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that displays metadata, etc
Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page
Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
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MySQL query.
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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
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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).
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'get_trait_info' call from search_result_page.py because its query was already being run
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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.
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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
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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.
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with no description
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Conflicts:
wqflask/base/trait.py
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error for phenotype traits
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get it working with Scroller correctly
Added code getting the description, etc to trait.py since it was missed from last commit
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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
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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)
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Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
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Still slower than preferable due to having to query the gn1 database for every trait in the search results
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trait.py. Since I couldn't find the purpose of the assert statement I removed it.
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Fixes #69
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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some others)
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* 'aliases' and 'location' are shown only where relevant
* descriptions for phenotype datasets are provided at the top
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where rat trait pages wouldn't work
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Fixed the header so that it looks fine when resizing
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On branch master
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Improved the "scatterplot matrix" feature on the trait page so that
it matches the chosen trait against every selected trait
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Suggestive/significant bars and additive effect curve added
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that will be used to color the bar graph
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on hover
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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
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Improved the templates for a couple pages related to changing user
password, etc
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Got human mapping mostly working
Fixed dataset dropdown menus
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dataset; previously we could not view traits in datasets that
were not in the DBType table in the database
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Conflicts:
wqflask/requirements.txt
wqflask/wqflask/correlation/show_corr_results.py
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Added docstring test to normalize_values
Number of overlapping samples column now displays correctly in the
correlation results page
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