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2023-04-25auth: Roles: Check for editability...Some roles should not be user-editable, and as such, we need to check before allowing any edits on such roles. This commit makes that possible. Frederick Muriuki Muriithi
2023-04-10Migrations for linking genotype files.Frederick Muriuki Muriithi
2023-04-06Fix linting issuesFrederick Muriuki Muriithi
2023-04-06Remove deprecated `gn3.db_utils.database_connector` function...Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils Frederick Muriuki Muriithi
2023-04-04Add tables to link genotype dataFrederick Muriuki Muriithi
2023-03-23tests: Set up fixture and mock out config variableFrederick Muriuki Muriithi
2023-03-22auth: Remove the tables used for linking data to resources...The way data is linked to the resources needs to be reworked. This commit removes all the existing migration scripts that created the tables formerly used for linking data in preparation for reworking the system. Frederick Muriuki Muriithi
2023-03-20Fix get_all_species testzsloan
2023-03-09auth: redis data: migrate data in redis...Implement the code to migrate the data from redis to SQLite. Frederick Muriuki Muriithi
2023-03-08auth: users: Use the same basic functions for password hashing...To avoid repeating the same thing in multiple places, leading to errors and breakages, reuse the same basic functions for password hashing. Frederick Muriuki Muriithi
2023-03-06auth: privileges/roles: fix issues caught by tests.Frederick Muriuki Muriithi
2023-02-21auth: 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
2023-02-10Return 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
2023-02-08auth: 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 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
2023-01-24tests: 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
2023-01-24search: 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
2023-01-23auth: 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
2023-01-21tests: roles - Extract values from Maybe objectFrederick Muriuki Muriithi
2023-01-21tests: Fix linting errorsFrederick Muriuki Muriithi
2023-01-19tests: Add unit tests for search....* tests/unit/test_search.py: New file. Arun Isaac
2023-01-18auth: 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
2023-01-16auth: 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
2023-01-11auth: 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
2023-01-03auth: 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
2023-01-03auth: 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
2022-12-22tests: 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
2022-12-22auth: 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_flowFrederick Muriuki Muriithi
2022-12-21migrations: 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
2022-12-21migrations: 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
2022-12-21migrations: 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
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts....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 Frederick Muriuki Muriithi
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 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
2022-12-08auth: 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
2022-12-08tests: 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
2022-12-08auth: 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
2022-12-08auth: 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
2022-12-08migrations: 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
2022-12-06migrations: 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
2022-12-06mypy 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 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
2022-11-24auth: 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