| Age | Commit message (Expand) | Author |
|---|
| 2018-04-09 | Removed the basicStatistics directory/contents because nothing there was bein......Removed box plot code from Plot.py since we no longer use it either
| zsloan |
| 2018-04-06 | See #308....Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
| Pjotr Prins |
| 2018-04-05 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te... | Muriithi Frederick Muriuki |
| 2018-04-04 | ES: doc | Pjotr Prins |
| 2018-03-31 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te......* Fix conflicts
| Muriithi Frederick Muriuki |
| 2018-03-29 | Type checking in its own file | Pjotr Prins |
| 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 https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
| Pjotr Prins |
| 2018-03-26 | Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build.
| Pjotr Prins |
| 2018-03-26 | Update module to make it more testable...* Update functions to make them more testable.
* Update code using updated functions.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Check elasticsearch at point of use...* 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.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add check for elasticsearch...* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Refactor common items to more generic methods....* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add SMTP configuration variables...* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Fail safely if elasticsearch is down or unconfigured...* 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.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Set to None if no value provided...* 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.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Update configurations...* Have the authorisation URLs build up from the client id and client
secret values.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Delay after save for indexing...* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add more configuration variables....* Add configurations for elasticsearch and github.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add save_user() function...* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in
a separate module.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration
variables.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add 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 |
| 2018-03-22 | Change raise statement...* Change the raise statement to use an Exception object rather than
using a string for compatibility with Python3.
| Muriithi Frederick Muriuki |
| 2018-02-15 | Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build.
| Pjotr Prins |
| 2018-02-15 | Fix conflict | Pjotr Prins |
| 2018-02-13 | Update module to make it more testable...* Update functions to make them more testable.
* Update code using updated functions.
| Muriithi Frederick Muriuki |
| 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...* 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.
| Muriithi Frederick Muriuki |
| 2018-02-09 | Add check for elasticsearch...* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
| Muriithi Frederick Muriuki |
| 2018-02-05 | Refactor common items to more generic methods....* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
| Muriithi Frederick Muriuki |
| 2018-02-05 | Add SMTP configuration variables...* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
| Muriithi Frederick Muriuki |
| 2018-01-30 | Fail safely if elasticsearch is down or unconfigured...* 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.
| Muriithi Frederick Muriuki |
| 2018-01-30 | Set to None if no value provided...* 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.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Update configurations...* Have the authorisation URLs build up from the client id and client
secret values.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Delay after save for indexing...* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add more configuration variables....* Add configurations for elasticsearch and github.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add save_user() function...* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
| Muriithi Frederick Muriuki |
| 2018-01-12 | Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in
a separate module.
| Muriithi Frederick Muriuki |
| 2018-01-12 | Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration
variables.
| Muriithi Frederick Muriuki |
| 2018-01-10 | Add 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 |
| 2017-12-20 | tools: find path for JS and gemma_wrapper | Pjotr Prins |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins |
| 2017-09-04 | gemma-wrapper: find binary in profile | Pjotr Prins |
| 2017-06-12 | Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND | Pjotr Prins |
| 2017-06-02 | settings: do not enforce JS paths | Pjotr Prins |
