| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-28 | fix: cleaner handling for gsearch errors | John Nduli | |
| 2024-08-28 | Add link to GeneCup to tool buttons | zsloan | |
| This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py | |||
| 2024-08-28 | Link to global search syntax document as markdown on github | zsloan | |
| 2024-08-28 | Put 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) | |||
| 2024-08-28 | Automatically 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 | |||
| 2024-08-28 | Increase MAX_SEARCH_RESULTS to 50000 | zsloan | |
| 2024-08-28 | Fix LRS/LOD Xapian searches when there are 5 terms (where position range is ↵ | zsloan | |
| included) | |||
| 2024-08-28 | Fix some issues with handling Xapian search output | zsloan | |
| - 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 | |||
| 2024-08-28 | Set default value for Mean and Additive Effect | zsloan | |
| 2024-08-28 | Add default value for location and symbol | zsloan | |
| Adding these in the DataTables column definitions is convenient because it means they don't need to be dealt with in the Python code | |||
| 2024-08-28 | Create trait objects from Xapian search results to pass to DataTables | zsloan | |
| 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. | |||
| 2024-08-28 | Raise ValueError if dataset type isn't ProbeSet/Publish/Geno | zsloan | |
| 2024-08-28 | Add doctstrings for new functions in search_results.py | zsloan | |
| Replace dataset name with fullname (this will need to be changed back when the Xapian indexing is rerun) | |||
| 2024-08-28 | Begin adding Xapian queries for the non-global search and submit request to GN3 | zsloan | |
| Still need to handle the output and address a bug that is also affecting the global search | |||
| 2024-08-28 | Add separate button for Xapian search | zsloan | |
| This will be temporary in the longer run, but can stay until all functionality is reproduced. | |||
| 2024-08-28 | Make UI items more flexible. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Remove flawed "group role" idea: use just "role". | Frederick Muriuki Muriithi | |
| 2024-08-28 | Remove deprecated endpoints/views and templates | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fix error display logic | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fetch the active user's roles on a particular resource. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Use privilege objects rather than IDS. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Delete request to obsoleted endpoint. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Create a new resource role. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Update URI forms | Frederick Muriuki Muriithi | |
| 2024-08-28 | Use json for communication with gn-auth | Frederick Muriuki Muriithi | |
| 2024-08-28 | Provide UI to delete role. | Frederick Muriuki Muriithi | |
| 2024-08-28 | List user assigned role of interest. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Organise UI into rows: each row holding related data. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Unassign privilege from resource role. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Import the UUID class directly. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Implement "Resource Role Page" | Frederick Muriuki Muriithi | |
| Show the page, providing all UI elements necessary, even if the elements themselves are not active. | |||
| 2024-08-28 | Generalise `render_ur` for the resources pages | Frederick Muriuki Muriithi | |
| 2024-08-28 | Set default headers for OAuth2Client requests. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Simplify 'View-Resource page' UI | Frederick Muriuki Muriithi | |
| Get rid of the resource role details and provide button-like elements to help navigate to view more details. | |||
| 2024-08-28 | PoC: Display resource roles on View-Resource page. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Update UI: Use resource roles rather than obsolete group roles | Frederick 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. | |||
| 2024-08-28 | UI: Add placeholder for resource roles | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fix displayed error message | Frederick Muriuki Muriithi | |
| 2024-08-28 | Remove the "Roles" page. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Deactivate the "create_role" function | Frederick Muriuki Muriithi | |
| The `create_role` function could lead to privilege escalation. This commit deactivates it completely to prevent the chance of that happening. | |||
| 2024-08-28 | Bug: Add missing data to search query. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Build search URI endpoint on server rather than on JS | Frederick Muriuki Muriithi | |
| To help with maintenance, build the search URI on the server rather than in the javascript. | |||
| 2024-08-28 | Build phenotype results template URI on backend | Frederick 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. | |||
| 2024-08-28 | Provide client data used for user verification. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Handle generic OAuthError gracefully | Frederick Muriuki Muriithi | |
| 2024-08-28 | Ensure endpoint returns a response. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Enable NA sorting for case attributes | zsloan | |
| 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) | |||
| 2024-08-28 | Restore collections endpoints | zsloan | |
| 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. | |||
| 2024-08-28 | Bug: Compute numeric timestamp for the claims. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Check if case attribute for RRID is a list, to prevent it being added twice ↵ | zsloan | |
| in situations where a sample appears in both the parent/f1 file and the .geno file | |||
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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