Add superseded_calibration in Calibration. Modified related functions and tests.

alembic/versions/adb481b7c60b_add_calibration_superseded_column.py

@@ -0,0 +1,31 @@
+"""add_calibration_superseded_column
+
+Revision ID: adb481b7c60b
+Revises: 398067c53257
+Create Date: 2026-06-01 16:45:35.507837
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = 'adb481b7c60b'
+down_revision = 'a7f3c2e9b104'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('score_calibrations', sa.Column('replaces_id', sa.Integer(), nullable=True))
+    op.create_index(op.f('ix_score_calibrations_replaces_id'), 'score_calibrations', ['replaces_id'], unique=False)
+    op.create_foreign_key(None, 'score_calibrations', 'score_calibrations', ['replaces_id'], ['id'])
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(None, 'score_calibrations', type_='foreignkey')
+    op.drop_index(op.f('ix_score_calibrations_replaces_id'), table_name='score_calibrations')
+    op.drop_column('score_calibrations', 'replaces_id')
+    # ### end Alembic commands ###

src/mavedb/lib/permissions/actions.py

@@ -14,3 +14,4 @@ class Action(Enum):
     ADD_BADGE = "add_badge"
     CHANGE_RANK = "change_rank"
     ADD_CALIBRATION = "add_calibration"
+    SUPERSEDE_CALIBRATION = "supersede_calibration"

src/mavedb/lib/permissions/score_calibration.py

@@ -61,6 +61,7 @@ def has_permission(user_data: Optional[UserData], entity: ScoreCalibration, acti
         Action.DELETE: _handle_delete_action,
         Action.PUBLISH: _handle_publish_action,
         Action.CHANGE_RANK: _handle_change_rank_action,
+        Action.SUPERSEDE_CALIBRATION: _handle_supersede_action
     }
 
     if action not in handlers:
@@ -293,3 +294,50 @@ def _handle_change_rank_action(
 
     user_may_view_private = user_is_owner or (entity.investigator_provided and user_is_contributor_to_score_set)
     return deny_action_for_entity(entity, private, user_data, user_may_view_private, "score calibration")
+
+
+def _handle_supersede_action(
+    user_data: Optional[UserData],
+    entity: ScoreCalibration,
+    user_is_owner: bool,
+    user_is_contributor_to_score_set: bool,
+    private: bool,
+    active_roles: list[UserRole],
+) -> PermissionResponse:
+    """
+    Handle SUPERSEDE action permission check for ScoreCalibration entities.
+
+    Only public score calibrations are allowed to be superseded.
+    Only superseding the calibration from the same score set.
+    Admin, owner, or investigator-provided plus a contributor to the score set can be the users who have permissions to
+    supersede a calibration.
+
+    Args:
+        user_data: The user's authentication data.
+        entity: The ScoreCalibration entity being accessed.
+        user_is_owner: Whether the user created the ScoreCalibration.
+        user_is_contributor_to_score_set: Whether the user is a contributor to the associated ScoreSet.
+        private: Whether the ScoreCalibration is private.
+        active_roles: List of the user's active roles.
+
+    Returns:
+        PermissionResponse: Permission result with appropriate HTTP status.
+    """
+    ## Allow read access under the following conditions:
+    # Only public score calibrations are allowed to be superseded.
+    if private:
+        return PermissionResponse(False)
+    # Owners of the ScoreCalibration may supersede it.
+    if user_is_owner:
+        return PermissionResponse(True)
+    # System admins may supersede any ScoreCalibration.
+    if roles_permitted(active_roles, [UserRole.admin]):
+        return PermissionResponse(True)
+    # If the calibration is investigator provided, contributors to the ScoreCalibration may supersede it.
+    if entity.investigator_provided and user_is_contributor_to_score_set:
+        return PermissionResponse(True)
+    # Only non superseded calibration can be superseded.
+    if entity.superseding_calibration:
+        return PermissionResponse(False)
+
+    return deny_action_for_entity(entity, private, user_data, False, "score calibration")