| Age | Commit message (Expand) | Author |
|---|
| 2023-01-21 | GN3: pylint - Check more files and directories | Frederick Muriuki Muriithi |
| 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 |
| 2022-10-06 | 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 | 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 |
| 2022-09-08 | Set genenetwork3 API endpoint used by genenetwork2 to /api3....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL to /api3.
| Arun Isaac |
| 2022-08-16 | 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 | Set GN_SERVER_URL when running genenetwork2....* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Set
GN_SERVER_URL.
| 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 |
| 2022-06-29 | 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 |
| 2022-06-14 | 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 |
| 2022-04-15 | Initial commit | Arun Isaac |
