Refactor validate_json-> validate_db_update for real-time ref integ checks

[PeopleMakeCulture]

We are refactoring the util validate_json to be a multi-step process where we:

• validate_json with Draft7Validator
• validate_linkml_nmdcdb validates schema with linkML constructor
• validate_transaction which treats the change set as a db transaction, and checks for referential integrity in the post-update state of the database

[dwinston]

part of #318

[PeopleMakeCulture]

On pause until #576 resolved

[eecavanna]

validate_json with Draft7Validator

FYI: In the most recent migration notebook (here), I started using LinkML's Validator class (docs) instead of directly using jsonschema's Draft7Validator class — this was in accordance with guidance from our teammates that work on LinkML.