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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
2023-01-18auth: Enable FOREIGN KEY constraint for the connectionsFrederick Muriuki Muriithi
Enable the FOREIGN KEY constraints for the connections to the database to help with queries that would otherwise lead to data corruption.
2023-01-18Tolerate WEIGHT operator in parsed search queries.Arun Isaac
* gn3/api/search.py (remove_synteny_field): Tolerate WEIGHT operator in parsed search queries.
2023-01-18Implement synteny search.Arun Isaac
* gn3/api/search.py: Import gzip, Path from pathlib and curry from pymonad.tools. (IntervalLiftoverFunction): New variable. (query_subqueries, query_terms, field_processor_or, liftover, liftover_interval, parse_synteny_field, is_synteny_on, remove_synteny_field): New functions. (parse_location_field): Generalize to support synteny searches. (parse_query): Support synteny search queries. (search_results): Pass synteny files directory to parse_query.
2023-01-18Support location shorthands in search queries.Arun Isaac
* gn3/api/search.py: Import partial and reduce from functools. Import Callable from typing. (ChromosomalPosition, ChromosomalInterval, FieldProcessor): New classes. (apply_si_suffix, combine_queries, parse_location_field, interval_start, interval_end): New functions. (parse_query): Add field processors for location shorthands.
2023-01-18Split off search query parsing into separate function.Arun Isaac
* gn3/api/search.py (parse_query): New function. (search_results): Use parse_query.
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
2023-01-11auth: Add missing importFrederick Muriuki Muriithi
2023-01-05auth: Persist the user's registration detailsFrederick Muriuki Muriithi
If the registration details pass the validations steps, then persist the details in the database and respond with details about the newly created user. * gn3/auth/authentication/users.py: new functions * `save_user`: create and persist a new user * `set_user_password`: hash and persist the new password for the given user * gn3/auth/authorisation/views.py: Persist the user details and respond with the newly persisted user details.
2023-01-04auth: Add `/register-user` endpointFrederick Muriuki Muriithi
* gn3/app.py: register top-level error handlers. reorganise oauth2 blueprint. * gn3/auth/__init__.py: reorganise oaut2 blueprint. * gn3/auth/authentication/oauth2/views.py: reorganise oauth2 blueprint. * gn3/auth/authorisation/exceptions.py -> gn3/auth/authorisation/errors.py * gn3/auth/authorisation/groups.py: rename file/module * gn3/auth/authorisation/resources.py: rename file/module * gn3/auth/authorisation/views.py: Add `/register-user` endpoint * gn3/auth/blueprint.py: reorganise oauth2 blueprint. * gn3/errors.py: register top-level error handlers.
2023-01-04auth: return group info as part of user detailsFrederick Muriuki Muriithi
* gn3/app.py: import blueprint from authorisation views inorder to get all endpoints * gn3/auth/authentication/oauth2/views.py: remove the `/user` endpoint * gn3/auth/authorisation/views.py: add the `/user` endpoint and add the group information to the user details.
2023-01-04auth: Return only non-resource roles on `/user-roles` endpointFrederick Muriuki Muriithi
Resource roles will be returned as part of the resources request. * gn3/auth/authorisation/roles.py: Simplify query - only get non-resource roles * gn3/auth/authorisation/views.py: update docstring
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
2022-12-28auth: Add resource server and /user endpointFrederick Muriuki Muriithi
Add a resource server with the validator for the bearer token to protect the resources endpoints. Add a protected `/user` endpoint that returns the user details for valid tokens. * gn3/auth/authentication/oauth2/resource_server.py: new file * gn3/auth/authentication/oauth2/views.py: add /user endpoint
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.
2022-12-21auth: 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.
2022-12-12auth: 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
2022-12-08Remove 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
2022-12-06Use 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.
2022-12-06mypy and pylint fixesAlexander_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
2022-11-28Catch 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.
2022-11-17auth: 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
2022-11-16auth: 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
2022-11-16Inject 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
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