Correlations: Remove top_n argument
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* 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
* 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.
* tests/unit/auth/test_create_user_credentials_table.py: new tests
* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking
* main.py: Provide the `apply-migrations` CLI command to run the migrations
against the auth database.
The command can be invoked with:
$ flask apply-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
* migrations/auth/20221108_02_wxTr9-create-privileges-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
* migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py: new migration. * tests/unit/auth/test_create_table_migrations.py: test new migration.
* 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.
* 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.
selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again.
* 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
* migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
* migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test for new migration
* migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
* 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
* migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py: new migration * tests/unit/auth/test_create_table_migrations.py: test new migration
* tests/unit/auth/test_create_table_migrations.py: new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
* migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py: new migration Commit ee72678 only contains tests for this migration.
* 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
* .gitignore: ignore all yoyo configuration files * README.md: Update documentation * yoyo.auth.ini: stop tracking the yoyo configuration file.
* migrations/auth/20221113_01_7M0hv-enumerate-initial-privileges.py: new migration. * tests/unit/auth/test_migrations_insert_data_into_empty_table.py: test new migration.
Add table `generic_role_privileges` table to link the generic roles to the privileges they provide. * migrations/auth/20221114_01_n8gsF-create-generic-role-privileges-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
* gn3/auth/authorisation/__init__.py: delete function * gn3/auth/authorisation/checks.py: move function to `checks` module
Use specified types for privileges, roles and types rather than using strings to help with limiting bugs. * gn3/auth/authorisation/groups.py: Specify and use the `Group` type * gn3/auth/authorisation/privileges.py: Specify and use the `Privilege` type * gn3/auth/authorisation/roles.py: Specify the `Role` type. Add the `create_role` function.
* 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
* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto.
* tests/unit/auth/test_roles.py: new tests.
* 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
* migrations/auth/20221116_01_nKUmX-add-privileges-to-group-leader-role.py: new migration to fix data errors. * tests/unit/auth/test_privileges.py: test privileges
* migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py: new migration * tests/unit/auth/test_migrations_add_remove_columns.py: test new migration
* gn3/auth/authentication.py -> gn3/auth/authentication/__init__.py: Convert module to package * gn3/auth/authentication/users.py: Define the `User` type
* tests/unit/auth/conftest.py: Add fixtures to help with testing * tests/unit/auth/test_groups.py: Add incomplete and failing test
* migrations/auth/20221117_02_fmuZh-create-group-users-table.py: new migration * tests/unit/auth/test_migrations_create_tables.py: test new migration * tests/unit/auth/test_migrations_indexes.py: test new migration
* 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.
* 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.
The `top_n` argument is used to pick the top `n` results of the computation, but in this function, it is way too early to do that, since you need to run filters against the computation results before you pick the results. * gn3/computations/rust_correlation.py: Remove `top_n` argument
BonfaceKilz
approved these changes
Nov 25, 2022
|
The metadata fetching issue probably needs to be resolved before this is
merged; currently I think it will always result in metadata being fetched
for the entire target dataset (even if we decide to do this when using the
filtering options, the filtering options usually aren't used, so it doesn't
make sense to fetch all the metadata in those situations).
…On Fri, Nov 25, 2022 at 7:18 AM BonfaceKilz ***@***.***> wrote:
***@***.**** approved this pull request.
Nothing seems off to me with this. You could have this merged if you are
happy with it.
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The
top_nargument is used to pick the topnresults of the computation, but in this function, it is way too early to do that, since you need to run filters against the computation results before you pick the results.top_nargument