feat: Enhance medical report generation with new features and improved data handling
- Added body fat percentage input and optional muscle oxygenation CSV upload in the upload form. - Implemented TSI chart generation based on muscle oxygenation data. - Updated report generation to include metabolism and fuel source charts. - Refactored context generation to eliminate reliance on SECA data, using patient info directly instead. - Improved error handling and logging for graph generation processes. - Enhanced HTML templates for better user experience and functionality.
This commit is contained in:
bolade
+211
-99
@@ -13,10 +13,13 @@ from pathlib import Path
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from fastapi import FastAPI, File, Form, HTTPException, Request, UploadFile
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from fastapi.responses import FileResponse, HTMLResponse, RedirectResponse
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from fastapi.staticfiles import StaticFiles
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from jinja2 import Environment, FileSystemLoader
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from pydantic import BaseModel
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from starlette.middleware.sessions import SessionMiddleware
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from services.report_generator import ReportGeneratorService
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from starlette.middleware.base import BaseHTTPMiddleware
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from starlette.middleware.sessions import SessionMiddleware
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from starlette.requests import Request as StarletteRequest
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app = FastAPI(
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title="Medical Report Generation API",
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@@ -25,7 +28,32 @@ app = FastAPI(
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)
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# Add session middleware
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app.add_middleware(SessionMiddleware, secret_key=os.getenv("SECRET_KEY", "your-secret-key-change-in-production"))
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app.add_middleware(
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SessionMiddleware,
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secret_key=os.getenv("SECRET_KEY", "your-secret-key-change-in-production"),
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)
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# Add security headers middleware to allow external scripts
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class SecurityHeadersMiddleware(BaseHTTPMiddleware):
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async def dispatch(self, request: StarletteRequest, call_next):
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response = await call_next(request)
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# Allow external scripts and styles (for Tailwind CDN)
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# Only add CSP for HTML responses
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content_type = response.headers.get("content-type", "").lower()
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if "text/html" in content_type:
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response.headers["Content-Security-Policy"] = (
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"default-src 'self'; script-src 'self' 'unsafe-inline' https://cdn.tailwindcss.com https:; style-src 'self' 'unsafe-inline' https://cdn.tailwindcss.com https:; img-src 'self' data: https:;"
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)
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return response
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app.add_middleware(SecurityHeadersMiddleware)
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# Mount static files (if static directory exists)
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static_dir = Path("static")
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if static_dir.exists():
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app.mount("/static", StaticFiles(directory="static"), name="static")
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# Setup templates
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jinja_env = Environment(loader=FileSystemLoader("app/templates"))
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@@ -59,13 +87,15 @@ def render_template(template_name: str, context: dict) -> HTMLResponse:
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"""Helper function to render Jinja2 templates"""
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template = jinja_env.get_template(template_name)
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html_content = template.render(**context)
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return HTMLResponse(content=html_content)
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return HTMLResponse(content=html_content, media_type="text/html")
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@app.get("/", response_class=HTMLResponse)
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async def root(request: Request):
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"""Root endpoint - Upload form page"""
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return render_template("upload.html", {"request": request, "session": request.session})
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return render_template(
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"upload.html", {"request": request, "session": request.session}
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)
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@app.post("/upload")
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@@ -77,56 +107,73 @@ async def upload_files(
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height: str = Form(...),
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weight: str = Form(...),
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gender: str = Form(...),
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fat_percentage: float = Form(...),
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focus: str = Form(default="Endurance"),
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session_id: str = Form(default="default"),
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spirometry_pdf: UploadFile = File(...),
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pnoe_csv: UploadFile = File(...),
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seca_excel: UploadFile = File(...),
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oxygenation_csv: UploadFile = File(None),
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):
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"""Handle file upload and generate report"""
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# Validate file types
