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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 some code to set up the path for the python-elasticsearch module.
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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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* Change the raise statement to use an Exception object rather than
using a string for compatibility with Python3.
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* End the 'def' statement with a colon (:)
* Add an empty line between lines at different indentation levels for
clarity.
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https://github.com/genenetwork/genenetwork2/issues/296
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* Navigation depends on Javascript to render the elements being tested.
That would require selenium and its ilk to run such tests, meaning
such packages would need to be defined for Guix first.
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* Start working on navigation tests.
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* Add tests for the R/qtl and CIM mapping tools.
* Fix tests for in-page links.
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https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
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Testing
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* Add mapping tests, and build the first of the tests.
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* Mainly to tell the dependencies easily.
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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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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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* Add the module that will hold the code to test the links on the
system.
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* Use argparse to handle commandline arguments.
* Create initial layout of how the code might end up - lots of the code
is currently commented out.
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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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* Check that the links for OAuth2 logins via ORCID and GitHub are setup
correctly.
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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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* With the parameterized module, the testcase cannot be run
independently at this time.
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* The test functions were very similar, so this commit refactors out the
common test code to a single method, and passes in the data to the
test using the parameterized package.
* Check that the page content after a login attempt is the expected
content, rather than checking the url.
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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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* Add an integration test to test that the login process for users
registered locally to genenetwork2 works as expected.
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