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2018-03-26Add functions to help handle github login...* Add functions to help with the github OAuth2 login process Muriithi Frederick Muriuki
2018-03-26Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in a separate module. Muriithi Frederick Muriuki
2018-03-26Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration variables. Muriithi Frederick Muriuki
2018-03-26Add template elements for OAuth login...* Add html elements that will be used to prompt users to login with either GitHub or ORCID. Muriithi Frederick Muriuki
2018-03-26Add configuration variables for external services...* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login. Muriithi Frederick Muriuki
2018-03-21Use logger.info instead of logger.debug, fixes https://github.com/genenetwork...Pjotr Prins
2018-03-21Skip automatic use of EXPLAIN_TEMPLATE_LOADING.Pjotr Prins
2018-03-20Refactor startup config for gunicorn and werkzeugPjotr Prins
2018-03-20FixPjotr Prins
2018-03-20Authentication: some mods around defaultsPjotr Prins
2018-03-19RELEASENOTESPjotr Prins
2018-03-19- Disabled PYTHONPATH injection - fix Guix instead, see https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS Pjotr Prins
2018-03-19Merge pull request #5 from fredmanglis/testing...TestingPjotr Prins
2018-03-18Initialise mapping tests...* Add mapping tests, and build the first of the tests. Muriithi Frederick Muriuki
2018-03-18Move import to the top of the page....* Mainly to tell the dependencies easily. Muriithi Frederick Muriuki
2018-03-18Check that key exists before using it...* Ensure the key exists in the json object/dictionary, before trying to use it to retrieve a value. Muriithi Frederick Muriuki
2018-03-16Just undoing tabulator changes so I can push other changeszsloan
2018-03-15Changed appearance of mapping and correlation options on trait page...Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping") Loading factors and their plot are hidden in situations where there's some error with calculating principal components Added GEMMA description and changed order of descriptions for mapping options on trait page zsloan
2018-03-14Add tests for main web functionalityMuriithi Frederick Muriuki
2018-03-12Add tests to check links.Muriithi Frederick Muriuki
2018-03-09Add link_checker module...* Add the module that will hold the code to test the links on the system. Muriithi Frederick Muriuki
2018-03-09Use argparse to handle arguments...* Use argparse to handle commandline arguments. * Create initial layout of how the code might end up - lots of the code is currently commented out. Muriithi Frederick Muriuki
2018-03-02Added option to display selected covariates for GEMMA mapping...Changed layout/appearance of mapping options Partially fixed issue with deleting collections Changes to correlation table still in progress; having trouble getting tabulator to load JSON zsloan
2018-02-26Merge /home/lei/gene into testingzsloan
2018-02-26Committing some in-progress changes related to loading correlation page from ...zsloan
2018-02-23Add tests to check that the UI is setup correctly...* Check that the links for OAuth2 logins via ORCID and GitHub are setup correctly. Muriithi Frederick Muriuki
2018-02-23Provide connections to elasticsearch...* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests. Muriithi Frederick Muriuki
2018-02-23Add new tests for orcid loginsMuriithi Frederick Muriuki
2018-02-23Add new test for github loginsMuriithi Frederick Muriuki
2018-02-23Remove failing code...* With the parameterized module, the testcase cannot be run independently at this time. Muriithi Frederick Muriuki
2018-02-23update corr scatterplot interfaceLei Yan
2018-02-21Simplify test. Check for content, rather than url...* 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. Muriithi Frederick Muriuki
2018-02-21Fix assumption of existing collection...* 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. Muriithi Frederick Muriuki
2018-02-19Add more login tests.Muriithi Frederick Muriuki
2018-02-19Add a runner for all integration tests.Muriithi Frederick Muriuki
2018-02-19Add test for local login...* Add an integration test to test that the login process for users registered locally to genenetwork2 works as expected. Muriithi Frederick Muriuki
2018-02-19Create parametrized superclass for tests...* 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. Muriithi Frederick Muriuki
2018-02-19Rename file and move common code...* Rename the file to make it an importable module * Refactor the test to move common code out to a super class. Muriithi Frederick Muriuki
2018-02-16Add registration test...* Add integration test to check the registration process. Muriithi Frederick Muriuki
2018-02-16Merge branch 'pjotrp-gn-testing-es' into testingMuriithi Frederick Muriuki
2018-02-15Requests addedPjotr Prins
2018-02-15Added unittest examplePjotr Prins
2018-02-15Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build. Pjotr Prins
2018-02-15Fix conflictPjotr Prins
2018-02-14Added empty collection error page to git, since it wasn't on productionzsloan
2018-02-13Resolved conflictzsloan
2018-02-13Just committing very minor change to correlation table so I can pull other ch...zsloan
2018-02-13Merge pull request #285 from pjotrp/testing...@zsloan: we should introduce full parameter checking and sensible defaultszsloan
2018-02-13Add tests for Registration process.Muriithi Frederick Muriuki
2018-02-13Update module to make it more testable...* Update functions to make them more testable. * Update code using updated functions. Muriithi Frederick Muriuki