genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-01-03	Created template for marek regression page and made the compute button direct	Zachary Sloan
	to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-18	Created new file species.py and species class object TheSpecies	Zachary Sloan
	Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
2012-12-07	Got basic statistics in show_trait to display the correct number	Zachary Sloan
	of samples for each group Got show_trait page to display for genotype traits
2012-12-06	Added minimum/maximum to basic statistics table	Zachary Sloan
	Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06	Got show_trait running again for MrnaAssay traits	Zachary Sloan

2012-12-06	Made many small changes to show_trait/data_set/search_results/trait to	Zachary Sloan
	remove use of the formData object and cursor
2012-12-05	Renamed webqtlTrait.py to trait.py	Zachary Sloan
	Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)
2012-12-05	Continued to make changes related to getting rid of cursor/db_conn	Zachary Sloan
	and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again
2012-12-04	Changed parser to allow quotes (i.e. name="rw williams")	Zachary Sloan
	Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy
2012-12-04	Began changing references to cursor/db_conn to use sqlalchemy	Zachary Sloan
	Wrote function for phenotype author searches
2012-11-30	Added example of escaping strings now that trasitioning to simple SQLAlchemy	Zachary Sloan

2012-11-30	Started switching to using basic sqlalchemy to handle db connection/queries	Zachary Sloan
	Began fixing bugs related to this fix, still in progress
2012-11-29	Changed a number of variables (riset to group, db to dataset)	Zachary Sloan
	Put most of the code for cisLRS and transLRS searches into the class CisTransLrsSearch (might change this name to something else later) Simplified escape code for searches in do_search.py Got search_results working again after some changes
2012-11-28	Made some small changes to get code working for genotype searches	Zachary Sloan

2012-11-27	Created subclass for each main data set type and moved the code	Zachary Sloan
	for getting trait info that was in search_results.py into its respective class Renamed webqtlDataset to DataSet/create_dataset in webqtlTrait.py, webqtlDatabaseFunction.py, and CorrelationPage.py Got search page running again for mRNA assay data sets with these changes
2012-11-27	Renamed webqtlDataSet.py to data_set.py	Zachary Sloan
	Renamed the class webqtlDataset to DataSet Finished cisLRS and transLRS search types in d_search.py Fixed parent/f1 issue in show_trait.py
2012-10-30	Worked on search_result.py code related to adding clause item to queries	Zachary Sloan
	Continued work on redesigning the trait data page design
2012-10-26	Got search page working for mice with a single gene search	Zachary Sloan

2012-10-25	Worked on search page code; got to the part that actually does the search	Zachary Sloan
	Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py
2012-10-24	Now builds json datastructure for menus correctly	Zachary Sloan

2012-10-23	Finished coffeescript that handles the home page dataset selection dropdowns	Zachary Sloan

2012-09-28	Removed show_trait_page.py and moved relevant code over to ↵	Zachary Sloan
	DataEditingPage.py (though the user security stuff still needs to be moved over)
2012-09-28	Finished getting extra attributes to display correctly in the trait data table	Zachary Sloan

2012-09-27	Worked on getting attributes in the SampleList object to display data ↵	Zachary Sloan
	properly, changed SampleList from an object list to object
2012-09-25	Got trait data page running for human dataset, changed list of sample ↵	Zachary Sloan
	objects to a SampleList object
2012-09-25	Fixed issue with parent strains appearing twice and began replacing variable ↵	Zachary Sloan
	names (strain -> sample, for example)
2012-09-19	Made pearson/spearman options disappear if lit correlation is chosen, began ↵	Zachary Sloan
	to address how to deal with Trait object in CorrelationPage
2012-09-14	Got the dynamic javascript stats table working	Zachary Sloan

2012-09-13	Worked on improving readData and informativeStrains functions in ↵	Zachary Sloan
	webqtlFormData while trying to get correlation page running
2012-09-12	Worked towards correctly passing form data to correlation page and addressed ↵	Zachary Sloan
	various bugs that arose while doing so
2012-09-07	Worked with passing form data to correlation page	Zachary Sloan

2012-08-29	Fixed so that outliers are now correctly highlighted	Zachary Sloan

2012-08-28	Various changes related to the webqtlCaseData object and the way ↵	Zachary Sloan
	values/variances/num_cases are called in DataEditingPage.py
2012-08-23	Various minor changes	Zachary Sloan

2012-06-06	Most of the top fields working	Sam Ockman

2012-06-05	Ran reindent.py recursively on wqflask directory	Sam Ockman

2012-06-04	Checkpoint along modifying for data trait and analysis	Sam Ockman

2012-06-03	Now using modified webqtlformdata for trait analysis	Sam Ockman

2012-06-03	Before changing fd for trait analysis into a webQTLFormData object	Sam Ockman

2012-06-03	Cleaning up trait stuff in flask	Sam Ockman

2012-05-24	Trying to get stuff working under new structure	Sam Ockman