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2023-03-08Replace Bcrypt with Argon2 for better security....Bcrypt is now somewhat vulnerable to offline cracking, so we move our password hashing over to Argon2. Frederick Muriuki Muriithi
2023-03-02auth: user registration: Rework error checking. Add email validationFrederick Muriuki Muriithi
2023-01-28auth: Enable retrieval of a role by id.Frederick Muriuki Muriithi
2023-01-20mypy: minor fixes to typing errorsFrederick Muriuki Muriithi
2023-01-18auth: Fix tests after enforcing FOREIGN KEY constraint...Fix a number of tests and fixtures that were not conforming to the FOREIGN KEY constraints: * Each test that creates a new "object" needs to clean up after itself * Each fixture that sets up test data needs to clean up after itself Frederick Muriuki Muriithi
2022-12-22auth: implement OAuth2 flow....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 oauth2_auth_flowFrederick Muriuki Muriithi
2022-11-03Initialise the Auth(entic|oris)ation packages...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 Frederick Muriuki Muriithi
2022-11-02Fix pylint and mypy errors...* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query directly to cursor.execute. Rename value to _value in for loop to make mypy pass. * gn3/db_utils.py (Connection): Add class docstring. (Connection.cursor): Add docstring. * mypy.ini: Add an entry for xapian. Munyoki Kilyungi
2022-11-02Add type stubs for Maybe...This allows Maybe[T] to be used as a type. Both Nothing and Just are of type Maybe. * mypy.ini: Add default location for stub files. * stubs/pymonad/__init__.pyi: New file. * stubs/pymonad/maybe.pyi: Ditto. Munyoki Kilyungi
2022-07-29Fix failing tests...* gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function Frederick Muriuki Muriithi
2022-06-21mypy.ini: Ignore missing lmdb mypy stubsBonfaceKilz
2022-03-15Feature/refactored pca (#79)...* compute zscore function * test case for computing zscore * function to compute pca * generate scree plot data * generate new pca trait data from zscores and eigen_vec * remove redundant functions * generate factor loading table data * generate pca temp dataset dict * variable naming and error fixes * unit test for processing factor loadings * minor fixes for generating temp pca dataset * pass datetime as argument to generate_pca temp dataset function * add unittest for caching pca datasets * cache temp datasets * ignore missing imports for sklearn * mypy fixes * pylint fixes * refactor tests for pca * remove ununsed imports * fix for generating pca traits vals * mypy and code refactoring * pep8 formatting and add docstrings * remove comments /pep8 formatting * sort eigen vectors based on eigen values * minor fix for zscores * fix for rounding variance ratios * refactor tests * rename module to pca * rename datasets to traits * fix failing tests * fix caching function * fixes return x and y coordinates for scree plot * expand exception scope * fix for deprecated numpy.matrix function * fix for failing tests * pep8 fixes * remove comments * fix merge conflict * pylint fixes * rename module name to test_pcaAlexander Kabui
2022-03-11Fix typing errorsFrederick Muriuki Muriithi
2021-12-14mypy: ignore some imports and errors...* Ignore some missing library stubs * Ignore some typing errors * Fix obvious typing errors Frederick Muriuki Muriithi
2021-11-01Fix mypy issuesBonfaceKilz
2021-10-29Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixesAlexander Kabui
2021-06-18add ignore_missing_imports for numpy in mypy.ini since it complains about tha...zsloan
2021-05-08Ignore missing stub imports from MySQLdbBonfaceKilz
2021-03-23Re-add mypy conf file...Deleted in 56ce88a BonfaceKilz
2021-03-16delete unwanted correlation stuff (#5)...* delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>Alexander Kabui
2021-03-15Add a basic mypy init fileBonfaceKilz