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2022-12-23Update how to set configurations in READMEzsloan
2022-12-23Add a couple necessary environment variableszsloan
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
2022-12-21auth: oauth2: users: Add expected propertyFrederick Muriuki Muriithi
* gn3/auth/authentication/users.py: authlib expects the user object to have a `get_user_id` method.
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
2022-12-21auth: Add default row_factory to sqlite3Frederick Muriuki Muriithi
* gn3/auth/db.py: For easier setting up of objects after querying, set the default row_factory object that allows indexing by database field name.
2022-12-21Enable authenticationFrederick Muriuki Muriithi
* gn3/auth/authentication/routes.py: Add `/login` endpoint and a function to validate the login credentials. * gn3/auth/authentication/users.py: add function to fetch user details by email
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
2022-12-12auth: functions to get user resourcesFrederick Muriuki Muriithi
* gn3/auth/authorisation/resources.py: add function to get the resources that the user has access to.
2022-12-12tests: Update fixtures to use for testing resources functionsFrederick Muriuki Muriithi
2022-12-12auth: Add a way to check whether a user is a group leaderFrederick Muriuki Muriithi
* gn3/auth/authorisation/groups.py: Add `is_group_leader` function
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
2022-12-08Remove unused importFrederick Muriuki Muriithi
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
2022-12-06Use a dataset's name to fetch it's metadata from RDFMunyoki Kilyungi
* gn3/api/metadata.py (jsonify_dataset_metadata): Rewrite metadata end-point to use a dataset's name instead of it's accession_id. * gn3/db/rdf.py (get_dataset_metadata): Replace accession_id with name. Use one single RDF query instead of multiple queries.
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
2022-12-02correlations: return `None` rather than zero for missing lit corrsFrederick Muriuki Muriithi
* gn3/computations/correlations.py: Return `None` for missing literature correlations rather than zero. Update the sorting key to avoid issues with comparing floats to NoneType objects
2022-11-29remove trailing whitespaceAlexanderKabui
2022-11-29remove unused function parameterAlexanderKabui
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.
2022-11-28Catch a URLError when virtuoso isn't running at allMunyoki Kilyungi
* gn3/api/metadata.py: Import URLError. (jsonify_dataset_metadata): Add URLError in except block.
2022-11-28Fix pylint errorsMunyoki Kilyungi
* gn3/api/general.py: Delete rdf import. Delete trailing white spaces. * gn3/api/metadata.py: Delete trailing white spaces.
2022-11-28Fail gracefully when virtuoso is not accessibleMunyoki Kilyungi
* gn3/api/metadata.py: import RemoteDisconnected. (jsonify_dataset_metadata): Wrap get_dataset_metadata in try block.
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.
2022-11-24auth: Define base exceptionsFrederick Muriuki Muriithi
* gn3/auth/authentication/exceptions.py: define `AuthenticationError` * gn3/auth/authorisation/exceptions.py: define `AuthorisationError`
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
2022-11-23Create a new REST endpoint for fetching a phenotype's metadataMunyoki Kilyungi
* gn3/api/general.py: (dataset_metadata) Delete. * gn3/api/metadata.py: Import Blueprint, jsonify, current_app, SPARQLWrapper and get_dataset_metadata. (metadata): New Blueprint (jsonify_dataset_metadata): New function/end-point. * gn3/app.py: Import metadata (create_app): Register metadata blueprint.
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
2022-11-17auth: Define the `User` typeFrederick Muriuki Muriithi
* gn3/auth/authentication.py -> gn3/auth/authentication/__init__.py: Convert module to package * gn3/auth/authentication/users.py: Define the `User` type
2022-11-17Tests: Make test failure messages clearer.Frederick Muriuki Muriithi
2022-11-17Migrations: Add column `group_role_id` to `group_roles` tableFrederick Muriuki Muriithi
* 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
2022-11-17tests: test for addition of data to non-empty tableFrederick Muriuki Muriithi
2022-11-16pylint: fix some linting errorsFrederick Muriuki Muriithi
2022-11-16tests: Add tests for privilegesFrederick Muriuki Muriithi
* 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
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