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2024-01-17fix pylint errorsAlexander_Kabui
2024-01-17temp fix:disable pylint checkAlexander_Kabui
2024-01-17Feature/gn llm refactoring (#147)...* refactor code for processing response from fahamu client * Add tests for gn-llmAlexander Kabui
2023-10-10Remove authentication from GN3...Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system. Frederick Muriuki Muriithi
2023-09-05Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove pylint skip...* gn3/auth/authentication/oauth2/models/oauth2token.py (introspect_token, check_permission): Delete "pylint: disable=[no-self-use]". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py (delete_authorization_code): Ditto. * tests/unit/test_heatmaps.py (test_cluster_traits): Delete "pylint: disable=R0201". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * tests/unit/computations/test_partial_correlations.py (test_tissue_correlation): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove unused import...* tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Delete IPFS tests...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit, test_cache_ipfs_file_cache_miss): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-17Fix tests to work with changeszsloan
2023-08-04Remove unused importFrederick Muriuki Muriithi
2023-08-04Remove tests for deleted function.Frederick Muriuki Muriithi
2023-08-02Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it being used in the code down the line. Frederick Muriuki Muriithi
2023-08-02Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone` so as to prevent theirs use in the code moving forward. Frederick Muriuki Muriithi
2023-07-19Extract code dealing with ProbeSets to their own module.Frederick Muriuki Muriithi
2023-07-11Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07. Frederick Muriuki Muriithi
2023-07-05Skip tests broken by Python-3.10 temporarily...Skip the tests that have been broken by the migrations to Python-3.10 temporarily, until we can fix them. Frederick Muriuki Muriithi
2023-07-05Update test: create throw-away variable...* Commit `b529c700` changes the return value to a tuple of values rather than a single string value. Handle that in the test. Frederick Muriuki Muriithi
2023-05-30Fix linting errors and failing tests...* scripts/register_sys_admin.py: fix linting error * tests/unit/auth/fixtures/oauth2_client_fixtures.py: hash client secret in database. The code expects it hashed in the database. Frederick Muriuki Muriithi
2023-05-25Set whether resource is publicly viewable on creationFrederick Muriuki Muriithi
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