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eb83689 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 | """NoteGuard FastAPI backend — PHI-safe REST endpoint for the LangGraph agent.
Exposes:
GET / -> index.html (clinician web UI)
GET /health -> {"status": "ok"}
GET /samples -> paginated list of synthetic notes (requires data/ dir)
GET /sample/random -> one random synthetic note
GET /sample/{id} -> full note by clinical_note_id
POST /summarise -> {clinician_answer, identifiers_removed, residual_risk,
deidentified_excerpt, ok}
POST /process -> {clinician_note, ai_note, identifiers, discharge_summary, metrics}
The assert_clean() guarantee is preserved: the graph raises ValueError if any
identifier survives de-identification, which surfaces here as HTTP 422.
Run: uvicorn app.api:app --reload --port 8000
"""
from __future__ import annotations
import csv
import random
from pathlib import Path
from dotenv import load_dotenv
load_dotenv(override=True)
from fastapi import FastAPI, HTTPException, Query
from fastapi.responses import FileResponse
from fastapi.staticfiles import StaticFiles
from langchain_core.messages import HumanMessage
from pydantic import BaseModel
from src.deid import NoteGuard, load_known_from_csv
STATIC_DIR = Path(__file__).parent / "static"
_DATA_DIR = Path(__file__).parent.parent / "data"
app = FastAPI(title="NoteGuard API", version="1.2.4")
# ---------------------------------------------------------------------------
# Dataset — loaded once at startup; degrades gracefully when data/ is absent
# ---------------------------------------------------------------------------
_NOTES: list[dict] = []
_DEFAULT_KNOWN: dict | None = None
try:
_patients_csv = str(_DATA_DIR / "patients.csv")
_admissions_csv = str(_DATA_DIR / "admissions.csv")
_DEFAULT_KNOWN = load_known_from_csv(_patients_csv, _admissions_csv)
with open(_DATA_DIR / "synthetic_clinical_notes.csv", newline="", encoding="utf-8-sig") as _f:
for _row in csv.DictReader(_f):
_text = NoteGuard._fix_mojibake(_row["clean_note_text"])
_NOTES.append(
{
"clinical_note_id": _row["clinical_note_id"],
"person_id": _row["person_id"],
"note_type": _row.get("note_type", ""),
"note_subject": _row.get("note_subject", ""),
"excerpt": _text[:120].strip(),
"note_text": _text,
}
)
except Exception:
pass # data/ not present — /samples returns empty, /process still works
# ---------------------------------------------------------------------------
# Per-vault graph cache — key is a hashable snapshot of the known-identifier dict.
# ---------------------------------------------------------------------------
_graph_cache: dict = {}
def _vault_key(known: dict | None) -> tuple | None:
if not known:
return None
return tuple(sorted((k, tuple(sorted(v))) for k, v in known.items()))
def _get_graph(known: dict | None):
"""Return a compiled NoteGuard graph, building it once per distinct vault."""
key = _vault_key(known)
if key not in _graph_cache:
from agent.graph import build_graph
_graph_cache[key] = build_graph(known=known)
return _graph_cache[key]
# ---------------------------------------------------------------------------
# Models
# ---------------------------------------------------------------------------
class SummariseRequest(BaseModel):
note: str
question: str = "Draft an NHS eDischarge summary."
known: dict | None = None
class SummariseResponse(BaseModel):
clinician_answer: str
identifiers_removed: int
residual_risk: float
deidentified_excerpt: str
ok: bool
class ProcessRequest(BaseModel):
note: str
question: str = "Draft an NHS eDischarge summary."
known: dict | None = None
person_id: str | None = None # accepted for UI compatibility; unused (patient is never named)
class ProcessResponse(BaseModel):
clinician_note: str
ai_note: str
identifiers: list[str]
discharge_summary: str
metrics: dict
class SampleItem(BaseModel):
clinical_note_id: str
person_id: str
note_type: str
excerpt: str
class SamplesResponse(BaseModel):
total: int
items: list[SampleItem]
class SampleDetail(BaseModel):
clinical_note_id: str
person_id: str
note_type: str
note_subject: str
note_text: str
# ---------------------------------------------------------------------------
# Endpoints
# ---------------------------------------------------------------------------
@app.get("/")
def index():
return FileResponse(STATIC_DIR / "index.html")
@app.get("/health")
def health():
"""Liveness probe — no API keys required."""
