genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-04-04	Merge pull request #303 from pjotrp/testing	zsloan
	Minor edits and document on ES
2018-04-04	Authentication: comments added	Pjotr Prins

2018-04-04	ES: doc	Pjotr Prins

2018-04-04	Switched to plotly probability plot	zsloan
	Removed a variety of scripts that weren't being used on the trait page
2018-04-02	Fixed link for staging server	zsloan

2018-04-02	Fixed error that caused server to not start with new user code	zsloan

2018-04-02	Merge pull request #301 from pjotrp/testing-rm-bloat	zsloan
	Testing rm bloat (jqplot and ckeditor)
2018-04-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2018-04-02	Just added link to staging branch to header bar	zsloan

2018-04-02	Config files are store in https://github.com/genenetwork/gn-deploy-servers repo	Pjotr Prins

2018-04-02	Remove file	Pjotr Prins

2018-04-02	User manager no longer uses SQL	Pjotr Prins

2018-04-02	js: rm ckeditor - need to replace	Pjotr Prins

2018-04-02	js: removed jqplot	Pjotr Prins

2018-04-02	user_session add output	Pjotr Prins

2018-03-30	Collections: use logging instead of print (@zsloan)	Pjotr Prins

2018-03-30	Fixes related to E-mail forgotten password	Pjotr Prins

2018-03-30	Fixes related to E-mail forgotten password	Pjotr Prins

2018-03-30	Fixes forgotten password error, see #257	Pjotr Prins

2018-03-29	Can now add markers to collection from mapping results page	zsloan

2018-03-29	Resolved conflict in views.py	zsloan

2018-03-29	Fixed box plots and got them to update with changed sample data	zsloan
	Removed fast correlation option because it doesn't work well with gunicorn Changed the type of logger from error to debug when logging which page is being visited in views.py
2018-03-29	Fixed gsearch blowout https://github.com/genenetwork/genenetwork2/issues/295	Pjotr Prins

2018-03-29	Type checking in its own file	Pjotr Prins

2018-03-29	Search: improved regex and some debug info	Pjotr Prins

2018-03-29	Disable caching of search errors	Pjotr Prins

2018-03-29	Checking search error terms with regex	Pjotr Prins

2018-03-29	Illegal search term corrected treatment and no longer shows as error in logs	Pjotr Prins

2018-03-26	Remove flask_security module - not used	Pjotr Prins

2018-03-26	Use logger.info instead of logger.debug, fixes ↵	Pjotr Prins
	https://github.com/genenetwork/genenetwork2/issues/296
2018-03-26	Skip automatic use of EXPLAIN_TEMPLATE_LOADING.	Pjotr Prins

2018-03-26	Refactor startup config for gunicorn and werkzeug	Pjotr Prins

2018-03-26	Fix	Pjotr Prins

2018-03-26	Authentication: some mods around defaults	Pjotr Prins

2018-03-26	- Disabled PYTHONPATH injection - fix Guix instead, see ↵	Pjotr Prins
	https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-26	Check that key exists before using it	Muriithi Frederick Muriuki
	* Ensure the key exists in the json object/dictionary, before trying to use it to retrieve a value.
2018-03-26	Provide connections to elasticsearch	Muriithi Frederick Muriuki
	* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests.
2018-03-26	Fix assumption of existing collection	Muriithi Frederick Muriuki
	* When logging in, if a user selects "Import existing collections", the system would throw an exception, since Redis would return a NoneType, which would then be accessed by json.loads(), which doesn't seem to know how to process that. This fixes that, by providing a string representing an empty json array ("[]"), in place of the NoneType.
2018-03-26	Add more login tests.	Muriithi Frederick Muriuki

2018-03-26	Added unittest example	Pjotr Prins

2018-03-26	Fixing authentication stuff so it uses parameters properly. Also no ↵	Pjotr Prins
	PYTHONPATH needed as it is now in the Guix build.
2018-03-26	Add tests for Registration process.	Muriithi Frederick Muriuki

2018-03-26	Update module to make it more testable	Muriithi Frederick Muriuki
	* Update functions to make them more testable. * Update code using updated functions.
2018-03-26	Check elasticsearch at point of use	Muriithi Frederick Muriuki
	* Instead of checking for the state of elasticsearch at startup, check the state at the moment the user requests a feature that depends on elasticsearch. This reduces the chances that the user is dropped onto an exception page when elasticsearch server goes down.
2018-03-26	Add check for elasticsearch	Muriithi Frederick Muriuki
	* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-03-26	Add code to allow user to change password	Muriithi Frederick Muriuki
	* After the email is sent to the user, there is need to provide a way for the user to actually change their password, and have the results saved.
2018-03-26	Refactor common items to more generic methods.	Muriithi Frederick Muriuki
	* Refactor code that can be used in more than one place to a more generic method/function that's called by other methods
2018-03-26	Send emails for forgotten passwords	Muriithi Frederick Muriuki
	* Update the code so that it sends out emails for the "forgot password" feature.
2018-03-26	Add SMTP configuration variables	Muriithi Frederick Muriuki
	* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
2018-03-26	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.