genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-11-04	remove whitespace and assertIs	Alexanderlacuna

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

2020-11-01	Merge pull request #472 from Alexanderlacuna/test-branch	BonfaceKilz
	Adding more Test for show_trait module
2020-10-31	Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵	Alexanderlacuna
	test-branch
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	Merge pull request #474 from zsloan/mapping_y_axis_fix	zsloan
	Mapping Y Axis Fix
2020-10-30	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
2020-10-30	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	Merge pull request #473 from zsloan/reaper_bootstrap_fix	zsloan
	Reaper bootstrap fix
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.
2020-10-28	Add new test for hmac_creation with latin-1 secret	BonfaceKilz
	* wqflask/tests/utility/test_hmac.py (test_hmac_creation_with_cookie): New test. For this test, use a secret that behaves differently when encoded to either utf-8 or latin-1.
2020-10-28	Add tests for cookie verification	BonfaceKilz

2020-10-28	Merge pull request #468 from zsloan/export_fix	zsloan
	Fixed trait page export issue caused by Scroller
2020-10-28	Fixed trait page export to work with Scroller + added metadata for ↵	zsloan
	non-Phenotype traits and column headers * wqflask/wqflask/show_trait/export_trait_data.py - Added metadata for non-Phenotype traits and column headers (which didn't previously exist) * wqflask/wqflask/static/new/javascript/show_trait.js - Changed export_sample_table_data to use DataTables API instead of just selecting from the DOM with JQuery
2020-10-27	Merge pull request #467 from zsloan/gsearch_encoding_fix	zsloan
	Remaining gsearch encoding fix for ProbeSet description
2020-10-27	Cast ProbeSet description as binary to fix encoding issue on global search page	zsloan
	* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary
2020-10-27	Merge pull request #466 from zsloan/show_trait_attributes_fix	zsloan
	Fix issue where attribute values were displayed in the wrong columns
2020-10-27	Get the "first_attr_start_pos" from a samplelist instead of from each ↵	zsloan
	individual sample, because it was previously causing problems when only some samples had an N * wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos * wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed
2020-10-27	Cast post and pre-publication descriptions into binary	BonfaceKilz
	* wqflask/wqflask/gsearch.py (GSearch): There's an exception thrown when the decode method is called on that description string. If the casting is absent, and the decode statements are removed, the some characters get broken.
2020-10-27	Merge pull request #465 from Alexanderlacuna/test-branch	BonfaceKilz
	add test for trait_data
2020-10-27	switch from single quote to double quote	Alexanderlacuna