genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-08-12	Fix some issues with the tests. Add notes in code for improvements.	Frederick Muriuki Muriithi

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.
2022-08-08	remove unnessary append to list	Alexander_Kabui

2022-08-08	remove test;test is redundant	Alexander_Kabui

2022-08-08	tests refactoring	Alexander_Kabui

2022-08-05	Include partial_correlations.js in the search page template	zsloan

2022-08-01	Remove console logs from scatterplot.js	zsloan

2022-08-01	Change Make Default button to Save Settings	zsloan

2022-08-01	Add date/time to trait page export	zsloan

2022-08-01	Add header/description to partial correlation page	zsloan

2022-08-01	Add index column and phenotype group code to trait export	zsloan

2022-07-28	Use external process to compute sample correlations	Frederick Muriuki Muriithi

2022-07-27	Disable PCA when fewer than 3 traits	zsloan

2022-07-27	Change some text/formatting on Correlation Matrix page	zsloan

2022-07-27	Change capitalization on index page	zsloan

2022-07-27	Change some text/formatting for the Scree Plot	zsloan

2022-07-27	Change search result text/formatting	zsloan

2022-07-27	Change formatting for search term + add line break in description text	zsloan

2022-07-25	new file module for preprocessing input	Alexander_Kabui

2022-07-25	add test route	Alexander_Kabui

2022-07-25	enable test route	Alexander_Kabui

2022-07-25	Fix BNW link	zsloan

2022-07-25	Remove Comparison Bar Chart button	zsloan

2022-07-25	Change Interval Analyst genome browser link to use mm10 instead of mm9	zsloan

2022-07-25	Return config in app.config or None	Frederick Muriuki Muriithi
	Update the code to return the setting already set up in the app.config dictionary if it exists or None if it does not exist.
2022-07-14	Remove column toggle JS from show_trait.html since it's in ↵	zsloan
	initialize_show_trait_tables.js
2022-07-14	Call DataTable() on the table id instead of referring to the_table; not	zsloan
	sure why this is necessary, but the search doesn't work otherwise
2022-07-12	Include genotypes for F1s/reference/non-reference strains when fetching	zsloan
	sample data for genotype traits
2022-07-11	Increase min-width for div containing tool buttons on search page	zsloan

2022-07-08	Add python for exporting case attributes	zsloan

2022-07-08	Add JS for exporting case attributes (sample metadata)	zsloan

2022-07-04	wqflask: Remove DebugToolbarExtension	BonfaceKilz
	This functionality, at least how we use it, is already provided natively in python's pdb. Should someone need this, they can add it manually. * wqflask/runserver.py (app_config): Remove "flask_debugtoolbar" import and instantiation. * wqflask/utility/startup_config.py (app_config): Ditto.