| Age | Commit message (Expand) | Author |
|---|
| 2022-11-10 | Migrations: Add columns to 'privileges' table•••* 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
| Frederick Muriuki Muriithi |
| 2022-11-10 | Tests: Generalise tests for adding/removing columns to/from tables | Frederick Muriuki Muriithi |
| 2022-11-10 | Migrations: migration for `role_privileges` table•••* tests/unit/auth/test_create_table_migrations.py: new migration
* tests/unit/auth/test_migrations_indexes.py: test new migration
| Frederick Muriuki Muriithi |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-10 | Migrations: 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 |
| 2022-11-09 | Migrations: Add `resource_meta` field to `resource_categories` table | Frederick Muriuki Muriithi |
| 2022-11-09 | Tests: Provide backend fixture to (apply|rollback)_single_migration | Frederick Muriuki Muriithi |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Migrations: 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 |
| 2022-11-08 | Tests: Fix test name. | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: Fix typo: remove variable from quotes. | Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: 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 |
| 2022-11-08 | Tests: 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 |
| 2022-11-08 | Tests: Test migration to create user_credentials table•••* tests/unit/auth/test_create_user_credentials_table.py: new tests
| Frederick Muriuki Muriithi |
| 2022-11-08 | Tests: 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 |
| 2022-11-03 | Add 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 |
| 2022-11-03 | Rename migration test. | Frederick Muriuki Muriithi |
| 2022-11-03 | Initialise 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 |
| 2022-11-02 | Add tests for monadic_dict•••* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases
for MonadicDict.
| Munyoki Kilyungi |
| 2022-08-30 | Update test: include port in parsed data from mysql uri | Frederick Muriuki Muriithi |
| 2022-08-10 | update test;parse output | Alexander_Kabui |
| 2022-07-29 | Fix 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 |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui |
| 2022-07-22 | add unittests | Alexander_Kabui |
| 2022-06-29 | use explicit parameters | Alexander_Kabui |
| 2022-06-29 | fix issues | Alexander_Kabui |
| 2022-06-29 | lint test file | Alexander |
| 2022-06-29 | add tests | Alexander |
| 2022-06-29 | add test data | Alexander |
| 2022-06-29 | parse output data | Alexander |
| 2022-06-29 | init test correlation rust module | Alexander |
| 2022-06-21 | tests: 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 |
| 2022-06-21 | test_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 |
| 2022-06-21 | integration: test_gemma: Skip "GemmaAPITest" | BonfaceKilz |
| 2022-05-30 | Pass 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 |
| 2022-05-27 | Move sql for CRUD operations on case-attrs from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Move sql for modifying case-attributes from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Return 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 |
| 2022-05-26 | Add Endpoint to get menu items for use in UI | Frederick Muriuki Muriithi |
| 2022-05-05 | Extract common error checking. Rename function.•••* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
| Frederick Muriuki Muriithi |
| 2022-04-12 | Delete "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 |
| 2022-04-12 | Test 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 |
| 2022-04-07 | Use 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 |