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if not spirometry_pdf.filename.endswith(".pdf"):
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return render_template("upload.html", {
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"request": request,
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"session": request.session,
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"error": "Spirometry file must be a PDF"
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})
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return render_template(
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"upload.html",
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{
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"request": request,
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"session": request.session,
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"error": "Spirometry file must be a PDF",
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},
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)
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if not pnoe_csv.filename.endswith(".csv"):
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return render_template("upload.html", {
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"request": request,
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"session": request.session,
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"error": "Pnoe file must be a CSV"
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})
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if not seca_excel.filename.endswith((".xlsx", ".xls")):
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return render_template("upload.html", {
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"request": request,
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"session": request.session,
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"error": "SECA file must be an Excel file (.xlsx or .xls)"
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})
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return render_template(
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"upload.html",
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{
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"request": request,
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"session": request.session,
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"error": "Pnoe file must be a CSV",
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},
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)
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# Validate oxygenation CSV if provided
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if oxygenation_csv and oxygenation_csv.filename:
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if not oxygenation_csv.filename.endswith(".csv"):
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return render_template(
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"upload.html",
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{
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"request": request,
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"session": request.session,
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"error": "Oxygenation file must be a CSV",
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},
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)
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# Create session-specific temp directory
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session_uuid = str(uuid.uuid4())
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session_temp_dir = TEMP_DIR / session_uuid
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session_temp_dir.mkdir(exist_ok=True, parents=True)
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# Save uploaded files
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spirometry_path = session_temp_dir / f"spirometry_{spirometry_pdf.filename}"
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pnoe_path = session_temp_dir / f"pnoe_{pnoe_csv.filename}"
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seca_path = session_temp_dir / f"seca_{seca_excel.filename}"
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oxygenation_path = None
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try:
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# Write files
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with open(spirometry_path, "wb") as f:
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shutil.copyfileobj(spirometry_pdf.file, f)
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with open(pnoe_path, "wb") as f:
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shutil.copyfileobj(pnoe_csv.file, f)
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with open(seca_path, "wb") as f:
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shutil.copyfileobj(seca_excel.file, f)
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# Save oxygenation CSV if provided
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if oxygenation_csv and oxygenation_csv.filename:
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oxygenation_path = (
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session_temp_dir / f"oxygenation_{oxygenation_csv.filename}"
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)
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with open(oxygenation_path, "wb") as f:
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shutil.copyfileobj(oxygenation_csv.file, f)
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# Prepare patient information
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patient_name = f"{first_name} {last_name}"
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patient_info = {
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@@ -137,76 +184,100 @@ async def upload_files(
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"height": height,
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"weight": weight,
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"gender": gender,
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"fat_percentage": fat_percentage,
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"focus": focus,
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"session_id": session_id,
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}
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# Generate report
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oxygenation_csv_path = str(oxygenation_path) if oxygenation_path else None
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result = await report_service.generate_report(
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spirometry_pdf_path=str(spirometry_path),
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pnoe_csv_path=str(pnoe_path),
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seca_excel_path=str(seca_path),
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patient_info=patient_info,
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oxygenation_csv_path=oxygenation_csv_path,
