genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-09-19	Check for file size before attempting parsing	Frederick Muriuki Muriithi
	Empty files lead to json encoding errors; this commit checks whether the file is empty before attempting to parse the file.
2022-09-19	Display correct error for missing file/directory	Frederick Muriuki Muriithi
	Provide the user with the missing file/directory in the error message to make debugging easier.
2022-09-19	Refactor: raise appropriate error	Frederick Muriuki Muriithi
	If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`.
2022-09-16	Add example code to docstring of MonadicDictCursor.	Arun Isaac
	* wqflask/utility/monads.py (MonadicDictCursor): Add example code to docstring.
2022-09-16	Add example code to docstring of MonadicDict.	Arun Isaac
	* wqflask/utility/monads.py (MonadicDict): Add example code to docstring.
2022-09-16	Initialize empty MonadicDict by default.	Arun Isaac
	* wqflask/utility/monads.py (MonadicDict)[__init__]: Set default dictionary argument to the empty dictionary.
2022-09-14	Add monadic utilities MonadicDict and MonadicDictCursor.	Arun Isaac
	* wqflask/utility/monads.py: New file.
2022-09-12	Add glyphicon for trait page Download table	zsloan

2022-09-12	Add glyphicons for sample table Export/Reset buttons	zsloan

2022-09-12	Add glyphicon for GEMMA compute button	zsloan

2022-09-12	Add glyphicons to Export/Reset buttons in Transform and Filter form	zsloan

2022-09-12	Move global search button and add glyphicon	zsloan

2022-09-12	Add search glyphicons + index_page.css for the Info button styling	zsloan

2022-09-12	Set Species drop-down to same width as Group/Type dropdowns	zsloan

2022-09-13	Increase table marker limit to 25000	zsloan

2022-09-13	Fix bug where passing LOCO into the mapping API endpoint didn't work	zsloan

2022-09-12	Fix query: Add comma to separate columns.	Frederick Muriuki Muriithi

2022-09-12	Check for species before calling `lower()`	Frederick Muriuki Muriithi

2022-09-12	Check there is target data before running correlations	Frederick Muriuki Muriithi

2022-09-12	Fix query: Remove extraneous bracket	Frederick Muriuki Muriithi

2022-09-12	Check for traits before computing	Frederick Muriuki Muriithi

2022-09-12	Fix query: remove wrongly-placed comma	Frederick Muriuki Muriithi

2022-09-12	Check db resultset before indexing into it	Frederick Muriuki Muriithi
	The assumption that the resultset will never be empty was leading to a lot of errors.
2022-09-12	Check data is truthy before indexing into it.	Frederick Muriuki Muriithi

2022-09-09	Fix bug in display_mapping_results chromosome query	zsloan
	A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome
2022-09-09	Fix bug in retrieve_other_names	zsloan
	After a recent change, it always tries to unpack 6 values from the query, but it should only be unpacking 4 values if not type ProbeSet (so it was throwing an error for anything not ProbeSet)
2022-09-09	handle cases where tissue dataset vals are empty list	Alexander_Kabui

2022-09-09	tissue:fetch for query formatting	Alexander_Kabui

2022-09-09	Fix query: remove string interpolation.	Frederick Muriuki Muriithi

2022-09-09	Retain only a single import of the same module	Frederick Muriuki Muriithi

2022-09-09	Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlations	Muriithi Frederick Muriuki
	Bug/fix broken correlations
2022-09-09	Fetch sample values correctly	Munyoki Kilyungi
	* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation.
2022-09-09	Add missing import	Munyoki Kilyungi
	* wqflask/base/trait.py: Import utility.hmac
2022-09-09	Import missing module.	Frederick Muriuki Muriithi

2022-09-09	Check whether trait_list and sample_data exist before operations	Frederick Muriuki Muriithi

2022-09-09	Remove `None` values from dataset	Frederick Muriuki Muriithi

2022-09-09	Filter out Samples without values	Frederick Muriuki Muriithi

2022-09-09	Refactor: Add tests and handle edge case	Frederick Muriuki Muriithi
	Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence.
2022-09-09	Use `database_connection()`	Frederick Muriuki Muriithi
	Call the `database_connection()` function to get a connection to the database.
2022-09-09	Replace `g.db.execute` with `cursor.execute`	Frederick Muriuki Muriithi

2022-09-09	Comment out pickling to avoid error	Frederick Muriuki Muriithi
	Pickling was failing with "TypeError: cannot pickle 'Connection' object" This commit avoids the error by temporarily commenting out the line to prevent the pickling to actually test the working of the system on the CI/CD server.
2022-09-09	If port is null, use MySQL's default 3306	Frederick Muriuki Muriithi

2022-09-09	Use `urllib.parse.urljoin` for urls	Frederick Muriuki Muriithi
	Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity.
2022-09-08	Filter export by checked rows (when any rows are checked)	zsloan

2022-09-08	Fix getCheckedRows so that it only selects checkbox input elements	zsloan

2022-09-08	Convert variables to camelCase and remove some unused variables	zsloan

2022-09-08	Remove commented out code	zsloan

2022-09-08	Remove console log	zsloan

2022-09-08	Remove some unused initialized variables	zsloan

2022-09-08	Make GN_SERVER_URL the genenetwork3 API endpoint.	Arun Isaac
	From now on, GN_SERVER_URL will be the genenetwork3 API endpoint. For example, GN_SERVER_URL=https://gn3.genenetwork.org/api * wqflask/wqflask/collect.py (view_collection), wqflask/wqflask/partial_correlations_views.py (partial_correlations, poll_partial_correlation_results), wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js (defaultStatusCodeFunctions): Do not append api to GN_SERVER_URL. * etc/default_settings.py (GN_SERVER_URL): Append /api.