| Age | Commit message (Expand) | Author |
|---|
| 2022-11-15 | pylint: Fix a myriad of linting errors | 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: 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 |
| 2022-11-10 | 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...* 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 | 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 | 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 | 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 |
| 2022-11-03 | Add 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 |
| 2022-11-03 | Rename migration test. | Frederick Muriuki Muriithi |
| 2022-11-03 | Initialise 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 |
| 2022-11-02 | Add tests for monadic_dict...* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases
for MonadicDict.
| Munyoki Kilyungi |
| 2022-08-30 | Update test: include port in parsed data from mysql uri | Frederick Muriuki Muriithi |
| 2022-08-10 | update test;parse output | Alexander_Kabui |
| 2022-07-29 | Fix 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 |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui |
| 2022-07-22 | add unittests | Alexander_Kabui |
| 2022-06-29 | use explicit parameters | Alexander_Kabui |
| 2022-06-29 | fix issues | Alexander_Kabui |
| 2022-06-29 | lint test file | Alexander |
| 2022-06-29 | add tests | Alexander |