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)
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# Store in session
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request.session["patient_info"] = patient_info
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request.session["temp_dir"] = str(session_temp_dir)
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request.session["report_path"] = result["report_path"]
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request.session["graphs_generated"] = result["graphs_generated"]
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request.session["analysis_data"] = result["analysis_data"]
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# Extract spirometry CSV path (it's saved in data_dir by the service)
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from services.spirometry_table_extractor import extract_spirometry_table_from_pdf
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from services.context_generator import ContextGenerator
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from pathlib import Path as PathLib
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from services.context_generator import ContextGenerator
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from services.spirometry_table_extractor import (
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extract_spirometry_table_from_pdf,
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)
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# The spirometry CSV is extracted during report generation
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# We need to find it or extract it again
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data_dir = PathLib("data")
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spirometry_csv_path = data_dir / f"spirometry_{Path(spirometry_pdf.filename).stem}.csv"
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spirometry_csv_path = (
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data_dir / f"spirometry_{Path(spirometry_pdf.filename).stem}.csv"
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)
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# If it doesn't exist, extract it
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if not spirometry_csv_path.exists():
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spirometry_csv_path = extract_spirometry_table_from_pdf(
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str(spirometry_path), output_dir=str(data_dir)
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)
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spirometry_csv_path = PathLib(spirometry_csv_path)
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# Get calculated metrics for display and editing
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context_gen = ContextGenerator()
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context_gen.load_data(
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str(pnoe_path),
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str(spirometry_csv_path),
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str(seca_path)
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None, # No SECA file needed anymore
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)
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context_gen.extract_patient_info(last_name) # Extract patient info
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# Set patient info manually since we're not reading from SECA
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weight_kg = float(weight.replace("lbs", "").replace("kg", "").strip())
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if "lbs" in weight.lower():
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weight_kg = weight_kg / 2.20462 # Convert lbs to kg
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context_gen.patient_info = {
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"name": first_name,
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"last_name": last_name,
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"age": age,
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"weight": weight_kg,
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"fat_percentage": fat_percentage,
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"gender": gender,
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}
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spirometry_metrics = context_gen.calculate_spirometry_metrics()
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pnoe_metrics = context_gen.calculate_pnoe_metrics()
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# Store metrics in session
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request.session["metrics"] = {
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"spirometry": spirometry_metrics,
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"pnoe": pnoe_metrics,
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}
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request.session["spirometry_csv_path"] = str(spirometry_csv_path)
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return RedirectResponse(url="/preview", status_code=303)
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except Exception as e:
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import traceback
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error_details = traceback.format_exc()
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print(f"ERROR: {error_details}")
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return render_template("upload.html", {
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"request": request,
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"session": request.session,
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"error": f"Error generating report: {str(e)}"
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})
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return render_template(
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"upload.html",
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{
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"request": request,
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"session": request.session,
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"error": f"Error generating report: {str(e)}",
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},
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)
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finally:
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# Close file handles
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spirometry_pdf.file.close()
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pnoe_csv.file.close()
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seca_excel.file.close()
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if oxygenation_csv and oxygenation_csv.filename:
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oxygenation_csv.file.close()
