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Various changes/fixes
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files and how it writes the phenotype file)
Y-axis for GEMMA now says -log(p)
Updated the style of the trait sample data table in the trait page
Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs)
Updated dataset menu json file
Added option to show and hide columns to regular search page using colVis
Changed regular and global search result table styles/column widths
Began work on user trait submission code (not working yet though)
Began work on static loading page for mapping results
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Various changes
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loading a collection or doing ctl analysis
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be there and changed the code that calls them accordingly
Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)
Removed some unused code from show_trait.py
changed appearance of table headers some, though needs a little more work
Updated dataset_menu_structure.json
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(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
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which would result in wrong correlation results
Fixed issue where the mean would sometimes be displayed into of the additive effect
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results pages
Improved the way the table width is set for search results page
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Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
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increases table load speed
In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip
Increased table width for non-Geno DBs
Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches
Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little
Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
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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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Throw error when TMPDIRs are not writable
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MySQL query.
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settings
Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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GN2 and third party links when clicking a node, view scatterplot when clicking an edge, and edges appearance varies based upon correlation
Fixed issue that caused error with correlation page
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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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seems to be related to some strains being renamed in the genofiles
Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days
Updated genofiles
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fetch1 to return a tuple
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'get_trait_info' call from search_result_page.py because its query was already being run
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selected Tissue correlation with traits from data sets without 'data_ids'
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occasional error with correlation page
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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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