genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-10-23	Adding new collections works	Sam

2013-10-22	Bunch of work on collections and user management	Sam

2013-10-16	security code cleanup	Sam

2013-10-15	Merge /home/zas1024/gene	Sam

2013-10-15	Password reset now works...but needs some error checking still	Sam

2013-10-15	Before getting rid of query_string in DecodeUser	Sam

2013-10-15	Changed templates to call the header macro	Zachary Sloan
	Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-15	* Redid mail sending service to set a ping showing it's alive	Sam
	* Redid server so it wouldn't start unless mail service recently pinged * Wrote a bunch of forgot password code * Refactored sending email about verification and forgotten passwords
2013-10-11	Merge /home/sam/gene	Zachary Sloan

2013-10-11	Small changes around logging in	Sam

2013-10-11	Merge /home/lei/gene	Zachary Sloan
	Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10	Almost have correlation working for non-primary strain/group	Lei Yan
	There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.
2013-10-09	Improved some of the code related to the correlation page	Lei Yan
	For example, changed the two functions getting gene symbols and ids for a dataset into one function that can take a column name as a parameter
2013-10-08	Literature correlation works when it is selected as the sorted	Lei Yan
	correlation type (that is, when it is run again all traits in a database) Added a function to data_set.py that gets all the gene_ids in the data set. Not sure if having a separate function for getting the gene_ids and another for getting the gene symbols makes sense.
2013-10-08	Did some work with interval mapping page; will use qtl reaper to do	Zachary Sloan
	the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-10-07	Worked on logins, session_ids, flash messages, etc.	Sam

2013-10-06	Before writing login code	Sam

2013-10-03	Much more progess on logging in:	Sam
	* Verifying emails now works * Redid user manager
2013-10-02	Half the verification code for email addresses is done	Sam

2013-09-27	Downloaded the TableTools library so tables can be exported/saved	Lei Yan

2013-09-27	Added trait links to correlation results	Lei Yan
	Began adding the code that does the initial sort by literature correlation
2013-09-27	User registration beginning to work (at least the first stage)	Sam

2013-09-27	Before fixing an issue in pbkdf2	Sam

2013-09-24	Did some work towards doing the tissue correlation for all traits	root
	in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-09-24	before deleting more of the security flask stuff	Sam

2013-09-24	Just committing a few additions to the interval mapping code	Zachary Sloan

2013-09-24	Fixed the db_tools import in mrna_assay_tissue_data.py	Zachary Sloan
	Added file for the interval mapping page and wrote code that gets/sets some parameters
2013-09-20	Tissue correlation results work for sample r/rho correlation page	Lei Yan
	and are written to the template
2013-09-13	Merge /home/lei/gene	Zachary Sloan

2013-09-13	Added file that will convert genofiles to plink ped/map files	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
2013-09-06	Registration form validaiton without js works	Sam

2013-09-05	Missed some files in last checkin so adding them now	Sam

2013-09-05	Switched registration form to no longer be modal, but instead it's own page	Sam
	Added validation of form using parsley.js Added password strength indicator using zxcvbn
2013-09-05	Adjusting to using our own registariton package	Sam

2013-09-04	Trying to trace through files	Sam

2013-08-28	Various changes to track down what happens with security modules	Sam

2013-08-23	Finally figured out where to put flask_security into the code	Sam
	Various registration template changes
2013-08-23	Working on user registration and added nginx conf for my branch	Sam

2013-08-21	Fixed an issue where correlationFunction was being imported	Zachary Sloan
	instead of its updated name correlation_function
2013-08-21	Just removed a couple print statements	Zachary Sloan

2013-08-15	Removed the markers with no variance (and thus no p-values) from the	Zachary Sloan
	manhattan plot
2013-08-14	Merge branch 'master' of https://github.com/zsloan/genenetwork	Zachary Sloan

2013-08-14	Made some changes related to getting marker regression working for	Zachary Sloan
	some datasets
2013-08-14	Removed some duplicate files in the maintenance folder	Zachary Sloan

2013-08-13	Added several test files and the file with the class that	Zachary Sloan
	they import (browser_test.py)
2013-08-08	Fixed issue where points in marker regression manhattan plot	Zachary Sloan
	weren't positioned on the x-axis
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
2013-08-02	Fixed a bug related to groups with genofiles (not sure if it makes sense	Zachary Sloan
	for them not to have genofiles yet)
2013-07-30	Just added some print statements to debug an issue with LMM code	Zachary Sloan
	Also added some to notes