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2022-11-21auth: Prevent group leader from being a member of multiple groups...* gn3/auth/authorisation/groups.py: Assign the group leader at group creation time. * tests/unit/auth/test_groups.py: Ensure the group leader is only ever a member of a single group. Frederick Muriuki Muriithi
2022-11-17auth: Finish implementation of `create_group_role`...* gn3/auth/authorisation/groups.py: Add `GroupRole` type. Fix typing annotations. Fix bugs. * tests/unit/auth/conftest.py: Fix bugs. * tests/unit/auth/test_groups.py: Fix test to run. Frederick Muriuki Muriithi
2022-11-17Migrations: Create `group_users` table...* migrations/auth/20221117_02_fmuZh-create-group-users-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 Frederick Muriuki Muriithi
2022-11-17tests: Add test to check creation of roles attached to groups...* tests/unit/auth/conftest.py: Add fixtures to help with testing * tests/unit/auth/test_groups.py: Add incomplete and failing test Frederick Muriuki Muriithi
2022-11-17Tests: Make test failure messages clearer.Frederick Muriuki Muriithi
2022-11-17Migrations: Add column `group_role_id` to `group_roles` table...* migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py: new migration * tests/unit/auth/test_migrations_add_remove_columns.py: test new migration Frederick Muriuki Muriithi
2022-11-17tests: test for addition of data to non-empty tableFrederick Muriuki Muriithi
2022-11-16pylint: fix some linting errorsFrederick Muriuki Muriithi
2022-11-16tests: Add tests for privileges...* migrations/auth/20221116_01_nKUmX-add-privileges-to-group-leader-role.py: new migration to fix data errors. * tests/unit/auth/test_privileges.py: test privileges Frederick Muriuki Muriithi
2022-11-16auth: fix bugs in the code...* 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 Frederick Muriuki Muriithi
2022-11-16tests: Test role creation...* tests/unit/auth/test_roles.py: new tests. Frederick Muriuki Muriithi
2022-11-15auth: Return results of calling function directly...* 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 Frederick Muriuki Muriithi
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 cursor...* 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. Frederick Muriuki Muriithi
2022-11-15tests: Fix cause of `DeprecationWarning`...* 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`. Frederick Muriuki Muriithi
2022-11-14auth: Implement `create_group`Frederick Muriuki Muriithi
2022-11-14tests: split test app and test client...* The test app and the test client are both needed as fixtures in different places Frederick Muriuki Muriithi
2022-11-14Migrations: Create `user_roles` table...* 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 Frederick Muriuki Muriithi
2022-11-14auth: Add test for `create_group`...* 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` Frederick Muriuki Muriithi
2022-11-14Migrations: Create the `group-leader` role and give it privileges...* 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 Frederick Muriuki Muriithi
2022-11-14Migrations: Create `group_roles` table...* 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 Frederick Muriuki Muriithi
2022-11-14Migrations: Drop `generic_role*` tables...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 Frederick Muriuki Muriithi
2022-11-14Rename files for consistency...* Name all tests that test migrations to start with `test_migrations_` Frederick Muriuki Muriithi
2022-11-14Migrations: Add generic_role_privileges table...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 Frederick Muriuki Muriithi
2022-11-14Migrations: Migration for initial privileges...* 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. Frederick Muriuki Muriithi
2022-11-10Migrations: Add columns to 'privileges' table...* 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 Frederick Muriuki Muriithi
2022-11-10Tests: Generalise tests for adding/removing columns to/from tablesFrederick Muriuki Muriithi
2022-11-10Migrations: migration for `role_privileges` table...* tests/unit/auth/test_create_table_migrations.py: new migration * tests/unit/auth/test_migrations_indexes.py: test new migration Frederick Muriuki Muriithi
2022-11-10Migrations: migration for 'generic_roles' table...* migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-10Migrations: migration for 'roles' table...* 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 Frederick Muriuki Muriithi
2022-11-10Migrations: migration for 'genotype_resources' table...* migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for 'phenotype_resources' table...* migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for mrna_resources table...* migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for 'resources' table...* 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 Frederick Muriuki Muriithi
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....* 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. Frederick Muriuki Muriithi
2022-11-08Migrations: Init `resource_categories` with initial categories...* 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. Frederick Muriuki Muriithi
2022-11-08Migrations: Create `resource_categories` table....* migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py: new migration. * tests/unit/auth/test_create_table_migrations.py: test new migration. Frederick Muriuki Muriithi
2022-11-08Migrations: Create `privileges` table....* migrations/auth/20221108_02_wxTr9-create-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
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' migrations...* 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 Frederick Muriuki Muriithi
2022-11-08Tests: Tests the credentials check system...* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking Frederick Muriuki Muriithi
2022-11-08Tests: Test migration to create user_credentials table...* tests/unit/auth/test_create_user_credentials_table.py: new tests Frederick Muriuki Muriithi
2022-11-08Tests: Separate *ALL* unit test fixtures from auth-specific ones...* 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. Frederick Muriuki Muriithi
2022-11-03Add credentials checking...* 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 Frederick Muriuki Muriithi
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