genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-06-18	Logging settings	Pjotr Prins

2016-06-18	Logger	Pjotr Prins

2016-06-18	Logger: replacing print statements	Pjotr Prins

2016-06-18	Changed file permssions to non-executable	Pjotr Prins

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

2016-06-03	Changed appearance of tables to more easily differentiate them from the rest ↵	zsloan
	of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-05-31	Fixed error when MrnaAssay search results didn't have a geneid	zsloan

2016-05-31	Allow the json dir to be in the old location.	Pjotr Prins

2016-05-26	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-05-26	Issue with certain samples (like BXD65a, ones were there are multiple for a ↵	zsloan
	single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23	Reaper mapping results are now correct and account for samples with two ↵	zsloan
	names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18	Merge branch 'staging' of https://github.com/genenetwork/genenetwork2	zsloan

2016-05-18	Updated dataset selection dropdown menus and fixed error caused by traits ↵	zsloan
	with no description
2016-05-17	Merge branch 'staging' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-05-13	Removing ref. to HTMLPATH	Pjotr Prins

2016-05-13	WebqtlConfig.py: Constant handling	Pjotr Prins

2016-05-13	Fix paths for images	Pjotr Prins

2016-04-29	Merge	Pjotr Prins

2016-04-28	Added option to export permutation results for mapping page	zsloan
	Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border
2016-04-20	Add file	Pjotr Prins

2016-04-20	-a	Pjotr Prins
	[PATCH 039/100] Removing commented code
2016-04-20	-a	Pjotr Prins
	[PATCH 038/100] Fix compile errors
2016-04-20	[PATCH 037/100] WebQtlConfig: sanitizing naming and used vars	Pjotr Prins

2016-04-20	[PATCH 033/100] Refactored file searching	Pjotr Prins

2016-04-20	[PATCH 032/100] file locating: error checking is built-in	Pjotr Prins

2016-04-20	[PATCH 024/100] Sanitizing file handling	Pjotr Prins

2016-04-20	[PATCH 023/100] WIP fixing all paths	Pjotr Prins

2016-04-19	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan
	Conflicts: wqflask/base/trait.py
2016-04-13	Moved the code getting the description/location because it was throwing an ↵	zsloan
	error for phenotype traits
2016-04-13	Global search should be able to return description and location columns now	zsloan

2016-04-11	Figured out how to load results into dataTable using AJAX, but still need to ↵	zsloan
	get it working with Scroller correctly Added code getting the description, etc to trait.py since it was missed from last commit
2016-04-11	Changed the way trait data is retrieved for the global search page (it now ↵	zsloan
	gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-03-29	Forgot to add GeneralObject file needed for haplotype analyst in last commit	zsloan

2016-03-18	Replaced header with other information in qtl map	zsloan
	Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
2016-03-15	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-03-15	Fixed the mapping figure track that lets you zoom into a smaller range	zsloan
	Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
2016-03-14	Changed the way headers look across all pages	zsloan
	Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-03	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-03-02	Increased gsearch speed by removing unnecessary query for sample data	zsloan
	Still slower than preferable due to having to query the gn1 database for every trait in the search results
2016-02-25	fixed untracked files	zsloan

2016-02-04	Most importantly, this commit fixes an issue that caused the trait page to ↵	zsloan
	not work because of the new dataset_menu_structure.json file An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
2015-12-14	GN1 mapping full genome figure now correct for pylmm and output to web page	zsloan

2015-12-12	Changed loop drawing qtl curve to fix some issues; still need to make it ↵	zsloan
	draw to different chr areas though
2015-11-18	Fixed issue where literature and tissue correlation didn't work	zsloan
	Scatterplot matrix feature only appears if user is logged in now Committing current progress on mapping page (it can at least import the file now, but there are still errors)
2015-11-09	Fixed issue that caused mapping to not work; for some reason the path to ↵	zsloan
	pylmm was wrong
2015-10-12	Changed the location filter for correlation page	zsloan

2015-09-11	Comment out some excessive stdout spam	DannyArends

2015-09-10	Fixed "TypeError: float argument required, not NoneType" about mean.	Lei Yan
	Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2015-08-26	Fixed issue with colums for the gene global search (still need to change for ↵	zsloan
	phenotype) Fixed issue where LRS and LOD are sometimes labeled incorrectly Changed the header of the trait page Added link to GN1 in header Fixxed an issue that made permutations not work with pylmm Fixed "sign in" button when creating a collection while not logged in
2015-07-20	Fixed the code that generates the dataset selection drop-down for correlations	zsloan
	Made changes to the tables of correlation results, collections, and search results: - Added resizeable columns to correlation results and collections, but not to search results because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling to the search results) - Correlation results and collections are now in scrolling tables - The style is the same across all of these tables now Remaining issues: - It doesn't seem like I can set the column width when initializing dataTables in correlation results. I don't know why this is; it might be due to the table already being the size of a full page. I want to be able to default to some good widths, even if the user can resize them - I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is due to having to put the text in a div.