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* wqflask/base/trait.py: Remove unused imports
* wqflask/db/call.py (Bench): Add urllib2 fallback for python2
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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* wqflask/base/trait.py: See
<https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
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Run `2to3-3.8 -f raise -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
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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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figure out the real solution to that issue
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where a trait is authenticated twice
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something that automatically inserts resources with default privileges
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and also simplified the check_owner_or_admin function a little
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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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queries and a missing import for the hmac functions
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index page header style a little
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just unpublished ones
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ordering phenotype results from searches
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Added option to download as JPEG in addition to SVG for basic stats figures
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Fixed year to not be a hyperlink when no pubmed id
Fixed first column width so it doesn't go onto two lines for trait details
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Added some information to the mapping loading page
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Fixed a bug that sometimes occurred in search results
Changed order of items on index page
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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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Made the outlier notification appear for all mapping methods
Removed some misleading text saying "Block samples" from the Transform and Filter Data section
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Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
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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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Added Phenogen track to mapping results
Added comparison bar chart figure
Simplified global search to not build trait/dataset objects, which speeds thing up considerably
Fixed correlation matrix to correctly deal with 0 values
Fixed issue where anonymous collections couldn't be created if none already existed
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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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appearance for mRNA assay data sets (still need to improve it for others)
Fixed minor logic issue in trait.py
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- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits
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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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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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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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