|
|
|
|
|
|
|
|
import sys, os, json, gradio as gr, pandas as pd, pdfplumber, hashlib, shutil, re, time |
|
|
from concurrent.futures import ThreadPoolExecutor, as_completed |
|
|
from threading import Thread |
|
|
|
|
|
|
|
|
base_dir = "/data" |
|
|
model_cache_dir = os.path.join(base_dir, "txagent_models") |
|
|
tool_cache_dir = os.path.join(base_dir, "tool_cache") |
|
|
file_cache_dir = os.path.join(base_dir, "cache") |
|
|
report_dir = os.path.join(base_dir, "reports") |
|
|
vllm_cache_dir = os.path.join(base_dir, "vllm_cache") |
|
|
|
|
|
for d in [model_cache_dir, tool_cache_dir, file_cache_dir, report_dir, vllm_cache_dir]: |
|
|
os.makedirs(d, exist_ok=True) |
|
|
|
|
|
|
|
|
os.environ.update({ |
|
|
"HF_HOME": model_cache_dir, |
|
|
"TRANSFORMERS_CACHE": model_cache_dir, |
|
|
"VLLM_CACHE_DIR": vllm_cache_dir, |
|
|
"TOKENIZERS_PARALLELISM": "false", |
|
|
"CUDA_LAUNCH_BLOCKING": "1" |
|
|
}) |
|
|
|
|
|
|
|
|
LOCAL_TXAGENT_PATH = os.path.join(model_cache_dir, "mims-harvard", "TxAgent-T1-Llama-3.1-8B") |
|
|
LOCAL_RAG_PATH = os.path.join(model_cache_dir, "mims-harvard", "ToolRAG-T1-GTE-Qwen2-1.5B") |
|
|
|
|
|
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "src"))) |
|
|
from txagent.txagent import TxAgent |
|
|
|
|
|
def file_hash(path): return hashlib.md5(open(path, "rb").read()).hexdigest() |
|
|
def sanitize_utf8(text): return text.encode("utf-8", "ignore").decode("utf-8") |
|
|
MEDICAL_KEYWORDS = {"diagnosis", "assessment", "plan", "results", "medications", "summary", "findings"} |
|
|
|
|
|
def extract_priority_pages(file_path, max_pages=20): |
|
|
try: |
|
|
with pdfplumber.open(file_path) as pdf: |
|
|
pages = [] |
|
|
for i, page in enumerate(pdf.pages[:3]): |
|
|
pages.append(f"=== Page {i+1} ===\n{(page.extract_text() or '').strip()}") |
|
|
for i, page in enumerate(pdf.pages[3:max_pages], start=4): |
|
|
text = page.extract_text() or "" |
|
|
if any(re.search(rf'\\b{kw}\\b', text.lower()) for kw in MEDICAL_KEYWORDS): |
|
|
pages.append(f"=== Page {i} ===\n{text.strip()}") |
|
|
return "\n\n".join(pages) |
|
|
except Exception as e: |
|
|
return f"PDF processing error: {str(e)}" |
|
|
|
|
|
def convert_file_to_json(file_path, file_type): |
|
|
try: |
|
|
h = file_hash(file_path) |
|
|
cache_path = os.path.join(file_cache_dir, f"{h}.json") |
|
|
if os.path.exists(cache_path): return open(cache_path, "r", encoding="utf-8").read() |
|
|
|
|
|
if file_type == "pdf": |
|
|
text = extract_priority_pages(file_path) |
|
|
result = json.dumps({"filename": os.path.basename(file_path), "content": text, "status": "initial"}) |
|
|
Thread(target=full_pdf_processing, args=(file_path, h)).start() |
|
|
elif file_type == "csv": |
|
|
df = pd.read_csv(file_path, encoding_errors="replace", header=None, dtype=str) |
|
|
result = json.dumps({"filename": os.path.basename(file_path), "rows": df.fillna('').astype(str).values.tolist()}) |
|
|
elif file_type in ["xls", "xlsx"]: |
|
|
df = pd.read_excel(file_path, engine="openpyxl", header=None, dtype=str) |
|
|
result = json.dumps({"filename": os.path.basename(file_path), "rows": df.fillna('').astype(str).values.tolist()}) |
|
|
else: |
|
|
return json.dumps({"error": f"Unsupported file type: {file_type}"}) |
|
|
|
|
|
with open(cache_path, "w", encoding="utf-8") as f: f.write(result) |
|
|
return result |
|
|
except Exception as e: |
|
|
return json.dumps({"error": str(e)}) |
|
|
|
|
|
def full_pdf_processing(file_path, h): |
