Release 2025.1.0#390

Merged

bencap merged 66 commits intomainfrom

release-2025.1.0

Feb 25, 2025

Commits on Dec 5, 2024

Only show unpublished superseding score set to the users who have permissions to view it. The current version to other users will only be the published one.
EstelleDa
committed

Commits on Dec 13, 2024

Commits on Dec 20, 2024

Fix listing score set in experiment if these score sets' superseding score sets are unpublished yet. Haven't fixed the search score set codes.
EstelleDa
committed
Handle poetry run mypy src/ error so that add next_version
EstelleDa
committed

Commits on Jan 13, 2025

Convert the file format back.
EstelleDa
committed

Commits on Jan 22, 2025

Find a potential bug from the failed tests. Haven't add related new tests yet.
EstelleDa
committed

Commits on Jan 27, 2025

Modify multiple functions that relates to superseding score set and add some related tests.
EstelleDa
committed
Collections Data Model
bencap
committed
DB Migration for Collections Data Model
bencap
committed
Move collection urn property to SavedCollection

sallybg
and
bencap
committed
Add method to create a collection

sallybg
and
bencap
committed
Add permissions for actions on collections

sallybg
authored and
bencap
committed
Allow deletion of a public collection

sallybg
authored and
bencap
committed
Add methods for modification and deletion of collections

sallybg
authored and
bencap
committed
Add documentation for select collection fields

sallybg
authored and
bencap
committed
Add tables to associate collections with data sets

sallybg
authored and
bencap
committed
squash: remove collection association tables from collection.py

sallybg
authored and
bencap
committed
squash: add collections and official collections to score set and experiment models

sallybg
authored and
bencap
committed
Add official collections to score set and experiment view models

sallybg
authored and
bencap
committed
Add view models to request addition of data sets to collections

sallybg
authored and
bencap
committed
Get my collections ordered by user role, and fix add data set to collection

sallybg
authored and
bencap
committed
Add router to get limited user information by Orcid ID

sallybg
authored and
bencap
committed
Automatically assign collection creator as admin

sallybg
authored and
bencap
committed
Only show collections' data sets for which user has read permissions

sallybg
authored and
bencap
committed
Do not separately include owned collections in my collections

sallybg
authored and
bencap
committed
Remove owned collections from view model

sallybg
authored and
bencap
committed
Change collection modify date when adding/removing a data set

sallybg
authored and
bencap
committed
Filter data sets based on user permissions when fetching my collections

sallybg
authored and
bencap
committed
Add users to Collection view model

sallybg
authored and
bencap
committed
Collections routers: use body instead of query param to specify user to add/remove

sallybg
authored and
bencap
committed
Make all fields optional in body of update collection request, and allow null values

sallybg
authored and
bencap
committed
Make update collection a patch request. Fix bugs with some routers

sallybg
authored and
bencap
committed
Add collection permissions to permissions API

sallybg
authored and
bencap
committed
Include official collection names and URNs in experiment and score set responses.

jstone-dev
authored and
bencap
committed
Cleaned up TODOs and pluralized API paths for collection user permissions.

jstone-dev
authored and
bencap
committed
Changed the collection URN format.

jstone-dev
authored and
bencap
committed
Added collection unit tests.

jstone-dev
authored and
bencap
committed
Formatted code with ruff.

jstone-dev
authored and
bencap
committed
Fixes for MyPy and preexisting unit tests

jstone-dev
authored and
bencap
committed
Cleanup and response to PR feedback

jstone-dev
authored and
bencap
committed
Add recordType Property to Collection View Models
bencap
committed
Use Sequence type for Collection user lists
bencap
committed
Merge pull request #374 from VariantEffect/feature/bencap/288/data-collections
bencap
authored

Commits on Feb 11, 2025

Commits on Feb 12, 2025

Commits on Feb 13, 2025

Place collections data model updates at alembic HEAD
bencap
committed

Commits on Feb 19, 2025

Merge pull request #366 from VariantEffect/estelle/debugShowTmpSupersedingScoreSet
EstelleDa
authored

Commits on Feb 25, 2025