Rajan Sharma
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# app.py - Complete Dual-Mode Healthcare Analysis System
import os, re, json, traceback, pathlib
from functools import lru_cache
from typing import List, Dict, Any, Tuple, Optional
import pandas as pd
import numpy as np
import gradio as gr
import torch
import regex as re2
# Import necessary modules
from settings import (
SNAPSHOT_PATH, PERSIST_CONTENT, HEALTHCARE_SETTINGS, MODEL_SETTINGS,
HEALTHCARE_SYSTEM_PROMPT, GENERAL_CONVERSATION_PROMPT
)
from audit_log import log_event, hash_summary
from privacy import redact_text, safety_filter, refusal_reply
from data_registry import DataRegistry
from upload_ingest import extract_text_from_files
from healthcare_analysis import HealthcareAnalyzer
# ---- NEW: scenario-first engine (keeps general chat intact)
from scenario_engine import ScenarioEngine
# (Optional) keep old formatter if you want a fallback:
try:
from response_formatter import ResponseFormatter # noqa: F401
except Exception:
ResponseFormatter = None # type: ignore
# ---------- Writable caches (HF Spaces-safe) ----------
HOME = pathlib.Path.home()
HF_HOME = str(HOME / ".cache" / "huggingface")
HF_HUB_CACHE = str(HOME / ".cache" / "huggingface" / "hub")
HF_TRANSFORMERS = str(HOME / ".cache" / "huggingface" / "transformers")
ST_HOME = str(HOME / ".cache" / "sentence-transformers")
GRADIO_TMP = str(HOME / "app" / "gradio")
GRADIO_CACHE = GRADIO_TMP
os.environ.setdefault("HF_HOME", HF_HOME)
os.environ.setdefault("HF_HUB_CACHE", HF_HUB_CACHE)
os.environ.setdefault("TRANSFORMERS_CACHE", HF_TRANSFORMERS)
os.environ.setdefault("SENTENCE_TRANSFORMERS_HOME", ST_HOME)
os.environ.setdefault("GRADIO_TEMP_DIR", GRADIO_TMP)
os.environ.setdefault("GRADIO_CACHE_DIR", GRADIO_CACHE)
os.environ.setdefault("HF_HUB_ENABLE_XET", "0")
os.environ.setdefault("HF_HUB_ENABLE_HF_TRANSFER", "1")
for p in [HF_HOME, HF_HUB_CACHE, HF_TRANSFORMERS, ST_HOME, GRADIO_TMP, GRADIO_CACHE]:
try:
os.makedirs(p, exist_ok=True)
except Exception:
pass
# Optional Cohere
try:
import cohere
_HAS_COHERE = True
except Exception:
_HAS_COHERE = False
from transformers import AutoTokenizer, AutoModelForCausalLM
from huggingface_hub import login
# ---------- Config ----------
MODEL_ID = os.getenv("MODEL_ID", "microsoft/Phi-3-mini-4k-instruct")
HF_TOKEN = os.getenv("HUGGINGFACE_HUB_TOKEN") or os.getenv("HF_TOKEN")
COHERE_API_KEY = os.getenv("COHERE_API_KEY")
USE_HOSTED_COHERE = bool(COHERE_API_KEY and _HAS_COHERE)
MAX_NEW_TOKENS = int(os.getenv("MAX_NEW_TOKENS", MODEL_SETTINGS.get("max_new_tokens", 2048)))
# ---- NEW: feature flag to toggle engines without code edits
USE_SCENARIO_ENGINE = os.getenv("USE_SCENARIO_ENGINE", "1") not in ("0", "false", "False")
# ---------- Helper Functions ----------
def find_column(df, patterns):
"""Find the first column in df that matches any of the patterns."""
if df is None or df.empty:
return None
for col in df.columns:
if any(pattern.lower() in col.lower() for pattern in patterns):
return col
return None
def extract_scenario_tasks(scenario_text):
"""Extract specific tasks from scenario text."""