return {"status": "ok", "notes_loaded": len(_NOTES)}
@app.get("/samples", response_model=SamplesResponse)
def samples(
limit: int = Query(50, ge=1, le=200),
offset: int = Query(0, ge=0),
q: str = Query(""),
note_type: str = Query(""),
):
"""Paginated list of synthetic notes with optional text/type filter."""
hits = _NOTES
if note_type:
hits = [n for n in hits if n["note_type"] == note_type]
if q:
ql = q.lower()
hits = [n for n in hits if ql in n["note_text"].lower() or ql in n["note_subject"].lower()]
page = hits[offset : offset + limit]
return SamplesResponse(
total=len(hits),
items=[
SampleItem(
clinical_note_id=n["clinical_note_id"],
person_id=n["person_id"],
note_type=n["note_type"],
excerpt=n["excerpt"],
)
for n in page
],
)
@app.get("/sample/random", response_model=SampleDetail)
def sample_random():
"""Return one random synthetic note."""
if not _NOTES:
raise HTTPException(status_code=404, detail="No notes loaded — run src/fetch_dataset.py first.")
note = random.choice(_NOTES)
return SampleDetail(**{k: note[k] for k in SampleDetail.model_fields})
@app.get("/sample/{clinical_note_id}", response_model=SampleDetail)
def sample_by_id(clinical_note_id: str):
"""Return a single synthetic note by its clinical_note_id."""
for note in _NOTES:
if note["clinical_note_id"] == clinical_note_id:
return SampleDetail(**{k: note[k] for k in SampleDetail.model_fields})
raise HTTPException(status_code=404, detail=f"Note {clinical_note_id!r} not found.")
@app.post("/summarise", response_model=SummariseResponse)
def summarise(req: SummariseRequest):
"""Run the NoteGuard agent and return a PHI-safe discharge summary.
Raises:
HTTPException 422: assert_clean() detected surviving PHI.
HTTPException 500: unexpected agent error.
"""
known = req.known if req.known is not None else _DEFAULT_KNOWN
try:
g = _get_graph(known)
state = g.invoke({"messages": [HumanMessage(content=req.note + "\n\n" + req.question)]})
except ValueError as exc:
raise HTTPException(status_code=422, detail=str(exc)) from exc
except Exception as exc:
raise HTTPException(status_code=500, detail=str(exc)) from exc
# De-id is correct iff nothing leaked to the model AND every surrogate reverses.
residual_pii = state.get("residual_pii") or []
leaked = state.get("leaked_tokens") or []
ok = not residual_pii and not leaked
return SummariseResponse(
clinician_answer=state.get("clinician_answer", ""),
identifiers_removed=len(state.get("forward", {})),
residual_risk=0.0 if ok else 1.0,
deidentified_excerpt=(state.get("deid_text") or "")[:400],
ok=ok,
)
@app.post("/process", response_model=ProcessResponse)
def process(req: ProcessRequest):
"""Run NoteGuard and return rich output for the clinician UI.
When req.known is omitted, uses the pre-built vault from data/patients.csv
so residual-leakage is measured against ground truth identifiers.
"""
known = req.known if req.known is not None else _DEFAULT_KNOWN
try:
g = _get_graph(known)
state = g.invoke({"messages": [HumanMessage(content=req.note + "\n\n" + req.question)]})
except ValueError as exc:
raise HTTPException(status_code=422, detail=str(exc)) from exc
except Exception as exc:
raise HTTPException(status_code=500, detail=str(exc)) from exc
forward = state.get("forward") or {}
leaked = state.get("leaked_tokens") or []
residual_pii = state.get("residual_pii") or []
reversible = not leaked
deid_ok = not residual_pii and reversible
return ProcessResponse(
clinician_note=req.note,
ai_note=state.get("deid_text", ""),
identifiers=list(forward.keys()),
discharge_summary=state.get("clinician_answer", ""),
metrics={
# Every metric reports whether reversible pseudonymisation was done correctly.
"deid_ok": deid_ok, # overall verdict: nothing leaked AND fully reversible
"identifiers_removed": len(forward), # PII spans pseudonymised this turn
"residual_pii": residual_pii, # [{type, text}] PII the model still saw
"residual_pii_count": len(residual_pii),
"reversible": reversible, # every surrogate restores to a real value
"leaked_tokens": leaked, # orphaned/unresolved surrogate tokens
},
)
if STATIC_DIR.exists():
app.mount("/static", StaticFiles(directory=str(STATIC_DIR)), name="static")
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