genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-03-19	Merge pull request #5 from fredmanglis/testing	Pjotr Prins
	Testing
2018-03-18	Initialise mapping tests	Muriithi Frederick Muriuki
	* Add mapping tests, and build the first of the tests.
2018-03-18	Move import to the top of the page.	Muriithi Frederick Muriuki
	* Mainly to tell the dependencies easily.
2018-03-18	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.
2018-03-14	Add tests for main web functionality	Muriithi Frederick Muriuki

2018-03-12	Add tests to check links.	Muriithi Frederick Muriuki

2018-03-09	Add link_checker module	Muriithi Frederick Muriuki
	* Add the module that will hold the code to test the links on the system.
2018-03-09	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.
2018-02-23	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.
2018-02-23	Provide connections to elasticsearch	Muriithi Frederick Muriuki
	* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests.
2018-02-23	Add new tests for orcid logins	Muriithi Frederick Muriuki

2018-02-23	Add new test for github logins	Muriithi Frederick Muriuki

2018-02-23	Remove failing code	Muriithi Frederick Muriuki
	* With the parameterized module, the testcase cannot be run independently at this time.
2018-02-21	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.
2018-02-21	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.
2018-02-19	Add more login tests.	Muriithi Frederick Muriuki

2018-02-19	Add a runner for all integration tests.	Muriithi Frederick Muriuki

2018-02-19	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.
2018-02-19	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.
2018-02-19	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.
2018-02-16	Add registration test	Muriithi Frederick Muriuki
	* Add integration test to check the registration process.
2018-02-16	Merge branch 'pjotrp-gn-testing-es' into testing	Muriithi Frederick Muriuki

2018-02-15	Requests added	Pjotr Prins

2018-02-15	Added unittest example	Pjotr Prins

2018-02-15	Fixing authentication stuff so it uses parameters properly. Also no ↵	Pjotr Prins
	PYTHONPATH needed as it is now in the Guix build.
2018-02-15	Fix conflict	Pjotr Prins

2018-02-13	Add tests for Registration process.	Muriithi Frederick Muriuki

2018-02-13	Update module to make it more testable	Muriithi Frederick Muriuki
	* Update functions to make them more testable. * Update code using updated functions.
2018-02-13	@zsloan: we should introduce full parameter checking and sensible defaults ↵	Pjotr Prins
	for every page we work on. It will help bug tracking. Probably fixes #279
2018-02-12	Merge pull request #277 from pjotrp/gn-production	zsloan
	Gn production
2018-02-11	Added gunicorn pid so we can not run twice	Pjotr Prins

2018-02-11	Using eventlet workers	zsloan

2018-02-10	Fix env variable $GEMMA_WRAPPER_COMMAND	Pjotr Prins

2018-02-10	Fixing GEMMA LOCO	Pjotr Prins

2018-02-10	Fixed finding PATHs - one return statement!	Pjotr Prins

2018-02-10	Check for bimbam path and bail out if it is missing	Pjotr Prins

2018-02-09	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.
2018-02-09	Add check for elasticsearch	Muriithi Frederick Muriuki
	* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-02-05	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.
2018-02-05	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
2018-02-05	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	Check each part of the PYTHONPATH	Muriithi Frederick Muriuki
	* PYTHONPATH may be composed of multiple locations in the filesystem, thus the need to test that each location exists and is a directory.
2018-02-05	Merge remote-tracking branch 'origin/testing' into testing	Muriithi Frederick Muriuki

2018-01-31	Merge pull request #275 from pjotrp/pjotr	zsloan
	Added cli swith and set timeout to 3 minutes for gunicorn-dev mode
2018-01-31	Startup: longer timeout for gunicorn-dev mode	Pjotr Prins

2018-01-31	Startup: added -cli option	Pjotr Prins

2018-01-30	Merge pull request #274 from pjotrp/pjotr	zsloan
	Add gunicorn support
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.