tasks = []
lines = scenario_text.split('\n')
in_tasks = False
for line in lines:
line = line.strip()
if line.lower().startswith('tasks'):
in_tasks = True
continue
if in_tasks:
if line.lower().startswith('operational recommendations') or line.lower().startswith('future integration'):
in_tasks = False
continue
if line and (line.startswith(('1.', '2.', '3.', '4.', '5.')) or line.startswith(('•', '-', '*'))):
tasks.append(line)
return tasks
# ---------- Session RAG Class ----------
class SessionRAG:
def __init__(self):
self.docs = []
self.artifacts = []
self.csv_columns = []
def add_docs(self, chunks):
self.docs.extend(chunks)
def register_artifacts(self, artifacts):
self.artifacts.extend(artifacts)
def get_latest_csv_columns(self):
return self.csv_columns
def retrieve(self, query, k=5):
return self.docs[:k] if self.docs else []
def clear(self):
self.docs.clear()
self.artifacts.clear()
self.csv_columns.clear()
# ---------- Healthcare-specific functions ----------
def is_healthcare_scenario(text: str, uploaded_files_paths) -> bool:
"""Detect if this is a healthcare scenario with specific indicators."""
t = (text or "").lower()
# Check for healthcare keywords
has_healthcare_keywords = any(keyword in t for keyword in HEALTHCARE_SETTINGS["healthcare_keywords"])
# Check for healthcare facility types
has_facility_types = (
any(ftype in t for ftype in ["hospital", "medical center", "health centre"]) or
any(ftype in t for ftype in ["nursing", "residential", "care facility", "long-term care"]) or
any(ftype in t for ftype in ["ambulatory", "clinic", "surgery center", "outpatient"])
)
# Check for healthcare-specific tasks
has_healthcare_tasks = any(
phrase in t for phrase in [
"bed capacity", "occupancy rates", "facility distribution",
"long-term care", "health operations", "resource allocation"
]
)
# Check for healthcare data files
has_healthcare_files = any(
"health" in path.lower() or "facility" in path.lower() or "bed" in path.lower()
for path in uploaded_files_paths
)
# Check for structured scenario format
has_scenario_structure = any(
section in t for section in ["background", "situation", "tasks"]
)
return (has_healthcare_keywords or has_facility_types or has_healthcare_tasks) and \
(has_healthcare_files or has_scenario_structure)
def is_general_conversation(text: str, uploaded_files_paths) -> bool:
"""Determine if this is a general conversation rather than a scenario analysis."""
# If there are uploaded files, it's likely a scenario
if uploaded_files_paths:
return False
# Check for scenario indicators
scenario_indicators = [
"scenario", "analyze", "analysis", "assess", "evaluate", "recommend",
"tasks", "background", "situation", "dataset", "data"
]
# If no scenario indicators, it's likely general conversation
text_lower = text.lower()
return not any(indicator in text_lower for indicator in scenario_indicators)
def process_healthcare_data(uploaded_files_paths, data_registry):
"""Process healthcare data files with robust error handling."""
for file_path in uploaded_files_paths:
try:
if data_registry.add_path(file_path):
print(f"Successfully processed: {file_path}")
else:
print(f"Failed to process: {file_path}")
except Exception as e:
print(f"Error processing {file_path}: {e}")
log_event("data_processing_error", None, {
"file": file_path,
"error": str(e)
})
def handle_healthcare_scenario(scenario_text, data_registry, history):
"""Handle healthcare scenarios with enhanced analysis"""
try:
# Initialize analyzer
analyzer = HealthcareAnalyzer(data_registry)
# Perform comprehensive analysis (returns dict of datasets/results)
results = analyzer.comprehensive_analysis(scenario_text)
# ---- NEW: Scenario-first exact-output engine
if USE_SCENARIO_ENGINE:
response = ScenarioEngine.render(scenario_text, results)
else:
# Optional fallback to legacy formatter if desired
if ResponseFormatter is None:
raise RuntimeError("ResponseFormatter not available and USE_SCENARIO_ENGINE is disabled.")
