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2024-08-26Allow '@' and '.' characters in searcheszsloan
This is mainly so e-mail searches work
2024-08-26Set fixed width of 500px for phenotype descriptionszsloan
2024-08-21Fix timestamp attribute nameszsloan
They were previously stored as 'created_timestamp' and 'changed_timestamp', but are now stored as 'created' and 'changed'
2024-08-19Edit 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
2024-08-19Change 'Sequence Site' text to 'Gene Location'zsloan
2024-08-19Only 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)
2024-08-19Remove javascript escape function from View Collection page to fix encoding ↵zsloan
issues
2024-08-16Add Wiki and RIF search terms to Xapian normal searchzsloan
2024-08-07Merge pull request #855 from jnduli/gn2_profiles_pagesMuriithi Frederick Muriuki
Gn2 Fix profiles pages dashboard
2024-08-07chore: remove passing bearer token to end userJohn Nduli
2024-08-07fix: remove bearer token from html and javascriptJohn Nduli
2024-08-06fix: use bearer token to query auth serverJohn Nduli
2024-08-06fix: pass in proper list of priviledge_idsJohn Nduli
2024-08-05Fix typo.Frederick Muriuki Muriithi
2024-08-05minor code formatting.Frederick Muriuki Muriithi
2024-08-05Update JWKs endpoint documentation.Frederick Muriuki Muriithi
2024-08-05Fix URLFrederick Muriuki Muriithi
2024-08-05Override '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.
2024-08-05Move 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
2024-08-02Consistently use JSON for all endpoints.Frederick Muriuki Muriithi
2024-08-01Remove obsolete configurations.Frederick Muriuki Muriithi
2024-08-01bug: add missing `count_per_page` variable.Frederick Muriuki Muriithi
2024-08-01Use auto-created and auto-rotated JSON Web KeysFrederick Muriuki Muriithi
Use auto-created JWKs for better security.
2024-08-01Use 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
2024-08-01Add module to help with rotation of JSON Web Keys.Frederick Muriuki Muriithi
2024-08-01Fix correlation bug caused by a result trait not having a locationzsloan
2024-08-01Fix misnamed variable that caused correlation location filter to not workzsloan
2024-07-31Fix collections import by allowing GET method for collections/add endpointzsloan
2024-07-31Improve loggingFrederick Muriuki Muriithi
Add more logging information to help with tracking and fixing bugs.
2024-07-31Synchronise 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.
2024-07-30Fix GN3 URIs for case attribute editingzsloan
Also improve error logging somewhat (but still need to properly display the error in a template)
2024-07-29Include 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
2024-07-27Include CaseAttribute.InbredSetId in the query that fetches case attributeszsloan
Previously issues could occur if a difference InbredSet had the same CaseAtribute Id
2024-07-27Add BXD-JAX-OFS to BXD_GROUP_EXCEPTIONzsloan
2024-07-26Use JSON rather than X-Form-URL-encoded data with auth server.Frederick Muriuki Muriithi
2024-07-23Run 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.
2024-07-22Provide PoC public-jwks endpoint.Frederick Muriuki Muriithi
2024-07-20Stop 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.
2024-07-20Also 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