app/app.py

# app/app.py
import os, sys, time, csv, re
from pathlib import Path
import yaml
import pandas as pd
import numpy as np
from dotenv import load_dotenv

load_dotenv()

ANTHROPIC_API_KEY = os.getenv("ANTHROPIC_API_KEY")
print("ANTHROPIC in env:", bool(os.getenv("ANTHROPIC_API_KEY")), flush=True)

if not ANTHROPIC_API_KEY:
    raise SystemExit("Missing ANTHROPIC_API_KEY in environment or .env file.")


# os.environ.setdefault("HF_HUB_DISABLE_TELEMETRY", "1")
# os.environ.setdefault("TRANSFORMERS_OFFLINE", "1")

# --- Resolve paths (works both as .py and PyInstaller .exe)
APP_DIR = Path(__file__).resolve().parent          # .../app
if hasattr(sys, "_MEIPASS"):                       
    ROOT = Path(sys._MEIPASS)                      
else:
    ROOT = APP_DIR.parent                          

CFG_PATH = ROOT / "app" / "config" / "app.yaml"
MODELS_DIR = ROOT / "models"
INDEX_DIR = ROOT / "outputs" / "index"
LOGS_DIR = ROOT / "local_logs"
DOCS_DIR = ROOT / "docs"

LOGS_DIR.mkdir(parents=True, exist_ok=True)

# --- Read config
DEFAULT_CFG = {
    "retrieval": {"top_k": 12, "evidence_shown": 3, "answerability_threshold": 0.2},
    "generator": {
        "enabled_default": False,
        "use_top_evidence": 5,
        "temperature": 0.1,
        "max_answer_sentences": 20,
        "n_ctx": 4096,
        "threads": max(2, (os.cpu_count() or 4) - 1)
    },
    "models": {
        "embedding_model": "sentence-transformers/all-MiniLM-L6-v2",
        "embedding_local_dir": None,  
        "anthropic_model": "claude-3-5-sonnet-latest"
    },
    "ui": {"show_online_badge": True, "performance_mode": "standard"}  # quick|standard
}
cfg = DEFAULT_CFG
if CFG_PATH.exists():
    cfg = {**cfg, **yaml.safe_load(CFG_PATH.read_text(encoding="utf-8"))}

# --- Load FAISS index & embeddings
import faiss
from sentence_transformers import SentenceTransformer

META_PATH = INDEX_DIR / "meta.parquet"
FAISS_PATH = INDEX_DIR / "chunks.faiss"

if not META_PATH.exists() or not FAISS_PATH.exists():
    raise SystemExit("Index not found. Ensure outputs/index/meta.parquet and chunks.faiss exist.")

df = pd.read_parquet(META_PATH)
df["text"] = df["text"].fillna("").astype(str)

#loading sentence transformer
emb_dir = cfg["models"].get("embedding_local_dir")
if emb_dir:
    EMBED_MODEL_PATH = Path(emb_dir)
    if not EMBED_MODEL_PATH.exists():
        raise SystemExit(f"Embedding model folder not found: {EMBED_MODEL_PATH}")
    embed_model = SentenceTransformer(str(EMBED_MODEL_PATH), trust_remote_code=False)
else:
    
    embed_model = SentenceTransformer(cfg["models"]["embedding_model"], trust_remote_code=False)

index = faiss.read_index(str(FAISS_PATH))

def _format_citation(row):
    p = int(row["page"]) if pd.notna(row.get("page")) else None
    return f"{row['title']} (p.{p})" if p else f"{row['title']}"

def retrieve(query, top_k=6):
    qv = embed_model.encode([query], convert_to_numpy=True, normalize_embeddings=True).astype("float32")
    scores, idxs = index.search(qv, top_k)
    out = []
    for s, ix in zip(scores[0], idxs[0]):
        r = df.iloc[int(ix)]
        out.append({
            "score": float(s),
            "citation": _format_citation(r),
            "doc_id": r.get("doc_id", ""),
            "page": None if pd.isna(r.get("page")) else int(r["page"]),
            "chunk_id": int(r["chunk_id"]),
            "text": r["text"]
        })
    return out

# Anthropic (Claude) LLM
from anthropic import Anthropic, APIError

ANTHROPIC_API_KEY = os.environ.get("ANTHROPIC_API_KEY")
if not ANTHROPIC_API_KEY:
    raise SystemExit("Missing ANTHROPIC_API_KEY environment variable.")

anthropic_client = Anthropic(api_key=ANTHROPIC_API_KEY)
CLAUDE_MODEL = cfg["models"].get("anthropic_model", "claude-3-5-sonnet-latest")