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@app.get("/preview", response_class=HTMLResponse)
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@@ -214,7 +285,9 @@ async def preview(request: Request):
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"""Preview generated report"""
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if not request.session.get("report_path"):
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return RedirectResponse(url="/", status_code=303)
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return render_template("preview.html", {"request": request, "session": request.session})
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return render_template(
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"preview.html", {"request": request, "session": request.session}
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)
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@app.get("/graphs/{filename}")
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@@ -231,7 +304,9 @@ async def edit_form(request: Request):
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"""Display edit metrics form"""
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if not request.session.get("metrics"):
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return RedirectResponse(url="/", status_code=303)
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return render_template("edit.html", {"request": request, "session": request.session})
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return render_template(
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"edit.html", {"request": request, "session": request.session}
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)
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@app.post("/edit")
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@@ -239,16 +314,13 @@ async def edit_metrics(request: Request):
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"""Handle metric edits and regenerate report"""
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if not request.session.get("temp_dir") or not request.session.get("patient_info"):
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return RedirectResponse(url="/", status_code=303)
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# Get form data
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form_data = await request.form()
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# Build metric overrides
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metric_overrides = {
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"pnoe": {},
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"spirometry": {}
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}
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metric_overrides = {"pnoe": {}, "spirometry": {}}
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# Pnoe overrides
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if form_data.get("vo2_max"):
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metric_overrides["pnoe"]["vo2_max"] = float(form_data["vo2_max"])
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@@ -262,28 +334,36 @@ async def edit_metrics(request: Request):
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metric_overrides["pnoe"]["fat_max_value"] = float(form_data["fat_max_value"])
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if form_data.get("fat_max_hr"):
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metric_overrides["pnoe"]["fat_max_hr"] = float(form_data["fat_max_hr"])
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# VT1 and VT2 overrides
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if form_data.get("vt1_hr") or form_data.get("vt1_speed") or form_data.get("vt1_time"):
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if (
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form_data.get("vt1_hr")
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or form_data.get("vt1_speed")
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or form_data.get("vt1_time")
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):
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metric_overrides["pnoe"]["vt1"] = {
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"HeartRate": float(form_data.get("vt1_hr", 0)),
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"Speed": float(form_data.get("vt1_speed", 0)),
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"Time": float(form_data.get("vt1_time", 0))
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"Time": float(form_data.get("vt1_time", 0)),
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}
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if form_data.get("vt2_hr") or form_data.get("vt2_speed") or form_data.get("vt2_time"):
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if (
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form_data.get("vt2_hr")
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or form_data.get("vt2_speed")
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or form_data.get("vt2_time")
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):
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metric_overrides["pnoe"]["vt2"] = {
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"HeartRate": float(form_data.get("vt2_hr", 0)),
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"Speed": float(form_data.get("vt2_speed", 0)),
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"Time": float(form_data.get("vt2_time", 0))
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"Time": float(form_data.get("vt2_time", 0)),
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}
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# Heart rate zones
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for i in range(1, 6):
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zone_key = f"zone{i}_bpm"
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if form_data.get(zone_key):
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metric_overrides["pnoe"][zone_key] = form_data[zone_key]
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# Spirometry overrides
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if form_data.get("fvc_best"):
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metric_overrides["spirometry"]["fvc_best"] = float(form_data["fvc_best"])
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@@ -294,88 +374,120 @@ async def edit_metrics(request: Request):
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if form_data.get("fev1_pred"):
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metric_overrides["spirometry"]["fev1_pred"] = float(form_data["fev1_pred"])
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if form_data.get("fev1_fvc_pct_best"):
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metric_overrides["spirometry"]["fev1_fvc_pct_best"] = float(form_data["fev1_fvc_pct_best"])
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metric_overrides["spirometry"]["fev1_fvc_pct_best"] = float(
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form_data["fev1_fvc_pct_best"]
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)