formatter = ResponseFormatter()
response = formatter.format_healthcare_response(scenario_text, results)
return response
except Exception as e:
log_event("healthcare_scenario_error", None, {"error": str(e)})
# Log the full traceback for better debugging
tb_str = traceback.format_exc()
log_event("healthcare_scenario_traceback", None, {"traceback": tb_str})
return f"Error analyzing healthcare scenario: {str(e)}\n\nTechnical details:\n{tb_str}"
# ---------- Model loading helpers ----------
def pick_dtype_and_map():
if torch.cuda.is_available():
return torch.float16, "auto"
if torch.backends.mps.is_available():
return torch.float16, {"": "mps"}
return torch.float32, "cpu"
@lru_cache(maxsize=1)
def load_local_model():
if not HF_TOKEN:
raise RuntimeError("HUGGINGFACE_HUB_TOKEN is not set.")
login(token=HF_TOKEN, add_to_git_credential=False)
dtype, device_map = pick_dtype_and_map()
tok = AutoTokenizer.from_pretrained(
MODEL_ID, token=HF_TOKEN, use_fast=True, model_max_length=8192,
padding_side="left", trust_remote_code=True,
cache_dir=os.environ.get("TRANSFORMERS_CACHE")
)
try:
mdl = AutoModelForCausalLM.from_pretrained(
MODEL_ID, token=HF_TOKEN, device_map=device_map,
low_cpu_mem_usage=True, torch_dtype=dtype, trust_remote_code=True,
cache_dir=os.environ.get("TRANSFORMERS_CACHE")
)
except Exception:
mdl = AutoModelForCausalLM.from_pretrained(
MODEL_ID, token=HF_TOKEN,
low_cpu_mem_usage=True, torch_dtype=dtype, trust_remote_code=True,
cache_dir=os.environ.get("TRANSFORMERS_CACHE")
)
mdl.to("cuda" if torch.cuda.is_available() else "cpu")
if mdl.config.eos_token_id is None and tok.eos_token_id is not None:
mdl.config.eos_token_id = tok.eos_token_id
return mdl, tok
# ---------- Chat helpers ----------
def is_identity_query(message, history):
patterns = [
r"\bwho\s+are\s+you\b", r"\bwhat\s+are\s+you\b", r"\bwhat\s+is\s+your\s+name\b",
r"\bwho\s+is\s+this\b", r"\bidentify\s+yourself\b", r"\btell\s+me\s+about\s+yourself\b",
r"\bdescribe\s+yourself\b", r"\band\s+you\s*\?\b", r"\byour\s+name\b",
r"\bwho\s+am\s+i\s+chatting\s+with\b",
]
def match(t): return any(re.search(p, (t or "").strip().lower()) for p in patterns)
if match(message): return True
if history:
last_user = history[-1][0] if isinstance(history[-1], (list, tuple)) else None
if match(last_user): return True
return False
def _iter_user_assistant(history):
for item in (history or []):
if isinstance(item, (list, tuple)):
u = item[0] if len(item) > 0 else ""
a = item[1] if len(item) > 1 else ""
yield u, a
def _sanitize_text(s: str) -> str:
if not isinstance(s, str):
return s
return re2.sub(r'[\p{C}--[\n\t]]+', '', s)
def cohere_chat(message, history):
if not USE_HOSTED_COHERE:
return None
try:
client = cohere.Client(api_key=COHERE_API_KEY)
parts = []
for u, a in _iter_user_assistant(history):
if u: parts.append(f"User: {u}")
if a: parts.append(f"Assistant: {a}")
parts.append(f"User: {message}")
prompt = "\n".join(parts) + "\nAssistant:"
resp = client.chat(
model="command-r7b-12-2024",
message=prompt,
temperature=MODEL_SETTINGS.get("temperature", 0.3),
max_tokens=MAX_NEW_TOKENS,
)
if hasattr(resp, "text") and resp.text: return resp.text.strip()
if hasattr(resp, "reply") and resp.reply: return resp.reply.strip()
if hasattr(resp, "generations") and resp.generations: return resp.generations[0].text.strip()
return None
