genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-01-06	README: Fix typo.	Arun Isaac
	* README.md: Change clinians to clinicians.
2022-01-06	bin: Stop execution on error.	Arun Isaac
	* bin/genenetwork2: Pass -e flag to sh.
2022-01-06	bin: Set shebang to sh instead of bash.	Arun Isaac
	/bin/sh is present on Guix System and other distros while /bin/bash is present only on other distros. * bin/genenetwork2: Set shebang to sh instead of bash.
2022-01-06	bin: Do not set environment variables set by guix shell.	Arun Isaac
	The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
2022-01-06	bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.	Arun Isaac
	`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
2022-01-05	metadata_edits.py: Remove duplicate imports	BonfaceKilz

2022-01-05	Display correct message on the # of edits	BonfaceKilz

2022-01-05	Insert data to db by checking the tracked deletions, mods, or adds	BonfaceKilz
	Prior to this, we only checked for the json files with contained the modifications. However, in the case of double deletions, and double inserts, the data would have been stored in the db anyway; which is a false representation of changes.
2022-01-05	Check for any double-inserts or double-deletions	BonfaceKilz
	Track any double-inserts or double-deletions
2022-01-05	Remove pudb debug statements	BonfaceKilz

2022-01-05	metadata_edits: Return early if uploaded csv has not been edited	BonfaceKilz

2022-01-05	display_diffs: Remove in-line styling from "pre" tag	BonfaceKilz

2022-01-05	Remove pudb line	BonfaceKilz

2022-01-05	display_diffs: Use datatables for every table	BonfaceKilz

2022-01-05	Make "Files for approval:" text a "h2"	BonfaceKilz

2022-01-05	Add interface for displaying diffs in a html page	BonfaceKilz

2022-01-05	Use datatables to display approved and rejected files	BonfaceKilz

2022-01-03	Added something that should work as a 'universal' solution for decoding ↵	zsloan
	trait descriptions in search results, since there were still some traits with encoding issues
2022-01-03	Fixed wrong logic for checking for null or empty string trait descriptions ↵	zsloan
	in search results
2021-12-23	If phenotype metadata is cached, authenticate for those traits (otherwise ↵	zsloan
	authentication happens in create_trait at line 105)
2021-12-23	Set new_traits_metadata so caching is used (previously was always an empty dict)	zsloan

2021-12-20	This should fix ProbeSet trait descriptions in the search results, which ↵	zsloan
	previousluy weren't showing the proper description
2021-12-17	Some updates to the DOL genotypes conversion script	zsloan

2021-12-15	Edited html for index page	zsloan

2021-12-14	Removed min-width from container div, since it seems to have preventd ↵	zsloan
	horizontal scrolling when the window is small
2021-12-14	Includes dataset name when creating SimpleNamespace dataset_ob, since it's ↵	zsloan
	needed during authentication
2021-12-13	Fixes issue that caused LRS searches that specify position to not work ↵	zsloan
	properly; the queries had to be changed after integrating the change that also pulls the Max LRS info in the original query
2021-12-13	pep8 formatting	Alexander Kabui

2021-12-13	modify endpoint for test wgcna	Alexander Kabui

2021-12-13	modify template to show error generated	Alexander Kabui

2021-12-13	handle connection error & other exceptions	Alexander Kabui

2021-12-13	parse powers to use from form data	Alexander Kabui

2021-12-13	add new endpoint:for test gn3 wgcna	Alexander Kabui

2021-12-07	Made some changes to the index page HTML	Arthur Centeno

2021-12-03	Add mapping_scale to mapping_results.html forum inputs	zsloan

2021-12-03	Properly set start position for cM mapping, to prevent overflow + remove ↵	zsloan
	some unnecessary commented out lines
2021-12-03	Make sure mapping_scale is always physic when using GEMMA	zsloan

2021-12-03	Prevent points prior to the X axis from being displayed in mapping figure ↵	zsloan
	when zoomed into a sub-range on a chromosome
2021-12-02	Gave the twitter feed div a background color to make it more visually ↵	zsloan
	distinct from surrounding content + removed top margin from ul elements that was added by uikit
2021-12-02	Moved the UIkit CSS from base.html to index_page.html (btw Arthur, never add ↵	zsloan
	CSS files to base.html - it makes their styling apply to every single GN page)
2021-12-02	Removed colons from Links headers and removed margin-bottom for H2 elements	zsloan

2021-12-02	Made Affiliates a subcategory of Links	zsloan

2021-12-02	Changed index pagee HTML to be more consistent, adding indentation, removed ↵	zsloan
	commented out HTML
2021-12-02	Increased min-width for showtrait-main-div to prevent mapping description ↵	zsloan
	text from overflowing
2021-12-02	Increased mid-width for container element for mapping figure to prevent it ↵	zsloan
	from shrinking when the browser window is smaller (which prevents the links, etc, from overlapping properly with the image)
2021-12-01	Figure out that we are using the wrong db_webqtl_s!	Pjotr Prins

2021-12-01	Introduce GN3_PYTHONPATH environment variable	Pjotr Prins

2021-11-27	display_files.html: Place "approved" before "rejected" section	BonfaceKilz

2021-11-25	wqflask: metadata_edits: Support deletions and insertions from csv	BonfaceKilz

2021-11-25	Remove useless comment	BonfaceKilz