| Age | Commit message (Expand) | Author |
|---|
| 2023-02-21 | auth: migrations: Link to data in main db...Provide the `linked_group_data` table to be used to link to data in the main
database.
Update the `mrna_resources`, `genotype_resources` and `phenotype_resources`
tables to rely on the `linked_group_data` table.
| Frederick Muriuki Muriithi |
| 2023-02-10 | Return empty tuple rather than Nothing...When user has no roles assigned, return an empty tuple rather than
pymonad.maybe.Nothing to ease maintenance.
| Frederick Muriuki Muriithi |
| 2023-02-08 | auth: groups: handle join requests. | Frederick Muriuki Muriithi |
| 2023-02-07 | auth: groups: Enable users to request to join group. | Frederick Muriuki Muriithi |
| 2023-02-06 | auth: resource: Enable viewing the details of a resource. | Frederick Muriuki Muriithi |
| 2023-02-03 | auth: tests: mock token acquisition. Fix minor bugs. | Frederick Muriuki Muriithi |
| 2023-02-02 | auth: Reorganise modules/packages for easier dev and maintenance...Split the views/routes into separate modules each dealing with a narrower
scope of the application to aid in maintenance, and help with making the
development easier.
| Frederick Muriuki Muriithi |
| 2023-01-24 | tests: Expect exact integer value when applying SI suffix....* tests/unit/test_search.py (test_apply_si_suffix_kilo,
test_apply_si_suffix_mega, test_apply_si_suffix_giga): Update docstring
indicating that we expect the exact integer value.
| Arun Isaac |
| 2023-01-24 | search: Abstract out parsing of position spec into separate function....* gn3/api/search.py (parse_position): New function.
(parse_location_field): Use parse_position.
* tests/unit/test_search.py: Import parse_position from gn3.api.search.
(test_parse_position_close_to_zero_location): New test.
| Arun Isaac |
| 2023-01-23 | auth: create group: Fix group creation....* gn3/auth/authorisation/checks.py: Enable passing user to authorisation
checking function. Raise error on authorisation failure for consistent error
handling.
* gn3/auth/authorisation/groups.py: Add user to group, updating the privileges
as appropriate.
* gn3/auth/authorisation/resources.py: Fix resources querying
* gn3/auth/authorisation/roles.py: Assign/revoke roles by name
* gn3/auth/authorisation/views.py: Create group
* migrations/auth/20221108_01_CoxYh-create-the-groups-table.py: Add
group_metadata field
* tests/unit/auth/fixtures/group_fixtures.py: fix tests
* tests/unit/auth/test_groups.py: fix tests
* tests/unit/auth/test_resources.py: fix tests
* tests/unit/auth/test_roles.py: fix tests
| Frederick Muriuki Muriithi |
| 2023-01-21 | tests: roles - Extract values from Maybe object | Frederick Muriuki Muriithi |
| 2023-01-21 | tests: Fix linting errors | Frederick Muriuki Muriithi |
| 2023-01-19 | tests: Add unit tests for search....* tests/unit/test_search.py: New file.
| Arun Isaac |
| 2023-01-18 | auth: Fix tests after enforcing FOREIGN KEY constraint...Fix a number of tests and fixtures that were not conforming to the FOREIGN KEY
constraints:
* Each test that creates a new "object" needs to clean up after itself
* Each fixture that sets up test data needs to clean up after itself
| Frederick Muriuki Muriithi |
| 2023-01-16 | auth: update privileges format...Save privileges with ids of the form <top-level>:<sub-level>:<privilege-name>
rather than using a UUID, to reduce indirection levels.
* migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py: new migration
to change the schema and IDs for the privileges.
* Update code to use new privileges format
* gn3/auth/authorisation/checks.py
* gn3/auth/authorisation/groups.py
* gn3/auth/authorisation/privileges.py
* gn3/auth/authorisation/resources.py
* gn3/auth/authorisation/roles.py
* migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py
* tests/unit/auth/fixtures/role_fixtures.py
* tests/unit/auth/test_groups.py
* tests/unit/auth/test_privileges.py
* tests/unit/auth/test_roles.py
| Frederick Muriuki Muriithi |
| 2023-01-11 | auth: assign default role. separate group creation from group admin...A newly registered user will have the ability to create a group.
Once a user is a member of a group, either by creating a new group, or being
added to a group, they should not be able to create any more groups, i.e. they
lose the 'create-group' (and/or equivalent) privileges.