except Exception:
return None
def build_inputs(tokenizer, message, history, system_prompt):
msgs = [{"role": "system", "content": system_prompt}]
for u, a in _iter_user_assistant(history):
if u: msgs.append({"role": "user", "content": u})
if a: msgs.append({"role": "assistant", "content": a})
msgs.append({"role": "user", "content": message})
return tokenizer.apply_chat_template(
msgs, tokenize=True, add_generation_prompt=True, return_tensors="pt"
)
def local_generate(model, tokenizer, input_ids, max_new_tokens=MAX_NEW_TOKENS):
input_ids = input_ids.to(model.device)
with torch.no_grad():
out = model.generate(
input_ids=input_ids, max_new_tokens=max_new_tokens,
do_sample=True, temperature=MODEL_SETTINGS.get("temperature", 0.3),
top_p=MODEL_SETTINGS.get("top_p", 0.9),
repetition_penalty=MODEL_SETTINGS.get("repetition_penalty", 1.15),
pad_token_id=tokenizer.eos_token_id,
eos_token_id=tokenizer.eos_token_id,
)
gen_only = out[0, input_ids.shape[-1]:]
return tokenizer.decode(gen_only, skip_special_tokens=True).strip()
# ---------- Core chat logic ----------
def clarityops_reply(user_msg, history, tz, uploaded_files_paths, awaiting_answers=False):
try:
log_event("user_message", None, {"sizes": {"chars": len(user_msg or "")}})
safe_in, blocked_in, reason_in = safety_filter(user_msg, mode="input")
if blocked_in:
ans = refusal_reply(reason_in)
return history + [(user_msg, ans)], awaiting_answers
if is_identity_query(safe_in, history):
ans = "I am an AI analytical system designed to help with both general conversations and healthcare scenario analysis. I can answer your questions and also analyze healthcare data when you upload files and describe a scenario."
return history + [(user_msg, ans)], awaiting_answers
# Initialize data registry and session RAG
data_registry = DataRegistry()
session_rag = SessionRAG()
# Process uploaded files if any
if uploaded_files_paths:
process_healthcare_data(uploaded_files_paths, data_registry)
# Also extract text for RAG
ing = extract_text_from_files(uploaded_files_paths)
if ing.get("chunks"):
session_rag.add_docs(ing["chunks"])
if ing.get("artifacts"):
session_rag.register_artifacts(ing["artifacts"])
# Update session RAG with CSV columns
for file_name in data_registry.names():
if file_name.endswith('.csv'):
df = data_registry.get(file_name)
session_rag.csv_columns = list(df.columns)
# Determine the mode: healthcare scenario or general conversation
if is_healthcare_scenario(safe_in, uploaded_files_paths):
# Healthcare scenario mode (ScenarioEngine enforces exact asks)
response = handle_healthcare_scenario(safe_in, data_registry, history)
return history + [(user_msg, response)], False
else:
# General conversation mode with enhanced handling (unchanged)
if USE_HOSTED_COHERE:
out = cohere_chat(safe_in, history)
if out:
out = _sanitize_text(out)
safe_out, blocked_out, reason_out = safety_filter(out, mode="output")
if blocked_out:
safe_out = refusal_reply(reason_out)
log_event("assistant_reply", None, {
**hash_summary("prompt", safe_in if not PERSIST_CONTENT else ""),
**hash_summary("reply", safe_out if not PERSIST_CONTENT else ""),
"mode": "general_cohere",
})
return history + [(user_msg, safe_out)], False
# Enhanced local model generation
try:
model, tokenizer = load_local_model()
# Use general conversation prompt
inputs = build_inputs(tokenizer, safe_in, history, GENERAL_CONVERSATION_PROMPT)
