| Age | Commit message (Expand) | Author |
|---|---|---|
| 2022-11-16 | Inject SPARQLWrapper as a parameter...* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto. | Munyoki Kilyungi |
| 2022-11-15 | auth: Add `create_group_role` function. | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: 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 |
| 2022-11-15 | auth: Specify types for privileges, roles, groups...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. | Frederick Muriuki Muriithi |
| 2022-11-15 | Add missing module __init__.py to mitigate the mypy errors | Frederick Muriuki Muriithi |
| 2022-11-15 | pylint: Fix a myriad of linting errors | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Add some typing information to the functions | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Reorganise package - move function to `checks` module...* gn3/auth/authorisation/__init__.py: delete function * gn3/auth/authorisation/checks.py: move function to `checks` module | Frederick Muriuki Muriithi |
| 2022-11-15 | pylint: Fix linting errors. | Frederick Muriuki Muriithi |
| 2022-11-15 | tests: typo: fix migration script file name | Frederick Muriuki Muriithi |
| 2022-11-15 | tests: 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 |
| 2022-11-15 | tests: 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 |
| 2022-11-14 | auth: Implement `create_group` | Frederick Muriuki Muriithi |
| 2022-11-14 | tests: split test app and test client...* The test app and the test client are both needed as fixtures in different places | Frederick Muriuki Muriithi |
| 2022-11-14 | Migrations: 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 |
| 2022-11-14 | auth: 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 |
| 2022-11-14 | Migrations: Add `user_editable` field to roles table...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 | Frederick Muriuki Muriithi |
| 2022-11-14 | Migrations: 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 |
| 2022-11-14 | Migrations: 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 |
| 2022-11-14 | Migrations: 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 |
| 2022-11-14 | Rename files for consistency...* Name all tests that test migrations to start with `test_migrations_` | Frederick Muriuki Muriithi |
| 2022-11-14 | Migrations: 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 |
| 2022-11-14 | Migrations: 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 |
| 2022-11-13 | Documentation: Explain how to run migrations...* .gitignore: ignore all yoyo configuration files * README.md: Update documentation * yoyo.auth.ini: stop tracking the yoyo configuration file. | Frederick Muriuki Muriithi |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Tests: Generalise tests for adding/removing columns to/from tables | Frederick Muriuki Muriithi |
| 2022-11-10 | Migrations: migration for `role_privileges` table...* migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py: new migration Commit ee72678fabb86d66ba7d61d26643cc73df94ee5d only contains tests for this migration. | Frederick Muriuki Muriithi |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-09 | Migrations: Add `resource_meta` field to `resource_categories` table | Frederick Muriuki Muriithi |
| 2022-11-09 | Tests: Provide backend fixture to (apply|rollback)_single_migration | Frederick Muriuki Muriithi |
| 2022-11-08 | Fix issue where only primary samples were used when all samples are...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. | zsloan |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Tests: Fix test name. | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: Fix typo: remove variable from quotes. | Frederick Muriuki Muriithi |
| 2022-11-08 | Add migration to create the groups table. | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: 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 |
| 2022-11-08 | CLI: Provide `apply-migrations` command for flask...* main.py: Provide the `apply-migrations` CLI command to run the migrations against the auth database. The command can be invoked with: $ flask apply-migrations | Frederick Muriuki Muriithi |
| 2022-11-08 | Settings: Provide default `AUTH_DB` setting. | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: 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 |
| 2022-11-08 | Tests: Test migration to create user_credentials table...* tests/unit/auth/test_create_user_credentials_table.py: new tests | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: 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 |
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