genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-03-23	conf: use flask.current_app.config not in gn3.settings	Frederick Muriuki Muriithi
	The configuration in gn3.settings can (and does) get overwritten by values in the environment variable `GN3_CONF` and any configurations passed in the call to the `gn3.app.create_app` function; as such, this commit changes the configuration used in the code to user the final configuration values that are in the running application's `flask.current_app.config` object.
2023-02-23	auth: Link data in MySQL to the groups (in SQLite)	Frederick Muriuki Muriithi
	In order for the group leaders (and other resource creators) to be able to link data to the resources, the data needs to be first linked to the relevant group. This commit enables the system admin to link the data in MySQL to the groups.
2022-11-02	Fix pylint and mypy errors	Munyoki Kilyungi
	* 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.
2022-10-28	Use Xapian index path from app settings.	Arun Isaac
	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.
2022-10-28	Disable various pylint checks on Connection class.	Arun Isaac
	* gn3/db_utils.py (Connection): Disable missing-class-docstring, missing-function-docstring and too-few-public-methods pylint checks.
2022-10-26	Add xapian database connection context manager.	Arun Isaac
	* 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.
2022-10-18	Add database connection context manager.	Arun Isaac
	* 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.
2022-08-22	Use non-default MySQL port if present	Frederick Muriuki Muriithi
	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.
2022-03-11	Fix some linting issues	Frederick Muriuki Muriithi

2022-03-08	Create database connections within context managers	Frederick Muriuki Muriithi
	Use the `with` context manager to open database connections, so as to ensure that those connections are closed once the call is completed. This hopefully avoids the 'too many connections' error
2021-05-08	gn3: db_utils: Remove mypy ignore stub	BonfaceKilz
	MySQLdb is already ignored in ".mypy.ini", added in 88c33df.
2021-05-08	Fix pep-8 errors	BonfaceKilz

2021-04-12	Integrate correlation API	Alexander Kabui
	- add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn