genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-05-31	Remove unnecessary statement	Frederick Muriuki Muriithi

2022-05-24	Run partial correlations with external script	Frederick Muriuki Muriithi
	Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits
2022-05-21	Fix linting errors	Frederick Muriuki Muriithi

2022-05-16	Run computation in one-shot asynchronous process	Frederick Muriuki Muriithi
	After reworking the worker/runner to have a one-shot mode, add a function that queues up the task and then runs the worker in the one-shot mode to process the computation in the background.
2022-03-11	Fix some linting issues	Frederick Muriuki Muriithi

2022-03-08	Fix tests, and issues caught by tests	Frederick Muriuki Muriithi
	Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration
2022-03-03	Run partial correlations in an external process	Frederick Muriuki Muriithi
	Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the genenetwork3 path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run
2021-06-29	Replace list with a tuple as an argument when setting success_codes	BonfaceKilz
	* gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd".
2021-06-29	gn3: commands: Add extra arg that sets the success codes to check	BonfaceKilz
	* gn3/commands.py (run_cmd): Some commands like "diff" return non-standard error codes. To make this fn more robust, add an extra optional argument that sets what successful codes to check.
2021-06-25	Check for the correct result code	BonfaceKilz
	When programs terminate with an error, they usually return a -1!
2021-06-18	Fix R/qtl command and the way keyword arguments are passed	zsloan

2021-05-18	Removed len from this if statement, since an empty list evaluates to False ↵	zsloan
	by itself
2021-05-18	Account for boolean kwargs in compose_rqtl_cmd	zsloan

2021-05-17	Created compose_rqtl_command and generate_rqtl_command to create the actual ↵	zsloan
	command to be run from the command line; used the same pattern as for GEMMA for consistency
2021-03-10	Queue the command only once	BonfaceKilz

2021-03-10	Call Redis hset correctly in the right order	BonfaceKilz

2021-03-10	Apply yapf file formatting to file	BonfaceKilz

2021-03-08	bug: Put a space between gemma-wrapper args	BonfaceKilz

2021-03-08	gn3: commands: Update docstring	BonfaceKilz

2021-03-08	Make the name of the redis job queue configurable	BonfaceKilz

2021-02-24	gn3: commands: Remove token and metadata_filename args	BonfaceKilz

2021-02-16	Add extra option to set email when queueing CMD	BonfaceKilz
	The e-mail field will be used to send the results of the computation when it is completed.
2021-02-16	gn3: commands: Add new procedure for running a command	BonfaceKilz
	* gn3/commands.py (run_command): New procedure.
2021-02-12	Add new procedure for queueing a command	BonfaceKilz
	* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^.
2021-02-12	Add new procedure for composing a gemma cmd	BonfaceKilz
	* gn3/commands.py: New file * tests/unit/test_commands.py: New test-cases for ^^.