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2024-08-29Add htmx js api for delete functionality.Alexander_Kabui
2024-08-29integrate gnqa history delete functionality.Alexander_Kabui
2024-08-29Handle attributeError when getting error codes.Alexander_Kabui
2024-08-29BugFix: return correct status code for generic exceptions handler.Alexander_Kabui
2024-08-29Fix bug: Update DOM correctly when rating error occurs.Alexander_Kabui
2024-08-29Mark answer and references as safe to render a tags.Alexander_Kabui
2024-08-29Add UI code for gnqa history search delete functionality.Alexander_Kabui
2024-08-29Update endpoints and add search history functionality.Alexander_Kabui
2024-08-29View file code cleanup for gnqa.Alexander_Kabui
2024-08-29Refactor template code for gnqa search historyAlexander_Kabui
2024-08-28Allow '@' and '.' characters in searcheszsloan
This is mainly so e-mail searches work
2024-08-28Set fixed width of 500px for phenotype descriptionszsloan
2024-08-28Fix timestamp attribute nameszsloan
They were previously stored as 'created_timestamp' and 'changed_timestamp', but are now stored as 'created' and 'changed'
2024-08-28Edit Haplotype Analyst legend contentzsloan
- Change order from Pat/Mat to Mat/Pat - Increase width of example color bars - Change 'Unk' to 'Unknown' and shift everything to the left so it fits
2024-08-28Change 'Sequence Site' text to 'Gene Location'zsloan
2024-08-28Only draw position marker if position existszsloan
Previous it was drawing the marker at the end of the map even when mapping with traits that don't have a position (like Publish/phenotype traits)
2024-08-28Remove javascript escape function from View Collection page to fix encoding ↵zsloan
issues
2024-08-28Add Wiki and RIF search terms to Xapian normal searchzsloan
2024-08-28chore: remove passing bearer token to end userJohn Nduli
2024-08-28fix: remove bearer token from html and javascriptJohn Nduli
2024-08-28fix: use bearer token to query auth serverJohn Nduli
2024-08-28fix: pass in proper list of priviledge_idsJohn Nduli
2024-08-28Fix typo.Frederick Muriuki Muriithi
2024-08-28minor code formatting.Frederick Muriuki Muriithi
2024-08-28Update JWKs endpoint documentation.Frederick Muriuki Muriithi
2024-08-28Fix URLFrederick Muriuki Muriithi
2024-08-28Override 'client_secret_post' auth with a JSON equivalentFrederick Muriuki Muriithi
In order to use JSON consistently across the board, we make even the authentication method use JSON rather than FORMDATA.
2024-08-28Move check for target_trait mb/chr into the if statement for ProbeSet/Geno ↵zsloan
datasets Previously it would throw an error for Publish datasets, since they don't have a location
2024-08-28Consistently use JSON for all endpoints.Frederick Muriuki Muriithi
2024-08-28Add mariadb package to database development container.Arun Isaac
* containers/db-container.scm (operating-system)[packages]: Add mariadb.
2024-08-28Remove obsolete configurations.Frederick Muriuki Muriithi
2024-08-28bug: add missing `count_per_page` variable.Frederick Muriuki Muriithi
2024-08-28Use auto-created and auto-rotated JSON Web KeysFrederick Muriuki Muriithi
Use auto-created JWKs for better security.
2024-08-28Use JWKs from auth server public endpointFrederick Muriuki Muriithi
* Fetch keys from auth server * Validate token is signed with one of the keys from server * Ensure refreshing of token is still synchronised
2024-08-28Add module to help with rotation of JSON Web Keys.Frederick Muriuki Muriithi
2024-08-28Fix correlation bug caused by a result trait not having a locationzsloan
2024-08-28Fix misnamed variable that caused correlation location filter to not workzsloan
2024-08-28Fix collections import by allowing GET method for collections/add endpointzsloan
2024-08-28Improve loggingFrederick Muriuki Muriithi
Add more logging information to help with tracking and fixing bugs.
2024-08-28Synchronise token refreshesFrederick Muriuki Muriithi
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.
2024-08-28Fix GN3 URIs for case attribute editingzsloan
Also improve error logging somewhat (but still need to properly display the error in a template)
2024-08-28Include trait and dataset name in hmac passed to search results page for ↵zsloan
non-xapian results Previously it only had the hmac, which caused adding to a collection to not work for such searches
2024-08-28Include CaseAttribute.InbredSetId in the query that fetches case attributeszsloan
Previously issues could occur if a difference InbredSet had the same CaseAtribute Id
2024-08-28Add BXD-JAX-OFS to BXD_GROUP_EXCEPTIONzsloan
2024-08-28Use JSON rather than X-Form-URL-encoded data with auth server.Frederick Muriuki Muriithi
2024-08-28Run GN2 multithreaded by defaultFrederick Muriuki Muriithi
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.
2024-08-28Provide PoC public-jwks endpoint.Frederick Muriuki Muriithi
2024-08-28Stop using the escape function for descriptions on the search result pagezsloan
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.
2024-08-28Also address the issue with trait IDs being detected as substrings for ↵zsloan
searches including the group codes, like BXD_27538
2024-08-28Change text for Block filtering options to Filter to more accurately reflect ↵zsloan
their current use