genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-02-05	Send emails for forgotten passwords	Muriithi Frederick Muriuki
	* Update the code so that it sends out emails for the "forgot password" feature.
2018-02-05	Add SMTP configuration variables	Muriithi Frederick Muriuki
	* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
2018-02-05	Merge remote-tracking branch 'origin/testing' into testing	Muriithi Frederick Muriuki

2018-01-30	gunicorn dev and prod modes added	Pjotr Prins

2018-01-30	Fail safely if elasticsearch is down or unconfigured	Muriithi Frederick Muriuki
	* If elasticsearch server is down, or the configuration variables are not provided at startup or in a configuration file, then do not allow the system to simply crash, but instead, inform the user that they cannot use the services that depend on elasticsearch to be running.
2018-01-30	Set to None if no value provided	Muriithi Frederick Muriuki
	* Add a method to set the configuration variables to None if the configuration values are not provided at startup or in the configuration files. The system already checks for these values, and if they are absent, it simply fails to display the OAuth service as available for use to login.
2018-01-29	Gunicorn works	Pjotr Prins

2018-01-29	startup script: adapting for gunicorn	Pjotr Prins

2018-01-24	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2018-01-24	Added links for markers in mapping results table when genotypes exist in DB	zsloan
	Added more info to trait details for phenotype traits Changed order of mapping methods Fixed layout of mapping loading screen to hopefully be centered on different screen sizes Improved layout of some elements in mapping results page
2018-01-19	Use elasticsearch rather than mysql for local accounts	Muriithi Frederick Muriuki
	* Register local accounts onto elasticsearch rather than mysql. * Login from the accounts on elasticsearch * Harmonise local and oauth2 logins to use the same code.
2018-01-19	Add OAuth2 login code for ORCID	Muriithi Frederick Muriuki
	* Add code to handle the login via ORCID
2018-01-19	Update configurations	Muriithi Frederick Muriuki
	* Have the authorisation URLs build up from the client id and client secret values.
2018-01-19	Add code to enable OAuth2 login	Muriithi Frederick Muriuki
	* Add some code to handle the login if the user chooses to login via GitHub or ORCID.
2018-01-19	Delay after save for indexing	Muriithi Frederick Muriuki
	* Elasticsearch need a short delay after adding document for it to index the document for subsequent access.
2018-01-19	Add more configuration variables.	Muriithi Frederick Muriuki
	* Add configurations for elasticsearch and github.
2018-01-19	Add save_user() function	Muriithi Frederick Muriuki
	* On successful login via OAuth2, save the details of the user in elasticsearch store, to avoid hitting the external provider for the basic details.
2018-01-12	Add functions to help handle github login	Muriithi Frederick Muriuki
	* Add functions to help with the github OAuth2 login process
2018-01-12	Add elasticsearch_tools module	Muriithi Frederick Muriuki
	* Collect variables and functions for using the elasticsearch system in a separate module.
2018-01-12	Add client_id and client_secret configurations	Muriithi Frederick Muriuki
	* Provide the OAuth2 client_id and client_secret values in configuration variables.
2018-01-10	Add template elements for OAuth login	Muriithi Frederick Muriuki
	* Add html elements that will be used to prompt users to login with either GitHub or ORCID.
2018-01-10	Add configuration variables for external services	Muriithi Frederick Muriuki
	* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login.
2018-01-04	Merge pull request #270 from pjotrp/testing	zsloan
	Merge some older commits
2017-12-20	Added submit_bnw even though it isn't working yet, just so views.py doesn't ↵	zsloan
	throw an error
2017-12-20	Fixed issue that caused Mb ticks to get out of alignment for mapping figure	zsloan

2017-12-20	Fixed the way PLINK outputs phenotype files (though there's still some ↵	zsloan
	problem preventing it from working) Added some code related to new plotly probability plot, though it's commented out until it looks how I want it to Added some code for adding the BNW link to GN2, though it's not working yet Updated dataset menu structure JSON file
2017-12-20	tools: find path for JS and gemma_wrapper	Pjotr Prins

2017-12-20	Bring in some earlier work - mostly documentation and startup handling	Pjotr Prins

2017-12-06	Fixed drop-down group order	zsloan

2017-12-04	Fixed drop-down scripts to more appropriately deal with BXD300 groups ↵	zsloan
	(though there's still a minor issue with a few datasets) Added some header data to mapping output file Fixed links in Network Group nodes/edges
2017-11-22	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2017-11-22	Added option to export csv of full mapping results	zsloan

2017-11-21	Merge pull request #258 from lyan6/master	zsloan
	improved scatter plots
2017-11-17	Fixed issue that caused GEMMA LOCO to not work on production	zsloan

2017-11-06	Replaced Histogram and Bar Chart with Plotly version and added new Box Plot ↵	zsloan
	with Plotly GEMMA now has option to select genotypes Updated dataset select dropdowns to be ordered correctly Fixed dataset select dropdowns for correlations to not show confidential datasets Added Skewness and Kurtosis to Basic Statistics table Fixed Verify and RNA-seq buttons on trait page Temporarily hardcoded Reference page until we get it to link with database
2017-10-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2	Lei Yan

2017-10-02	save as svg button work	Lei Yan

2017-09-22	Fixed issue that caused covariates to not work for certain data set groups	zsloan

2017-09-22	Fixed issue that caused LOCO to not work when remapping or using single ↵	zsloan
	chromosome view
2017-09-21	LOCO should work with GEMMA (when BIMBAM available), though I still need to ↵	zsloan
	do more testing
2017-09-14	Committing current progress towards implementing LOCO for GEMMA, not done yet	zsloan

2017-09-13	update Correlation Scatterplot format	Lei Yan

2017-09-12	Merge branch 'testing' of github.com:genenetwork/genenetwork2	Lei Yan

2017-09-12	change corr_scatterplot precision format	Lei Yan

2017-09-07	Updated show trait page to correctly show GEMMA options for certain data sets	zsloan

2017-09-07	Added the script to convert bimbam to kinship matrices	zsloan

2017-09-05	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2017-09-05	Added file converting genofiles to bimbam	zsloan

2017-09-04	gemma-wrapper: find binary in profile	Pjotr Prins

2017-08-29	Mostly changes related to getting gemma working with covariates and BIMBAM ↵	zsloan
	file format Other changes include: - Fixing links in the network graph - Changing button colors on show trait page - Changing color scheme for heatmap - Making rows highlight in yellow when clicked on - Some changes to table appearance (like giving gene global search a horizontal scroll)