This means that the group-administration privileges should be separated from
the group-creation privilege.
* gn3/auth/authorisation/roles.py: assign default roles to user on
registration
* gn3/auth/authorisation/views.py: assign default roles to user on
registration
* migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py:
separate group-creation role from group-administration role.
* tests/unit/auth/fixtures/user_fixtures.py: Add group-creation role to test
user
* tests/unit/auth/test_roles.py: Add the group-creation role explicitly in the
expected results for the test
| Frederick Muriuki Muriithi |
| 2023-01-03 | auth: Fetch all of a user's roles....* gn3/auth/authorisation/roles.py: Fetch roles from DB
* gn3/auth/authorisation/views.py: Provide API endpoint for user roles
* tests/unit/auth/test_roles.py: Tests to check fetching roles works correctly
Fix linting and typing issues in the following files:
* gn3/auth/authentication/oauth2/resource_server.py
* gn3/auth/authentication/oauth2/views.py
* tests/unit/auth/fixtures/oauth2_client_fixtures.py
| Frederick Muriuki Muriithi |
| 2023-01-03 | auth: rename fixtures: test_* -> fxtr_*...Since test functions are defined starting with "test_", rename the fixture to
more clearly indicate it is a fixture (fxtr_*), an not a test in itself.
| Frederick Muriuki Muriithi |
| 2022-12-22 | tests: Setup environment variables and configs...* gn3/settings.py: leave `OAUTH2_ACCESS_TOKEN_GENERATOR` in its default
setting
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: setup
`AUTHLIB_INSECURE_TRANSPORT` before running the OAuth2 tests
* tests/unit/conftest.py: setup the test application's configuration correctly
for the tests.
| Frederick Muriuki Muriithi |
| 2022-12-22 | auth: implement OAuth2 flow....Add code to implement the OAuth2 flow.
* Add test fixtures for setting up users and OAuth2 clients
* Add tests for token generation with the "Password Grant" flow
* Fix some issues with test due to changes in the database connection's
row_factory
oauth2_auth_flow | Frederick Muriuki Muriithi |
| 2022-12-21 | migrations: create the authorisation_code table...* migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py: new
migration
* tests/unit/auth/test_migrations_create_tables.py: test new migration
| Frederick Muriuki Muriithi |
| 2022-12-21 | migrations: create oauth2_tokens table...* migrations/auth/20221219_02_buSEU-create-oauth2-tokens-table.py
* tests/unit/auth/test_migrations_create_tables.py
| Frederick Muriuki Muriithi |
| 2022-12-21 | migrations: New migration...* migrations/auth/20221219_01_CI3tN-create-oauth2-clients-table.py: New
migration
* tests/unit/auth/test_migrations_create_tables.py: tests for new migration
| Frederick Muriuki Muriithi |
| 2022-12-12 | tests: Update fixtures to use for testing resources functions | Frederick Muriuki Muriithi |
| 2022-12-12 | auth: pass cursor object to `user_group` function | Frederick Muriuki Muriithi |
| 2022-12-12 | auth: Attach group to GroupRole, rather than group_id | Frederick Muriuki Muriithi |
| 2022-12-12 | tests: Reorganise fixtures...Split the fixtures into separate modules for easier management
* tests/unit/auth/conftest.py: Import all from the `fixtures` package. Delete
all fixtures from the file
* tests/unit/auth/fixtures/__init__.py: new `fixtures` package
* tests/unit/auth/fixtures/group_fixtures.py: new groups fixtures module
* tests/unit/auth/fixtures/migration_fixtures.py: new migrations fixtures
module
* tests/unit/auth/fixtures/resource_fixtures.py: new resources fixtures module
* tests/unit/auth/fixtures/role_fixtures.py: new roles fixtures module
* tests/unit/auth/fixtures/user_fixtures.py: new users fixtures module
| Frederick Muriuki Muriithi |
| 2022-12-08 | auth: test for `user_resources` function (incomplete)...* gn3/auth/authorisation/resources.py: dummy `user_resources` function
* tests/unit/auth/conftest.py: (incomplete): Add some fixtures for testing the
`user_resources` function
* tests/unit/auth/test_resources.py: test the `user_resources` function
| Frederick Muriuki Muriithi |
| 2022-12-08 | tests: Fix issues caught by tests...The addition of the `public` field in the `resources` table, led to some
previously passing tests to fail. This commit fixes the failures, and cleans
up some pylint issues.
