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* Instead of checking for the state of elasticsearch at startup, check
the state at the moment the user requests a feature that depends on
elasticsearch.
This reduces the chances that the user is dropped onto an exception
page when elasticsearch server goes down.
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* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
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* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
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* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
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* If elasticsearch server is down, or the configuration variables are
not provided at startup or in a configuration file, then do not allow
the system to simply crash, but instead, inform the user that they
cannot use the services that depend on elasticsearch to be running.
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* Add a method to set the configuration variables to None if the
configuration values are not provided at startup or in the
configuration files.
The system already checks for these values, and if they are absent, it
simply fails to display the OAuth service as available for use to
login.
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* Have the authorisation URLs build up from the client id and client
secret values.
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* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
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* Add configurations for elasticsearch and github.
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* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
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* Collect variables and functions for using the elasticsearch system in
a separate module.
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* Provide the OAuth2 client_id and client_secret values in configuration
variables.
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* Add configuration variables for GitHub and ORCID which will be used by
the system to allow users to login.
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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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Temporarily removed second sample table for CFW traits
Fixed location of global search bar to work with wider screens
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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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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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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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fetch1 to return a tuple
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