| Age | Commit message (Expand) | Author |
|---|
| 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 | Use a dataset's name to fetch it's metadata from RDF...* 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.
| Munyoki Kilyungi |
| 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 |
| 2022-12-02 | correlations: return `None` rather than zero for missing lit corrs...* 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
| Frederick Muriuki Muriithi |
| 2022-11-29 | remove trailing whitespace | AlexanderKabui |
| 2022-11-29 | remove unused function parameter | AlexanderKabui |
| 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 |
| 2022-11-28 | Catch a URLError when virtuoso isn't running at all...* gn3/api/metadata.py: Import URLError.
(jsonify_dataset_metadata): Add URLError in except block.
| Munyoki Kilyungi |
| 2022-11-28 | Fix pylint errors...* gn3/api/general.py: Delete rdf import. Delete trailing white
spaces.
* gn3/api/metadata.py: Delete trailing white spaces.
| Munyoki Kilyungi |
| 2022-11-28 | Fail gracefully when virtuoso is not accessible...* gn3/api/metadata.py: import RemoteDisconnected.
(jsonify_dataset_metadata): Wrap get_dataset_metadata in try block.
| Munyoki Kilyungi |
| 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 | auth: Define base exceptions...* gn3/auth/authentication/exceptions.py: define `AuthenticationError`
* gn3/auth/authorisation/exceptions.py: define `AuthorisationError`
| 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 |
| 2022-11-23 | Create a new REST endpoint for fetching a phenotype's metadata...* 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.
| Munyoki Kilyungi |
| 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 | auth: Define the `User` type...* gn3/auth/authentication.py -> gn3/auth/authentication/__init__.py: Convert
module to package
* gn3/auth/authentication/users.py: Define the `User` type
| 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 |
| 2022-11-16 | tests: Test role creation...* tests/unit/auth/test_roles.py: new tests.
| Frederick Muriuki Muriithi |
| 2022-11-16 | Inject SPARQLWrapper as a parameter...* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import.
(sparql_query): Inject SPARQLWrapper.
(get_dataset_metadata): Ditto.
| Munyoki Kilyungi |
| 2022-11-15 | auth: Add `create_group_role` function. | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Return results of calling function directly...* 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
| Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Specify types for privileges, roles, groups...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.
| Frederick Muriuki Muriithi |
| 2022-11-15 | Add missing module __init__.py to mitigate the mypy errors | Frederick Muriuki Muriithi |
| 2022-11-15 | pylint: Fix a myriad of linting errors | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Add some typing information to the functions | Frederick Muriuki Muriithi |
| 2022-11-15 | auth: Reorganise package - move function to `checks` module...* gn3/auth/authorisation/__init__.py: delete function
* gn3/auth/authorisation/checks.py: move function to `checks` module
| Frederick Muriuki Muriithi |
| 2022-11-15 | pylint: Fix linting errors. | Frederick Muriuki Muriithi |
| 2022-11-15 | tests: typo: fix migration script file name | Frederick Muriuki Muriithi |
| 2022-11-15 | tests: Use `gn3.auth.db` functions for db connection and cursor...* 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.
| Frederick Muriuki Muriithi |
| 2022-11-15 | tests: Fix cause of `DeprecationWarning`...* 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`.
| Frederick Muriuki Muriithi |
| 2022-11-14 | auth: Implement `create_group` | Frederick Muriuki Muriithi |
| 2022-11-14 | tests: split test app and test client...* The test app and the test client are both needed as fixtures in different
places
| Frederick Muriuki Muriithi |
| 2022-11-14 | Migrations: Create `user_roles` table...* 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
| Frederick Muriuki Muriithi |
| 2022-11-14 | auth: Add test for `create_group`...* 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`
| Frederick Muriuki Muriithi |
