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2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2013-01-03Began working on marker_regression.py and created Chromosomes classZachary Sloan
in species.py
2013-01-03marker_regression page is up againZachary Sloan
2013-01-03Created template for marek regression page and made the compute button directZachary 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
2012-12-20Changed layout of marker regression optionsZachary Sloan
2012-12-20The control locus field in the interval mapping settings is now disabled ifZachary Sloan
"choose closest control" is set to "yes"
2012-12-20Made composite mapping options show/hide for the interval mapping sectionZachary Sloan
2012-12-20More changes to the layout of interval mapping optionsZachary Sloan
2012-12-20Continued to customize the interval mapping menuZachary Sloan
2012-12-20Improved appearance/layout of the interval mapping tab using bootstrapZachary Sloan
2012-12-20Form data passed via POST for marker regressionZachary Sloan
Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan
2012-12-18Changed html for the marker regression tabZachary Sloan
Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form"
2012-12-18Created new file species.py and species class object TheSpeciesZachary 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
2012-12-07Got links working for statistics table labelsZachary Sloan
2012-12-07Got basic statistics in show_trait to display the correct numberZachary Sloan
of samples for each group Got show_trait page to display for genotype traits
2012-12-07Got show_trait page to appear again for phenotype traitsZachary Sloan
Need to see why other samples list doesn't appear for traits in BXDPublishedPhenotypes
2012-12-06All 10 stats workingZachary Sloan
2012-12-06Continued work on basic statistics table in show_traitZachary Sloan
Continued work towards getting show_trait to work with phenotype traits
2012-12-06Added minimum/maximum to basic statistics tableZachary Sloan
Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06Got show_trait running again for MrnaAssay traitsZachary Sloan
2012-12-06Made many small changes to show_trait/data_set/search_results/trait toZachary Sloan
remove use of the formData object and cursor
2012-12-05Renamed webqtlTrait.py to trait.pyZachary 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)
2012-12-05Continued to make changes related to getting rid of cursor/db_connZachary Sloan
and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again
2012-12-04Changed 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
2012-12-04Began changing references to cursor/db_conn to use sqlalchemyZachary Sloan
Wrote function for phenotype author searches
2012-11-30Added example of escaping strings now that trasitioning to simple SQLAlchemyZachary Sloan
2012-11-30Started switching to using basic sqlalchemy to handle db connection/queriesZachary Sloan
Began fixing bugs related to this fix, still in progress
2012-11-30Finished pValue searchZachary Sloan
Got headers working in search page
2012-11-30Got searches working for RANGE and MEAN commandsZachary Sloan
Created a file where renamed variables will be listed for future reference
2012-11-29Changed 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
2012-11-29Got LRS searches working with 5 parametersZachary Sloan
2012-11-28Got cisLRS search working (in web service) for searches with > or < (ex. LRS>99)Zachary Sloan
search_term is always a list now ([99] in the example LRS>99)
2012-11-28Changed parser to split by ">=" and "<="Zachary Sloan
2012-11-28Changed parser.py to deal with the wild card character (*) and to split byZachary Sloan
">" and "<" in addition to "=" and ":"
2012-11-28Made some small changes to get code working for genotype searchesZachary Sloan
2012-11-27Created subclass for each main data set type and moved the codeZachary 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
2012-11-27Renamed webqtlDataSet.py to data_set.pyZachary 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
2012-11-21Changed parser to allow for bother square brackets and parenthesesZachary Sloan
Changed show_trait.coffee to get the stats table working again Still need to get stats table to work with changed values
2012-11-21Trimmed a large amount of code from search_results.pyZachary Sloan
Removed everything related to drawing html; finished code for getting info for Phenotype and Genotype result tables Did some more with CisLRS and TransLRS searches Put something in parser about using square brackets as well as parentheses Edited template for other table types (Geno and Pheno)
2012-11-16Made small change to parser to have it detect square brackets '[' along withZachary Sloan
round ones '('; need to ask Sam about rewriting the regular expression stuff Trimmed a lot of code from search_results.py
2012-11-09Did some work with adding code for LRS-related searchesZachary Sloan
2012-11-02Created search objects for GeneRIF and GeneWiki searchesZachary Sloan
Got search results to display Refactored the template for show_trait page
2012-11-01Changed the if/elif statements for the different dataset types toZachary Sloan
use a dictionary instead
2012-11-01Began integrating do_search.py's DoSearch object into search_results.py,Zachary Sloan
with simple searches returning correct results Still need to make results display in the table Sam also did some work with the bootstrap styling
2012-10-31Did work with writing the search page query functions for some ProbeSet and ↵Zachary Sloan
Phenotype searches
2012-10-30Worked on search_result.py code related to adding clause item to queriesZachary Sloan
Continued work on redesigning the trait data page design
2012-10-30Did some work converting show_trait.html to using bootstrap for stylingZachary Sloan
2012-10-26Changed search page appearance using bootstrapZachary Sloan
Headers/information displays correctly for single mRNA expression trait searches
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