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models.py — Pydantic request / response models for the RareDx diagnosis API.
"""
from pydantic import BaseModel, Field
from typing import Optional
class DiagnoseRequest(BaseModel):
note: str = Field(
...,
min_length=10,
description="Plain-text clinical note describing the patient's presentation.",
examples=["18 year old male, extremely tall, displaced lens, heart murmur, scoliosis"],
)
top_n: int = Field(default=10, ge=1, le=50, description="Max candidates to return.")
threshold: float = Field(
default=0.55, ge=0.3, le=0.95,
description="Minimum BioLORD cosine similarity to accept an HPO match.",
)
class HPOMatch(BaseModel):
phrase: str
hpo_id: str
term: str
score: float
class Candidate(BaseModel):
rank: int
orpha_code: str
name: str
definition: Optional[str]
rrf_score: float
graph_rank: Optional[int]
chroma_rank: Optional[int]
graph_matches: Optional[int] # number of HPO terms matched in graph
chroma_sim: Optional[float] # cosine similarity from ChromaDB
matched_hpo: list[dict] = [] # HPO terms matched via graph
hallucination_flag: bool = False
flag_reason: Optional[str] = None
evidence_score: float = 0.0
class DiagnoseResponse(BaseModel):
note: str
phrases_extracted: list[str]
hpo_matches: list[HPOMatch]
hpo_ids_used: list[str]
candidates: list[Candidate] # all candidates (flag fields attached)
passed_candidates: list[Candidate] # guard passed
flagged_candidates: list[Candidate] # guard flagged
top_diagnosis: Optional[Candidate]
graph_backend: str
chroma_backend: str
elapsed_seconds: float
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