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2024-10-02Move sparql-auth URIs to gn3-conf in documentation.Munyoki Kilyungi
We want to strictly keep secrets in the secret file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-28Update documentation on how to run tests.Frederick Muriuki Muriithi
2024-09-23Add section on setting up virtuoso locally.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs to use default virtuoso ports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs on how to use SPARQL default ports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs to highlight sparql conf params in SECRETS file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Update docs with extra conf vars for updating virtuoso.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-12rqtl_wrapper: minor fixesPjotr Prins
2024-09-12READMEPjotr Prins
2023-12-19README: Replace pylint and mypy CI badges with all-tests CI badge.Arun Isaac
2023-09-05Update instructions on how to run pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-14auth: Remove documentationFrederick Muriuki Muriithi
The authentication/authorisation stuff is being moved to a separate repository. This commit removes the documentation for how to run migrations from this repository since it has been moved over to the new repository.
2023-05-26Document CLI Utility CommandsFrederick Muriuki Muriithi
Document some CLI utility commands useful for development and for supporting the operation of the GN3 app.
2023-05-25Script to assign existing data to publicly-visible resourcesFrederick Muriuki Muriithi
A script to assign existing data not assigned to any group to publicly-visible resources.
2023-05-23Document how to log out information in GN3Frederick Muriuki Muriithi
2023-03-23Docs: Add a note on how the configuration system works.Frederick Muriuki Muriithi
2023-03-13Add 'ON UPDATE/DELETE' clauses to foreign keys.Frederick Muriuki Muriithi
2023-03-13auth: cURL: Add some docs on using cURLFrederick Muriuki Muriithi
2023-03-08Replace Bcrypt with Argon2 for better security.Frederick Muriuki Muriithi
Bcrypt is now somewhat vulnerable to offline cracking, so we move our password hashing over to Argon2.
2023-01-25Some commentsPjotr Prins
2023-01-24docs: Add information on running the OAuth2 server without HTTPSFrederick Muriuki Muriithi
2022-12-23Update how to set configurations in READMEzsloan
2022-12-23Add a couple necessary environment variableszsloan
2022-12-22auth: implement OAuth2 flow.oauth2_auth_flowFrederick Muriuki Muriithi
Add code to implement the OAuth2 flow. * Add test fixtures for setting up users and OAuth2 clients * Add tests for token generation with the "Password Grant" flow * Fix some issues with test due to changes in the database connection's row_factory
2022-11-13Documentation: Explain how to run migrationsFrederick Muriuki Muriithi
* .gitignore: ignore all yoyo configuration files * README.md: Update documentation * yoyo.auth.ini: stop tracking the yoyo configuration file.
2022-11-03Initialise the Auth(entic|oris)ation packagesFrederick Muriuki Muriithi
Initialise the authentication/authorisation system packages and set up the initial database migrations to set up the system. * README.md: Add documentation on migrations * gn3/auth/__init__.py: init package * gn3/auth/authentication/__init__.py: init package * gn3/auth/authorisation/__init__.py: init package * gn3/migrations.py: provide migration utilities * migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py: new migration * tests/unit/auth/test_init_database.py: test new migration applies and rolls back as expected * tests/unit/conftest.py: fixtures for unit tests * yoyo.auth.ini: basic configuration for yoyo-migration for auth system migrations
2022-10-08README: a note on designPjotr Prins
2022-09-06Update link to continuous deployment.Arun Isaac
* README.md: Update link to continuous deployment.
2022-07-29New script to run sample correlationsFrederick Muriuki Muriithi
* README.md: update mypy's invocation * scripts/argparse_actions.py: new file - implement custom FileCheck action for argparse * scripts/sample_correlations.py: new file - implement new script to run sample correlations in an external process
2022-06-20Update README: export env variables explicitlyFrederick Muriuki Muriithi
2022-05-24New script to compute partial correlationsFrederick Muriuki Muriithi
* Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order.
2022-05-05Link to continuous deployment in README.Arun Isaac
* README.md: Link to continuous deployment.
2022-03-18README: Update CI badge subdomain.Arun Isaac
The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org. * README.md: Update CI badge subdomain.
2022-03-12README: Replace "unit-test" instructions with "pytest"BonfaceKilz
2022-03-04Document basic partial correlations dependenciesFrederick Muriuki Muriithi
* Document the things that the partial correlations feature depends on to work
2022-02-02Revert "Use guix shell shortcut with guix.scm file"BonfaceKilz
This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
2022-01-27Use guix shell shortcut with guix.scm filejgart
2022-01-24README: Add pylint and mypy CI badges.Arun Isaac
We now have separate CI jobs for the pylint and mypy tests. * README.md: Add pylint and mypy CI badges.
2022-01-21README: Update link to CI badge.Arun Isaac
The CI has been moved to penguin2, and this is accompanied by a URI change. * README.md: Update link to CI badge.
2022-01-01guix_deployPjotr Prins
2021-12-09README: Link CI badge to CI status page.Arun Isaac
* README.md: Link CI badge to CI status page.
2021-12-09README: Add CI badge.Arun Isaac
* README.md: Add CI badge.
2021-11-19Replace guix environment with guix shell.Arun Isaac
* README.md, guix.scm: Replace guix environment with guix shell.
2021-11-11Disuse absolute paths to guix.Arun Isaac
It is safe to assume that the user has correctly set up guix in their PATH. * README.md: Disuse absolute paths to guix in command invocations.
2021-11-11Disuse GUIX_PACKAGE_PATH.Arun Isaac
guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is no need to specify it explicitly using GUIX_PACKAGE_PATH. * README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command.
2021-08-31Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_generation
2021-08-30Update documentation on genotype filesMuriithi Frederick Muriuki
* Provide documentation on downloading and using the genotype files.
2021-08-30Fix issues with traits file formatMuriithi Frederick Muriuki
* README.md: update header: Traits ==> Trait * gn3/computations/qtlreaper.py: update header: Traits ==> Trait * qtlfilesexport.py: Choose only BXD strains Rename the first column header from "Traits" to "Trait" to correspond with what `rust-qtlreaper` expects. Choose only the BXD strains for the proof-of-concept example - this helped bring out the fact that the traits file SHOULD NOT contain a strain column for a strain that does not exist in the genotype file in consideration. If the traits file has a strain column which does not exist in the genotype file, then `rust-qtlreaper` fails with a panic, since, from what I can tell, it tries to get a value from the genotype file for the non-existent strain, which results to a `None` type. Subsequent attempts at running an operation on the `None` type lead to the panic.
2021-08-30Document acquired knowledge on `rust-qtlreaper`Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: document format of the traits file To assist future developers, and development of the system, this commit documents some of the hard-won knowledge about the operation of the system to ease future development of the system. The documentation, if good, might also help with future onboarding of new developers to the system.
2021-08-28README: updated install instructionsPjotr Prins
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