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https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
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* Ensure the key exists in the json object/dictionary, before trying to
use it to retrieve a value.
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* Provide connections to elasticsearch at various points in the code.
These oversight was caught while running tests.
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* When logging in, if a user selects "Import existing collections", the
system would throw an exception, since Redis would return a NoneType,
which would then be accessed by json.loads(), which doesn't seem to
know how to process that.
This fixes that, by providing a string representing an empty json
array ("[]"), in place of the NoneType.
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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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* 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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* 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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Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping")
Loading factors and their plot are hidden in situations where there's some error with calculating principal components
Added GEMMA description and changed order of descriptions for mapping options on trait page
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Changed layout/appearance of mapping options
Partially fixed issue with deleting collections
Changes to correlation table still in progress; having trouble getting tabulator to load JSON
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JSON
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changes
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for every page we
work on. It will help bug tracking.
Probably fixes #279
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correct p-values
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suddenly decided to start running it when it wasn't in the past.
Switched correlation table to tabulator
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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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