out = local_generate(model, tokenizer, inputs, max_new_tokens=MAX_NEW_TOKENS)
if isinstance(out, str):
for tag in ("Assistant:", "System:", "User:"):
if out.startswith(tag):
out = out[len(tag):].strip()
out = _sanitize_text(out or "")
safe_out, blocked_out, reason_out = safety_filter(out, mode="output")
if blocked_out:
safe_out = refusal_reply(reason_out)
log_event("assistant_reply", None, {
**hash_summary("prompt", safe_in if not PERSIST_CONTENT else ""),
**hash_summary("reply", safe_out if not PERSIST_CONTENT else ""),
"mode": "general_local",
})
return history + [(user_msg, safe_out)], False
except Exception as e:
err = f"Error generating response: {str(e)}"
log_event("model_error", None, {"error": str(e)})
return history + [(user_msg, err)], False
except Exception as e:
err = f"Error: {e}"
try:
traceback.print_exc()
except Exception:
pass
return history + [(user_msg, err)], awaiting_answers
# ---------- UI Setup ----------
theme = gr.themes.Soft(primary_hue="teal", neutral_hue="slate", radius_size=gr.themes.sizes.radius_lg)
custom_css = """
:root { --brand-bg: #0f172a; --brand-accent: #0d9488; --brand-text: #0f172a; --brand-text-light: #ffffff; }
html, body, .gradio-container { height: 100vh; }
.gradio-container { background: var(--brand-bg); display: flex; flex-direction: column; }
/* HERO (landing) */
#hero-wrap { height: 70vh; display: grid; place-items: center; }
#hero { text-align: center; }
#hero h2 { color: #0f172a; font-weight: 800; font-size: 32px; margin-bottom: 22px; }
#hero .search-row { width: min(860px, 92vw); margin: 0 auto; display: flex; gap: 8px; align-items: stretch; }
#hero .search-row .hero-box { flex: 1 1 auto; }
#hero .search-row .hero-box textarea { height: 52px !important; }
#hero-send > button { height: 52px !important; padding: 0 18px !important; border-radius: 12px !important; }
#hero .hint { color: #334155; margin-top: 10px; font-size: 13px; opacity: 0.9; }
/* CHAT */
#chat-container { position: relative; }
.chatbot header, .chatbot .label, .chatbot .label-wrap { display: none !important; }
.message.user, .message.bot { background: var(--brand-accent) !important; color: var(--brand-text-light) !important; border-radius: 12px !important; padding: 8px 12px !important; }
textarea, input, .gr-input { border-radius: 12px !important; }
/* Chat input row equal heights */
#chat-input-row { align-items: stretch; }
#chat-msg textarea { height: 52px !important; }
#chat-send > button, #chat-clear > button { height: 52px !important; padding: 0 18px !important; border-radius: 12px !important; }
"""
# ---------- Main App ----------
with gr.Blocks(theme=theme, css=custom_css, analytics_enabled=False) as demo:
# --- HERO (initial screen) ---
with gr.Column(elem_id="hero-wrap", visible=True) as hero_wrap:
with gr.Column(elem_id="hero"):
gr.HTML("<h2>How can I help you today?</h2>")
with gr.Row(elem_classes="search-row"):
hero_msg = gr.Textbox(
placeholder="Ask me anything or upload healthcare data files for scenario analysis…",
show_label=False,
lines=1,
elem_classes="hero-box"
)
hero_send = gr.Button("➤", scale=0, elem_id="hero-send")
# ---- NEW: hint that directive-driven scenarios are supported
gr.Markdown(
'<div class="hint">I can chat normally or run directive-based analyses. '
