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2024-08-29Add initial template for gn editor UIAlexander_Kabui
2024-08-29Add initial endpoint for serving edit filesAlexander_Kabui
2024-08-29refactor: drop monad_requests and mark required fieldsJohn Nduli
2024-08-29feat: add post actions for editting wiki contentJohn Nduli
2024-08-29feat: add template for editting wikiJohn Nduli
2024-08-29Handle errors correctly during wiki entry fetch.Munyoki Kilyungi
* gn2/wqflask/templates/wiki/genewiki.html: Flash messages during errors. * gn2/wqflask/views.py (display_genewiki_page): Use "raise_for_status()" to handle errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Move genewiki template to wiki template folder.Munyoki Kilyungi
* gn2/wqflask/templates/genewiki.html: Move this... * gn2/wqflask/templates/genewiki.html: ... here. * gn2/wqflask/views.py (display_genewiki_page): Update the render_template page. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Delete un-used css block in genewiki html template.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Update genewiki page to be the same as GN1.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Add type annotation for symbol.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Use updated GN3 endpoint for wiki.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Rename entries -> wiki.Munyoki Kilyungi
* gn2/wqflask/views.py (display_genewiki_page)[entries]: Rename entries to wiki. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Remove gn-entries from NCBI.Munyoki Kilyungi
Will re-add this section once the API is finalised. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Apply dj-lint jinja linter against genewiki.html.Munyoki Kilyungi
* 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>
2024-08-29Rename generif -> genewiki.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Auto-pep8 file.Munyoki Kilyungi
* gn2/wqflask/views.py: Run auto-pep8 against file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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
2024-07-26Use JSON rather than X-Form-URL-encoded data with auth server.Frederick Muriuki Muriithi