| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-29 | Rename generif -> genewiki. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-29 | Auto-pep8 file. | Munyoki Kilyungi | |
| * gn2/wqflask/views.py: Run auto-pep8 against file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-26 | Allow '@' and '.' characters in searches | zsloan | |
| This is mainly so e-mail searches work | |||
| 2024-08-26 | Set fixed width of 500px for phenotype descriptions | zsloan | |
| 2024-08-21 | Fix timestamp attribute names | zsloan | |
| They were previously stored as 'created_timestamp' and 'changed_timestamp', but are now stored as 'created' and 'changed' | |||
| 2024-08-19 | Edit Haplotype Analyst legend content | zsloan | |
| - 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 | |||
| 2024-08-19 | Change 'Sequence Site' text to 'Gene Location' | zsloan | |
| 2024-08-19 | Only draw position marker if position exists | zsloan | |
| 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) | |||
| 2024-08-19 | Remove javascript escape function from View Collection page to fix encoding ↵ | zsloan | |
| issues | |||
| 2024-08-16 | Add Wiki and RIF search terms to Xapian normal search | zsloan | |
| 2024-08-07 | Merge pull request #855 from jnduli/gn2_profiles_pages | Muriithi Frederick Muriuki | |
| Gn2 Fix profiles pages dashboard | |||
| 2024-08-07 | chore: remove passing bearer token to end user | John Nduli | |
| 2024-08-07 | fix: remove bearer token from html and javascript | John Nduli | |
| 2024-08-06 | fix: use bearer token to query auth server | John Nduli | |
| 2024-08-06 | fix: pass in proper list of priviledge_ids | John Nduli | |
| 2024-08-05 | Fix typo. | Frederick Muriuki Muriithi | |
| 2024-08-05 | minor code formatting. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Update JWKs endpoint documentation. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Fix URL | Frederick Muriuki Muriithi | |
| 2024-08-05 | 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. | |||
| 2024-08-05 | 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 | |||
| 2024-08-02 | Consistently use JSON for all endpoints. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Add mariadb package to database development container. | Arun Isaac | |
| * containers/db-container.scm (operating-system)[packages]: Add mariadb. | |||
| 2024-08-01 | Remove obsolete configurations. | Frederick Muriuki Muriithi | |
| 2024-08-01 | bug: add missing `count_per_page` variable. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Use auto-created and auto-rotated JSON Web Keys | Frederick Muriuki Muriithi | |
| Use auto-created JWKs for better security. | |||
| 2024-08-01 | 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 | |||
| 2024-08-01 | Add module to help with rotation of JSON Web Keys. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Fix correlation bug caused by a result trait not having a location | zsloan | |
| 2024-08-01 | Fix misnamed variable that caused correlation location filter to not work | zsloan | |
| 2024-07-31 | Fix collections import by allowing GET method for collections/add endpoint | zsloan | |
| 2024-07-31 | Improve logging | Frederick Muriuki Muriithi | |
| Add more logging information to help with tracking and fixing bugs. | |||
| 2024-07-31 | 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. | |||
| 2024-07-30 | Fix GN3 URIs for case attribute editing | zsloan | |
| Also improve error logging somewhat (but still need to properly display the error in a template) | |||
| 2024-07-29 | 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 | |||
| 2024-07-27 | Include CaseAttribute.InbredSetId in the query that fetches case attributes | zsloan | |
| Previously issues could occur if a difference InbredSet had the same CaseAtribute Id | |||
| 2024-07-27 | Add BXD-JAX-OFS to BXD_GROUP_EXCEPTION | zsloan | |
| 2024-07-26 | Use JSON rather than X-Form-URL-encoded data with auth server. | Frederick Muriuki Muriithi | |
| 2024-07-23 | 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. | |||
| 2024-07-22 | Provide PoC public-jwks endpoint. | Frederick Muriuki Muriithi | |
| 2024-07-20 | 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. | |||
| 2024-07-20 | Also address the issue with trait IDs being detected as substrings for ↵ | zsloan | |
| searches including the group codes, like BXD_27538 | |||
| 2024-07-20 | Change text for Block filtering options to Filter to more accurately reflect ↵ | zsloan | |
| their current use | |||
| 2024-07-20 | 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) | |||
| 2024-07-17 | 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. | |||
| 2024-07-17 | Remove redundant import. | Frederick Muriuki Muriithi | |
| 2024-07-17 | 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. | |||
| 2024-07-17 | 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. | |||
| 2024-07-12 | Add two new links to tutorials page | zsloan | |
| 2024-07-12 | Add Peak Chr and Peak Mb columns to ProbeSet export in the GN2 REST API | zsloan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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