| Age | Commit message (Expand) | Author |
|---|
| 2024-06-28 | Make secrets dirs writable by relevant services. | Frederick Muriuki Muriithi |
| 2024-06-28 | Remove duplicated, and wrong settings. | Frederick Muriuki Muriithi |
| 2024-06-28 | Fix permissions: Only files are read-only...Directories need the execute bit set to actually be accessible to the
owner.
| Frederick Muriuki Muriithi |
| 2024-06-28 | Make relevant services available to each service. | Frederick Muriuki Muriithi |
| 2024-06-28 | Set secrets as directories for services with multiple secrets. | Frederick Muriuki Muriithi |
| 2024-06-28 | Add JWT SSL keys configurations. | Frederick Muriuki Muriithi |
| 2024-06-12 | gn-uploader: Setup profile path...The profile path is necessary for use retrieving the included
bootstrap content.
| Frederick Muriuki Muriithi |
| 2024-05-07 | gn-uploader: Serve static files via nginx....* genenetwork/services/genenetwork.scm: Import nginx from (gnu
packages web), python from (gnu packages python), (guix build
python-build-system) and (guix packages).
(gn-uploader-nginx-server-block): Serve static files via nginx.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-04-12 | gn-uploader: use installed entry-point. | Frederick Muriuki Muriithi |
| 2024-04-12 | gn-uploader: use defined app in wsgi.py to pick up logging configs. | Frederick Muriuki Muriithi |
| 2024-04-12 | Set up log level in gunicornadd-gunicorn-logging | Frederick Muriuki Muriithi |
| 2024-04-10 | gn-uploader: Enable changing of log-level for container....This commit enables us to change the logging level of the gn-uploader
service within the container: this will help in the instances when we
need to debug events in the application that are unexpected.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Change ownership of data-directory...While the share is technically writable from the container, the
service was running as an unprivileged user, and thus could not write
to the data-directory. This commit changes the ownership of the
data-directory to the same user that runs the service.
| Frederick Muriuki Muriithi |
| 2024-04-09 | gn-uploader: Made datadir writable and set up uploads directory. | Frederick Muriuki Muriithi |
| 2024-04-05 | Document configuration settings | Pjotr Prins |
| 2024-04-03 | Set up SQL_URI for gn-auth. | Frederick Muriuki Muriithi |
| 2024-04-03 | gendev: special machine for Pjotr | Pjotr Prins |
| 2024-04-01 | Share TMPDIR between GN2 and GN3 | Pjotr Prins |
| 2024-04-01 | fallback: have gn2 and gn3 share a source directory so we can update/debug so......topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
| Pjotr Prins |
| 2024-03-28 | gn-uploader: Increment maximum size of uploadable files. | Frederick Muriuki Muriithi |
| 2024-03-25 | Add gn-uploader service....* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>):
New type.
(gn-uploader-activation, gn-uploader-gunicorn-app,
gn-uploader-nginx-server-block): New functions.
(gn-uploader-service-type): New variable.
* uploader.scm, uploader-deploy.sh: New files.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-03-21 | Add timeout for proxies | Pjotr Prins |
| 2024-03-05 | Let the gunicorn-gn-auth user own the auth database....gn-auth runs as the gunicorn-gn-auth user, not the genenetwork user.
* genenetwork/services/genenetwork.scm (genenetwork-activation): Let
the gunicorn-gn-auth user own the auth database.
Reported-by: Frederick M. Muriithi <fredmanglis@protonmail.com>
| Arun Isaac |
| 2024-03-05 | Pass on the request scheme to GN2 app...This is useful to enable building URIs with the correct scheme in the
application. These URIs are important when redirection to and from
external services such as the gn-auth service.
| Frederick Muriuki Muriithi |
| 2024-03-01 | Set AUTH_SERVER_URL on production genenetwork2....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set AUTH_SERVER_URL on production genenetwork2.
| Arun Isaac |
| 2024-03-01 | Reverse proxy gn-auth on production....*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth-server-name]:
New field.
*
genenetwork/services/genenetwork.scm (genenetwork-nginx-server-block):
Rename to ...
(genenetwork-nginx-server-blocks): ... this. Return list of reverse
proxy blocks including one for gn-auth.
* genenetwork/services/genenetwork.scm (genenetwork-service-type): Use
genenetwork-nginx-server-blocks instead of
genenetwork-nginx-server-block.
*
production.scm (operating-system)[services]{genenetwork-service-type}:
Add gn-auth-server-name.
| Arun Isaac |
| 2024-03-01 | Set owner-only permissions on secrets files....* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
owner-only permissions on secrets files.
| Arun Isaac |
| 2024-03-01 | Set ownership of secrets files....* genenetwork/services/genenetwork.scm (genenetwork-activation): Set
ownership of secrets files.
* production-deploy.sh: Mount secrets files read-write.
| Arun Isaac |
| 2024-03-01 | Add gn-auth to production genenetwork service....* genenetwork/services/genenetwork.scm: Import gn-auth from (gn
packages genenetwork).
*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[gn-auth,
gn-auth-port, gn-auth-secrets]: New fields.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add gn-auth gunicorn app.
| Arun Isaac |
| 2024-01-09 | genenetwork: Increase gunicorn timeout for genenetwork3....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Increase gunicorn timeout for genenetwork3 to 1200 seconds.
| Arun Isaac |
| 2024-01-08 | Increase gunicorn timeout for genenetwork3....* genenetwork-development.scm (genenetwork3-cd-gexp): Increase
gunicorn timeout to 1200 seconds.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add TODO note to increase gunicorn timeout to 1200 seconds.
| Arun Isaac |
| 2024-01-03 | Add GeneNetwork service....* genenetwork/services/genenetwork.scm: New file.
| Arun Isaac |
| 2023-12-20 | Use guix-channel-job-gexp for gn-transform-databases CI job....* genenetwork-development.scm: Import (guix ci).
(transform-genenetwork-database-tests): Delete variable.
(%default-guix-channel-with-substitutes): New variable.
(transform-genenetwork-database-project): Use guix-channel-job-gexp
for transform-genenetwork-database-tests CI job.
* genenetwork/development-helper.scm: Delete file.
| Arun Isaac |
| 2023-12-19 | Delete unused qc-tests variable....* genenetwork-development.scm (qc-tests): Delete variable.
* genenetwork/development-helper.scm (asdf-test-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for gn-auth pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-tests): Delete function.
(gn-auth-pylint): Delete variable.
(genenetwork-projects): Build only the gn-auth variable in the gn-auth
CI job. Combine gn-auth-mypy and gn-auth-pylint CI jobs into a
gn-auth-all-tests job that uses guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for genenetwork3 pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-mypy,
genenetwork3-pylint): Delete variables.
(genenetwork-projects): Build only genenetwork3 variable in
genenetwork3 CI job. Combine genenetwork3-mypy and genenetwork3-pylint
CI jobs into a genenetwork3-all-tests job that uses
guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork3-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-09-16 | Add CI/CD definitions for gn-auth | Frederick Muriuki Muriithi |
| 2023-09-05 | Update arguments to pylint...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 |
