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2024-07-20Also address the issue with trait IDs being detected as substrings for ↵zsloan
searches including the group codes, like BXD_27538
2024-07-20Change text for Block filtering options to Filter to more accurately reflect ↵zsloan
their current use
2024-07-20This 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)
2024-07-17Fix premature session expirationFrederick 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.
2024-07-17Remove redundant import.Frederick Muriuki Muriithi
2024-07-17Remove token and user detail handling from @app.before_requestFrederick 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.
2024-07-17Reorganise code to do ALL configs at the top and then loggingFrederick Muriuki Muriithi
In order to ensure that logging works as expected, make sure it is set up after all settings are in place.
2024-07-12Add two new links to tutorials pagezsloan
2024-07-12Add Peak Chr and Peak Mb columns to ProbeSet export in the GN2 REST APIzsloan
2024-07-05fix: show no_data instead of Loading when there is no results from searchJohn Nduli
2024-07-05fix: correct javascript if statementJohn Nduli
2024-07-05fix: datatables error when search returns empty resultJohn Nduli
2024-07-05fix: cleaner handling for gsearch errorsJohn Nduli
2024-07-03Add 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
2024-07-01Link 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