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It's in-efficient to have a sql query executed in a loop. As data
grows, the query becomes slower. It's better to let sql handle such
queries.
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input string
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring>
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Run `2to3-3.8 -f dict -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and
<https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
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- Now use proxy to pull trait data and hide traits/results that the user
doesn't have view permission for
- Created a factory method for creating trait ob so it can return None
when user doesn't have view permissions (this is why such a large number
of files are changed)
- Added metadata to permutation export
- Added current group management code
- Added fixed password verification e-mail code
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or add them to a collection from the corr matrix page,
but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well,
but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better
way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch
- Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc
- Fixed some appearance issue where the network graph options were too wide if a trait name was too long
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just clicking their row in collection
- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
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Temporarily removed second sample table for CFW traits
Fixed location of global search bar to work with wider screens
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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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Added the option to display the rqtl results (and soon other mapping results)
as either a manhattan plot or "interval map" style curve chart
Removed a couple unnecessary javascript imports
Changed the function in helper_functions.py that creates the trait and dataset
objects, making it to where the trait object also gets qtl info
Fixed color by trait after it was broken by the "scatterplot matrix" function
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Changed order of tabs in statistics panel on trait page
Started working on heatmap
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adding the correlation matrix page
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withouot using reaper and caches results so it doesn't need
to read the file every single time someone loads a page
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dataset object for each trait in the correlation results
Added new fields/columns for each trait in the correlation result table
(max LRS, max LRS location, mean expression)
Fixed error if trait doesn't have these fields
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of the marker regression calculations
Storing progress of kinship matrix calculation in variable as
portion of 45 (the rough percent of total marker regression calculation
time
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page to work, but will change all references to the dataset name to
'dataset_name' in future to avoid confusion between the dataset name
and the actual dataset object
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Worked with correlation code; got to the code that
begins to do the actual correlations
Created a function "get_dataset_and_trait" in
the new file "helper_functions.py" because the
code initializing the dataset and trait objects
was repeated in multiple places
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