genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-09-23	Remove click handler on global search.	Arun Isaac
	check_search_term is not relevant to global search. It checks search terms in the unrelated #or_search and #and_search fields. * wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js: Do not call check_search_term on clicking global search button.
2022-09-22	Fix bug in GeneUtil.py query where extra quotes caused an error	zsloan

2022-09-22	Use passed in cursor instead of initialising a new cursor.	Frederick Muriuki Muriithi

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.
2022-09-22	Update tests: pass in missing arguments.	Frederick Muriuki Muriithi

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	Make -logP columns uniform	zsloan

2022-09-20	Make -logP columns uniform	zsloan

2022-09-20	Re-add collect import to views.py	zsloan
	Not sure why this was removed...I guess it looked like an unused import?
2022-09-20	Make Search and Global Search Max -logP columns uniform	zsloan

2022-09-20	Fix gsearch ProbeSet query	zsloan

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	Revert "Use member variable `self.conn` to avoid test failure"	Frederick Muriuki Muriithi
	This reverts commit 4fafdfd8487ddf61105b2a5ca92534c8014c1db4. While using `self.conn.cursor()` works in the tests, it will not work in the application since the point of initialisation could be very different from the point where the 'property' is called.
2022-09-20	Use member variable `self.conn` to avoid test failure	Frederick Muriuki Muriithi
	Use the `self.conn` variable to prevent test from failing.
2022-09-20	integrate use of text files	Alexander_Kabui

2022-09-20	store text files in TMPDIR	Alexander_Kabui

2022-09-20	write probeset datasets to text files	Alexander_Kabui

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.
2022-09-19	Remove commented-out html	zsloan

2022-09-19	Provide fixtures for test. Fix error to pass test.	Frederick Muriuki Muriithi
	Provide the following (empty) files to be used for the test * wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt * wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt Rework the paths in `wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py` such that they point to the files added above for testing. Do not require that the phenotype file exists in `wqflask/wqflask/marker_regression/gemma_mapping.py` before attempting the mapping.
2022-09-19	Remove "wrong" assertions	Frederick Muriuki Muriithi
	The assertions was checking that the function was implemented a certain way, rather than whether the function was doing the correct thing.
2022-09-19	Check paths before running gemma command	Frederick Muriuki Muriithi
	* Check that the required file paths exist * Check the bimbam directory path only once
2022-09-19	Improve error reporting for no mapping results	Frederick Muriuki Muriithi
	* wqflask/wqflask/marker_regression/exceptions.py: new NoMappingResultsError exception * wqflask/wqflask/templates/mapping_error.html: reword display of the errors * wqflask/wqflask/views.py: Raise the NoMappingResultsError exception in the case where there are no results for the mapping.
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)