genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-04-06	See #308.	Pjotr Prins
	Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
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	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 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	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	Update configurations	Muriithi Frederick Muriuki
	* Have the authorisation URLs build up from the client id and client secret values.
2018-03-26	Add more configuration variables.	Muriithi Frederick Muriuki
	* Add configurations for elasticsearch and github.
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 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.
2018-02-10	Fixed finding PATHs - one return statement!	Pjotr Prins

2018-02-10	Check for bimbam path and bail out if it is missing	Pjotr Prins

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

2017-05-31	JS_GUIX_PATH may not be there	Pjotr Prins

2017-05-31	JS module handling	Pjotr Prins

2017-05-21	Merge from the diet branch.	Pjotr Prins
	* refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile
2017-02-06	Fixed appearance of several tables (search, mapping results, sample data)	zsloan
	Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
2017-01-26	GEMMA now works with CFW data (had to update where it looks for the input ↵	zsloan
	files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
2016-10-11	Merge branch 'pjotr-gn2' into testing	Pjotr Prins

2016-10-09	Add version information	Pjotr Prins

2016-10-07	Make sure JS path exists	Pjotr Prins

2016-10-07	Changed error output	Pjotr Prins

2016-10-07	Saner handling of TMPDIR and TEMPDIR	Pjotr Prins
	Throw error when TMPDIRs are not writable
2016-10-03	Config: supporting JSON OVERRIDES	Pjotr Prins

2016-10-03	Debug: sanitize some output	Pjotr Prins

2016-09-25	Make sure MAPPING_PATH exists	Pjotr Prins

2016-09-25	tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2	Pjotr Prins

2016-09-10	Support for running maintenance scripts so they can pick up all webserver ↵	Pjotr Prins
	settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
2016-06-24	Log: and document SQL calls	Pjotr Prins

2016-06-23	Logger: improved logging	Pjotr Prins

2016-06-23	Settings: add GN_SERVER_URL	Pjotr Prins

2016-06-21	logger: add format field (reserve)	Pjotr Prins

2016-06-21	Logger: switch for logging SQLALCHEMY	Pjotr Prins

2016-06-21	Benchmarking: allow output select with LOG_BENCH	Pjotr Prins

2016-06-19	gn_server: SQL handling	Pjotr Prins

2016-06-19	Renamed settings so they are grouped together	Pjotr Prins

2016-06-18	Logging settings	Pjotr Prins

2016-06-18	Logger: more info	Pjotr Prins

2016-06-18	Logger: introducing logging	Pjotr Prins

2016-06-18	Logging: behaviours	Pjotr Prins

2016-06-18	Logger: improving output	Pjotr Prins

2016-06-18	Logger: introducing logging	Pjotr Prins

2016-06-17	Conflict	Pjotr Prins

2016-06-17	Removed trailing spaces in .py and .js files	Pjotr Prins