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* wqflask/wqflask/collect.py: Add and remove traits to and from
collections.
* wqflask/wqflask/oauth2/client.py: Add functions for POST and GET
that do the right thing depending on whether or not the user is
logged in.
* wqflask/wqflask/oauth2/request_utils.py: Add some common utility
function to create the data extraction functions for
`pymonads.either.Either` objects.
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Enable the deletion of selected collections via the GN3 api.
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Show the total number of collections available in the active session
in the collections badge at the top of the page.
Also do some minor UI tweaks to differentiate the user and anonymous
collections.
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Integrate import/delete of anonymous collection when user is
authenticated.
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Retrieve a specific collection's details from the GN3 endpoint rather
than from the session, as was done previously.
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* wqflask/wqflask/collect.py: Send data to the GN3 API to create the
new collections.
* wqflask/wqflask/oauth2/client.py: Ensure request is sent as a json
request.
* wqflask/wqflask/static/new/javascript/search_results.js: use "POST"
rather than "GET" and send the traits also, in addition to the hash
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Rework the sessions to do what was handled by the soon-to-be-obsolete
`wqflask.user_sessions` module.
This is necessary in order to retain the expected functionality of the
user collections, especially:
* anonymous user collections
* authenticated user collections
* import of anonymous collections when user authenticates
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Fetch the user collections from GN3 for users that have authenticated.
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The `logged_in` symbol was changed from a plain variable into a
function, so we need to call it to get its actual value.
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Update the templates to make use of the OAuth2 authentication rather
than the older authentication that used Redis.
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The `Edit` button was unnecessary, since the `View` button gives the
user access to a UI that allows them to edit the role.
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Surround the UI elements with the check for any authorisation errors
to avoid trying to access non-existent data (this leads to an
exception).
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As a proof-of-concept, add some sort of wrapper to check whether the
user has access to the given trait/dataset.
This will probably need some improvement to check for edit access,
curation access, etc.
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For some reason xanchor=right does this
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This allows the scatterplots to use edited sample data
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This is so edited sample values can be used in the additive effect scatterplots
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If a role is not user-editable, disable the UI elements that allow
editting of the role to prevent that as an option in the first place.
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Add missing `wqflask.oauth2.ui` module
Make arguments to the menu-generation macro mandatory going forward.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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This commit generalises the code for selecting and deselecting items
making it usable even for the phenotype traits. Now we can switch
items from the search table to the linking table and vice versa.
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chores/minor-fixes
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* wqflask/wqflask/templates/generif.html: New template.
* wqflask/wqflask/views.py (display_diffs_users): New route.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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At this point, the code fails with a 404, despite the appropriate
endpoint existing. Will need further debugging.
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This reverts commit b8b62aea1c7924e2ee7455c6fe8b34eee7cb8e74.
We do need to decouple the entire `gn3.db_utils` from the
`flask.current_app` object, and as such, the use of `SQL_URI` from the
`utility.tools` module in GN2 was on purpose. This is also to help
towards fixing issue
https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
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This was just caused by the correlation code not directly being passed the PMID (and instead only being passed the link and the text), so the logic in the table code needed to be changed to check for the link instead of the PMID
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I think it now gets the SQL_URI from settings
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