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2022-11-16auth: fix bugs in the codeFrederick Muriuki Muriithi
* gn3/auth/authorisation/privileges.py: Set id to UUID type * gn3/auth/authorisation/roles.py: fix parameters to types that sqlite3 supports * gn3/auth/db.py: add logging for errors and re-raise the exception * tests/unit/auth/test_roles.py: fix test
2022-11-16tests: Test role creationFrederick Muriuki Muriithi
* tests/unit/auth/test_roles.py: new tests.
2022-11-15auth: Return results of calling function directlyFrederick Muriuki Muriithi
* gn3/auth/authorisation/checks.py: Return results of calling the function rather than a dict of values that include the results. * gn3/auth/authorisation/groups.py: Use the newer form of `authorised_p` decorator. * tests/unit/auth/test_groups.py: Update tests
2022-11-15Add missing module __init__.py to mitigate the mypy errorsFrederick Muriuki Muriithi
2022-11-15pylint: Fix a myriad of linting errorsFrederick Muriuki Muriithi
2022-11-15pylint: Fix linting errors.Frederick Muriuki Muriithi
2022-11-15tests: typo: fix migration script file nameFrederick Muriuki Muriithi
2022-11-15tests: Use `gn3.auth.db` functions for db connection and cursorFrederick Muriuki Muriithi
* tests/unit/auth/conftest.py: use the functions in `gn3.auth.db` to acquire the database connection and cursor since they handle some of the basic issues like rollback and commit, meaning we do not have to explicitly handle said issues in the fixtures.
2022-11-15tests: Fix cause of `DeprecationWarning`Frederick Muriuki Muriithi
* tests/unit/auth/test_groups.py: use Flask's application context directly rather than the request context to access `g` in order to get rid of the `DeprecationWarning`.
2022-11-14auth: Implement `create_group`Frederick Muriuki Muriithi
2022-11-14tests: split test app and test clientFrederick Muriuki Muriithi
* The test app and the test client are both needed as fixtures in different places
2022-11-14Migrations: Create `user_roles` tableFrederick Muriuki Muriithi
* migrations/auth/20221114_05_hQun6-create-user-roles-table.py: new migration * tests/unit/auth/test_migrations_create_tables.py: test new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
2022-11-14auth: Add test for `create_group`Frederick Muriuki Muriithi
* gn3/auth/authorisation/__init__.py: Add `authorised_p` decorator to be used for all function requiring authorisation. * gn3/auth/authorisation/groups.py: Add `create_group` function stub * tests/unit/auth/conftest.py: Add fixture for test users * tests/unit/auth/test_groups.py: Add tests for `create_group`
2022-11-14Migrations: Create the `group-leader` role and give it privilegesFrederick Muriuki Muriithi
* migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py: new migration * tests/unit/auth/test_migrations_insert_data_into_empty_table.py: test new migration
2022-11-14Migrations: Create `group_roles` tableFrederick Muriuki Muriithi
* migrations/auth/20221110_05_BaNtL-create-roles-table.py: modify migration * migrations/auth/20221114_03_PtWjc-create-group-roles-table.py: new migration * tests/unit/auth/test_migrations_create_tables.py: test new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
2022-11-14Migrations: Drop `generic_role*` tablesFrederick Muriuki Muriithi
Drop the `generic_role*` tables, since what they were envisioned for can be handled a different, (arguably) more simple way. * migrations/auth/20221114_02_DKKjn-drop-generic-role-tables.py: new migration * tests/unit/auth/test_migrations_drop_tables.py: test new migration
2022-11-14Rename files for consistencyFrederick Muriuki Muriithi
* Name all tests that test migrations to start with `test_migrations_`
2022-11-14Migrations: Add generic_role_privileges tableFrederick Muriuki Muriithi
Add table `generic_role_privileges` table to link the generic roles to the privileges they provide. * migrations/auth/20221114_01_n8gsF-create-generic-role-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
2022-11-14Migrations: Migration for initial privilegesFrederick Muriuki Muriithi
* migrations/auth/20221113_01_7M0hv-enumerate-initial-privileges.py: new migration. * tests/unit/auth/test_migrations_insert_data_into_empty_table.py: test new migration.
