genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-07-25	The variable is never defined, so let's default to "none"	Pjotr Prins

2020-07-24	Merge pull request #409 from BonfaceKilz/Build/add-tests	zsloan
	Build/add tests
2020-07-24	Revert "Add work-around for failed imports in unittest"	BonfaceKilz
	This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
2020-07-24	Add work-around for failed imports in unittest	BonfaceKilz
	* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app` and the gn2 script will use `from wqflask import app`
2020-07-24	Apply autopep-8	BonfaceKilz
	* wqflask/utility/formatting.py: apply it
2020-07-24	Add zero to num_repr dictionary	BonfaceKilz
	* wqflask/utility/formatting.py(numify): Update `num_repr` to have a zero
2020-07-24	Remove redundant variable	BonfaceKilz
	* wqflask/utility/corr_result_helpers.py(normalize_values_with_values): Remove `num_overlap`
2020-07-24	Remove unused assert	BonfaceKilz
	* wqflask/utility/corr_result_helpers.py(normalize_values): At no one point will that assert be hit
2020-07-24	Remove unused doc-tests	BonfaceKilz
	* wqflask/utility/corr_result_helpers.py: Delete doc-test
2020-07-24	Simplify normalize_values	BonfaceKilz
	* wqflask/utility/corr_result_helpers.py(normalize_values): Replace loop with zip form
2020-07-24	Remove unused doc-tests	BonfaceKilz
	* wqflask/utility/chunks.py: Remove test code from module
2020-07-24	Revert "Add work-around for failed imports in unittest"	BonfaceKilz
	This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
2020-07-24	Add work-around for failed imports in unittest	BonfaceKilz
	* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app` and the gn2 script will use `from wqflask import app`
2020-07-22	It should add new resources to Redis automatically now	zsloan

2020-07-16	Expose elastic-search variables for tests to pass	BonfaceKilz

2020-07-08	Removed remaining unused references to the old qtlreaper	zsloan

2020-07-06	Fixed some of the logic with how traits are authenticated to avoid situation ↵	zsloan
	where a trait is authenticated twice
2020-06-24	Temporary partial fix to issue of resources without info; need to add ↵	zsloan
	something that automatically inserts resources with default privileges
2020-06-20	Fixed ports for proxy (though I need to add the port to global variables) ↵	zsloan
	and also simplified the check_owner_or_admin function a little
2020-06-20	Added some admin functionality and fixed issue with temp traits	zsloan

2020-06-17	A user's id is now set as a parameter if it doesn't already existauthentication_test	zsloan

2020-06-17	Adding all the authentication stuff	zsloan

2020-06-05	Commiting other current group/resource management code, plus the new files	zsloan

2020-06-04	Really should have split this into many more commits:	zsloan
	- Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code
2020-05-28	Added lines calling proxy for publish datasets + added some resource redis ↵	zsloan
	queries and a missing import for the hmac functions
2020-05-12	Merging Danny's changes and Bonface's changes to js imports	zsloan

2020-05-12	Added change for F2s in r/qtl and fixed minor issue in save_user in redis_tools	zsloan

2020-05-07	Committing current progress on group manager + a minor fix in dataset.py	zsloan

2020-05-06	Commiting a few minor changes plus returning rqtl_mapping.py to the same as ↵	zsloan
	on testing branch before merging Danny's changes and testing them
2020-05-06	Replace CSS dependencies for datatables	BonfaceKilz

2020-04-26	Merge master and testingmaster	Pjotr Prins

2020-04-24	Replaced hard-coded instances of GN2 urls with ones pulled from settings file	zsloan

2020-04-22	Fixed a variety of issues related to users registering and logging in	zsloan
	GN2 should now work when Redis is empty
2020-04-16	Many changes, including:	zsloan
	- Added permutation strata option for R/qtl - Made a variety of aesthetic changes to collections-related pages - Made a variety of aesthetic changes to the multi-trait tool options on the search result and correlation pages - Made some functional changes to collections that prevent duplicate traits and ensure new traits are at the top - The "Default Collection" is now always at the bottom of the collection list and renamed to "Your Default Collection"
2020-04-03	Added option to select cofactors from collection for R/qtl	zsloan
	Fixed some issues with displaying the R/qtl results from the RData HET3-ITP dataa
2020-03-27	Added integration for using RData files with R/qtl, plus some other changes ↵	zsloan
	to how it decides which mapping methods to display on the trait page
2020-03-10	Fixed issue that caused some problems when verifying hmac	zsloan

2020-03-09	I think this should complete consolidating all the collections code.	zsloan

2020-03-03	Missed one more reference in helper_functions	zsloan

2020-03-03	was missing a couple files in last commit	zsloan

2020-03-03	Refactored all the anonymous (not logged-in) user stuff so that both ↵	zsloan
	logged-in and anonymous users share the same code
2020-02-12	Fixed issue that broke some logins with the new redis user code	zsloan

2020-01-23	Forgot to commit new file containing Redis functions	zsloan

2019-10-18	Fixed issue with collections ordering	zsloan

2019-10-08	Fixed serious issue that caused output to be wrong for new reaper mapping	zsloan
	Haplotype analyst now works for GEMMA Increased margin a bit to fix minor issue with buttons getting cut off on certain Safari versions for bar chart
2019-09-24	Fixed issue that caused GEMMA to not work with genotype files without cM, ↵	zsloan
	though this issue still needs to be dealt with to get the new qtlreaper working
2019-09-06	Fix name of javascript-twitter-post-fetcher	Pjotr Prins

2019-07-23	Added change to automatically update datasets list using rest api instead of ↵	zsloan
	json file Removed option to edit certain html pages, like news, policies, etc
2019-06-07	Global search and correlation results can handle null expression now	zsloan

2019-06-05	Fixed issue that caused interval mapping to not work because the python ↵	zsloan
	implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)