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2018-03-26Refactor 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
2018-03-26Send emails for forgotten passwordsMuriithi Frederick Muriuki
* Update the code so that it sends out emails for the "forgot password" feature.
2018-03-26Add SMTP configuration variablesMuriithi Frederick Muriuki
* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
2018-03-26Fix conflictPjotr Prins
2018-03-26Fail safely if elasticsearch is down or unconfiguredMuriithi 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.
2018-03-26Set to None if no value providedMuriithi 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.
2018-03-26Use elasticsearch rather than mysql for local accountsMuriithi 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.
2018-03-26Add OAuth2 login code for ORCIDMuriithi Frederick Muriuki
* Add code to handle the login via ORCID
2018-03-26Update configurationsMuriithi Frederick Muriuki
* Have the authorisation URLs build up from the client id and client secret values.
2018-03-26Add code to enable OAuth2 loginMuriithi Frederick Muriuki
* Add some code to handle the login if the user chooses to login via GitHub or ORCID.
2018-03-26Delay after save for indexingMuriithi Frederick Muriuki
* Elasticsearch need a short delay after adding document for it to index the document for subsequent access.
2018-03-26Add more configuration variables.Muriithi Frederick Muriuki
* Add configurations for elasticsearch and github.
2018-03-26Add save_user() functionMuriithi 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.
2018-03-26Add elasticsearch module to the pathMuriithi Frederick Muriuki
* Add some code to set up the path for the python-elasticsearch module.
2018-03-26Add functions to help handle github loginMuriithi Frederick Muriuki
* Add functions to help with the github OAuth2 login process
2018-03-26Add elasticsearch_tools moduleMuriithi Frederick Muriuki
* Collect variables and functions for using the elasticsearch system in a separate module.
2018-03-26Add client_id and client_secret configurationsMuriithi Frederick Muriuki
* Provide the OAuth2 client_id and client_secret values in configuration variables.
2018-03-26Add template elements for OAuth loginMuriithi Frederick Muriuki
* Add html elements that will be used to prompt users to login with either GitHub or ORCID.
2018-03-26Add configuration variables for external servicesMuriithi Frederick Muriuki
* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login.
2018-03-22Change raise statementMuriithi Frederick Muriuki
* Change the raise statement to use an Exception object rather than using a string for compatibility with Python3.
2018-03-22Fix 'def' statementMuriithi Frederick Muriuki
* End the 'def' statement with a colon (:) * Add an empty line between lines at different indentation levels for clarity.
2018-03-21Use logger.info instead of logger.debug, fixes ↵Pjotr Prins
https://github.com/genenetwork/genenetwork2/issues/296
2018-03-21Skip automatic use of EXPLAIN_TEMPLATE_LOADING.Pjotr Prins
2018-03-21Deactivate navigation testsMuriithi Frederick Muriuki
* Navigation depends on Javascript to render the elements being tested. That would require selenium and its ilk to run such tests, meaning such packages would need to be defined for Guix first.
2018-03-20Refactor startup config for gunicorn and werkzeugPjotr Prins
2018-03-20FixPjotr Prins
2018-03-20Authentication: some mods around defaultsPjotr Prins
2018-03-19Initialise navigation tests.Muriithi Frederick Muriuki
* Start working on navigation tests.
2018-03-19* Add mapping tests. Fix link-checker tests.Muriithi Frederick Muriuki
* Add tests for the R/qtl and CIM mapping tools. * Fix tests for in-page links.
2018-03-19RELEASENOTESPjotr Prins
2018-03-19- Disabled PYTHONPATH injection - fix Guix instead, see ↵Pjotr Prins
https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-19Merge pull request #5 from fredmanglis/testingPjotr Prins
Testing
2018-03-18Initialise mapping testsMuriithi Frederick Muriuki
* Add mapping tests, and build the first of the tests.
2018-03-18Move import to the top of the page.Muriithi Frederick Muriuki
* Mainly to tell the dependencies easily.
2018-03-18Check that key exists before using itMuriithi Frederick Muriuki
* Ensure the key exists in the json object/dictionary, before trying to use it to retrieve a value.
2018-03-16Just undoing tabulator changes so I can push other changeszsloan
2018-03-15Changed appearance of mapping and correlation options on trait pagezsloan
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
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 moduleMuriithi Frederick Muriuki
* Add the module that will hold the code to test the links on the system.
2018-03-09Use argparse to handle argumentsMuriithi 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.
2018-03-02Added option to display selected covariates for GEMMA mappingzsloan
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
2018-02-26Merge /home/lei/gene into testingzsloan
2018-02-26Committing some in-progress changes related to loading correlation page from ↵zsloan
JSON
2018-02-23Add tests to check that the UI is setup correctlyMuriithi Frederick Muriuki
* Check that the links for OAuth2 logins via ORCID and GitHub are setup correctly.
2018-02-23Provide connections to elasticsearchMuriithi Frederick Muriuki
* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests.
2018-02-23Add new tests for orcid loginsMuriithi Frederick Muriuki
2018-02-23Add new test for github loginsMuriithi Frederick Muriuki
2018-02-23Remove failing codeMuriithi Frederick Muriuki
* With the parameterized module, the testcase cannot be run independently at this time.
2018-02-23update corr scatterplot interfaceLei Yan
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