api/app/routes/biomarkers.py

"""
Biomarkers List Endpoint
"""

import json
from datetime import datetime
from pathlib import Path

from fastapi import APIRouter, HTTPException

from app.models.schemas import BiomarkerInfo, BiomarkerReferenceRange, BiomarkersListResponse

router = APIRouter(prefix="/api/v1", tags=["biomarkers"])


@router.get("/biomarkers", response_model=BiomarkersListResponse)
async def list_biomarkers():
    """
    Get list of all supported biomarkers with reference ranges.

    Returns comprehensive information about all 24 biomarkers:
    - Name and unit
    - Normal reference ranges (gender-specific if applicable)
    - Critical thresholds
    - Clinical significance

    Useful for:
    - Frontend validation
    - Understanding what biomarkers can be analyzed
    - Getting reference ranges for display
    """

    try:
        # Load biomarker references
        config_path = Path(__file__).parent.parent.parent.parent / "config" / "biomarker_references.json"

        with open(config_path, encoding="utf-8") as f:
            config_data = json.load(f)

        biomarkers_data = config_data.get("biomarkers", {})

        biomarkers_list = []

        for name, info in biomarkers_data.items():
            # Parse reference range
            normal_range_data = info.get("normal_range", {})

            if "male" in normal_range_data or "female" in normal_range_data:
                # Gender-specific ranges
                reference_range = BiomarkerReferenceRange(
                    min=None, max=None, male=normal_range_data.get("male"), female=normal_range_data.get("female")
                )
            else:
                # Universal range
                reference_range = BiomarkerReferenceRange(
                    min=normal_range_data.get("min"), max=normal_range_data.get("max"), male=None, female=None
                )

            biomarker_info = BiomarkerInfo(
                name=name,
                unit=info.get("unit", ""),
                normal_range=reference_range,
                critical_low=info.get("critical_low"),
                critical_high=info.get("critical_high"),
                gender_specific=info.get("gender_specific", False),
                description=info.get("description", ""),
                clinical_significance=info.get("clinical_significance", {}),
            )

            biomarkers_list.append(biomarker_info)

        return BiomarkersListResponse(
            biomarkers=biomarkers_list, total_count=len(biomarkers_list), timestamp=datetime.now().isoformat()
        )

    except FileNotFoundError as exc:
        raise HTTPException(status_code=500, detail="Biomarker configuration file not found") from exc

    except Exception as e:
        raise HTTPException(status_code=500, detail=f"Failed to load biomarkers: {e!s}") from e