Migrations: Update notebook to perform LinkML validation and allow database name configuration

[eecavanna]

In this branch:

1. I made it so the migration notebook gets the database name from the notebook configuration file instead of from strings hard-coded in the notebook. This will allow people to use a single MongoDB server when running the notebook, instead of requiring them to use two separate MongoDB servers.
2. I made it so the migration notebook uses LinkML's Validator class instead of using the jsonschema package directly, to validate the transformed data.
3. Delete some obsolete variables from a test.

Fixes #749 and #746

Type of change

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

• I performed a migration locally, using a single MongoDB server as both the origin and transformation server

Definition of Done (DoD) Checklist:

• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have added tests that prove my fix is effective or that my feature works, incl. considering downstream usage (e.g. https://github.com/microbiomedata/notebook_hackathons) if applicable.