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2018-03-26Fix assumption of existing collectionMuriithi 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.
2018-03-26Add more login tests.Muriithi Frederick Muriuki
2018-03-26Add a runner for all integration tests.Muriithi Frederick Muriuki
2018-03-26Add test for local loginMuriithi Frederick Muriuki
* Add an integration test to test that the login process for users registered locally to genenetwork2 works as expected.
2018-03-26Create parametrized superclass for testsMuriithi 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.
2018-03-26Rename file and move common codeMuriithi Frederick Muriuki
* Rename the file to make it an importable module * Refactor the test to move common code out to a super class.
2018-03-26Add registration testMuriithi Frederick Muriuki
* Add integration test to check the registration process.
2018-03-26Requests addedPjotr Prins
2018-03-26Added unittest examplePjotr Prins
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-03-26Add tests for Registration process.Muriithi Frederick Muriuki
2018-03-26Update module to make it more testableMuriithi Frederick Muriuki
* Update functions to make them more testable. * Update code using updated functions.
2018-03-26Check elasticsearch at point of useMuriithi 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.
2018-03-26Add check for elasticsearchMuriithi Frederick Muriuki
* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-03-26Add code to allow user to change passwordMuriithi 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.
2018-03-26Refactor 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.
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