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if form_data.get("fev1_fvc_pct_pred"):
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metric_overrides["spirometry"]["fev1_fvc_pct_pred"] = float(form_data["fev1_fvc_pct_pred"])
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metric_overrides["spirometry"]["fev1_fvc_pct_pred"] = float(
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form_data["fev1_fvc_pct_pred"]
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)
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try:
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# Get file paths from session
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temp_dir = Path(request.session["temp_dir"])
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patient_info = request.session["patient_info"]
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# Find files in temp directory
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spirometry_path = None
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pnoe_path = None
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seca_path = None
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oxygenation_path = None
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for file_path in temp_dir.iterdir():
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if file_path.name.startswith("spirometry_"):
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spirometry_path = file_path
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elif file_path.name.startswith("pnoe_"):
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pnoe_path = file_path
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elif file_path.name.startswith("seca_"):
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seca_path = file_path
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if not all([spirometry_path, pnoe_path, seca_path]):
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raise ValueError("Could not find all uploaded files")
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elif file_path.name.startswith("oxygenation_"):
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oxygenation_path = file_path
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if not all([spirometry_path, pnoe_path]):
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raise ValueError("Could not find all required uploaded files")
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# Regenerate report with overrides
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oxygenation_csv_path = str(oxygenation_path) if oxygenation_path else None
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result = await report_service.generate_report(
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spirometry_pdf_path=str(spirometry_path),
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pnoe_csv_path=str(pnoe_path),
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seca_excel_path=str(seca_path),
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patient_info=patient_info,
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metric_overrides=metric_overrides if (metric_overrides["pnoe"] or metric_overrides["spirometry"]) else None,
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metric_overrides=metric_overrides
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if (metric_overrides["pnoe"] or metric_overrides["spirometry"])
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else None,
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oxygenation_csv_path=oxygenation_csv_path,
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)
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# Update session with new report
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request.session["report_path"] = result["report_path"]
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request.session["graphs_generated"] = result["graphs_generated"]
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request.session["analysis_data"] = result["analysis_data"]
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# Recalculate metrics with overrides
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from services.context_generator import ContextGenerator
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context_gen = ContextGenerator()
|
||||
spirometry_csv_path = request.session.get("spirometry_csv_path", "")
|
||||
if not spirometry_csv_path or not Path(spirometry_csv_path).exists():
|
||||
from services.spirometry_table_extractor import extract_spirometry_table_from_pdf
|
||||
from pathlib import Path as PathLib
|
||||
|
||||
from services.spirometry_table_extractor import (
|
||||
extract_spirometry_table_from_pdf,
|
||||
)
|
||||
|
||||
data_dir = PathLib("data")
|
||||
spirometry_csv_path = extract_spirometry_table_from_pdf(
|
||||
str(spirometry_path), output_dir=str(data_dir)
|
||||
)
|
||||
spirometry_csv_path = str(PathLib(spirometry_csv_path))
|
||||
|
||||
|
||||
context_gen.load_data(
|
||||
str(pnoe_path),
|
||||
spirometry_csv_path,
|
||||
str(seca_path)
|
||||
None, # No SECA file
|
||||
)
|
||||
# Set patient info manually
|
||||
weight_str = patient_info.get("weight", "0")
|
||||
weight_kg = float(weight_str.replace("lbs", "").replace("kg", "").strip())
|
||||
if "lbs" in weight_str.lower():
|
||||
weight_kg = weight_kg / 2.20462 # Convert lbs to kg
|
||||
|
||||
context_gen.patient_info = {
|
||||
"name": patient_info.get("first_name", ""),
|
||||
"last_name": patient_info.get("last_name", ""),
|
||||
"age": patient_info.get("age", 25),
|
||||
"weight": weight_kg,
|
||||
"fat_percentage": patient_info.get("fat_percentage", 0),
|
||||
"gender": patient_info.get("gender", "female"),
|
||||
}
|
||||
context_gen.extract_patient_info(patient_info.get("last_name", ""))
|
||||
|
||||
|
||||
spirometry_overrides = metric_overrides.get("spirometry", {})
|
||||
pnoe_overrides = metric_overrides.get("pnoe", {})
|
||||
spirometry_metrics = context_gen.calculate_spirometry_metrics(spirometry_overrides)
|
||||
spirometry_metrics = context_gen.calculate_spirometry_metrics(
|
||||
spirometry_overrides
|
||||
)
|
||||
pnoe_metrics = context_gen.calculate_pnoe_metrics(pnoe_overrides)
|
||||
|
||||
|
||||
# Update metrics in session
|
||||
request.session["metrics"] = {
|
||||
"spirometry": spirometry_metrics,
|
||||
"pnoe": pnoe_metrics,
|
||||
}
|
||||
request.session["spirometry_csv_path"] = spirometry_csv_path
|
||||
|
||||
|
||||
return RedirectResponse(url="/preview", status_code=303)
|
||||
|
||||
|
||||
except Exception as e:
|
||||
import traceback
|
||||
|
||||
error_details = traceback.format_exc()
|
||||
print(f"ERROR: {error_details}")
|
||||
return render_template("edit.html", {
|
||||
"request": request,
|
||||
"session": request.session,
|
||||
"error": f"Error regenerating report: {str(e)}"
|
||||
})
|
||||
return render_template(
|
||||
"edit.html",
|
||||
{
|
||||
"request": request,
|
||||
"session": request.session,
|
||||
"error": f"Error regenerating report: {str(e)}",
|
||||
},
|
||||
)
|
||||
|
||||
|
||||
@app.get("/health")
|
||||
|
||||
Reference in New Issue
Block a user