genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-06-23	Logger: SQL	Pjotr Prins

2016-06-23	Refactored dir name dbFunction to db	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

2016-05-26	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	Updated dataset selection dropdown menus and fixed error caused by traits ↵	zsloan
	with no description
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
2016-03-18	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)
2016-03-14	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
2016-03-02	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
2015-07-09	Some phenotype searches were throwing an error due to an assert statement in ↵	zsloan
	trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-06-29	Merge pull request #72 from lomereiter/issue69	zsloan
	Fixes #69
2015-06-22	fixed a few potential security issues	Artem Tarasov

2015-06-18	fix all_samples_ordered	Artem Tarasov
	move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-05-22	Fixed issue where correlation didn't work for human traits (and probably ↵	zsloan
	some others)
2015-05-12	Fix #35	Artem Tarasov
	* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-04-10	Added git large file system (the .gitattributes files) and fixed an issue ↵	zsloan
	where rat trait pages wouldn't work
2014-12-12	Added a additive effect column to search result and collection tables	Zachary Sloan
	Fixed the header so that it looks fine when resizing
2014-10-02	Fixed an error when there's no locus for mRNA expression traits	Zachary Sloan

2014-08-21	Committer: Lei Yan <lei@penguin.uthsc.edu>	Lei Yan
	On branch master
2014-06-25	Added Karl's correlation matrix code	Zachary Sloan
	Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06	Implimented Karl Broman's lodchart code for the interval mapping function.	Zachary Sloan
	Suggestive/significant bars and additive effect curve added
2013-11-27	Clicking a trait in "color by trait" now gets all of its sample values	Zachary Sloan
	that will be used to color the bar graph
2013-11-26	Made some progress towards getting the traits inside a collection to display ↵	Zachary Sloan
	on hover
2013-11-25	Got the interval mapping results into a table	Zachary Sloan

2013-11-01	Merge /home/sam/gene	Zachary Sloan

2013-10-30	More work on collections	Sam

2013-10-25	Began working on color coding bar chart by extra attributes	Zachary Sloan

2013-09-13	Merge https://github.com/zsloan/genenetwork	Lei Yan
	Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
2013-08-07	Fixed things with the dataset dropdowns and mRNA datasets	Zachary Sloan
	Improved the templates for a couple pages related to changing user password, etc
2013-07-18	Added Amelie's rat data genotypes	Zachary Sloan
	Got human mapping mostly working Fixed dataset dropdown menus
2013-07-16	Wrote code that can get a dataset's type for every single GN	Zachary Sloan
	dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-25	Merge git://github.com/zsloan/genenetwork into flask	Lei Yan

2013-06-20	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19	Moved the normalize_values function to separate file corr_result_helpers.py	Lei Yan
	Added docstring test to normalize_values Number of overlapping samples column now displays correctly in the correlation results page
2013-06-19	Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columns	Lei Yan
	in the correlation page weren't displaying
2013-06-19	Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask	Lei Yan
	Conflicts: wqflask/base/data_set.py
2013-06-19	Changed QTL parameter name to "get_qtl_info" on trait.py and	Lei Yan
	other places it's called, like search_results.py Added other trait info fields to correlation results page
2013-06-19	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
2013-06-13	Fixed issue where too much memory was used as a result of creating a	Lei Yan
	dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-11	Put trait info for correlation results page into a dictionary instead	Lei Yan
	of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-31	Fixed the location column for the quick search page	Zachary Sloan
	Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
2013-05-30	Rewrote some code in get_trait_info in dataset.py	Lei Yan
	Added spearman correlation to show_corr_results and template