genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-03-30	Add --fail argument to test runner	Pjotr Prins

2018-03-30	Tests: all tests run	Pjotr Prins

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	Fix conflict	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	RELEASENOTES	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	Initialise mapping tests	Muriithi Frederick Muriuki
	* Add mapping tests, and build the first of the tests.
2018-03-26	Move import to the top of the page.	Muriithi Frederick Muriuki
	* Mainly to tell the dependencies easily.
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	Add tests for main web functionality	Muriithi Frederick Muriuki

2018-03-26	Add tests to check links.	Muriithi Frederick Muriuki

2018-03-26	Add link_checker module	Muriithi Frederick Muriuki
	* Add the module that will hold the code to test the links on the system.
2018-03-26	Use argparse to handle arguments	Muriithi Frederick Muriuki
	* Use argparse to handle commandline arguments. * Create initial layout of how the code might end up - lots of the code is currently commented out.
2018-03-26	Add tests to check that the UI is setup correctly	Muriithi Frederick Muriuki
	* Check that the links for OAuth2 logins via ORCID and GitHub are setup correctly.
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	Add new tests for orcid logins	Muriithi Frederick Muriuki

2018-03-26	Add new test for github logins	Muriithi Frederick Muriuki

2018-03-26	Remove failing code	Muriithi Frederick Muriuki
	* With the parameterized module, the testcase cannot be run independently at this time.
2018-03-26	Simplify test. Check for content, rather than url	Muriithi Frederick Muriuki
	* The test functions were very similar, so this commit refactors out the common test code to a single method, and passes in the data to the test using the parameterized package. * Check that the page content after a login attempt is the expected content, rather than checking the url.
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	Add a runner for all integration tests.	Muriithi Frederick Muriuki

2018-03-26	Add test for local login	Muriithi Frederick Muriuki
	* Add an integration test to test that the login process for users registered locally to genenetwork2 works as expected.
2018-03-26	Create parametrized superclass for tests	Muriithi Frederick Muriuki
	* Since the tests require that some parameters be provided while running the tests, create a class that helps abstract away the details of retrieving and setting the expected parameters.
2018-03-26	Rename file and move common code	Muriithi Frederick Muriuki
	* Rename the file to make it an importable module * Refactor the test to move common code out to a super class.
2018-03-26	Add registration test	Muriithi Frederick Muriuki
	* Add integration test to check the registration process.
2018-03-26	Requests added	Pjotr Prins

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	Fix conflict	Pjotr Prins

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.