block): New
functions.
(operating-system)[services]: Bind laminar service to 9089.
Add nginx service on 9090 to reverse proxy laminar.
| Arun Isaac |
| 2022-06-10 | Relabel issue tracker link as "Issues"....* genenetwork-development.scm (laminar-template-gexp): Relabel issue
tracker link as "Issues".
| Arun Isaac |
