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2022-11-10Migrations: Add migration for 'phenotype_resources' tableFrederick Muriuki Muriithi
* migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
2022-11-10Migrations: Add migration for mrna_resources tableFrederick Muriuki Muriithi
* migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
2022-11-10Migrations: Add migration for 'resources' tableFrederick Muriuki Muriithi
* 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
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.Frederick Muriuki Muriithi
* 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.
2022-11-08Migrations: Init `resource_categories` with initial categoriesFrederick Muriuki Muriithi
* 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.
2022-11-08Migrations: Create `resource_categories` table.Frederick Muriuki Muriithi
* migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py: new migration. * tests/unit/auth/test_create_table_migrations.py: test new migration.
2022-11-08Migrations: Create `privileges` table.Frederick Muriuki Muriithi
* migrations/auth/20221108_02_wxTr9-create-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
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' migrationsFrederick Muriuki Muriithi
* 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
2022-11-08Tests: Tests the credentials check systemFrederick Muriuki Muriithi
* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking
2022-11-08Tests: Test migration to create user_credentials tableFrederick Muriuki Muriithi
* tests/unit/auth/test_create_user_credentials_table.py: new tests
2022-11-08Tests: Separate *ALL* unit test fixtures from auth-specific onesFrederick Muriuki Muriithi
* 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.
2022-11-03Add credentials checkingFrederick Muriuki Muriithi
* 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
2022-11-03Rename migration test.Frederick Muriuki Muriithi
2022-11-03Initialise the Auth(entic|oris)ation packagesFrederick Muriuki Muriithi
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
2022-11-02Add tests for monadic_dictMunyoki Kilyungi
* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases for MonadicDict.
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 testsFrederick Muriuki Muriithi
* 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
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.skipBonfaceKilz
"python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3.
2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"BonfaceKilz
* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto.
2022-05-30Pass trait data as args to `fix_strains` and fix some bugsFrederick Muriuki Muriithi
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.
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 isBonfaceKilz
* 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.
2022-05-26Add Endpoint to get menu items for use in UIFrederick Muriuki Muriithi
2022-04-12Delete "get_allowable_sampledata_headers"BonfaceKilz
* 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.
2022-04-12Test that a carriage return is removed when generating csvBonfaceKilz
* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data". (test_get_trait_csv_sample_data): New test function.
2022-04-07Use case attribute id inside brackets if present during insertionsBonfaceKilz
* 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.
2022-04-07Use case attribute id inside brackets if present during insertionsBonfaceKilz
* 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.
2022-04-07Use case attribute id inside brackets if present during updatesBonfaceKilz
* 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.
2022-04-07Add method for fetching the case_attributesBonfaceKilz
* 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.
2022-04-07Add method for parsing a csv header from uploaded sample-data fileBonfaceKilz
* gn3/csvcmp.py (parse_csv_column): New function. * tests/unit/test_csvcmp.py: Test case for the above.
2022-04-01Run python-black in fileBonfaceKilz
* gn3/csvcmp.py: Run "black -l 79 ..." * tests/unit/db/test_sample_data.py: Ditto. * tests/unit/test_csvcmp.py: Ditto.
2022-03-18Clean all csv fields before diffingBonfaceKilz
There was a subtle bug where "csvdiff" generated an error related to "different column headings" caused something akin to diffing: "a, b \n, ..." with "a, b\n, ...". * gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing. * tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to capture aforementioned bug.
2022-03-18Create new function for cleaning individual fields in csv textBonfaceKilz
* gn3/csvcmp.py (clean_csv_text): New function. * tests/unit/test_csvcmp.py: Import "csv_text". (test_clean_csv_text): Test case for the above.
2022-03-15Feature/refactored pca (#79)Alexander Kabui
* compute zscore function * test case for computing zscore * function to compute pca * generate scree plot data * generate new pca trait data from zscores and eigen_vec * remove redundant functions * generate factor loading table data * generate pca temp dataset dict * variable naming and error fixes * unit test for processing factor loadings * minor fixes for generating temp pca dataset * pass datetime as argument to generate_pca temp dataset function * add unittest for caching pca datasets * cache temp datasets * ignore missing imports for sklearn * mypy fixes * pylint fixes * refactor tests for pca * remove ununsed imports * fix for generating pca traits vals * mypy and code refactoring * pep8 formatting and add docstrings * remove comments /pep8 formatting * sort eigen vectors based on eigen values * minor fix for zscores * fix for rounding variance ratios * refactor tests * rename module to pca * rename datasets to traits * fix failing tests * fix caching function * fixes return x and y coordinates for scree plot * expand exception scope * fix for deprecated numpy.matrix function * fix for failing tests * pep8 fixes * remove comments * fix merge conflict * pylint fixes * rename module name to test_pca
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