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2024-07-01Link to global search syntax document as markdown on githubzsloan
2024-06-27Put SQL search code into function, and default to that function if the ↵zsloan
Xapian search returns no results or throws an error (so search will still work if GN3 is down)
2024-06-27Automatically decide whether to use Xapian or SQL (uses Xapian if possible) ↵zsloan
+ remove separate search button Change logic so that SQL is used for non-term Publish searches, since searches for phenotype trait IDs currently don't work in Xapian
2024-06-27Increase MAX_SEARCH_RESULTS to 50000zsloan
2024-06-27Fix LRS/LOD Xapian searches when there are 5 terms (where position range is ↵zsloan
included)
2024-06-27Fix some issues with handling Xapian search outputzsloan
- Description trimming is now handled in the python code - HMAC generation function is changed to be the same as the one used by global search - Search terms that currently don't support Xapian searches are now 'routed' to the SQL search
2024-06-27Set default value for Mean and Additive Effectzsloan
2024-06-27Add default value for location and symbolzsloan
Adding these in the DataTables column definitions is convenient because it means they don't need to be dealt with in the Python code
2024-06-27Create trait objects from Xapian search results to pass to DataTableszsloan
This means the result table should be displayed now. The only issue is that this involves a significant amount of duplicated code from gsearch.py; I'm not sure how best to avoid this, but this is okay for now.
2024-06-27Raise ValueError if dataset type isn't ProbeSet/Publish/Genozsloan
2024-06-27Add doctstrings for new functions in search_results.pyzsloan
Replace dataset name with fullname (this will need to be changed back when the Xapian indexing is rerun)
2024-06-27Begin adding Xapian queries for the non-global search and submit request to GN3zsloan
Still need to handle the output and address a bug that is also affecting the global search
2024-06-27Add separate button for Xapian searchzsloan
This will be temporary in the longer run, but can stay until all functionality is reproduced.
2024-06-25Make UI items more flexible.Frederick Muriuki Muriithi
2024-06-25Remove flawed "group role" idea: use just "role".Frederick Muriuki Muriithi
2024-06-17Remove deprecated endpoints/views and templatesFrederick Muriuki Muriithi
2024-06-17Fix error display logicFrederick Muriuki Muriithi
2024-06-17Fetch the active user's roles on a particular resource.Frederick Muriuki Muriithi
2024-06-17Use privilege objects rather than IDS.Frederick Muriuki Muriithi
2024-06-17Delete request to obsoleted endpoint.Frederick Muriuki Muriithi
2024-06-17Create a new resource role.Frederick Muriuki Muriithi
2024-06-17Update URI formsFrederick Muriuki Muriithi
2024-06-17Use json for communication with gn-authFrederick Muriuki Muriithi
2024-06-11Provide UI to delete role.Frederick Muriuki Muriithi
2024-06-11List user assigned role of interest.Frederick Muriuki Muriithi
2024-06-11Organise UI into rows: each row holding related data.Frederick Muriuki Muriithi
2024-06-10Unassign privilege from resource role.Frederick Muriuki Muriithi
2024-06-10Import the UUID class directly.Frederick Muriuki Muriithi
2024-06-10Implement "Resource Role Page"Frederick Muriuki Muriithi
Show the page, providing all UI elements necessary, even if the elements themselves are not active.
2024-06-10Generalise `render_ur` for the resources pagesFrederick Muriuki Muriithi
2024-06-10Set default headers for OAuth2Client requests.Frederick Muriuki Muriithi
2024-06-10Simplify 'View-Resource page' UIFrederick Muriuki Muriithi
Get rid of the resource role details and provide button-like elements to help navigate to view more details.
2024-06-07PoC: Display resource roles on View-Resource page.Frederick Muriuki Muriithi
2024-06-07Update UI: Use resource roles rather than obsolete group rolesFrederick Muriuki Muriithi
In a fix to fix a privilege-escalation bug, the `…/group/roles` endpoint was entirely removed and replaced with the less error-prone `…/resource/…/roles` endpoint. This commit updates the code to use the new endpoint's data as appropriate. We also fix typos in some url_for routing arguments.
2024-06-06UI: Add placeholder for resource rolesFrederick Muriuki Muriithi
2024-06-06Fix displayed error messageFrederick Muriuki Muriithi
2024-06-06Remove the "Roles" page.Frederick Muriuki Muriithi
2024-06-06Deactivate the "create_role" functionFrederick Muriuki Muriithi
The `create_role` function could lead to privilege escalation. This commit deactivates it completely to prevent the chance of that happening.
2024-06-05Bug: Add missing data to search query.Frederick Muriuki Muriithi
2024-06-05Build search URI endpoint on server rather than on JSFrederick Muriuki Muriithi
To help with maintenance, build the search URI on the server rather than in the javascript.
2024-06-05Build phenotype results template URI on backendFrederick Muriuki Muriithi
Build the template URI on the backend to remove the need to remember to update the javascript if the URI changes in the future.
2024-06-04Provide client data used for user verification.Frederick Muriuki Muriithi
2024-06-03Handle generic OAuthError gracefullyFrederick Muriuki Muriithi
2024-06-03Ensure endpoint returns a response.Frederick Muriuki Muriithi
2024-05-31Enable NA sorting for case attributeszsloan
The NA-excluding sort functions were moved to table_functions.js (and removed from search_results.js) so they can be used by other pages (in this case the show_trait page)
2024-05-31Restore collections endpointszsloan
Import was removed in commit 7c77ff91f6530aca0865bd13025811f2f93e3541 because it wasn't being used in views.py, but it was providing the collections endpoints albeit indirectly. This commit makes it somewhat explicit that it is a needed module.
2024-05-30Fix redirection bug.Frederick Muriuki Muriithi
2024-05-29Handle attributeError when getting error codes.Alexander_Kabui
2024-05-28BugFix: return correct status code for generic exceptions handler.Alexander_Kabui
2024-05-23Bug: Compute numeric timestamp for the claims.Frederick Muriuki Muriithi