'In scenarios, add directives like <code>format:</code>, <code>data_key:</code>, '
'<code>filter:</code>, <code>group_by:</code>, <code>agg:</code>, <code>pivot:</code>, '
'<code>sort_by:</code>, <code>top:</code>, <code>fields:</code>, <code>chart:</code> to control the output exactly.</div>'
)
# --- MAIN APP (hidden until first message) ---
with gr.Column(elem_id="chat-container", visible=False) as app_wrap:
chat = gr.Chatbot(label="", show_label=False, height="80vh")
with gr.Row():
uploads = gr.Files(
label="Upload healthcare data files",
file_types=HEALTHCARE_SETTINGS["supported_file_types"],
file_count="multiple", height=68
)
with gr.Row(elem_id="chat-input-row"):
msg = gr.Textbox(
label="",
show_label=False,
placeholder="Ask me anything or continue your healthcare scenario analysis…",
scale=10,
elem_id="chat-msg",
lines=1,
)
send = gr.Button("Send", scale=1, elem_id="chat-send")
clear = gr.Button("Clear chat", scale=1, elem_id="chat-clear")
# ---- State
state_history = gr.State(value=[])
state_uploaded = gr.State(value=[])
state_awaiting = gr.State(value=False)
# ---- Uploads
def _store_uploads(files, current):
paths = []
for f in (files or []):
paths.append(getattr(f, "name", None) or f)
return (current or []) + paths
uploads.change(fn=_store_uploads, inputs=[uploads, state_uploaded], outputs=state_uploaded)
# ---- Core send (used by both hero input and chat input)
def _on_send(user_msg, history, up_paths, awaiting):
try:
if not user_msg or not user_msg.strip():
return history, "", history, awaiting
new_history, new_awaiting = clarityops_reply(
user_msg.strip(), history or [], None, up_paths or [], awaiting_answers=awaiting
)
return new_history, "", new_history, new_awaiting
except Exception as e:
err = f"Error: {e}"
try: traceback.print_exc()
except Exception: pass
new_hist = (history or []) + [(user_msg or "", err)]
return new_hist, "", new_hist, awaiting
# ---- Hero -> App transition + first send
def _hero_start(user_msg, history, up_paths, awaiting):
chat_o, msg_o, hist_o, await_o = _on_send(user_msg, history, up_paths, awaiting)
return (
chat_o, msg_o, hist_o, await_o,
gr.update(visible=False),
gr.update(visible=True),
""
)
hero_send.click(
_hero_start,
inputs=[hero_msg, state_history, state_uploaded, state_awaiting],
outputs=[chat, msg, state_history, state_awaiting, hero_wrap, app_wrap, hero_msg],
concurrency_limit=2, queue=True
)
hero_msg.submit(
_hero_start,
inputs=[hero_msg, state_history, state_uploaded, state_awaiting],
outputs=[chat, msg, state_history, state_awaiting, hero_wrap, app_wrap, hero_msg],
concurrency_limit=2, queue=True
)
# ---- Normal chat interactions after hero is gone
send.click(_on_send, inputs=[msg, state_history, state_uploaded, state_awaiting],
outputs=[chat, msg, state_history, state_awaiting],
concurrency_limit=2, queue=True)
msg.submit(_on_send, inputs=[msg, state_history, state_uploaded, state_awaiting],
outputs=[chat, msg, state_history, state_awaiting],
concurrency_limit=2, queue=True)
def _on_clear():
return (
[], "", [], False,
gr.update(visible=True),
gr.update(visible=False),
""
)
clear.click(_on_clear, None, [chat, msg, state_history, state_awaiting, hero_wrap, app_wrap, hero_msg])
if __name__ == "__main__":
port = int(os.environ.get("PORT", "7860"))
demo.launch(server_name="0.0.0.0", server_port=port, show_api=False, max_threads=40)