| Age | Commit message (Expand) | Author |
|---|
| 2024-08-28 | Consistently use JSON for all endpoints. | Frederick Muriuki Muriithi |
| 2024-08-28 | Add mariadb package to database development container....* containers/db-container.scm (operating-system)[packages]: Add
mariadb.
| Arun Isaac |
| 2024-08-28 | Remove obsolete configurations. | Frederick Muriuki Muriithi |
| 2024-08-28 | bug: add missing `count_per_page` variable. | Frederick Muriuki Muriithi |
| 2024-08-28 | Use auto-created and auto-rotated JSON Web Keys...Use auto-created JWKs for better security.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Use JWKs from auth server public endpoint...* Fetch keys from auth server
* Validate token is signed with one of the keys from server
* Ensure refreshing of token is still synchronised
| Frederick Muriuki Muriithi |
| 2024-08-28 | Add module to help with rotation of JSON Web Keys. | Frederick Muriuki Muriithi |
| 2024-08-28 | Fix correlation bug caused by a result trait not having a location | zsloan |
| 2024-08-28 | Fix misnamed variable that caused correlation location filter to not work | zsloan |
| 2024-08-28 | Fix collections import by allowing GET method for collections/add endpoint | zsloan |
| 2024-08-28 | Improve logging...Add more logging information to help with tracking and fixing bugs.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Synchronise token refreshes...The application can be run in a multi-threaded server, leading to a
situation where the multiple threads attempt to get a new JWT using
the exact same refresh token.
This synchronises the various threads ensuring only a single thread is
able to retrieve the new JWT that all the rest of the threads then
use.
| Frederick Muriuki Muriithi |
| 2024-08-28 | Fix GN3 URIs for case attribute editing...Also improve error logging somewhat (but still need to properly display the error in a template)
| zsloan |
| 2024-08-28 | Include trait and dataset name in hmac passed to search results page for non-......Previously it only had the hmac, which caused adding to a collection to not work for such searches
| zsloan |
| 2024-08-28 | Include CaseAttribute.InbredSetId in the query that fetches case attributes...Previously issues could occur if a difference InbredSet had the same CaseAtribute Id
| zsloan |
| 2024-08-28 | Add BXD-JAX-OFS to BXD_GROUP_EXCEPTION | zsloan |
| 2024-08-28 | Use JSON rather than X-Form-URL-encoded data with auth server. | Frederick Muriuki Muriithi |
| 2024-08-28 | Run GN2 multithreaded by default...The service runs multithreaded on production, thus running it
multithreaded during dev should help with exposing otherwise
difficult/impossible to debug issues if running single-threaded.
| Frederick Muriuki Muriithi |
| 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...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.
| zsloan |
| 2024-08-28 | Also address the issue with trait IDs being detected as substrings for search... | zsloan |
| 2024-08-28 | Change text for Block filtering options to Filter to more accurately reflect ... | zsloan |
| 2024-08-28 | This prevents phenotype trait IDs (numeric search terms that are 5 digits in ... | zsloan |
| 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 |
