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PYTHONPATH needed as
it is now in the Guix build.
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* Update functions to make them more testable.
* Update code using updated functions.
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for every page we
work on. It will help bug tracking.
Probably fixes #279
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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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* After the email is sent to the user, there is need to provide a way
for the user to actually change their password, and have the results
saved.
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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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* Update the code so that it sends out emails for the "forgot password"
feature.
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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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Added more info to trait details for phenotype traits
Changed order of mapping methods
Fixed layout of mapping loading screen to hopefully be centered on different screen sizes
Improved layout of some elements in mapping results page
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* Register local accounts onto elasticsearch rather than mysql.
* Login from the accounts on elasticsearch
* Harmonise local and oauth2 logins to use the same code.
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* Add code to handle the login via ORCID
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* Have the authorisation URLs build up from the client id and client
secret values.
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* Add some code to handle the login if the user chooses to login via
GitHub or ORCID.
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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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* Add functions to help with the github OAuth2 login process
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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 html elements that will be used to prompt users to login with
either GitHub or ORCID.
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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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Merge some older commits
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throw an error
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problem preventing it from working)
Added some code related to new plotly probability plot, though it's commented out until it looks how I want it to
Added some code for adding the BNW link to GN2, though it's not working yet
Updated dataset menu structure JSON file
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(though there's still a minor issue with a few datasets)
Added some header data to mapping output file
Fixed links in Network Group nodes/edges
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improved scatter plots
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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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