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2023-06-14Change plotly layout options for probability plotzsloan
2023-06-14Change CSS for mapping options/description for better fitzsloan
2023-06-14Make default unit_type value with lower-case vzsloan
2023-06-14Remove extra spacezsloan
2023-06-13Namespace session variable.Frederick Muriuki Muriithi
Namespace the session variable name to avoid conflicts with other systems served on the same domain.
2023-06-12Add phenotype pageMunyoki Kilyungi
* wqflask/wqflask/templates/phenotype.html: New template. * wqflask/wqflask/views.py (get_phenotype): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-08bug: Fix URI to prevent unnecessary redirect.Frederick Muriuki Muriithi
2023-06-08Remove authorization restriction on viewing sample datazsloan
2023-06-08Fix bug by providing anon_id to collections/addzsloan
2023-06-07Add publication pageMunyoki Kilyungi
* wqflask/wqflask/templates/publication.html: New page. * wqflask/wqflask/views.py (get_dataset): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Add 1 to LRS_LOD_MAX in order to prevent situations where a tick is missing ↵zsloan
for the highest points on the manhattan plot
2023-06-06Align probability plot title to the left ('xanchor: right' does this for ↵zsloan
some reason)
2023-06-06Make geoSeries a linkMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Put metadata name in a new lineMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Fix geoplatform link in datasets pageMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Fix some titles in INFOPAGEMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06If a title doesn't exist, use the metadata name insteadMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Update dataset page to match GN1Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Add dataset link that uses RDFMunyoki Kilyungi
* wqflask/wqflask/templates/dataset.html: New page. * wqflask/wqflask/templates/show_trait_details.html: Add link to GN2 datasets page. * wqflask/wqflask/views.py (get_dataset): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Delete trait metadata from the show_traits pageMunyoki Kilyungi
* wqflask/wqflask/templates/show_metadata_details.html: Delete. * wqflask/wqflask/templates/show_trait.html: Delete if block that checks includes trait metadata. * wqflask/wqflask/views.py: Remove "metadata". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-31Use utility.tools to get configuration variablesFrederick Muriuki Muriithi
Using flask.current_app.config for configurations does not give the appropriate configurations.
2023-05-31Compute dataset type from name.Frederick Muriuki Muriithi
2023-05-30Fix test: Sort values to avoid equality problems.Frederick Muriuki Muriithi
2023-05-30Fix test: Expect tuple not set.Frederick Muriuki Muriithi
2023-05-30Fix test: Expect tuple not set.Frederick Muriuki Muriithi
2023-05-25auth: Show publicly visible traits.Frederick Muriuki Muriithi
2023-05-25Rework UI. Set resource publicly viewable by default.Frederick Muriuki Muriithi
Reorganise the UI for resource creation. Add a checkbox that sets the resource as publicly viewable by default.
2023-05-24Add link to user-account registration page.Frederick Muriuki Muriithi
2023-05-23oauth2: Enable admins to masquerade as other usersFrederick Muriuki Muriithi
2023-05-22Initialize exonStarts and exonEnds for mouse, since it currently throws an ↵zsloan
error if there's nothing in the GeneList table for the interval selected
2023-05-22Allow for editing values of samples that don't currently have valueszsloan
Deletions aren't working yet. This is dependent on a GN3 chance that allows the sample_list to be passed to get_trait_csv_sample_data
2023-05-22Fix phenotype metadata template to only read in changed sample datazsloan
Also fix the display so it only shows 3 decimal places
2023-05-22Add support for editing sample data via an HTML tablezsloan
This doesn't yet support adding sample data for samples that don't already have values
2023-05-19auth: Integrate metadata editting with new authFrederick Muriuki Muriithi
2023-05-19auth: Use auth privileges to control UI displayFrederick Muriuki Muriithi
Use the privileges from the authorisation endpoint to control which elements of the UI are displayed to the user. * wqflask/base/trait.py: Remove unused import * wqflask/wqflask/show_trait/show_trait.py: Unhook from GN-PROXY * wqflask/wqflask/templates/show_trait.html: Display or hide UI elements depending on the privileges the user has. * wqflask/wqflask/templates/show_trait_details.html: Display or hide UI elements depending on the privileges the user has. * wqflask/wqflask/views.py: Pass privileges, user, and resource details on to the UI template to be used for controlling UI element display.
2023-05-18auth: Change collection nameFrederick Muriuki Muriithi
Enable the changing of the collection names. * wqflask/wqflask/collect.py: Send data to GN3 API * wqflask/wqflask/templates/collections/view.html: Use an actual form and submit it.
2023-05-18auth: Display flash messages.Frederick Muriuki Muriithi
2023-05-18auth: Add and remove traits from collectionsFrederick Muriuki Muriithi
* 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.
2023-05-17auth: Integrate deleting selected collections with authFrederick Muriuki Muriithi
Enable the deletion of selected collections via the GN3 api.
2023-05-17auth: Integrate collections badge with authFrederick Muriuki Muriithi
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.
2023-05-17auth: Import/Delete Anonymous CollectionsFrederick Muriuki Muriithi
Integrate import/delete of anonymous collection when user is authenticated.
2023-05-16auth: View collection details from GN3 endpointFrederick Muriuki Muriithi
Retrieve a specific collection's details from the GN3 endpoint rather than from the session, as was done previously.
2023-05-15Create new collection via GN3 APIFrederick Muriuki Muriithi
* 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
2023-05-12auth: Fetch anonymous collections from separate endpoint.Frederick Muriuki Muriithi
2023-05-12auth: Integrate sessions with authFrederick Muriuki Muriithi
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
2023-05-10auth: Fetch user collections from GN3Frederick Muriuki Muriithi
Fetch the user collections from GN3 for users that have authenticated.
2023-05-10auth: bug-fix: Call `logged_in` functionFrederick Muriuki Muriithi
The `logged_in` symbol was changed from a plain variable into a function, so we need to call it to get its actual value.
2023-05-09Integrate OAuth2 auth with GN2 UIhook-up-auth-to-traits-pageFrederick Muriuki Muriithi
Update the templates to make use of the OAuth2 authentication rather than the older authentication that used Redis.
2023-05-09auth: Handle authentication using the "Authorization Code Flow"Frederick Muriuki Muriithi
2023-05-08oauth2: UI - Remove `Edit` elementFrederick Muriuki Muriithi
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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