| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-28 | minor code formatting. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Update JWKs endpoint documentation. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fix URL | Frederick Muriuki Muriithi | |
| 2024-08-28 | Override 'client_secret_post' auth with a JSON equivalent | Frederick Muriuki Muriithi | |
| In order to use JSON consistently across the board, we make even the authentication method use JSON rather than FORMDATA. | |||
| 2024-08-28 | Move 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 | |||
| 2024-08-28 | Consistently use JSON for all endpoints. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Add mariadb package to database development container. | Arun Isaac | |
| * containers/db-container.scm (operating-system)[packages]: Add mariadb. | |||
| 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 | Frederick Muriuki Muriithi | |
| Use auto-created JWKs for better security. | |||
| 2024-08-28 | Use JWKs from auth server public endpoint | Frederick 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 | |||
| 2024-08-28 | 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 | Frederick Muriuki Muriithi | |
| Add more logging information to help with tracking and fixing bugs. | |||
| 2024-08-28 | Synchronise token refreshes | Frederick 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. | |||
| 2024-08-28 | Fix GN3 URIs for case attribute editing | zsloan | |
| Also improve error logging somewhat (but still need to properly display the error in a template) | |||
| 2024-08-28 | Include 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 | |||
| 2024-08-28 | Include CaseAttribute.InbredSetId in the query that fetches case attributes | zsloan | |
| Previously issues could occur if a difference InbredSet had the same CaseAtribute Id | |||
| 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 | Frederick 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. | |||
| 2024-08-28 | Provide PoC public-jwks endpoint. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Stop using the escape function for descriptions on the search result page | zsloan | |
| 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. | |||
| 2024-08-28 | Also address the issue with trait IDs being detected as substrings for ↵ | zsloan | |
| searches including the group codes, like BXD_27538 | |||
| 2024-08-28 | Change text for Block filtering options to Filter to more accurately reflect ↵ | zsloan | |
| their current use | |||
| 2024-08-28 | This 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) | |||
| 2024-08-28 | Fix premature session expiration | Frederick 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. | |||
| 2024-08-28 | Remove redundant import. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Remove token and user detail handling from @app.before_request | Frederick 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. | |||
| 2024-08-28 | Reorganise code to do ALL configs at the top and then logging | Frederick Muriuki Muriithi | |
| In order to ensure that logging works as expected, make sure it is set up after all settings are in place. | |||
| 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 | zsloan | |
| This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py | |||
| 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 ↵ | zsloan | |
| Xapian search returns no results or throws an error (so search will still work if GN3 is down) | |||
| 2024-08-28 | Automatically 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 | |||
| 2024-08-28 | Increase MAX_SEARCH_RESULTS to 50000 | zsloan | |
| 2024-08-28 | Fix LRS/LOD Xapian searches when there are 5 terms (where position range is ↵ | zsloan | |
| included) | |||
| 2024-08-28 | Fix some issues with handling Xapian search output | zsloan | |
| - 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 | |||
| 2024-08-28 | Set default value for Mean and Additive Effect | zsloan | |
| 2024-08-28 | Add default value for location and symbol | zsloan | |
| Adding these in the DataTables column definitions is convenient because it means they don't need to be dealt with in the Python code | |||
| 2024-08-28 | Create trait objects from Xapian search results to pass to DataTables | zsloan | |
| 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. | |||
| 2024-08-28 | Raise ValueError if dataset type isn't ProbeSet/Publish/Geno | zsloan | |
| 2024-08-28 | Add doctstrings for new functions in search_results.py | zsloan | |
| Replace dataset name with fullname (this will need to be changed back when the Xapian indexing is rerun) | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |