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2022-11-17auth: Define the `User` typeFrederick Muriuki Muriithi
* gn3/auth/authentication.py -> gn3/auth/authentication/__init__.py: Convert module to package * gn3/auth/authentication/users.py: Define the `User` type
2022-11-17Tests: Make test failure messages clearer.Frederick Muriuki Muriithi
2022-11-17Migrations: Add column `group_role_id` to `group_roles` tableFrederick Muriuki Muriithi
* 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
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 privilegesFrederick Muriuki Muriithi
* 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
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.
2022-11-16Inject SPARQLWrapper as a parameterMunyoki Kilyungi
* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto.
2022-11-15auth: Add `create_group_role` function.Frederick Muriuki Muriithi
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
2022-11-15auth: Specify types for privileges, roles, groupsFrederick Muriuki Muriithi
Use specified types for privileges, roles and types rather than using strings to help with limiting bugs. * gn3/auth/authorisation/groups.py: Specify and use the `Group` type * gn3/auth/authorisation/privileges.py: Specify and use the `Privilege` type * gn3/auth/authorisation/roles.py: Specify the `Role` type. Add the `create_role` function.
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
2022-11-15auth: Add some typing information to the functionsFrederick Muriuki Muriithi
2022-11-15auth: Reorganise package - move function to `checks` moduleFrederick Muriuki Muriithi
* gn3/auth/authorisation/__init__.py: delete function * gn3/auth/authorisation/checks.py: move function to `checks` module
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: Add `user_editable` field to roles tableFrederick Muriuki Muriithi
Some roles will not be user editable to prevent inconsistencies, and possible privilege escalation. * migrations/auth/20221110_05_BaNtL-create-roles-table.py: Add `user_editable` column to table * migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py: Set `group-leader` role as not user editable
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.
2022-11-13Documentation: 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.
2022-11-10Migrations: 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
* migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py: new migration Commit ee72678fabb86d66ba7d61d26643cc73df94ee5d only contains tests for this migration.
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
2022-11-08Fix issue where only primary samples were used when all samples arezsloan
selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again.
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
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