genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2021-10-09	add function to process image data	Alexander Kabui

2021-10-09	unittest for processing wgcna output	Alexander Kabui

2021-10-09	add function to process gn3 wgcna output	Alexander Kabui

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)
2021-10-06	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵	Frederick Muriuki Muriithi
	clustered_heatmaps
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	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	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	wqflask: resource_manager: Remove logger	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.
2021-09-22	Removed the Control for (marker) option from R/qtl for now since Danny ↵	zsloan
	mentioned it isn't working correctly
2021-09-22	Fixed issue where the control marker parameter was being passed incorrectly ↵	zsloan
	to GN3 (should be just 'control' but was previously passed as 'control_marker')
2021-09-22	Only show most search page options if results exist; otherwise provide a ↵	zsloan
	link back to the home page
2021-09-22	Added type='button' to the Delete Collection button within collections/view, ↵	zsloan
	since without it it attempts to submit the form encapsulating the button (export in this case)
2021-09-22	Remove references to reaper_version and code for running old qtlreaper	zsloan

2021-09-22	Cleanup code	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove unnecessary console.log(...) statements that were used in development * Re-arrange the html elements * Rename element id
2021-09-22	Test heatmap creation from serialized figure	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Attempt using the figure, serialized as JSON, to display the clustered heatmap.
2021-09-20	Returned the GN1 url to gn1.genenetwork.org since it's apparently working ↵	zsloan
	well enough again now that some issues have been fixed
2021-09-20	Removed the reaper_version selection option, since original qtlreaper is no ↵	zsloan
	longer supported
2021-09-20	Added back the option to edit privileges on trait pages, since the metadata ↵	zsloan
	edit button had replaced it
2021-09-20	Prevent the default submit action	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Prevent the default submit action.
2021-09-20	Fix id used.	Frederick Muriuki Muriithi

2021-09-20	Move "Clustered Heatmap" button to separate form	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move the button out of the "export_form" into a new "heatmaps_form" to avoid some weird JS interaction that showed up.
2021-09-20	Implement proof-of-concept code to submit data	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement some javascript to activate the "Clustered Heatmap" button. This commit provides a proof-of-concept implementation to help with identifying the requirements for sending and receiving of the heatmaps data.
2021-09-20	Provide UI elements for clustered heatmap generation	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * wqflask/wqflask/collect.py: provide hard-coded URL for testing * wqflask/wqflask/templates/collections/view.html: provide button Provide a button to trigger the heatmap generation. As a test, we also provide a hard-coded URL for the API endpoint to get the heatmap data.