* gn3/auth/authorisation/resources.py: add `public` to db queries
* tests/unit/auth/test_groups.py: fix pylint issues
| Frederick Muriuki Muriithi |
| 2022-12-08 | auth: add test to retrieve public resources...* gn3/auth/authorisation/resources.py: new functions
* resource_categories: retrieves all resource categories
* public_resources: retrieves all public resources
* tests/unit/auth/test_resources.py: test `public_resources` function
| Frederick Muriuki Muriithi |
| 2022-12-08 | auth: add function to retrieve a user's group...* gn3/auth/authorisation/groups.py: new `user_group` function
* tests/unit/auth/test_groups.py: test `user_group` function
| Frederick Muriuki Muriithi |
| 2022-12-08 | migrations: Add column `public` to `resources` table...* migrations/auth/20221208_01_sSdHz-add-public-column-to-resources-table.py:
new migration script.
* tests/unit/auth/test_migrations_add_remove_columns.py: test new migration
script
| Frederick Muriuki Muriithi |
| 2022-12-06 | migrations: Add `group_user_roles_on_resources` table...* migrations/auth/20221206_01_BbeF9-create-group-user-roles-on-resources-table.py:
new migration
* tests/unit/auth/test_migrations_create_tables.py: Test creation of table
* tests/unit/auth/test_migrations_indexes.py: Test creation of index
| Frederick Muriuki Muriithi |
| 2022-12-06 | mypy and pylint fixes | Alexander_Kabui |
| 2022-12-06 | remove noisy tests for constant array correlation | Alexander_Kabui |
| 2022-12-06 | update tests for lit correlation | Alexander_Kabui |
| 2022-11-29 | tests: fix failing test...* tests/unit/computations/test_rust_correlation.py: The underlying code
changed and the test needed to be updated to test the correct thing.
| Frederick Muriuki Muriithi |
| 2022-11-24 | auth: Check for authentication and fix errors...* gn3/auth/authorisation/groups.py: base `MembershipError` on new
`AuthorisationError` base exception. Use new authentication checking
decorator.
* gn3/auth/authorisation/privileges.py: Change argument to User object rather
than UUID object
* gn3/auth/authorisation/roles.py: Use new authentication checking decorator.
* tests/unit/auth/test_groups.py: use `conftest.TEST_USER`
* tests/unit/auth/test_privileges.py: use `conftest.TEST_USER`
* tests/unit/auth/test_roles.py: use `conftest.TEST_USER`
| Frederick Muriuki Muriithi |
| 2022-11-24 | auth: Implement `create_resource` function...* gn3/auth/authentication/checks.py: new `authenticated_p` decorator to apply
on any function that requires the user to be authenticated before it runs.
* gn3/auth/authorisation/checks.py: use a `auth.authentication.users.User`
object rather than a UUID object in the global `g`.
* gn3/auth/authorisation/groups.py: Implement the `authenticated_user_group`
function to get the group(s) in which the currently authenticated user
belongs.
* gn3/auth/authorisation/resources.py: Implement the `create_resource`
function correctly.
* tests/unit/auth/conftest.py: extract the User objects into a global variable
for reusability with the tests.
* tests/unit/auth/test_resources.py: Use global user objects from conftest in
the tests. Set a User object (rather than UUID) in the global `g` variable.
| Frederick Muriuki Muriithi |
| 2022-11-24 | tests: Add test for `create_resource`...* gn3/auth/authorisation/resources.py: Define Resource and ResourceCategory
classes. Create the `create_resource` stub.
* tests/unit/auth/test_resources.py: test for `create_resource` function
| Frederick Muriuki Muriithi |
| 2022-11-21 | auth: 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 |
| 2022-11-17 | auth: 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 |
| 2022-11-17 | Migrations: 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 |
| 2022-11-17 | tests: 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 |
| 2022-11-17 | Tests: Make test failure messages clearer. | Frederick Muriuki Muriithi |
| 2022-11-17 | Migrations: 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 |
| 2022-11-17 | tests: test for addition of data to non-empty table | Frederick Muriuki Muriithi |
| 2022-11-16 | pylint: fix some linting errors | Frederick Muriuki Muriithi |
| 2022-11-16 | tests: 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 |
| 2022-11-16 | auth: 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 |
