| Age | Commit message (Expand) | Author |
|---|
| 2024-08-28 | Fix premature session expiration...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.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Remove redundant import. | Frederick Muriuki Muriithi |
| 2024-08-28 | Remove token and user detail handling from @app.before_request...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.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Reorganise code to do ALL configs at the top and then logging...In order to ensure that logging works as expected, make sure it is set
up after all settings are in place.
| Frederick Muriuki Muriithi |
| 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...This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py
| zsloan |
| 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 Xapian... | zsloan |
| 2024-08-28 | Automatically decide whether to use Xapian or SQL (uses Xapian if possible) +......Change logic so that SQL is used for non-term Publish searches, since searches for phenotype trait IDs currently don't work in Xapian
| zsloan |
| 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 i... | zsloan |
| 2024-08-28 | Fix some issues with handling Xapian search output...- 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
| zsloan |
| 2024-08-28 | Set default value for Mean and Additive Effect | zsloan |
| 2024-08-28 | Add default value for location and symbol...Adding these in the DataTables column definitions is convenient
because it means they don't need to be dealt with in the Python code
| zsloan |
| 2024-08-28 | Create trait objects from Xapian search results to pass to DataTables...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.
| zsloan |
| 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...Replace dataset name with fullname (this will need to be changed back when the Xapian indexing is rerun)
| zsloan |
| 2024-08-28 | Begin adding Xapian queries for the non-global search and submit request to GN3...Still need to handle the output and address a bug that is also affecting the global search
| zsloan |
| 2024-08-28 | Add separate button for Xapian search...This will be temporary in the longer run, but can stay until all functionality is reproduced.
| zsloan |
| 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"...Show the page, providing all UI elements necessary, even if the
elements themselves are not active.
| Frederick Muriuki Muriithi |
| 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...Get rid of the resource role details and provide button-like elements
to help navigate to view more details.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 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...The `create_role` function could lead to privilege escalation. This
commit deactivates it completely to prevent the chance of that
happening.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Bug: Add missing data to search query. | Frederick Muriuki Muriithi |
