kemal
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End-to-end variant interpretation platform for rare genetic disease research: SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline, LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure. Public test data only; no clinical claims.
33 lines
868 B
Python
33 lines
868 B
Python
import asyncio
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from logging.config import fileConfig
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from alembic import context
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from sqlalchemy.ext.asyncio import async_engine_from_config
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from sqlalchemy import pool
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from app.config import settings
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from app.models import Base
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config = context.config
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config.set_main_option("sqlalchemy.url", settings.database_url)
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if config.config_file_name:
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fileConfig(config.config_file_name)
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target_metadata = Base.metadata
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def run_migrations(connection):
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context.configure(connection=connection, target_metadata=target_metadata)
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with context.begin_transaction():
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context.run_migrations()
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async def run_async():
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engine = async_engine_from_config(
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config.get_section(config.config_ini_section, {}), poolclass=pool.NullPool
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)
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async with engine.connect() as conn:
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await conn.run_sync(run_migrations)
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asyncio.run(run_async())
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