genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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
2013-07-23	Fixed a couple issues with he quick_search_table.py script	Zachary Sloan
	Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-19	Finished integrating code that reads sample list from geno files	Zachary Sloan
	withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19	Created file gen_group_samplelists that iterates through all genofiles	Zachary Sloan
	and builds each groups' samplelist