| Age | Commit message (Collapse) | Author |
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The names had been changed when refactoring the code but can now be restored.
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* Introduce flask Blueprints to help with decoupling the various
modules from the `wqflask/__init__.py` module
* Refactor settings: Create a function
`base.webqtlConfig.init_app(...)` to handle setting up the
configurations on the app correctly. Call this function at app
creation time.
* Move configuration utility functions from `utility.tools` module to
`utility.configuration` module.
* Use the `get_setting(...)` function to retrieve configuration
settings from the application.
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up in correlation drop-down)
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hardcoded into show_trait.build_correlation_tools (+ add BXD-Heart-Metals to that list)
I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
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Rules used are:
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242,
E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,
E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121,
E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
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Run:
python -m autopep8 --in-place --recrusive ./ --select\
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\
E242,E251,E252,E26,E265,E266,E27 -p 3
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lists (I think the proxy expects them to not be lists, but then returns them as lists; need to check about this)
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though later I need to go through and redo a bunch of CSS stuff
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correctly in certain situations
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Added a couple new third party links
Added link to GN1 trait page in trait pages
Fixed gene global search table appearance
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Changed text in several pages (submit trait, mapping error)
Changed header menu structure some
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Fixed issue that caused error when creating UCSC RefSeq link
Fixed issue that sometimes caused an error for phenotype searches
Changed some text on collections page
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Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets
Added icon for smartphones/tablets
Made error more informative for main search
Added gene symbol column to collections (need to add something that removes the column if it's all empty)
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chart if results exceed some number (5000 on GN1)
- Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over
- Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"
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in later when other third party links are implemented on the trait/collection pages
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with Plotly
GEMMA now has option to select genotypes
Updated dataset select dropdowns to be ordered correctly
Fixed dataset select dropdowns for correlations to not show confidential datasets
Added Skewness and Kurtosis to Basic Statistics table
Fixed Verify and RNA-seq buttons on trait page
Temporarily hardcoded Reference page until we get it to link with database
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file format
Other changes include:
- Fixing links in the network graph
- Changing button colors on show trait page
- Changing color scheme for heatmap
- Making rows highlight in yellow when clicked on
- Some changes to table appearance (like giving gene global search a horizontal scroll)
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* refactored ./bin/genenetwork2 and /etc/default_settings
- better detection of Guix
- removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
- removing some default settings, such as PYLMM_COMMAND
- rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
- added GUIX_JS_PATH for JS modules
* Added documentation on installing binary GN2
* Updated Twitter board to latest version in Guix - it had broken
* Updated many tools in the latest Guix profile
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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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Throw error when TMPDIRs are not writable
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settings
Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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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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draw to different chr areas though
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Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
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it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
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external settings
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Improved the templates for a couple pages related to changing user
password, etc
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and builds each groups' samplelist
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Got human mapping mostly working
Fixed dataset dropdown menus
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