genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-11-04	Add link markers to elements which are referenced from elsewhere	BonfaceKilz

2020-11-04	Update test_markdown_routes	BonfaceKilz
	* wqflask/tests/unit/wqflask/test_markdown_routes.py (test_render_markdown_when_fetching_locally): Fix failing test.
2020-11-04	Add an edit link button to glossary page	BonfaceKilz

2020-11-04	Wrap rendered content in div container	BonfaceKilz

2020-11-04	Update glossary markdown file	BonfaceKilz

2020-11-04	Use python3-genenetwork2 docker image on commit 0bf4ee6	BonfaceKilz

2020-11-03	Fix false-positive tests	BonfaceKilz
	* wqflask/tests/unit/wqflask/test_markdown_routes.py: (MockRequests404): Pass self in all properties. (MockRequests200): Ditto. (test_render_markdown): Rename to test_render_markdown_when_fetching_locally. (test_render_markdown_when_fetching_remotely): New test.
2020-11-03	Delete file	BonfaceKilz
	* wqflask/tests/integration/test_glossary.py: Delete it. Earlier renamed to test_markdown_routes.
2020-11-03	Add basic tests for rendering_markdown	BonfaceKilz
	* wqflask/tests/unit/wqflask/test_markdown_routes.py: New tests.
2020-11-03	Add basic structure for "/glossary" routes test	BonfaceKilz

2020-11-03	Move logic for fetching md files to it's own function	BonfaceKilz
	* wqflask/wqflask/markdown_routes.py (render_markdown): New function. (glossary): use render_markdown function.
2020-11-03	Use python3-genenetwork2 on commit bdce85d in container	BonfaceKilz
	* .github/workflows/main.yml: Update gn2 container.
2020-11-03	Add simple md content in glossary.md	BonfaceKilz

2020-11-03	Update glossary template with markdown content	BonfaceKilz

2020-11-03	Rename glossary.py to markdown_routes.py	BonfaceKilz
	Evary page with markdown content will have routes added in markdown_routes.py * markdown_routes.py: New file. * wqflask/wqflask/glossary.py: Delete it. * wqflask/wqflask/__init__.py: Update import.
2020-11-03	Remove encoding header for file	BonfaceKilz
	In python3 the default encoding is utf-8 so this is redundant.
2020-11-03	Separate unittests from integration tests	BonfaceKilz

2020-11-03	Add test for "/glossary" route	BonfaceKilz

2020-11-03	Add glossary template and use it	BonfaceKilz

2020-11-03	Add and register glossary blueprint	BonfaceKilz

2020-11-03	Apply PEP-8 to file	BonfaceKilz
	* wqflask/wqflask/__init__.py: Remove unused import and variables. Also add module docstring and pylint errors to ignore. (before_request): Use correct spacing.
2020-11-03	Remove stale file	BonfaceKilz
	* jquery.qtip.css: Delete it.
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
2020-11-01	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.