| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-28 | Provide PoC public-jwks endpoint. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Stop using the escape function for descriptions on the search result page | zsloan | |
| Apparently escape is deprecated, and it's also introducing some issues. We may encounter other descriptions with problems as a result of this, but they should be fixed in a different way. | |||
| 2024-08-28 | Also address the issue with trait IDs being detected as substrings for ↵ | zsloan | |
| searches including the group codes, like BXD_27538 | |||
| 2024-08-28 | Change text for Block filtering options to Filter to more accurately reflect ↵ | zsloan | |
| their current use | |||
| 2024-08-28 | This prevents phenotype trait IDs (numeric search terms that are 5 digits in ↵ | zsloan | |
| length) from being searched as a partial term (since some phenotype IDs were showing up in PubMed_IDs and corrupting search results) | |||
| 2024-08-28 | Fix premature session expiration | Frederick Muriuki Muriithi | |
| With the change to JWTs the time-to-live for each token is severely curtailed to help with security in case of a token theft. We, therefore, can no longer rely on the TTL for session expiration, rather, we will rely of the token-refresh mechanism to expire a token after a long while. | |||
| 2024-08-28 | Remove redundant import. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Remove token and user detail handling from @app.before_request | Frederick Muriuki Muriithi | |
| The token and user details information is handled in the `gn2.wqflask.oauth2.session`. Other parts of the system should make use of that. It also helps avoid some weird "action-at-a-distance" interactions - this forces the code to request what it needs when it needs it and not rely on some global variables. | |||
| 2024-08-28 | Reorganise code to do ALL configs at the top and then logging | Frederick Muriuki Muriithi | |
| In order to ensure that logging works as expected, make sure it is set up after all settings are in place. | |||
| 2024-08-28 | Add two new links to tutorials page | zsloan | |
| 2024-08-28 | Add Peak Chr and Peak Mb columns to ProbeSet export in the GN2 REST API | zsloan | |
| 2024-08-28 | fix: show no_data instead of Loading when there is no results from search | John Nduli | |
| 2024-08-28 | fix: correct javascript if statement | John Nduli | |
| 2024-08-28 | fix: datatables error when search returns empty result | John Nduli | |
| 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. | |||
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