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2023-03-20Fix get_all_species testzsloan
2023-03-09auth: redis data: migrate data in redisFrederick Muriuki Muriithi
Implement the code to migrate the data from redis to SQLite.
2023-03-08auth: users: Use the same basic functions for password hashingFrederick Muriuki Muriithi
To avoid repeating the same thing in multiple places, leading to errors and breakages, reuse the same basic functions for password hashing.
2023-03-06auth: privileges/roles: fix issues caught by tests.Frederick Muriuki Muriithi
2023-02-21auth: migrations: Link to data in main dbFrederick Muriuki Muriithi
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.
2023-02-10Return empty tuple rather than NothingFrederick Muriuki Muriithi
When user has no roles assigned, return an empty tuple rather than pymonad.maybe.Nothing to ease maintenance.
2023-02-08auth: groups: handle join requests.Frederick Muriuki Muriithi
2023-02-07auth: groups: Enable users to request to join group.Frederick Muriuki Muriithi
2023-02-06auth: resource: Enable viewing the details of a resource.Frederick Muriuki Muriithi
2023-02-03auth: tests: mock token acquisition. Fix minor bugs.Frederick Muriuki Muriithi
2023-02-02auth: Reorganise modules/packages for easier dev and maintenanceFrederick Muriuki Muriithi
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.
2023-01-24tests: Expect exact integer value when applying SI suffix.Arun Isaac
* 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.
2023-01-24search: Abstract out parsing of position spec into separate function.Arun Isaac
* 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.
2023-01-23auth: create group: Fix group creation.Frederick Muriuki Muriithi
* 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
2023-01-21tests: roles - Extract values from Maybe objectFrederick Muriuki Muriithi
2023-01-21tests: Fix linting errorsFrederick Muriuki Muriithi
2023-01-19tests: Add unit tests for search.Arun Isaac
* tests/unit/test_search.py: New file.
2023-01-18auth: Fix tests after enforcing FOREIGN KEY constraintFrederick Muriuki Muriithi
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
2023-01-16auth: update privileges formatFrederick Muriuki Muriithi
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
2023-01-11auth: assign default role. separate group creation from group adminFrederick Muriuki Muriithi
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
2023-01-03auth: Fetch all of a user's roles.Frederick Muriuki Muriithi
* 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
2023-01-03auth: rename fixtures: test_* -> fxtr_*Frederick Muriuki Muriithi
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.
2022-12-22tests: Setup environment variables and configsFrederick Muriuki Muriithi
* 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.
2022-12-22auth: implement OAuth2 flow.oauth2_auth_flowFrederick Muriuki Muriithi
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
2022-12-21migrations: create the authorisation_code tableFrederick Muriuki Muriithi
* migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py: new migration * tests/unit/auth/test_migrations_create_tables.py: test new migration
2022-12-21migrations: create oauth2_tokens tableFrederick Muriuki Muriithi
* migrations/auth/20221219_02_buSEU-create-oauth2-tokens-table.py * tests/unit/auth/test_migrations_create_tables.py
2022-12-21migrations: New migrationFrederick Muriuki Muriithi
* migrations/auth/20221219_01_CI3tN-create-oauth2-clients-table.py: New migration * tests/unit/auth/test_migrations_create_tables.py: tests for new migration
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.Frederick Muriuki Muriithi
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import
2022-12-12tests: Update fixtures to use for testing resources functionsFrederick Muriuki Muriithi
2022-12-12auth: pass cursor object to `user_group` functionFrederick Muriuki Muriithi
2022-12-12auth: Attach group to GroupRole, rather than group_idFrederick Muriuki Muriithi
2022-12-12tests: Reorganise fixturesFrederick Muriuki Muriithi
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
2022-12-08auth: test for `user_resources` function (incomplete)Frederick Muriuki Muriithi
* 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
2022-12-08tests: Fix issues caught by testsFrederick Muriuki Muriithi
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
2022-12-08auth: add test to retrieve public resourcesFrederick Muriuki Muriithi
* 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
2022-12-08auth: add function to retrieve a user's groupFrederick Muriuki Muriithi
* gn3/auth/authorisation/groups.py: new `user_group` function * tests/unit/auth/test_groups.py: test `user_group` function
2022-12-08migrations: Add column `public` to `resources` tableFrederick Muriuki Muriithi
* 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
2022-12-06migrations: Add `group_user_roles_on_resources` tableFrederick Muriuki Muriithi
* 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
2022-12-06mypy and pylint fixesAlexander_Kabui
2022-12-06remove noisy tests for constant array correlationAlexander_Kabui
2022-12-06update tests for lit correlationAlexander_Kabui
2022-11-29tests: fix failing testFrederick Muriuki Muriithi
* tests/unit/computations/test_rust_correlation.py: The underlying code changed and the test needed to be updated to test the correct thing.
2022-11-24auth: Check for authentication and fix errorsFrederick Muriuki Muriithi
* 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`
2022-11-24auth: Implement `create_resource` functionFrederick Muriuki Muriithi
* 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.
2022-11-24tests: Add test for `create_resource`Frederick Muriuki Muriithi
* 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
2022-11-21auth: Prevent group leader from being a member of multiple groupsFrederick Muriuki Muriithi
* 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.
2022-11-17auth: Finish implementation of `create_group_role`Frederick Muriuki Muriithi
* 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.
2022-11-17Migrations: Create `group_users` tableFrederick Muriuki Muriithi
* 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
2022-11-17tests: Add test to check creation of roles attached to groupsFrederick Muriuki Muriithi
* tests/unit/auth/conftest.py: Add fixtures to help with testing * tests/unit/auth/test_groups.py: Add incomplete and failing test
2022-11-17Tests: Make test failure messages clearer.Frederick Muriuki Muriithi
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