genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2023-12-29	Namespace all modules under gn2.	Arun Isaac
	We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
2023-06-22	Update calls to `database_connection` function	Frederick Muriuki Muriithi
	Pass in the database URI at call time.
2023-05-31	Compute dataset type from name.	Frederick Muriuki Muriithi

2023-03-17	Fix correlation bug caused by a NULL UPDATE_TIME in the DB	zsloan

2022-12-01	Fix Exception that's raised when query_sql returns None	Munyoki Kilyungi
	* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value.
2022-11-30	Remove check for shortnames/fullnames in probeset metadata query	Munyoki Kilyungi
	Some rows in InfoFiles have NULL values thereby causing an exception to be raised. All InfoFiles.DB_Name are unique. * wqflask/base/data_set/dataset.py (DataSet.get_accession_id): Remove shortname/fullname check in query.
2022-11-10	Use the Maybe Monad when fetching the accession_id of a dataset	Munyoki Kilyungi
	* wqflask/base/data_set/dataset.py: Import itertools, DictCursor, MonadicDict, Maybe, Nothing and query_sql. (DataSet.__init__): Initialize accession_id to Nothing. (DataSet.as_dict): Rename this to ... (Dataset.as_monadic_dict): ... this which returns a monadic dictionary. (DataSet.get_accession_id): Query for the accession_id and return it as a maybe monad.
2022-11-08	Remove string check for 'None' in HTML template	Munyoki Kilyungi
	In Jinja, you can use dot notation to check for values. If a value does not exist, you get None by default. * wqflask/base/data_set/dataset.py (Dataset.get_accession_id): Remove returning a string version of None. * wqflask/wqflask/templates/correlation_page.html: Delete `!= 'None'`.
2022-10-17	Fix bug when initializing Temp DatasetGroups	zsloan

2022-09-22	Provide database cursor as argument for TheSpecies and Chromosomes	Frederick Muriuki Muriithi
	Provide the database cursor as an argument to the methods of the two classes: * wqflask.base.species.TheSpecies * wqflask.base.species.Chromosomes Also update dependent code to initialise and pass the cursor where these classes are used.
2022-09-21	Added Markers/HumanMarkers import to datasetgroup.py and removed it from	zsloan
	__init__.py Previously it threw an error when it tried to use Markers/HumanMarkers in datasetgroup.py; since Markers/HumanMarkers doesn't seem to be used anywhere else, I think it's okay for the import to only be in datasetgroup.py
2022-09-21	Refactor: pass redis and db connections as argument	Frederick Muriuki Muriithi
	Pass the redis and database connection/cursors as arguments to the class methods, and do not retain a copy of the connections/cursors. This allows us to do the connection management in the context managers elsewhere - ideally, at the top-level. For now the context manager is within the `create_dataset` function, but this should be moved out to a higher level once the lower levels are verified to be working as expected.
2022-09-20	Remove global `Dataset_Getter` variable	Frederick Muriuki Muriithi
	Since the `__post_init__` method in the 'DatasetType' class checks whether data is in redis before hitting the database, it does not matter whether there is a global object of the type, as long as we make sure to call the object correctly. This commit makes that happen.
2022-09-20	Decompose file into separate modulesrefactor-data_set_py-20220920	Frederick Muriuki Muriithi
	To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently.