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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
2022-11-16auth: fix bugs in the codeFrederick Muriuki Muriithi
* 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
2022-11-16tests: Test role creationFrederick Muriuki Muriithi
* tests/unit/auth/test_roles.py: new tests.
2022-11-16Inject SPARQLWrapper as a parameterMunyoki Kilyungi
* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto.
2022-11-15auth: Add `create_group_role` function.Frederick Muriuki Muriithi
2022-11-15auth: Return results of calling function directlyFrederick Muriuki Muriithi
* gn3/auth/authorisation/checks.py: Return results of calling the function rather than a dict of values that include the results. * gn3/auth/authorisation/groups.py: Use the newer form of `authorised_p` decorator. * tests/unit/auth/test_groups.py: Update tests
2022-11-15auth: Specify types for privileges, roles, groupsFrederick Muriuki Muriithi
Use specified types for privileges, roles and types rather than using strings to help with limiting bugs. * gn3/auth/authorisation/groups.py: Specify and use the `Group` type * gn3/auth/authorisation/privileges.py: Specify and use the `Privilege` type * gn3/auth/authorisation/roles.py: Specify the `Role` type. Add the `create_role` function.
2022-11-15Add missing module __init__.py to mitigate the mypy errorsFrederick Muriuki Muriithi
2022-11-15pylint: Fix a myriad of linting errorsFrederick Muriuki Muriithi
2022-11-15auth: Add some typing information to the functionsFrederick Muriuki Muriithi
2022-11-15auth: Reorganise package - move function to `checks` moduleFrederick Muriuki Muriithi
* gn3/auth/authorisation/__init__.py: delete function * gn3/auth/authorisation/checks.py: move function to `checks` module
2022-11-15pylint: Fix linting errors.Frederick Muriuki Muriithi
2022-11-15tests: typo: fix migration script file nameFrederick Muriuki Muriithi
2022-11-15tests: Use `gn3.auth.db` functions for db connection and cursorFrederick Muriuki Muriithi
* 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.
2022-11-15tests: Fix cause of `DeprecationWarning`Frederick Muriuki Muriithi
* 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`.
2022-11-14auth: Implement `create_group`Frederick Muriuki Muriithi
2022-11-14tests: split test app and test clientFrederick Muriuki Muriithi
* The test app and the test client are both needed as fixtures in different places
2022-11-14Migrations: Create `user_roles` tableFrederick Muriuki Muriithi
* 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
2022-11-14auth: Add test for `create_group`Frederick Muriuki Muriithi
* 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`
2022-11-14Migrations: Add `user_editable` field to roles tableFrederick Muriuki Muriithi
Some roles will not be user editable to prevent inconsistencies, and possible privilege escalation. * migrations/auth/20221110_05_BaNtL-create-roles-table.py: Add `user_editable` column to table * migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py: Set `group-leader` role as not user editable
2022-11-14Migrations: Create the `group-leader` role and give it privilegesFrederick Muriuki Muriithi
* 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
2022-11-14Migrations: Create `group_roles` tableFrederick Muriuki Muriithi
* 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
2022-11-14Migrations: Drop `generic_role*` tablesFrederick Muriuki Muriithi
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
2022-11-14Rename files for consistencyFrederick Muriuki Muriithi
* Name all tests that test migrations to start with `test_migrations_`
2022-11-14Migrations: Add generic_role_privileges tableFrederick Muriuki Muriithi
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
2022-11-14Migrations: Migration for initial privilegesFrederick Muriuki Muriithi
* 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.
2022-11-13Documentation: Explain how to run migrationsFrederick Muriuki Muriithi
* .gitignore: ignore all yoyo configuration files * README.md: Update documentation * yoyo.auth.ini: stop tracking the yoyo configuration file.
2022-11-10Migrations: Add columns to 'privileges' tableFrederick Muriuki Muriithi
* 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
2022-11-10Tests: Generalise tests for adding/removing columns to/from tablesFrederick Muriuki Muriithi
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