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* gn3/auth/authorisation/__init__.py: delete function
* gn3/auth/authorisation/checks.py: move function to `checks` module
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* gn3/auth/authorisation/__init__.py: Add `authorised_p` decorator to be used
for all function requiring authorisation.
* gn3/auth/authorisation/groups.py: Add `create_group` function stub
* tests/unit/auth/conftest.py: Add fixture for test users
* tests/unit/auth/test_groups.py: Add tests for `create_group`
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* 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
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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.
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* 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
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* gn3/auth/authentication.py: Fix issues caught by tests
* tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials
checking
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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
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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
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* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf.
(dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with
rdf.get_dataset_metadata.
* gn3/db/datasets.py: Remove unused imports.
(sparql_query, dataset_metadata): Delete.
* gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
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* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query
directly to cursor.execute. Rename value to _value in for loop to
make mypy pass.
* gn3/db_utils.py (Connection): Add class docstring.
(Connection.cursor): Add docstring.
* mypy.ini: Add an entry for xapian.
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App settings should be accessed from current_app. It should not be hard-coded
to a variable in a module.
* gn3/db_utils.py: Do not import XAPIAN_DB_PATH from gn3.settings.
(xapian_database): Accept path argument.
* gn3/api/search.py: Import current_app from flask.
(search_results): Pass Xapian index path to xapian_database.
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* gn3/db_utils.py (Connection): Disable missing-class-docstring,
missing-function-docstring and too-few-public-methods pylint checks.
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* gn3/api/search.py: New file.
* gn3/app.py: Register the search blueprint.
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* gn3/settings.py (XAPIAN_DB_PATH): New variable.
* gn3/db_utils.py: Import xapian and XAPIAN_DB_PATH from gn3.settings.
(xapian_database): New function.
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* gn3/genodb.py (matrix): Reshape column major genotype database storage as
ncols x nrows instead of as nrows x ncols.
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* gn3/monads.py: Import SSDictCursor from MySQLdb.cursors.
(query_sql): Add server_side argument.
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* gn3/db_utils.py: Import contextlib. Import Any, Iterator, Protocol and Tuple
from typing.
(database_connector): Deprecate function.
(Connection): New class.
(database_connection): New function.
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* gn3/monads.py: New file.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function
was parsing data from a file, and then converting the parsed values into a
comma-separated string for output, despite the fact that the data parsed is
not output in this specific function. This is a really bad idea, and leads
to errors showing up down the line, far removed from the cause.
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Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
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* gn3/db/__init__.py (update): Delete conn.commit() and conn.rollback()
(insert): Ditto.
* gn3/db/case_attributes.py (insert_case_attribute_audit): Ditto.
(reject_case_attribute): Ditto.
(approve_case_attribute): Ditto.
* gn3/db/sample_data.py (update_sample_data): Ditto.
(delete_sample_data): Ditto.
(insert_sample_data): Ditto.
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By default, MySQL/Mariadb connects at port 3306, however, the configuration
variable `SQL_URI` could contain a different port. In that case, this commit
allows the system to connect to the non-default port.
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* Always return dict
* Fix internal '__parse_line__' to always have a valid return
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* remove extra iteration that is unnecessary
* remove unnecessary variables
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* 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
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* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
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