genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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.
2021-09-23	Clear any existing image on subsequent clicks	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * If the user clicks on the "Clustered Heatmap" button, the system should remove any previously existing clustered heatmap image and replace it with the new image.
2021-09-23	Move the heatmap display area to before the table	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move the heatmap area to before the data table, so that once the heatmap is generated, it shows up before the table, and the user is able to see what happened.