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Create the application and set up configs and other things within an
application factory function.
Fix obvious egregious errors preventing the application from starting
up correctly.
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Set up the mandatory settings in the `flask.current_app.config` object
rather than in the file itself.
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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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This functionality, at least how we use it, is already provided
natively in python's pdb. Should someone need this, they can add it
manually.
* wqflask/runserver.py (app_config): Remove "flask_debugtoolbar"
import and instantiation.
* wqflask/utility/startup_config.py (app_config): Ditto.
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* wqflask/runserver.py: Relative imports leads to import errors.
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-import>
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different from base dataset
Improved collection list and view table appearances
Added question mark image for glossary entries in table headers
Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values
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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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also I found out that there are two legends shown simultaneously,
but one is suitable only for discrete values, and the other for
continuous; now only the suitable one is shown
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Added GEMMA and necessary plink-format genotype files in gemma directory
Added the GEMMA genotype files to git LFS
Removed some unnecessary/duplicated code from interval_mapping.py
Separated GEMMA mapping code into its own file (will also do this for other methods) and fixed
and issue that caused it to not run
Added the table to the pair scan results page and wrote some code adding its attributes
to each marker object, but it still isn't working yet
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I figure out how to get it to read the port from the config file instead
Using runserver.py instead of secure_server.py because of an error with the latter
that I haven't figured out how to fix yet
Improved the appearance of several of the tables
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adding the correlation matrix page
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Changed "threaded" to True in runserver.py; this fixed issue
related to getting progress bar to work
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Small change to the code printing out fd in search_results.py
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