Implemented the memory fix.

Changed app.py:
•
process_pft_pdf() now uses the uploaded file stream directly instead of copying the PDF into bytes.
•
Output now uses SpooledTemporaryFile, so larger generated PDFs spill to disk instead of staying fully in RAM.
•
Explicitly closes PdfReader objects after writing.
•
Removed @app.teardown_request gc.collect(), which was running too early and could break send_file.
•
Added response.call_on_close() cleanup so the generated PDF stream is closed only after Flask/Werkzeug finishes sending it.
Changed Dockerfile:
•
Added Gunicorn --max-requests 50 --max-requests-jitter 10 as a production guardrail against PDF-library or allocator memory growth.

Dockerfile

@@ -15,4 +15,4 @@ COPY . .
 EXPOSE 5000
 
 # Command to run the application using Gunicorn (production ready)
-CMD ["gunicorn", "--bind", "0.0.0.0:5000", "app:app"]
+CMD ["gunicorn", "--bind", "0.0.0.0:5000", "--max-requests", "50", "--max-requests-jitter", "10", "app:app"]

app.py

@@ -2,15 +2,15 @@ import sys
 import gc
 import re
 import json
-import io
 import logging
+import tempfile
 from pathlib import Path
 from datetime import datetime
 import pdfplumber
 from pypdf import PdfReader, PdfWriter
 from pypdf.constants import UserAccessPermissions
 from pypdf.generic import NameObject, BooleanObject
-from typing import TypedDict, Literal
+from typing import BinaryIO, TypedDict, Literal
 from flask import Flask, request, send_file, abort
 from werkzeug.utils import secure_filename
 
@@ -45,7 +45,7 @@ class ParsedPdfData(TypedDict):
     highlighted_box: InterpretationType
 
 
-def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
+def process_pft_pdf(input_stream: BinaryIO) -> BinaryIO:
     text_mapping: dict[str, InterpretationType] = {
         "normal": "normal",
         "pv disorders": "pvd",
@@ -70,8 +70,11 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
         "highlighted_box": "normal"
     }
 
-    # Use a detached context for pdfplumber to read the file metadata
+    input_stream.seek(0)
-    with pdfplumber.open(io.BytesIO(input_bytes)) as pdf:
+
+    # Use the upload stream directly so each request does not duplicate the PDF
+    # in memory before parsing.
+    with pdfplumber.open(input_stream) as pdf:
         if len(pdf.pages) < 2:
             logger.error(
                 "Expected a 2-page PFT report, found %s page(s).", len(pdf.pages))
@@ -82,9 +85,8 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
         page2 = pdf.pages[1]
 
         # --- 1. FULL TEXT METADATA EXTRACTION (Page 1) ---
-        full_text_p1 = page1.extract_text()
+        full_text_p1 = page1.extract_text() or ""
 
-        if full_text_p1:
         lines = [line.strip()
                  for line in full_text_p1.split("\n") if line.strip()]
         for line in lines:
@@ -106,11 +108,11 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
             record["smoker"] = smoker_match.group(1).capitalize()
 
         # --- 2. INTERPRETATION DIAGRAM PROCESSING (Page 2) ---
-        text_p2 = page2.extract_text()
+        text_p2 = page2.extract_text() or ""
         detected_box: InterpretationType = "normal"
         box_found = False
 
-        if text_p2 and "System Summary Interpretation" in text_p2:
+        if "System Summary Interpretation" in text_p2:
             summary_text = text_p2.split(
                 "System Summary Interpretation")[-1].strip().lower()
             for phrase, token in text_mapping.items():
@@ -154,8 +156,10 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
             f"Template file '{TEMPLATE_NAME}' missing inside container workspace.")
 
     writer = PdfWriter()
-
     template_reader = PdfReader(TEMPLATE_NAME)
+    raw_results_reader: PdfReader | None = None
+
+    try:
         writer.append(template_reader)
 
         patient_data = {"patient_name": "",
@@ -230,7 +234,8 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
         writer.remove_annotations(subtypes="/Widget")
 
         # Append raw input pages directly onto the end of our current working context
-    raw_results_reader = PdfReader(io.BytesIO(input_bytes))
+        input_stream.seek(0)
+        raw_results_reader = PdfReader(input_stream)
         writer.append(raw_results_reader)
 
         # Secure document permissions
@@ -243,10 +248,14 @@ def process_pft_pdf(input_bytes: bytes) -> io.BytesIO:
             permissions_flag=permissions
         )
 
-    # Output final joined stream directly to Flask
+        # Keep small responses in memory, but spill larger PDFs to a temp file.
-    output_stream = io.BytesIO()
+        output_stream = tempfile.SpooledTemporaryFile(max_size=8 * 1024 * 1024, mode="w+b")
         writer.write(output_stream)
         output_stream.seek(0)
+    finally:
+        template_reader.close()
+        if raw_results_reader is not None:
+            raw_results_reader.close()
 
     logger.info("PDTR successfully prepended to PFT result PDF.")
     return output_stream
@@ -268,20 +277,24 @@ def upload_file():
         logger.info("Received PDF: %s", original_filename)
 
         try:
-            # Read input file directly into memory bytes
+            # Execute logic sequentially using the upload stream directly.
-            raw_input_bytes = file.read()
+            processed_file_stream = process_pft_pdf(file.stream)
-
-            # Execute logic sequentially
-            processed_file_stream = process_pft_pdf(raw_input_bytes)
 
             logger.info("Returning processed PDF file: %s", original_filename)
-            return send_file(
+            response = send_file(
                 processed_file_stream,
                 mimetype='application/pdf',
                 as_attachment=True,
                 download_name=original_filename
             )
 
+            @response.call_on_close
+            def close_processed_file_stream() -> None:
+                processed_file_stream.close()
+                gc.collect()
+
+            return response
+
         except Exception as e:
             logger.exception("Error during execution processing pipeline")
             return abort(500, f"Error processing file: {str(e)}")
@@ -323,12 +336,5 @@ def index():
     """
 
 
-@app.teardown_request
-def spi_clear_memory(exception=None):
-    """Runs automatically after every single request."""
-    # Force collection of unreferenced objects
-    gc.collect()
-
-
 if __name__ == "__main__":
     app.run(host='0.0.0.0', port=5000)