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path: root/wqflask/base/trait.py
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2016-09-29Fix global search "il6" for "Internal Server Error". Add single quotes into ↵Lei Yan
MySQL query.
2016-08-24Replaced post-publication description with pre-publication description for ↵zsloan
confidential phenotype traits in search results and trait pages Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases) Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale Removed some unused javascript libary imports from search/global search pages
2016-08-16Users can now select specific traits from collection when using collection ↵zsloan
tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc).
2016-06-26Resolve conflictsPjotr Prins
2016-06-24Removed function 'get_info' in trait.py that was never used and reomved ↵zsloan
'get_trait_info' call from search_result_page.py because its query was already being run
2016-06-23Logger: SQLPjotr Prins
2016-06-23Logger: SQLPjotr Prins
2016-06-23Refactored dir name dbFunction to dbPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-03Changed appearance of tables to more easily differentiate them from the rest ↵zsloan
of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-05-31Fixed error when MrnaAssay search results didn't have a geneidzsloan
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Issue with certain samples (like BXD65a, ones were there are multiple for a ↵zsloan
single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23Reaper mapping results are now correct and account for samples with two ↵zsloan
names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18Updated dataset selection dropdown menus and fixed error caused by traits ↵zsloan
with no description
2016-04-19Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
Conflicts: wqflask/base/trait.py
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Figured out how to load results into dataTable using AJAX, but still need to ↵zsloan
get it working with Scroller correctly Added code getting the description, etc to trait.py since it was missed from last commit
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-03-18Replaced header with other information in qtl mapzsloan
Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
2016-03-14Changed the way headers look across all pageszsloan
Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-02Increased gsearch speed by removing unnecessary query for sample datazsloan
Still slower than preferable due to having to query the gn1 database for every trait in the search results
2015-07-09Some phenotype searches were throwing an error due to an assert statement in ↵zsloan
trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-06-29Merge pull request #72 from lomereiter/issue69zsloan
Fixes #69
2015-06-22fixed a few potential security issuesArtem Tarasov
2015-06-18fix all_samples_orderedArtem Tarasov
move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-05-22Fixed issue where correlation didn't work for human traits (and probably ↵zsloan
some others)
2015-05-12Fix #35Artem Tarasov
* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-04-10Added git large file system (the .gitattributes files) and fixed an issue ↵zsloan
where rat trait pages wouldn't work
2014-12-12Added a additive effect column to search result and collection tablesZachary Sloan
Fixed the header so that it looks fine when resizing
2014-10-02Fixed an error when there's no locus for mRNA expression traitsZachary Sloan
2014-08-21Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added
2013-11-27Clicking a trait in "color by trait" now gets all of its sample valuesZachary Sloan
that will be used to color the bar graph
2013-11-26Made some progress towards getting the traits inside a collection to display ↵Zachary Sloan
on hover
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-11-01Merge /home/sam/geneZachary Sloan
2013-10-30More work on collectionsSam
2013-10-25Began working on color coding bar chart by extra attributesZachary Sloan
2013-09-13Merge https://github.com/zsloan/genenetworkLei 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
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-25Merge git://github.com/zsloan/genenetwork into flaskLei Yan
2013-06-20Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19Moved the normalize_values function to separate file corr_result_helpers.pyLei Yan
Added docstring test to normalize_values Number of overlapping samples column now displays correctly in the correlation results page
2013-06-19Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columnsLei Yan
in the correlation page weren't displaying
2013-06-19Merge branch 'flask' of git://github.com/zsloan/genenetwork into flaskLei Yan
Conflicts: wqflask/base/data_set.py
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