genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2017-01-26	Merge pull request #1 from genenetwork/testing	zsloan
	Various changes/fixes
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
2017-01-03	Fixed appearance of samples tables in show_trait to look like all the other ↵	zsloan
	tables Disabled sorting for the first column (check box) of the samples tables
2016-12-15	Merge pull request #234 from zsloan/master	zsloan
	Various changes
2016-12-15	Changed table appearance	zsloan
	Updated dataset_menu_structure.json
2016-12-13	Fixed a problem related to the last commit that caused a problem when ↵	zsloan
	loading a collection or doing ctl analysis
2016-12-12	Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵	zsloan
	be there and changed the code that calls them accordingly Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json
2016-11-29	Fixed loadings plot so it looks like the GN1 figure	zsloan

2016-11-21	Fixed correlation page so it correctly sorts by the scientific notation for ↵	zsloan
	sample p Set default sort for correlation page to sample p Improved appearance of correlation matrix some by decreasing line height Added labels to each figure/table on the correlation page
2016-11-18	Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) ↵	Lei Yan
	(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
2016-11-15	Fixed issue where sample values of 0 would sometimes be displayed as 'x', ↵	zsloan
	which would result in wrong correlation results Fixed issue where the mean would sometimes be displayed into of the additive effect
2016-11-11	Fixed error causing correlation matrix page to not work with 2 traits ↵	zsloan
	(related to factor loadings table) Also improved factor loads table to show only two factors when there are two traits Fixed error related to get_traits_from_collections.js being called in collections/list before jquery is defined
2016-11-11	Fixed problem that caused checkboxes to not work with Scroller search ↵	zsloan
	results pages Improved the way the table width is set for search results page
2016-11-08	Adding the joss badge	DannyArends

2016-11-07	Adding functions addNode and addEdge, to separate out the cytoscape graph ↵	DannyArends
	creation from the main CTL analysis code
2016-11-07	Adding the reference to the paper, and updating the output to show the ↵	DannyArends
	cytoscape.js network
2016-11-07	Adding code to the ctl analysis file to output nodes and edges for cytoscape	DannyArends

2016-11-07	Javascript file (based on the correlation file) to dsplay CTL networks using ↵	DannyArends
	cytoscape.js
2016-11-02	Fixed typos causing genofile selector to not show up in mapping options	zsloan

2016-11-02	Added toggleable short and long labels to correlation matrix	zsloan
	Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
2016-11-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-11-02	Added Scroller functionality to regular (but not global) search, which ↵	zsloan
	increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
2016-10-31	Merge branch 'lyan' into testing	Pjotr Prins

2016-10-31	Use existing GENODIR - the metadata can be stored there, next to the	Pjotr Prins
	.geno files.
2016-10-31	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	Pjotr Prins

2016-10-31	Fix spacing	Pjotr Prins

2016-10-31	Merge branch 'master' of github.com:lyan6/genenetwork2 into lyan	Pjotr Prins

2016-10-29	For those case that we have multiple genotypes we would like to add a selector.	Lei Yan

2016-10-25	Just removed some extraneous spaces in trait.py	zsloan

2016-10-25	Replaced the Download Table button for collection page with python version ↵	zsloan
	that displays metadata, etc Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
2016-10-21	Added CSV table download option to both gene and pheno global search	zsloan
	The "Database" part of the metadata isn't displayed for global search table downloads In both regular and global search, the table can not be sorted by whether the first column is checked Removed some unused datatables/javascript from the regular and global search page html
2016-10-21	Added metadata to "Download Table"	zsloan
	Only checked traits are now downloaded and all traits are downloaded if nothing is checked
2016-10-19	Rewrote export CSV in python	zsloan
	Still need to add metadata and change it to where only selected traits are exported
2016-10-17	Fixed issue where period sometimes appeared incorrectly in search results text.	zsloan
	Changed formatting of a couple things in search results text (capitalizing/underlining "terms" and bolding the search term) Changed "Gene" label on trait page to "NCBI" and removed GenBank link
2016-10-15	Remove all spacing introduced by merge	Pjotr Prins

2016-10-13	Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloan	Pjotr Prins

2016-10-12	Moved plink code out of marker_regression, though I don't think plink is ↵	zsloan
	working right now Ran some end of line conversion on rqtl_mapping because there were a few ^M's
2016-10-12	Removed unused gemma code from marker_regression.py and changed the order of ↵	zsloan
	a couple functions in collect.py to more accurately reflect when they're called
2016-10-11	Merge branch 'pjotr-gn2' into testing	Pjotr Prins

2016-10-09	Handle VERSION on different pages	Pjotr Prins

2016-10-09	Merge branch 'mechanize' into testing	Pjotr Prins

2016-10-09	Revert on Zach tabs and trailing spaces	Pjotr Prins

2016-10-09	CTL: show correct # of phenotypes also in results page	Pjotr Prins

2016-10-09	Add version information	Pjotr Prins

2016-10-09	Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloan	Pjotr Prins

2016-10-09	Changed mirrors & affiliates on wqflask/wqflask/templates/index_page_orig.html	Pjotr Prins

2016-10-09	Merge branch 'twitter' into pjotr-gn2	Pjotr Prins

2016-10-09	Merge branch 'testing' into twitter	Pjotr Prins

2016-10-09	Changed mirrors & affiliates on wqflask/wqflask/templates/index_page_orig.html	Pjotr Prins

2016-10-09	Added links to base.html	Pjotr Prins