import sys
import os
import pandas as pd
import pdfplumber
import gradio as gr
from typing import List
# ✅ Fix: Add src to Python path
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "src")))
from txagent.txagent import TxAgent
def extract_all_text_from_csv_or_excel(file_path: str, progress=None, index=0, total=1) -> str:
try:
if not os.path.exists(file_path):
return f"File not found: {file_path}"
if progress:
progress((index + 1) / total, desc=f"Reading spreadsheet: {os.path.basename(file_path)}")
if file_path.endswith(".csv"):
df = pd.read_csv(file_path, encoding="utf-8", errors="replace", low_memory=False)
elif file_path.endswith((".xls", ".xlsx")):
df = pd.read_excel(file_path, engine="openpyxl")
else:
return f"Unsupported spreadsheet format: {file_path}"
lines = []
for _, row in df.iterrows():
line = " | ".join(str(cell) for cell in row if pd.notna(cell))
if line:
lines.append(line)
return f"\ud83d\udcc4 {os.path.basename(file_path)}\n\n" + "\n".join(lines)
except Exception as e:
return f"[Error reading {os.path.basename(file_path)}]: {str(e)}"
def extract_all_text_from_pdf(file_path: str, progress=None, index=0, total=1) -> str:
try:
if not os.path.exists(file_path):
return f"PDF not found: {file_path}"
extracted = []
with pdfplumber.open(file_path) as pdf:
num_pages = len(pdf.pages)
for i, page in enumerate(pdf.pages):
try:
text = page.extract_text() or ""
extracted.append(text.strip())
if progress:
progress((index + (i / num_pages)) / total, desc=f"Reading PDF: {os.path.basename(file_path)} ({i+1}/{num_pages})")
except Exception as e:
extracted.append(f"[Error reading page {i+1}]: {str(e)}")
return f"\ud83d\udcc4 {os.path.basename(file_path)}\n\n" + "\n\n".join(extracted)
except Exception as e:
return f"[Error reading PDF {os.path.basename(file_path)}]: {str(e)}"
def create_ui(agent: TxAgent):
with gr.Blocks(theme=gr.themes.Soft()) as demo:
gr.Markdown("
\ud83d\udccb CPS: Clinical Patient Support System
")
chatbot = gr.Chatbot(label="CPS Assistant", height=600, type="messages")
file_upload = gr.File(
label="Upload Medical File",
file_types=[".pdf", ".txt", ".docx", ".jpg", ".png", ".csv", ".xls", ".xlsx"],
file_count="multiple"
)
message_input = gr.Textbox(placeholder="Ask a biomedical question or just upload the files...", show_label=False)
send_button = gr.Button("Send", variant="primary")
conversation_state = gr.State([])
def handle_chat(message: str, history: list, conversation: list, uploaded_files: list, progress=gr.Progress()):
context = (
"You are an expert clinical AI assistant reviewing medical form or interview data. "
"Your job is to analyze this data and reason about any information or red flags that a human doctor might have overlooked. "
"Provide a **detailed and structured response**, including examples, supporting evidence from the form, and clinical rationale for why these items matter. "
"Ensure the output is informative and helpful for improving patient care. "
"Do not hallucinate. Base the response only on the provided form content. "
"End with a section labeled '🧠 Final Analysis' where you summarize key findings the doctor may have missed."
)
try:
extracted_text = ""
if uploaded_files and isinstance(uploaded_files, list):
total_files = len(uploaded_files)
for index, file in enumerate(uploaded_files):
if not hasattr(file, 'name'):
continue
path = file.name
try:
if path.endswith((".csv", ".xls", ".xlsx")):
extracted_text += extract_all_text_from_csv_or_excel(path, progress, index, total_files) + "\n"
elif path.endswith(".pdf"):
extracted_text += extract_all_text_from_pdf(path, progress, index, total_files) + "\n"
else:
extracted_text += f"(Uploaded file: {os.path.basename(path)})\n"
except Exception as file_error:
extracted_text += f"[Error processing file: {os.path.basename(path)}] — {str(file_error)}\n"
continue
message = (
f"{context}\n\n--- Uploaded File Content ---\n\n{extracted_text.strip()}\n\n--- End of File ---\n\nNow begin your reasoning:"
)
generator = agent.run_gradio_chat(
message=message,
history=history,
temperature=0.3,
max_new_tokens=1024,
max_token=8192,
call_agent=False,
conversation=conversation,
uploaded_files=uploaded_files,
max_round=30
)
for update in generator:
try:
if isinstance(update, list):
cleaned = [
msg for msg in update
if hasattr(msg, 'role')
and not (
msg.role == "assistant"
and hasattr(msg, 'content')
and msg.content.strip().startswith("\ud83e\udde0")
)
]
if cleaned:
yield cleaned
elif isinstance(update, str) and not update.strip().startswith("\ud83e\udde0"):
yield update.encode("utf-8", "replace").decode("utf-8")
except Exception as update_error:
print(f"Error processing update: {update_error}")
continue
except Exception as chat_error:
print(f"Chat handling error: {chat_error}")
yield "An error occurred while processing your request. Please try again."
inputs = [message_input, chatbot, conversation_state, file_upload]
send_button.click(fn=handle_chat, inputs=inputs, outputs=chatbot)
message_input.submit(fn=handle_chat, inputs=inputs, outputs=chatbot)
gr.Examples([
["Upload your medical form and ask what the doctor might've missed."],
["This patient was treated with antibiotics for UTI. What else should we check?"],
["Is there anything abnormal in the attached blood work report?"]
], inputs=message_input)
return demo