Age | Commit message (Collapse) | Author |
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being used except corestats, which I moved to utility
Removed box plot code from Plot.py since we no longer use it either
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Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
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testing
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testing
* Fix conflicts
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https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
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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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* 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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* Change the raise statement to use an Exception object rather than
using a string for compatibility with Python3.
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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.
|
|
|
|
|
|
* 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.
|
|
* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
|
|
* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
|
|
* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
|
|
* 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.
|
|
* 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.
|
|
* Have the authorisation URLs build up from the client id and client
secret values.
|
|
* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
|
|
* Add configurations for elasticsearch and github.
|
|
* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
|
|
* Collect variables and functions for using the elasticsearch system in
a separate module.
|
|
* Provide the OAuth2 client_id and client_secret values in configuration
variables.
|
|
* Add configuration variables for GitHub and ORCID which will be used by
the system to allow users to login.
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