genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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	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 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 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
2016-10-06	Logger: add more granular debug messages	Pjotr Prins

2016-10-05	print statements should be logger	Pjotr Prins

2016-10-03	Config: supporting JSON OVERRIDES	Pjotr Prins

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

2016-10-02	Errors: added time stamps in UTC	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
2016-08-16	Users can now select specific traits from collection when using collection ↵	zsloan
	tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc).
2016-06-26	gn_server: introduced one new query to fetch a dataset record and force ↵	Pjotr Prins
	fetch1 to return a tuple
2016-06-24	Log: and document SQL calls	Pjotr Prins

2016-06-23	Log: SQL queries	Pjotr Prins

2016-06-23	Logger: improved logging	Pjotr Prins

2016-06-23	Logger: prettify	Pjotr Prins

2016-06-23	Settings: add GN_SERVER_URL	Pjotr Prins

2016-06-23	Add warnings for adding MySQLdb cursor	Pjotr Prins

2016-06-21	log: replace print statements	Pjotr Prins

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

2016-06-21	Use logger also for benchmarking	Pjotr Prins

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

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

2016-06-21	Logger: SQL	Pjotr Prins

2016-06-19	gn_server: Species info can be fetched from gn_server	Pjotr Prins

2016-06-19	gn_server: SQL handling	Pjotr Prins

2016-06-19	Logger: started logging SQL	Pjotr Prins