2022-11-10Migrations: Add columns to 'privileges' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_08_23psB-add-privilege-category-and-privilege-description-columns-to-privileges-table.py: new migration * tests/unit/auth/test_migrations_add_remove_columns.py: test new migration
2022-11-10Tests: Generalise tests for adding/removing columns to/from tablesFrederick Muriuki Muriithi
2022-11-10Migrations: migration for `role_privileges` tableFrederick Muriuki Muriithi
* tests/unit/auth/test_create_table_migrations.py: new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
2022-11-10Migrations: migration for 'generic_roles' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
2022-11-10Migrations: migration for 'roles' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_05_BaNtL-create-roles-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
2022-11-10Migrations: migration for 'genotype_resources' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
2022-11-10Migrations: Add migration for 'phenotype_resources' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
2022-11-10Migrations: Add migration for mrna_resources tableFrederick Muriuki Muriithi
* migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
2022-11-10Migrations: Add migration for 'resources' tableFrederick Muriuki Muriithi
* gn3/migrations.py: Minor change * migrations/auth/20221110_01_WtZ1I-create-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
2022-11-09Migrations: Add `resource_meta` field to `resource_categories` tableFrederick Muriuki Muriithi
2022-11-09Tests: Provide backend fixture to (apply|rollback)_single_migrationFrederick Muriuki Muriithi
2022-11-08Migrations: Improve `resource_categories` data tests.Frederick Muriuki Muriithi
* tests/unit/auth/test_migration_init_data_in_resource_categories_table.py: Test that the data is initialised properly. Test that rollback works as expected.
2022-11-08Migrations: Init `resource_categories` with initial categoriesFrederick Muriuki Muriithi
* migrations/auth/20221108_04_CKcSL-init-data-in-resource-categories-table.py: new migration. * tests/unit/auth/test_migration_init_data_in_resource_categories_table.py: test new migration.
2022-11-08Migrations: Create `resource_categories` table.Frederick Muriuki Muriithi
* migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py: new migration. * tests/unit/auth/test_create_table_migrations.py: test new migration.
2022-11-08Migrations: Create `privileges` table.Frederick Muriuki Muriithi
* migrations/auth/20221108_02_wxTr9-create-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
2022-11-08Tests: Fix test name.Frederick Muriuki Muriithi
2022-11-08Tests: Fix typo: remove variable from quotes.Frederick Muriuki Muriithi
2022-11-08Tests: Generalise testing 'CREATE TABLE' migrationsFrederick Muriuki Muriithi
* gn3/settings.py: Omit trailing slash * tests/unit/auth/test_create_table_migrations.py: Generalise testing migrations that create tables. * tests/unit/auth/test_create_user_credentials_table.py: delete * tests/unit/auth/test_migration_create_users_table.py: delete
2022-11-08Tests: Tests the credentials check systemFrederick Muriuki Muriithi
* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking
2022-11-08Tests: Test migration to create user_credentials tableFrederick Muriuki Muriithi
* tests/unit/auth/test_create_user_credentials_table.py: new tests
2022-11-08Tests: Separate *ALL* unit test fixtures from auth-specific onesFrederick Muriuki Muriithi
* tests/unit/auth/conftest.py: add fixtures specific to auth * tests/unit/auth/test_migration_create_users_table.py: import from new fixtures module * tests/unit/conftest.py: remove auth-specific fixtures from *ALL* unit tests fixture module.
2022-11-03Add credentials checkingFrederick Muriuki Muriithi
* gn3/auth/authentication.py: new function `credentials_in_database` * gn3/auth/authentication/__init__.py: replace package with module * gn3/settings.py: new `AUTH_MIGRATIONS` configuration variable * migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py: new migration * tests/unit/auth/test_credentials.py: test the `credentials_in_database` function * tests/unit/conftest.py: more test fixtures
2022-11-03Rename migration test.Frederick Muriuki Muriithi
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
2022-11-02Add tests for monadic_dictMunyoki Kilyungi
* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases for MonadicDict.
2022-08-30Update test: include port in parsed data from mysql uriFrederick Muriuki Muriithi
2022-08-10update test;parse outputAlexander_Kabui
2022-07-29Fix failing testsFrederick Muriuki Muriithi
* 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
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22add unittestsAlexander_Kabui
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