genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-11-06	Changed the show/hide column buttons to use DataTables API + a few other ↵	zsloan
	changes (for some reason none of my changes could be pushed from one of my local branches to origin/testing, so they're combined in this commit) - Fixed a couple column header glossary links to point to GN1 - Added trait_list.css for styling a couple elements common to similar pages (like correlations or view collection)
2020-11-06	Added min-width for the divs containing the analysis tools and table ↵	zsloan
	options, since they would look weird if the window shrunk below a certain width Also made some indentation more consistent
2020-11-06	Added new css file for pages that have trait list tables (not sure what else ↵	zsloan
	to call them, but pages like search results, view collection, and correlation results)
2020-11-06	Increased the min-width for the show_trait page container div for all the ↵	zsloan
	accordion sections, since previously it could get too narrow and cause text to extend beyong the borders of each accordion area
2020-11-06	After I changed some class names in the trait page to use - instead of _ (to ↵	zsloan
	keep naming consistent) I forgot to change the references in show_trait_mapping_tools.js (which broke the functionality of clicking a tab doing mapping)
2020-11-04	Changed numeric-html sorting for the Tissue/Lit r columns to ↵	zsloan
	natural-minus-na so it deals with the "--" values * wqflask/wqflask/templates/correlation_page.html - Replaced numeric-html sorting with natural-minus-na for the lit/tissue r columns
2020-11-04	Merge pull request #475 from Alexanderlacuna/test-showtrait	BonfaceKilz
	Add more tests for show trait module
2020-11-04	correct a typo	Alexanderlacuna

2020-11-04	remove extra whitespace	Alexanderlacuna

2020-11-04	remove whitespace in line 119-120	Alexanderlacuna

2020-11-04	remove whitespace	Alexanderlacuna

2020-11-04	remove whitespace and assertIs	Alexanderlacuna

2020-11-03	Merge pull request #479 from zsloan/bug/haplotype_analyst_error_fix	zsloan
	Bug/haplotype analyst error fix
2020-11-03	Changed the syntax for the "sort" function in the docstring of GeneralObject ↵	zsloan
	to be compatible with Python 3 syntax * wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
2020-11-03	Fixed a sort used when doing the haplotype analysis to be compatible with ↵	zsloan
	Python 3 * wqflask/wqflask/marker_regression/display_mapping_results.py - The arguments for sort are different in Python 3, so it was changed to be compatible
2020-11-03	Merge pull request #478 from zsloan/loading_page_n_fix	zsloan
	Joined sample names in primary_samples and all_samples with commas be…
2020-11-03	Joined sample names in primary_samples and all_samples with commas because ↵	zsloan
	this list was being split to get the N of samples; not sure why this was working before * wqflask/wqflask/show_trait/show_trait.py primary_samples and all_samples passed as hidden form inputs now have names split by commas so they can be counted correctly when displaying the N on the mapping loading screen
2020-11-03	Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵	Alexanderlacuna
	test-showtrait
2020-11-03	remove unnecessary comments	Alexanderlacuna

2020-11-03	add pep8 formatting	Alexanderlacuna

2020-11-03	add tests for the get_categorical_variables function	Alexanderlacuna

2020-11-03	switch from assertFalse to assertIs	Alexanderlacuna

2020-11-03	switch from assertTrue/False to assertIs to make the tests tighter	Alexanderlacuna

2020-11-03	use assertTrue and assertFalse in while testing boolean	Alexanderlacuna

2020-11-02	Merge pull request #476 from zsloan/correlation_errors_fix	zsloan
	Correlation errors fix
2020-11-02	Created function for encoding the column value as bytes when fetching from ↵	zsloan
	the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis
2020-11-02	Changed correlation page logic to skip over traits that share fewer than 6 ↵	zsloan
	samples + traits that user doesn't have permission to access * wqflask/wqflask/correlation/show_corr_results.py - Moved the num_overlap check so that it never attempts to calculate the correlation if it's too low + checked if trait_object is None in the main loop (since it would be returned as None if the user doesn't have permissions
2020-11-02	add better formatting	Alexanderlacuna

2020-11-02	add function docstring	Alexanderlacuna

2020-11-02	add tests for show trait module	Alexanderlacuna

2020-10-31	Removed a line adding the ceiling of the Max LRS to the Y axis, since it has ↵	zsloan
	the potential to cause an axis tick to appear above the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis
2020-10-31	remove redundant classes	Alexanderlacuna

2020-10-31	use descriptive variable names	Alexanderlacuna

2020-10-31	Use more descriptive variable and class names	Alexanderlacuna

2020-10-30	add test for get_export_metadata	Alexanderlacuna

2020-10-30	Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵	Alexanderlacuna
	test-branch
2020-10-29	Fixed issue with single-chromosome mapping after the bootstrap fix and fixed ↵	zsloan
	error that occurred if either bootstrap or permutations were set to 0 * wqflask/wqflask/marker_regression/display_mapping_results.py - Cast self.qtlresults 'chr' as a string since the comparison between it and the chromosome names was faililng due to numeric chromosomes being int type + used a list comprehension that converts None to an empty string when creating a comma-joined string from the list of mapping output files
2020-10-29	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵	zsloan
	reaper_bootstrap_fix
2020-10-29	add test for show_trait	Alexanderlacuna

2020-10-29	Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵	Alexanderlacuna
	test-branch
2020-10-29	Merge pull request #469 from BonfaceKilz/bug/fix-cookies-verification	BonfaceKilz
	Bug/Fix cookie verification bug
2020-10-29	resolve merge conflict	Alexanderlacuna

2020-10-29	format file	Alexanderlacuna

2020-10-29	remove print statement in for loop	Alexanderlacuna

2020-10-29	add test for show_trait/export_trait_data	Alexanderlacuna

2020-10-29	Merge pull request #471 from BonfaceKilz/bug/replace-map-on-strip-method	BonfaceKilz
	Bug/Replace map on strip with a list comprehension that calls strip()
2020-10-28	Merge pull request #470 from zsloan/mapping_chr_view_fix	zsloan
	Fixed error when zooming into a chromosome when mapping
2020-10-28	A non-string being used as a paramter in HT.Link caused an error after the ↵	zsloan
	Python3 switchover, so I converted it to a string * wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string
2020-10-29	Replace map on strip with a list comprehension that calls strip()	BonfaceKilz
	* scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map string.strip on a list of strings. Instead use a list comprehension and apply strip() on each element of the list. * wqflask/wqflask/marker_regression/plink_mapping.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
2020-10-28	Use latin-1 encoding when converting hmac secret to bytes	BonfaceKilz
	* wqflask/utility/hmac.py (hmac_creation): Use latin-1 when serializing the hmac secret. This ensures that the behaviour of verify_cookie remains the same as in the python2 tip.