# entrypoint.py
from Bio import SeqIO
from sqlalchemy.orm import Session
from app.database import engine, SessionLocal, Base
from app.models import Sequence, Feature
import json

# Tworzenie tabeli w bazie danych
Base.metadata.create_all(bind=engine)

def get_db():
    db = SessionLocal()
    try:
        yield db
    finally:
        db.close()

def load_genbank_to_db(file_path: str):
    db = next(get_db())
    with open(file_path, 'r') as file:
        record = SeqIO.read(file, "genbank")

        # Zapisz sekwencję do bazy danych
        sequence_data = Sequence(
            name=record.name,
            description=record.description,
            sequence=str(record.seq)
        )
        db.add(sequence_data)
        db.commit()

        # Zapisz cechy (features) do bazy danych
        for feature in record.features:
            feature_data = Feature(
                type=feature.type,
                location=str(feature.location),
                sequence=str(record.seq[feature.location.start:feature.location.end]),
                qualifiers=json.dumps(feature.qualifiers),
                sequence_id=sequence_data.id
            )
            db.add(feature_data)
        db.commit()
    print(f"Loaded {file_path} to database.")

if __name__ == "__main__":
    load_genbank_to_db("data/pET-28+(a).gb")