|
|
try: |
|
|
cache_path = os.path.join(file_cache_dir, f"{h}_full.json") |
|
|
if os.path.exists(cache_path): return |
|
|
with pdfplumber.open(file_path) as pdf: |
|
|
full_text = "\n".join([f"=== Page {i+1} ===\n{(p.extract_text() or '').strip()}" for i, p in enumerate(pdf.pages)]) |
|
|
with open(cache_path, "w", encoding="utf-8") as f: f.write(json.dumps({"content": full_text})) |
|
|
except: pass |
|
|
|
|
|
def init_agent(): |
|
|
target_tool_path = os.path.join(tool_cache_dir, "new_tool.json") |
|
|
if not os.path.exists(target_tool_path): |
|
|
shutil.copy(os.path.abspath("data/new_tool.json"), target_tool_path) |
|
|
|
|
|
agent = TxAgent( |
|
|
model_name=LOCAL_TXAGENT_PATH, |
|
|
rag_model_name=LOCAL_RAG_PATH, |
|
|
tool_files_dict={"new_tool": target_tool_path}, |
|
|
force_finish=True, |
|
|
enable_checker=True, |
|
|
step_rag_num=8, |
|
|
seed=100 |
|
|
) |
|
|
agent.init_model() |
|
|
return agent |
|
|
|
|
|
agent_container = {"agent": None} |
|
|
def get_agent(): |
|
|
if agent_container["agent"] is None: |
|
|
agent_container["agent"] = init_agent() |
|
|
return agent_container["agent"] |
|
|
|
|
|
def create_ui(): |
|
|
with gr.Blocks(theme=gr.themes.Soft()) as demo: |
|
|
gr.Markdown("""<h1 style='text-align:center;'>🩺 Clinical Oversight Assistant</h1>""") |
|
|
chatbot = gr.Chatbot(label="Analysis", height=600) |
|
|
msg_input = gr.Textbox(placeholder="Ask a question about the patient...") |
|
|
file_upload = gr.File(file_types=[".pdf", ".csv", ".xls", ".xlsx"], file_count="multiple") |
|
|
send_btn = gr.Button("Analyze", variant="primary") |
|
|
state = gr.State([]) |
|
|
|
|
|
def analyze(message, history, conversation, files): |
|
|
try: |
|
|
extracted, hval = "", "" |
|
|
if files: |
|
|
with ThreadPoolExecutor(max_workers=3) as pool: |
|
|
futures = [pool.submit(convert_file_to_json, f.name, f.name.split(".")[-1].lower()) for f in files] |
|
|
extracted = "\n".join([sanitize_utf8(f.result()) for f in as_completed(futures)]) |
|
|
hval = file_hash(files[0].name) |
|
|
|
|
|
prompt = f"""Review these medical records and identify exactly what might have been missed: |
|
|
1. Missed diagnoses |
|
|
2. Medication conflicts |
|
|
3. Incomplete assessments |
|
|
4. Abnormal results needing follow-up |
|
|
|
|
|
Medical Records:\n{extracted[:15000]} |
|
|
""" |
|
|
final_response = "" |
|
|
for chunk in get_agent().run_gradio_chat(prompt, history=[], temperature=0.2, max_new_tokens=1024, max_token=4096, call_agent=False, conversation=conversation): |
|
|
if isinstance(chunk, str): final_response += chunk |
|
|
elif isinstance(chunk, list): final_response += "".join([c.content for c in chunk if hasattr(c, 'content')]) |
|
|
cleaned = final_response.replace("[TOOL_CALLS]", "").strip() |
|
|
updated_history = history + [[message, cleaned]] |
|
|
return updated_history, None |
|
|
except Exception as e: |
|
|
return history + [[message, f"❌ Error: {str(e)}"]], None |
|
|
|
|
|
send_btn.click(analyze, inputs=[msg_input, chatbot, state, file_upload], outputs=[chatbot, gr.File()]) |
|
|
msg_input.submit(analyze, inputs=[msg_input, chatbot, state, file_upload], outputs=[chatbot, gr.File()]) |
|
|
return demo |
|
|
|
|
|
if __name__ == "__main__": |
|
|
ui = create_ui() |
|
|
ui.queue(api_open=False).launch( |
|
|
server_name="0.0.0.0", |
|
|
server_port=7860, |
|
|
show_error=True, |
|
|
allowed_paths=["/data/reports"], |
|
|
share=False |
|
|
) |
|
|
|
