Source code for modalysis.server.gff

"""FastAPI routes for GFF operations."""

import logging

from fastapi import APIRouter

from modalysis.core import gff as core_gff
from modalysis.server.models import GffAnnotateRequest, GffFormatRequest

logger = logging.getLogger(__name__)

router = APIRouter(prefix="/gff")




@router.post("/format")
def gff_format(request: GffFormatRequest) -> dict[str, str]:
    """Handle POST `/gff/format` and run core GFF formatting."""
    logger.info("Server received GFF format request: %s", request)
    core_gff.format(
        input_path=request.input_path,
        output_path=request.output_path,
        output_name=request.output_name,
        allowed_chromosomes=request.allowed_chromosomes,
    )
    return {"status": "success"}





@router.post("/annotate")
def gff_annotate(request: GffAnnotateRequest) -> dict[str, str]:
    """Handle POST `/gff/annotate` and run core GFF annotation."""
    logger.info("Server received GFF annotate request: %s", request)
    core_gff.annotate(
        gff_path=request.gff_path,
        expression_paths=request.expression_paths,
        expression_labels=request.expression_labels,
        output_path=request.output_path,
        output_name=request.output_name,
    )
    return {"status": "success"}