genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2021-10-08	Fixed some issues with scale and score_type in mapping export + include ↵	zsloan
	mapping method in export filename
2021-10-08	Fix issue where outliers weren't being highlighted for rows drawn by ↵	zsloan
	Scroller (so all rows beyond a certain point)
2021-10-08	Fixed the sort to account for both chr and pos in a kind of hack-y way + ↵	zsloan
	added some comments + changed EOL to LF because the file suddenly started including EOL characters
2021-10-08	Adding convert_dol_genotypes.py to scripts; everything is hard-coded in it ↵	zsloan
	since I was only writing it to generate a specific file and it probably won't be re-used
2021-10-06	scripts: resource: Add option for specifying a groups uuid	BonfaceKilz

2021-10-06	scripts: group: Replace args.group_name with data["field"]	BonfaceKilz

2021-10-06	scripts: group: Update docstrings for "create_group_data"	BonfaceKilz

2021-10-06	scripts: group: Break up long line	BonfaceKilz

2021-10-06	scripts: group: Fix indentation	BonfaceKilz

2021-10-06	workflows: main.yml: Disable link checking	BonfaceKilz

2021-10-06	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵	Frederick Muriuki Muriithi
	clustered_heatmaps
2021-10-06	scripts: group: Remove empty `""` value for data.get	BonfaceKilz
	data.get("field") will default to None if there is no value; and None is falsy.
2021-10-06	scripts: group: Remove unused import	BonfaceKilz

2021-10-06	scripts: group: Use a unique key to identify a group	BonfaceKilz

2021-10-06	display images	Alexander Kabui

2021-10-06	Enable selection of heatmap orientation	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Provide the user with the UI elements to enable them select the orientation of the heatmap that will be produced.
2021-10-06	doc: docker-container.org: Remove python2 gn2 docker set-up command	BonfaceKilz

2021-10-06	tests: test_run_mapping: Add missing "name" attribute to tests	BonfaceKilz

2021-10-06	tests: test_run_mapping: Add missing calls	BonfaceKilz
	After adding the missing attribute to "self.trait", we need to also need to update some missing calls.
2021-10-06	tests: test_run_mapping: Fix failing assert when getting perm strata	BonfaceKilz

2021-10-06	tests: test_run_mapping: Add missing attribute to "self.trait"	BonfaceKilz

2021-10-06	tests: test_run_mapping: Add missing positional argument "vals_hash"	BonfaceKilz

2021-10-06	add datatable for eigengenes	Alexander Kabui

2021-10-05	Merge branch 'testing' into feature/add_resizeable_columns	zsloan

2021-10-05	code format for wgcna results file	Alexander Kabui

2021-10-05	js formatting	Alexander Kabui

2021-10-05	move xterm code to setup	Alexander Kabui

2021-10-05	work on wgcna_setup form	Alexander Kabui

2021-10-04	Moved REDIS_CONN back into if __name__ == '__main__' since it doesn't need ↵	zsloan
	to be globally accessed anymore (I think I intiially moved it because I was calling it in create_group_data, but that ended up being unnecessary
2021-10-04	Changed the group.py script to replace user e-mails with IDs and to include ↵	zsloan
	id, name, changed_timestamp, and created_timestamp in group details
2021-10-04	Changed get_user_groups to pull both the ID and details in the for loop from ↵	zsloan
	group_list by using group_list.items()
2021-10-04	Add group link for user member groups	zsloan

2021-10-04	scripts: group.py: Modify exit message when displaying updated data	BonfaceKilz

2021-10-04	scripts: group.py: Remove "glom" dependency	BonfaceKilz

2021-10-04	Decode redis response by default	BonfaceKilz

2021-10-04	Modify resource editing script to enable data backups & restoration	BonfaceKilz

2021-10-04	wqflask: resource_manager: Remove logger	BonfaceKilz

2021-10-04	Add script that adds "editors" group to all resources in Redis	BonfaceKilz

2021-10-04	Add script for creating/ updating groups during authorisation	BonfaceKilz

2021-10-04	Remove "_scripts.html" and all it's references	BonfaceKilz

2021-10-04	new_security: login_user.html: Delete commented out block	BonfaceKilz

2021-10-04	Replace hard-coded e-mails with gn-proxy queries	BonfaceKilz
	* wqflask/wqflask/decorators.py (edit_access_required.wrap): Query the proxy to see the access rights of a given user.
2021-10-04	Rename "admin_login_required" to "edit_access_required"	BonfaceKilz

2021-10-01	add xterm web terminal	Alexander Kabui

2021-09-29	test template for gn3 wgcna	Alexander Kabui

2021-09-27	Apply pep-8 formatting	BonfaceKilz

2021-09-27	Remove variable-- named after a python keyword-- called "list"	BonfaceKilz

2021-09-27	Remove lengthy stack trace for 404, 400, 408 status codes	BonfaceKilz
	The stack trace causes the log file to grow into unmanageable sizes over time.
2021-09-25	Add progress indicator. Handle errors.	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add a progress indicator to show the user that there is some progress happening, so that they can wait. Add a function to handle any errors that arise.
2021-09-25	Remove hard-coded URL; use configured URL	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * etc/default_settings.py: remove duplicate configuration variable * wqflask/wqflask/collect.py: use the configured url for the API server Use the configured URL rather that the hard-coded URL that was used for testing out the clustered heatmap generation.