| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2018-04-02 | Config files are store in https://github.com/genenetwork/gn-deploy-servers repo | Pjotr Prins | |
| 2018-04-02 | Remove file | Pjotr Prins | |
| 2018-04-02 | User manager no longer uses SQL | Pjotr Prins | |
| 2018-04-02 | user_session add output | Pjotr Prins | |
| 2018-03-30 | Collections: use logging instead of print (@zsloan) | Pjotr Prins | |
| 2018-03-30 | Fixes related to E-mail forgotten password | Pjotr Prins | |
| 2018-03-30 | Fixes related to E-mail forgotten password | Pjotr Prins | |
| 2018-03-30 | Fixes forgotten password error, see #257 | 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 | 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 | - 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 | 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 | 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 | 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 | 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 | 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. | |||
| 2018-03-26 | Set to None if no value provided | Muriithi 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. | |||
| 2018-03-26 | Use elasticsearch rather than mysql for local accounts | Muriithi 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. | |||
| 2018-03-26 | Add OAuth2 login code for ORCID | Muriithi Frederick Muriuki | |
| * Add code to handle the login via ORCID | |||
| 2018-03-26 | Update configurations | Muriithi Frederick Muriuki | |
| * Have the authorisation URLs build up from the client id and client secret values. | |||
| 2018-03-26 | Add code to enable OAuth2 login | Muriithi Frederick Muriuki | |
| * Add some code to handle the login if the user chooses to login via GitHub or ORCID. | |||
| 2018-03-26 | Delay after save for indexing | Muriithi Frederick Muriuki | |
| * Elasticsearch need a short delay after adding document for it to index the document for subsequent access. | |||
| 2018-03-26 | Add more configuration variables. | Muriithi Frederick Muriuki | |
| * Add configurations for elasticsearch and github. | |||
| 2018-03-26 | Add save_user() function | Muriithi 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. | |||
| 2018-03-26 | Add functions to help handle github login | Muriithi Frederick Muriuki | |
| * Add functions to help with the github OAuth2 login process | |||
| 2018-03-26 | Add elasticsearch_tools module | Muriithi Frederick Muriuki | |
| * Collect variables and functions for using the elasticsearch system in a separate module. | |||
| 2018-03-26 | Add client_id and client_secret configurations | Muriithi Frederick Muriuki | |
| * Provide the OAuth2 client_id and client_secret values in configuration variables. | |||
| 2018-03-26 | Add template elements for OAuth login | Muriithi Frederick Muriuki | |
| * Add html elements that will be used to prompt users to login with either GitHub or ORCID. | |||
| 2018-03-26 | Add configuration variables for external services | Muriithi Frederick Muriuki | |
| * Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login. | |||
| 2018-03-16 | Just undoing tabulator changes so I can push other changes | zsloan | |
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