| Age | Commit message (Expand) | Author |
|---|
| 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 | Fix conflict | Pjotr Prins |
| 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 | Use elasticsearch rather than mysql for local accounts...* Register local accounts onto elasticsearch rather than mysql.
* Login from the accounts on elasticsearch
* Harmonise local and oauth2 logins to use the same code.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add OAuth2 login code for ORCID...* Add code to handle the login via ORCID
| 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 | Add code to enable OAuth2 login...* Add some code to handle the login if the user chooses to login via
GitHub or ORCID.
| 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 module to the path...* Add some code to set up the path for the python-elasticsearch module.
| Muriithi Frederick Muriuki |
| 2018-03-26 | Add functions to help handle github login...* Add functions to help with the github OAuth2 login process
| 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 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 |
| 2018-03-26 | 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 |
| 2018-03-22 | Fix 'def' statement...* End the 'def' statement with a colon (:)
* Add an empty line between lines at different indentation levels for
clarity.
| Muriithi Frederick Muriuki |
| 2018-03-21 | Use logger.info instead of logger.debug, fixes https://github.com/genenetwork... | Pjotr Prins |
| 2018-03-21 | Skip automatic use of EXPLAIN_TEMPLATE_LOADING. | Pjotr Prins |
| 2018-03-21 | Deactivate navigation tests...* 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.
| Muriithi Frederick Muriuki |
| 2018-03-20 | Refactor startup config for gunicorn and werkzeug | Pjotr Prins |
| 2018-03-20 | Fix | Pjotr Prins |
| 2018-03-20 | Authentication: some mods around defaults | Pjotr Prins |
| 2018-03-19 | Initialise navigation tests....* Start working on navigation tests.
| Muriithi Frederick Muriuki |
| 2018-03-19 | * Add mapping tests. Fix link-checker tests....* Add tests for the R/qtl and CIM mapping tools.
* Fix tests for in-page links.
| Muriithi Frederick Muriuki |
| 2018-03-19 | RELEASENOTES | Pjotr Prins |
| 2018-03-19 | - Disabled PYTHONPATH injection - fix Guix instead, see https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
| Pjotr Prins |
| 2018-03-19 | Merge pull request #5 from fredmanglis/testing...Testing | Pjotr Prins |
| 2018-03-18 | Initialise mapping tests...* Add mapping tests, and build the first of the tests.
| Muriithi Frederick Muriuki |
| 2018-03-18 | Move import to the top of the page....* Mainly to tell the dependencies easily.
| Muriithi Frederick Muriuki |
| 2018-03-18 | Check 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 |
| 2018-03-16 | Just undoing tabulator changes so I can push other changes | zsloan |
| 2018-03-15 | Changed 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 |
| 2018-03-14 | Add tests for main web functionality | Muriithi Frederick Muriuki |
| 2018-03-12 | Add tests to check links. | Muriithi Frederick Muriuki |
| 2018-03-09 | Add link_checker module...* Add the module that will hold the code to test the links on the
system.
| Muriithi Frederick Muriuki |
| 2018-03-09 | Use 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 |
| 2018-03-05 | rename draw_corr_scatterplot-2.js to draw_corr_scatterplot.js | Lei Yan |
| 2018-03-05 | update Correlation Scatterplot | Lei Yan |
| 2018-03-02 | Added 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 |
| 2018-02-28 | Forgot to import function assert_file | zsloan |
| 2018-02-28 | Fixed issue that caused some GEMMA results to appear incorrectly | zsloan |
| 2018-02-28 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 | zsloan |
| 2018-02-26 | Merge /home/lei/gene into testing | zsloan |
| 2018-02-26 | Committing some in-progress changes related to loading correlation page from ... | zsloan |
| 2018-02-23 | Add 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 |
| 2018-02-23 | Provide connections to elasticsearch...* Provide connections to elasticsearch at various points in the code.
These oversight was caught while running tests.
| Muriithi Frederick Muriuki |
| 2018-02-23 | Add new tests for orcid logins | Muriithi Frederick Muriuki |
