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2022-10-28Declutter stdoutFrederick Muriuki Muriithi
* wqflask/utility/tools.py: Output extraneous messages to stderr rather than stdout to avoid cluttering the output.
2022-09-19Refactor: raise appropriate errorFrederick Muriuki Muriithi
If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`.
2022-07-25Return config in app.config or NoneFrederick Muriuki Muriithi
Update the code to return the setting already set up in the app.config dictionary if it exists or None if it does not exist.
2021-11-25Delete noisy loggingBonfaceKilz
2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-10-22Fix line pulling GN3_LOCAL_URL from settingszsloan
2021-10-22Added proxy and local GN3 URLs in tools.py (which should be set in the ↵zsloan
settings file)
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2020-12-18Added redirect_uri to the ORCID_AUTH_URL since it wasn't working due to ↵zsloan
missing this parameter
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-08-18Wrap print statements in parenthesesBonfaceKilz
2020-07-24Revert "Add work-around for failed imports in unittest"BonfaceKilz
This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
2020-07-24Add work-around for failed imports in unittestBonfaceKilz
* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app` and the gn2 script will use `from wqflask import app`
2020-07-24Revert "Add work-around for failed imports in unittest"BonfaceKilz
This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
2020-07-24Add work-around for failed imports in unittestBonfaceKilz
* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app` and the gn2 script will use `from wqflask import app`
2020-07-16Expose elastic-search variables for tests to passBonfaceKilz
2020-05-06Replace CSS dependencies for datatablesBonfaceKilz
2020-04-26Merge master and testingmasterPjotr Prins
2020-04-24Replaced hard-coded instances of GN2 urls with ones pulled from settings filezsloan
2020-04-22Fixed a variety of issues related to users registering and logging inzsloan
GN2 should now work when Redis is empty
2020-03-03Refactored all the anonymous (not logged-in) user stuff so that both ↵zsloan
logged-in and anonymous users share the same code
2019-09-06Fix name of javascript-twitter-post-fetcherPjotr Prins
2019-07-23Added change to automatically update datasets list using rest api instead of ↵zsloan
json file Removed option to edit certain html pages, like news, policies, etc
2019-02-18Updated installation instructions and SERVER_PORT for single flask serverPjotr Prins
2019-02-13Removed pylmm references and related functionsPjotr Prins
2018-09-05ELASTICSEARCH settings and fix runserver.py to run without gunicornPjotr Prins
2018-04-06See #308.Pjotr Prins
Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
2018-03-26Refactor startup config for gunicorn and werkzeugPjotr Prins
2018-03-26FixPjotr Prins
2018-03-26Authentication: some mods around defaultsPjotr 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
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-03-26Add SMTP configuration variablesMuriithi Frederick Muriuki
* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
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.
2018-03-26Update configurationsMuriithi Frederick Muriuki
* Have the authorisation URLs build up from the client id and client secret values.
2018-03-26Add more configuration variables.Muriithi Frederick Muriuki
* Add configurations for elasticsearch and github.
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 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.
2018-02-10Fixed finding PATHs - one return statement!Pjotr Prins
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
2017-12-20tools: find path for JS and gemma_wrapperPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
2017-06-12Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMANDPjotr Prins
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-04 01:49:27 +0000