genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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	User registration beginning to work (at least the first stage)	Sam

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

2013-09-24	before deleting more of the security flask stuff	Sam

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
2013-07-18	Added Amelie's rat data genotypes	Zachary Sloan
	Got human mapping mostly working Fixed dataset dropdown menus
2013-07-18	Merge branch 'master' of https://github.com/zsloan/genenetwork	Zachary Sloan
	Conflicts: wqflask/base/webqtlConfigLocal.py wqflask/maintenance/gen_select_dataset.py wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
2013-07-18	Added to installation notes	Zachary Sloan
	Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)
2013-07-17	Fixed gen_select_dataset.py	Zachary Sloan
	Appended redis installation info to notes
2013-07-16	Merge branch 'master' of https://github.com/zsloan/genenetwork	Zachary Sloan
	Conflicts: misc/gn_installation_notes.txt
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
2013-07-10	Updated gn_installation_notes	Zachary Sloan

2013-07-09	Committing installation notes before editing them more	Zachary Sloan

2013-07-03	Updated notes and created requirements.txt file	Zachary Sloan

2013-07-03	Made the table in the group manager sortable, etc	Zachary Sloan

2013-06-27	Created a group manager page where user administrators can create	Zachary Sloan
	groups of datasets to give/add read privileges to
2013-06-26	Merge /home/sam/gene	Zachary Sloan

2013-06-26	More signin changes	Sam

2013-06-26	Moved code creating DataSets object to a function in dataset.py	Zachary Sloan
	Added caching to creating DataSets object
2013-06-26	Got code that creates DataSets object running	Zachary Sloan
	Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-06-25	Added DataSets class to dataset.py that will be used to create list of	Zachary Sloan
	confidential datasets
2013-06-21	Added a thank you for siging in message	Sam
	Fixed issues where homepage was reloaded in modal after siging in
2013-06-21	Merge /home/zas1024/gene	Sam

2013-06-21	Working on getting logins working again	Sam

2013-06-21	Fixed bug where cursor was still being used in query	Zachary Sloan

2013-06-20	Merge branch 'flask' of /home/sam/gene	Zachary Sloan
	Conflicts: wqflask/wqflask/templates/index_page.html