feat!: use vrs 2.0-alpha models in /normalize

[korikuzma]

Close #363
Going to wait to open until Disease Normalization PR is merged. But would still like your review @jsstevenson now . This PR is very similar to the gene/disease PRs.

Notes:

• Dependency updates
  • Pin pydantic to v2
  • Remove ga4gh.vrsatile.pydantic and switch to use ga4gh.vrs for core/vrs 2-alpha models
    *TherapeuticDescriptor --> TherapeuticAgent
  • Updates disease-normalizer version
• Set response_model_exclude_none=True in FastAPI response
• In QueryHandler, method _add_vod renamed to _add_therapeutic_agent

[jsstevenson]

A few changes:

In cli.py, change these lines

from disease.database import Database as DiseaseDatabase                                                                                                                                                                                                                                                           
from disease.cli import CLI as DiseaseCLI

to

from disease.database.dynamodb import DynamoDbDatabase as DiseaseDatabase                                                                                                                                                                                                                                          
from disease.cli import update_db as update_disease_db

and change

click.echo(msg)
                try:
                    DiseaseCLI().update_normalizer_db(

to

click.echo(msg)
                try:
                    update_disease_db(                                                                                                                                                                                                                                                                             
                        ["--update_all", "--update_merged", "--db_url", endpoint_url]

and in etl/base.py change

self.disease_normalizer = DiseaseNormalizer(self.database.endpoint_url)

to

db = DynamoDbDatabase(self.database.endpoint_url)                                                                                                                                                                                                                                                          
        self.disease_normalizer = DiseaseNormalizer(db)

I'm testing with imports of HemOnc and Wikidata and they appear to work with the changes above (minus a separate HemOnc error which I've made a new issue for).