genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-08-17	Merge branch 'chores/rust-enhancements' of ↵	Frederick Muriuki Muriithi
	github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/rust-enhancements
2022-08-16	Merge dicts into single result	Frederick Muriuki Muriithi

2022-08-16	Convert list items to single dict	Frederick Muriuki Muriithi

2022-08-16	rename boolean variables	Alexander_Kabui

2022-08-16	linter fixes	Alexander_Kabui

2022-08-16	enable compute all for test	Alexander_Kabui

2022-08-16	index error fix	Alexander_Kabui

2022-08-16	remove flask g object	Alexander_Kabui

2022-08-16	minor fixes for computing all correlations	Alexander_Kabui

2022-08-16	Setup default GN_PROXY setting	Frederick Muriuki Muriithi

2022-08-15	add default values for num overlap,corr_coeff	Alexander_Kabui

2022-08-14	init:perform top n sample for probes	Alexander_Kabui

2022-08-12	Update to newer lxml API	Frederick Muriuki Muriithi

2022-08-12	Revert "Check for keys before using them."	Frederick Muriuki Muriithi
	This reverts commit a1cbc12f843bbdc1759d5acac5ae3630fb5d4b81.
2022-08-12	Merge branch 'integrate-rust-correlations' of ↵	Frederick Muriuki Muriithi
	github.com:genenetwork/genenetwork2 into integrate-rust-correlations
2022-08-12	Add a profiling script	Frederick Muriuki Muriithi
	Add a script to enable profiling the code.
2022-08-12	Fix some issues with the tests. Add notes in code for improvements.	Frederick Muriuki Muriithi

2022-08-12	Refactor: separate the three correlation types	Frederick Muriuki Muriithi
	Refactor the code such that each correlation type (sample, tissue, literature) is computed in its own function. This makes the code clearer, and helps reduce repetition.
2022-08-12	Fix correlation tests: Fix the test message.	Frederick Muriuki Muriithi

2022-08-12	Check for keys before using them.	Frederick Muriuki Muriithi

2022-08-12	Update format to prevent tissue correlation from failing	Frederick Muriuki Muriithi
	Update the data format of returned values so that it conforms with expectatitions.
2022-08-12	Check that the correlations work as expected.	Frederick Muriuki Muriithi

2022-08-12	Fix formatting for legibility	Frederick Muriuki Muriithi

2022-08-12	code to merge results;minor fixes	Alexander_Kabui

2022-08-12	compute top n tissue results	Alexander_Kabui

2022-08-12	add code to compute top n tissue results	Alexander_Kabui

2022-08-12	Fix minor bug.	Frederick Muriuki Muriithi

2022-08-12	Integrate rust correlations. Deduplicate similar code.	Frederick Muriuki Muriithi
	- Use rust correlations rather than the slower python one - Remove code duplicated in the `wqflask/wqflask/correlation/rust_correlation.py` module within the `compute_correlation_rust` function.
2022-08-12	Add a profiling script	Frederick Muriuki Muriithi
	Add a script to enable profiling the code.
2022-08-12	Fix some issues with the tests. Add notes in code for improvements.	Frederick Muriuki Muriithi

2022-08-11	Add data-trait-info attribute to checkboxes on search results page	zsloan
	Currently there's a separate trait_info_str function in search_results.py, because search_results.py doesn't build the trait objects (so it can't use the one in collect.py unless I change that to accept traits as either a GeneralTrait class or dict - which might be better, I'm not sure)
2022-08-11	Refactor: separate the three correlation types	Frederick Muriuki Muriithi
	Refactor the code such that each correlation type (sample, tissue, literature) is computed in its own function. This makes the code clearer, and helps reduce repetition.
2022-08-11	Fix correlation tests: Fix the test message.	Frederick Muriuki Muriithi

2022-08-11	Check for keys before using them.	Frederick Muriuki Muriithi

2022-08-11	Update format to prevent tissue correlation from failing	Frederick Muriuki Muriithi
	Update the data format of returned values so that it conforms with expectatitions.
2022-08-10	Check that the correlations work as expected.	Frederick Muriuki Muriithi

2022-08-10	Fix formatting for legibility	Frederick Muriuki Muriithi

2022-08-10	code to merge results;minor fixes	Alexander_Kabui

2022-08-10	compute top n tissue results	Alexander_Kabui

2022-08-10	add code to compute top n tissue results	Alexander_Kabui

2022-08-09	Fix minor bug.	Frederick Muriuki Muriithi

2022-08-09	Integrate rust correlations. Deduplicate similar code.	Frederick Muriuki Muriithi
	- Use rust correlations rather than the slower python one - Remove code duplicated in the `wqflask/wqflask/correlation/rust_correlation.py` module within the `compute_correlation_rust` function.
2022-08-09	Display the probeset name in the editing form	Munyoki Kilyungi
	* wqflask/wqflask/templates/edit_probeset.html: Add probeset.name to the h1 tag.
2022-08-09	Make edit_probeset.html similar to corresponding phenotype page	Munyoki Kilyungi
	* wqflask/wqflask/templates/edit_probeset.html: Remove "reset" button. Make button green. Move form element into the "container" div. Add "container" class to form. Left justify labels, and the button. Remove ":" from labels.
2022-08-09	Delete "diff" section	Munyoki Kilyungi
	For both the edit phenotype and probeset pages, the diffs can be viewed from history.html. * wqflask/wqflask/templates/edit_phenotype.html: Delete "diffs" section. * wqflask/wqflask/templates/edit_probeset.html: Ditto.
2022-08-09	Remove "diff" logic from edit_probeset	Munyoki Kilyungi
	* wqflask/wqflask/metadata_edits.py (edit_probeset): Delete logic for fetching diff. Move that... (show_history): ... here * wqflask/wqflask/templates/edit_probeset.html: Update template to show diffs in a history.html. Reposition and rename the h1 tag of this page.
2022-08-09	Update h1 title of history page	Munyoki Kilyungi
	ATM, we don't show the name of the phenotype whose history we are changing. That may be updated in a future commit. * wqflask/wqflask/templates/edit_history.html: Reword h1 and remove "{{}}" which results in a jinja error.
2022-08-09	Fix circular import issue	Frederick Muriuki Muriithi

2022-08-09	Integrate rust correlation for "sample" correlation selection	Frederick Muriuki Muriithi
	Integrate the use of the rust code to compute the correlations for the "sample" correlation selection.
2022-08-09	Pass trait values (X) as list not string	Frederick Muriuki Muriithi
	The trait values (X values) are converted to JSON within the `run_correlation` call. Since JSON has the ability to represent lists of objects, there is no point for the added conversion to and from strings.