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2024-08-28Add two new links to tutorials pagezsloan
2024-08-28Add Peak Chr and Peak Mb columns to ProbeSet export in the GN2 REST APIzsloan
2024-08-28fix: show no_data instead of Loading when there is no results from searchJohn Nduli
2024-08-28fix: correct javascript if statementJohn Nduli
2024-08-28fix: datatables error when search returns empty resultJohn Nduli
2024-08-28fix: cleaner handling for gsearch errorsJohn Nduli
2024-08-28Add link to GeneCup to tool buttonszsloan
This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py
2024-08-28Link to global search syntax document as markdown on githubzsloan
2024-08-28Put 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)
2024-08-28Automatically 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
2024-08-28Increase MAX_SEARCH_RESULTS to 50000zsloan
2024-08-28Fix LRS/LOD Xapian searches when there are 5 terms (where position range is ↵zsloan
included)
2024-08-28Fix 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
2024-08-28Set default value for Mean and Additive Effectzsloan
2024-08-28Add 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
2024-08-28Create 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.
2024-08-28Raise ValueError if dataset type isn't ProbeSet/Publish/Genozsloan
2024-08-28Add 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)
2024-08-28Begin 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
2024-08-28Add separate button for Xapian searchzsloan
This will be temporary in the longer run, but can stay until all functionality is reproduced.
2024-08-28Make UI items more flexible.Frederick Muriuki Muriithi
2024-08-28Remove flawed "group role" idea: use just "role".Frederick Muriuki Muriithi
2024-08-28Remove deprecated endpoints/views and templatesFrederick Muriuki Muriithi
2024-08-28Fix error display logicFrederick Muriuki Muriithi
2024-08-28Fetch the active user's roles on a particular resource.Frederick Muriuki Muriithi
2024-08-28Use privilege objects rather than IDS.Frederick Muriuki Muriithi
2024-08-28Delete request to obsoleted endpoint.Frederick Muriuki Muriithi
2024-08-28Create a new resource role.Frederick Muriuki Muriithi
2024-08-28Update URI formsFrederick Muriuki Muriithi
2024-08-28Use json for communication with gn-authFrederick Muriuki Muriithi
2024-08-28Provide UI to delete role.Frederick Muriuki Muriithi
2024-08-28List user assigned role of interest.Frederick Muriuki Muriithi
2024-08-28Organise UI into rows: each row holding related data.Frederick Muriuki Muriithi
2024-08-28Unassign privilege from resource role.Frederick Muriuki Muriithi
2024-08-28Import the UUID class directly.Frederick Muriuki Muriithi
2024-08-28Implement "Resource Role Page"Frederick Muriuki Muriithi
Show the page, providing all UI elements necessary, even if the elements themselves are not active.
2024-08-28Generalise `render_ur` for the resources pagesFrederick Muriuki Muriithi
2024-08-28Set default headers for OAuth2Client requests.Frederick Muriuki Muriithi
2024-08-28Simplify '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.
2024-08-28PoC: Display resource roles on View-Resource page.Frederick Muriuki Muriithi
2024-08-28Update 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.
2024-08-28UI: Add placeholder for resource rolesFrederick Muriuki Muriithi
2024-08-28Fix displayed error messageFrederick Muriuki Muriithi
2024-08-28Remove the "Roles" page.Frederick Muriuki Muriithi
2024-08-28Deactivate 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.
2024-08-28Bug: Add missing data to search query.Frederick Muriuki Muriithi
2024-08-28Build 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.
2024-08-28Build 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.
2024-08-28Provide client data used for user verification.Frederick Muriuki Muriithi
2024-08-28Handle generic OAuthError gracefullyFrederick Muriuki Muriithi