| Age | Commit message (Expand) | Author |
|---|
| 2024-08-29 | Rename entries -> wiki....* gn2/wqflask/views.py (display_genewiki_page)[entries]: Rename
entries to wiki.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Remove gn-entries from NCBI....Will re-add this section once the API is finalised.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Apply dj-lint jinja linter against genewiki.html....* gn2/wqflask/templates/genewiki.html: Run:
```
djlint gn2/wqflask/templates/genewiki.html \
--profile=jinja --reformat --format-css \
--format-js
```
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Rename generif -> genewiki....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Auto-pep8 file....* gn2/wqflask/views.py: Run auto-pep8 against file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | Allow '@' and '.' characters in searches...This is mainly so e-mail searches work
| zsloan |
| 2024-08-26 | Set fixed width of 500px for phenotype descriptions | zsloan |
| 2024-08-21 | Fix timestamp attribute names...They were previously stored as 'created_timestamp' and 'changed_timestamp', but are now stored as 'created' and 'changed'
| zsloan |
| 2024-08-19 | Edit Haplotype Analyst legend content...- 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
| zsloan |
| 2024-08-19 | Change 'Sequence Site' text to 'Gene Location' | zsloan |
| 2024-08-19 | Only draw position marker if position exists...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)
| zsloan |
| 2024-08-19 | Remove javascript escape function from View Collection page to fix encoding i... | zsloan |
| 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...Gn2 Fix profiles pages dashboard | Muriithi Frederick Muriuki |
| 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...In order to use JSON consistently across the board, we make even the
authentication method use JSON rather than FORMDATA.
| Frederick Muriuki Muriithi |
| 2024-08-05 | Move check for target_trait mb/chr into the if statement for ProbeSet/Geno da......Previously it would throw an error for Publish datasets, since they don't have a location
| zsloan |
| 2024-08-02 | Consistently use JSON for all endpoints. | Frederick Muriuki Muriithi |
| 2024-08-01 | Add mariadb package to database development container....* containers/db-container.scm (operating-system)[packages]: Add
mariadb.
| Arun Isaac |
| 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...Use auto-created JWKs for better security.
| Frederick Muriuki Muriithi |
| 2024-08-01 | 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 |
| 2024-08-01 | 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...Add more logging information to help with tracking and fixing bugs.
| Frederick Muriuki Muriithi |
| 2024-07-31 | 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 |
| 2024-07-30 | Fix GN3 URIs for case attribute editing...Also improve error logging somewhat (but still need to properly display the error in a template)
| zsloan |
| 2024-07-29 | 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 |
| 2024-07-27 | Include CaseAttribute.InbredSetId in the query that fetches case attributes...Previously issues could occur if a difference InbredSet had the same CaseAtribute Id
| zsloan |
| 2024-07-27 | 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...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 |
| 2024-07-22 | Provide PoC public-jwks endpoint. | Frederick Muriuki Muriithi |
| 2024-07-20 | Stop using the escape function for descriptions on the search result page...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 |
| 2024-07-20 | Also address the issue with trait IDs being detected as substrings for search... | zsloan |
| 2024-07-20 | Change text for Block filtering options to Filter to more accurately reflect ... | zsloan |
| 2024-07-20 | This prevents phenotype trait IDs (numeric search terms that are 5 digits in ... | zsloan |
| 2024-07-17 | 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 |
| 2024-07-17 | Remove redundant import. | Frederick Muriuki Muriithi |
| 2024-07-17 | 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 |
