import sys import os import pandas as pd import pdfplumber import gradio as gr from tabulate import tabulate # ✅ 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, progress=None, index=0, total=1): try: if file_path.endswith(".csv"): df = pd.read_csv(file_path, low_memory=False) elif file_path.endswith((".xls", ".xlsx")): df = pd.read_excel(file_path) else: return f"Unsupported spreadsheet format: {file_path}" if progress: progress((index + 1) / total, desc=f"Processed table: {os.path.basename(file_path)}") if "Booking Number" in df.columns: groups = df.groupby("Booking Number") elif "Form Name" in df.columns: groups = df.groupby("Form Name") else: return tabulate(df, headers="keys", tablefmt="github", showindex=False).encode("utf-8", errors="replace").decode("utf-8") result = [] for group_name, group_df in groups: result.append(f"\n### Group: {group_name}\n") formatted = tabulate(group_df, headers="keys", tablefmt="github", showindex=False) result.append(formatted.encode("utf-8", errors="replace").decode("utf-8")) return "\n".join(result) except Exception as e: return f"Error parsing file: {e}" def extract_all_text_from_pdf(file_path, progress=None, index=0, total=1): extracted = [] try: with pdfplumber.open(file_path) as pdf: num_pages = len(pdf.pages) for i, page in enumerate(pdf.pages): tables = page.extract_tables() for table in tables: for row in table: if any(row): extracted.append("\t".join([cell or "" for cell in row])) if progress: progress((index + i / num_pages) / total, desc=f"Parsing PDF: {os.path.basename(file_path)} ({i+1}/{num_pages})") return "\n".join(extracted).encode("utf-8", errors="replace").decode("utf-8") except Exception as e: return f"Error parsing PDF: {e}" def create_ui(agent: TxAgent): with gr.Blocks(theme=gr.themes.Soft()) as demo: gr.Markdown("

📋 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, history, conversation, uploaded_files, 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." ) if uploaded_files: extracted_text = "" total_files = len(uploaded_files) for index, file in enumerate(uploaded_files): path = file.name 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" if progress: progress((index + 1) / total_files, desc=f"Skipping unsupported file: {os.path.basename(path)}") message = f"{context}\n\n---\n{extracted_text.strip()}\n---\n\nBegin 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: yield update 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