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2022-11-10Migrations: migration for 'generic_roles' table...* migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-10Migrations: migration for 'roles' table...* migrations/auth/20221110_05_BaNtL-create-roles-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 Frederick Muriuki Muriithi
2022-11-10Migrations: migration for 'genotype_resources' table...* migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for 'phenotype_resources' table...* migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for mrna_resources table...* migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration Frederick Muriuki Muriithi
2022-11-10Migrations: Add migration for 'resources' table...* gn3/migrations.py: Minor change * migrations/auth/20221110_01_WtZ1I-create-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-09Migrations: Add `resource_meta` field to `resource_categories` tableFrederick Muriuki Muriithi
2022-11-09Tests: Provide backend fixture to (apply|rollback)_single_migrationFrederick Muriuki Muriithi
2022-11-08Migrations: Improve `resource_categories` data tests....* tests/unit/auth/test_migration_init_data_in_resource_categories_table.py: Test that the data is initialised properly. Test that rollback works as expected. Frederick Muriuki Muriithi
2022-11-08Migrations: Init `resource_categories` with initial categories...* migrations/auth/20221108_04_CKcSL-init-data-in-resource-categories-table.py: new migration. * tests/unit/auth/test_migration_init_data_in_resource_categories_table.py: test new migration. Frederick Muriuki Muriithi
2022-11-08Migrations: Create `resource_categories` table....* migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py: new migration. * tests/unit/auth/test_create_table_migrations.py: test new migration. Frederick Muriuki Muriithi
2022-11-08Migrations: Create `privileges` table....* migrations/auth/20221108_02_wxTr9-create-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration Frederick Muriuki Muriithi
2022-11-08Tests: Fix test name.Frederick Muriuki Muriithi
2022-11-08Tests: Fix typo: remove variable from quotes.Frederick Muriuki Muriithi
2022-11-08Tests: Generalise testing 'CREATE TABLE' migrations...* gn3/settings.py: Omit trailing slash * tests/unit/auth/test_create_table_migrations.py: Generalise testing migrations that create tables. * tests/unit/auth/test_create_user_credentials_table.py: delete * tests/unit/auth/test_migration_create_users_table.py: delete Frederick Muriuki Muriithi
2022-11-08Tests: Tests the credentials check system...* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking Frederick Muriuki Muriithi
2022-11-08Tests: Test migration to create user_credentials table...* tests/unit/auth/test_create_user_credentials_table.py: new tests Frederick Muriuki Muriithi
2022-11-08Tests: Separate *ALL* unit test fixtures from auth-specific ones...* tests/unit/auth/conftest.py: add fixtures specific to auth * tests/unit/auth/test_migration_create_users_table.py: import from new fixtures module * tests/unit/conftest.py: remove auth-specific fixtures from *ALL* unit tests fixture module. Frederick Muriuki Muriithi
2022-11-03Add credentials checking...* gn3/auth/authentication.py: new function `credentials_in_database` * gn3/auth/authentication/__init__.py: replace package with module * gn3/settings.py: new `AUTH_MIGRATIONS` configuration variable * migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py: new migration * tests/unit/auth/test_credentials.py: test the `credentials_in_database` function * tests/unit/conftest.py: more test fixtures Frederick Muriuki Muriithi
2022-11-03Rename migration test.Frederick Muriuki Muriithi
2022-11-03Initialise the Auth(entic|oris)ation packages...Initialise the authentication/authorisation system packages and set up the initial database migrations to set up the system. * README.md: Add documentation on migrations * gn3/auth/__init__.py: init package * gn3/auth/authentication/__init__.py: init package * gn3/auth/authorisation/__init__.py: init package * gn3/migrations.py: provide migration utilities * migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py: new migration * tests/unit/auth/test_init_database.py: test new migration applies and rolls back as expected * tests/unit/conftest.py: fixtures for unit tests * yoyo.auth.ini: basic configuration for yoyo-migration for auth system migrations Frederick Muriuki Muriithi
2022-11-02Add tests for monadic_dict...* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases for MonadicDict. Munyoki Kilyungi
2022-08-30Update test: include port in parsed data from mysql uriFrederick Muriuki Muriithi
2022-08-10update test;parse outputAlexander_Kabui
2022-07-29Fix failing tests...* gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function Frederick Muriuki Muriithi
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22add unittestsAlexander_Kabui
2022-06-29use explicit parametersAlexander_Kabui
2022-06-29fix issuesAlexander_Kabui
2022-06-29lint test fileAlexander
2022-06-29add testsAlexander
2022-06-29add test dataAlexander
2022-06-29parse output dataAlexander
2022-06-29init test correlation rust moduleAlexander
2022-06-21tests: test_file_utils: Replace pytest.mark.skip with unittest.skip..."python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3. BonfaceKilz
2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto. BonfaceKilz
2022-05-30Pass trait data as args to `fix_strains` and fix some bugs...The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function. Frederick Muriuki Muriithi
2022-05-27Move sql for CRUD operations on case-attrs from gn2 to gn3BonfaceKilz
2022-05-27Move sql for modifying case-attributes from gn2 to gn3BonfaceKilz
2022-05-27Return all the results from CaseAttributes column as is...* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import. (get_case_attributes): Return the results of "fetchall" from the case attributes. * tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing test. BonfaceKilz
2022-05-26Add Endpoint to get menu items for use in UIFrederick Muriuki Muriithi
2022-04-12Delete "get_allowable_sampledata_headers"...* gn3/csvcmp.py (get_allowable_sampledata_headers): Delete it. * tests/unit/test_csvcmp.py: Remove "get_allowable_sampledata_headers" import. (test_get_allowable_csv_headers): Delete it. BonfaceKilz
2022-04-12Test that a carriage return is removed when generating csv...* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data". (test_get_trait_csv_sample_data): New test function. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to capture the above. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to capture the above. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during updates...* gn3/db/sample_data.py: Import "parse_csv_column". (update_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to capture the above. BonfaceKilz
2022-04-07Add method for fetching the case_attributes...* gn3/db/sample_data.py (get_case_attributes): New function. * tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for the above. BonfaceKilz
2022-04-07Add method for parsing a csv header from uploaded sample-data file...* gn3/csvcmp.py (parse_csv_column): New function. * tests/unit/test_csvcmp.py: Test case for the above. BonfaceKilz
2022-04-01Run python-black in file...* gn3/csvcmp.py: Run "black -l 79 ..." * tests/unit/db/test_sample_data.py: Ditto. * tests/unit/test_csvcmp.py: Ditto. BonfaceKilz