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# [Track A: Baseline]
"""
Tool: Patient Data Parser
Parses raw free-text patient case descriptions into a structured PatientProfile.
Uses MedGemma for intelligent extraction.
"""
from __future__ import annotations
import logging
from app.models.schemas import PatientProfile
from app.services.medgemma import MedGemmaService
logger = logging.getLogger(__name__)
SYSTEM_PROMPT = """You are a clinical data extraction assistant. Your job is to parse
free-text patient case descriptions into structured data. Extract all available clinical
information accurately. If a field is not mentioned, leave it empty or use defaults.
Never fabricate information that isn't present in the input."""
EXTRACTION_PROMPT = """Parse the following patient case into structured clinical data.
Patient Case:
{patient_text}
Extract:
- Age, gender
- Chief complaint (primary reason for visit)
- History of present illness (HPI)
- Past medical history (list of conditions)
- Current medications (name and dose)
- Allergies
- Lab results (test name, value, reference range, abnormal flag)
- Vital signs
- Social history
- Family history
- Any additional relevant notes"""
class PatientParserTool:
"""Parses raw patient text into a structured PatientProfile."""
def __init__(self):
self.medgemma = MedGemmaService()
async def run(self, patient_text: str) -> PatientProfile:
"""
Parse free-text patient description into structured profile.
Args:
patient_text: Raw patient case description
Returns:
Structured PatientProfile
"""
prompt = EXTRACTION_PROMPT.format(patient_text=patient_text)
try:
profile = await self.medgemma.generate_structured(
prompt=prompt,
response_model=PatientProfile,
system_prompt=SYSTEM_PROMPT,
temperature=0.1, # Low temp for factual extraction
max_tokens=1500,
)
logger.info(f"Parsed patient profile: {profile.chief_complaint}")
return profile
except Exception as e:
# Fallback: If any error occurs (API, parsing, etc.), do basic extraction
logger.warning(f"Patient parsing failed ({type(e).__name__}: {e}), using basic extraction")
return PatientProfile(
chief_complaint=patient_text[:200],
history_of_present_illness=patient_text,
additional_notes=f"Auto-extracted from raw text (structured parsing failed: {type(e).__name__})",
)
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