SYSTEM_PROMPT = (
    "You are a careful assistant for clinicians. "
    "Use ONLY the provided context to answer. "
    "Be concise. Add inline citations like [1], [2] matching the numbered context. "
    "If the context does not fully answer, provide the best supported guidance you can, and point to the closest relevant passages with citations"
)

def _citations_valid(text, k):
    nums = set(int(n) for n in re.findall(r"\[(\d+)\]", text))
    return bool(nums) and all(1 <= n <= k for n in nums)

def _join_cites(nums):
    nums = [f"[{n}]" for n in nums]
    if not nums:
        return ""
    if len(nums) == 1:
        return nums[0]
    return ", ".join(nums[:-1]) + " and " + nums[-1]

def _make_context_block(ctx, use_n):
    blocks = []
    for i, c in enumerate(ctx[:use_n], 1):
        blocks.append(f"[{i}] {c['citation']}\n{c['text']}\n")
    return "\n".join(blocks)

def generate_answer(question, ctx, use_n, temp=0.1, max_sentences=6):
    context_text = _make_context_block(ctx, use_n)
    user_prompt = (
        f"Context:\n\n{context_text}\n\n"
        f"Question: {question}\n"
        "Answer using ONLY the context above and cite with [1], [2], etc."
    )
    try:
        resp = anthropic_client.messages.create(
            model=CLAUDE_MODEL,
            system=SYSTEM_PROMPT,
            max_tokens=600,
            temperature=float(temp),
            messages=[{"role": "user", "content": [{"type": "text", "text": user_prompt}]}],
        )
    except APIError as e:
        return f"_API error from Anthropic: {e}_"

    # Claude returns a list of content blocks
    parts = []
    for blk in resp.content:
        if blk.type == "text":
            parts.append(blk.text)
    full = ("\n".join(parts)).strip()

    # # Log raw model output to console for debugging
    # print("\n===== RAW MODEL OUTPUT =====\n", full, "\n============================\n", flush=True)

    # Trim to ~N sentences to keep it short for testers
    sents = re.split(r'(?<=[.!?])\s+', full)
    short = " ".join(sents[:max_sentences]).strip()
    return short

# gradio
import gradio as gr
ONLINE_BADGE = "Standards of Practice & Code of Ethics" if cfg["ui"].get("show_online_badge", True) else ""
def _top_sentences(text, n=3):
    sents = re.split(r'(?<=[.!?])\s+', text.strip())
    return [s for s in sents if s][:n]

def answer_extractive(query, k=6, per_chunk_sents=2):
    ctx = retrieve(query, top_k=k)
    bullets, refs = [], []
    for i, c in enumerate(ctx, 1):
        for s in _top_sentences(c["text"], per_chunk_sents):
            bullets.append(f"- {s} [{i}]")
        refs.append(f"[{i}] {c['citation']}")
    if not bullets:
        return "I couldn’t find relevant text in the corpus.", refs
    return "\n".join(bullets) + "\n\nSources:\n" + "\n".join(refs), refs

def app_infer(question, do_generate, mode):
    start = time.time()
    if not question or not question.strip():
        return "", "", "", f"{ONLINE_BADGE}  Ready."

    # Retrieval
    top_k = int(cfg["retrieval"]["top_k"])
    shown = int(cfg["retrieval"]["evidence_shown"])
    use_n = int(cfg["generator"]["use_top_evidence"])
    if mode == "quick":
        shown = min(3, shown)
        use_n = min(3, use_n)

    ctx = retrieve(question, top_k=top_k)

    # Prepare evidence panel (currently hidden as shown == 0)
    if shown > 0:
        ev_md_lines = []
        for i, c in enumerate(ctx[:shown], 1):
            title = c["citation"]
            pg = f" (p.{c['page']})" if c["page"] else ""
            body = c["text"].strip()
            body_short = body if len(body) <= 1200 else body[:1200] + "..."
            ev_md_lines.append(f"**[{i}] {title}**\n\n{body_short}\n")
        evidence_md = "\n---\n".join(ev_md_lines)
    else:
        evidence_md = ""  
    # Decide if we should generate?
    answer = ""
    sources_md = ""
    conf = float(ctx[0]["score"]) if ctx else 0.0
    threshold = float(cfg["retrieval"].get("answerability_threshold", 0.01))

    if not ctx:
        status = f"{ONLINE_BADGE}  No evidence found."
        return evidence_md, answer, sources_md, status

    if do_generate and conf >= threshold:
        draft = generate_answer(
            question=question,
            ctx=ctx,
            use_n=use_n,
            temp=float(cfg["generator"]["temperature"]),
            max_sentences=int(cfg["generator"]["max_answer_sentences"])
        )
        # Validate citations
        # if not _citations_valid(draft, min(use_n, len(ctx))):
        #     answer = "_Not enough evidence to generate a reliable summary. See Evidence below._"
        # else:
        #     answer = draft
        
        if not _citations_valid(draft, min(use_n, len(ctx))):
            extractive, _ = answer_extractive(question, k=use_n, per_chunk_sents=2)
            answer = extractive
        else:
            answer = draft



    elif do_generate and conf < threshold:
        answer = "_Not enough evidence—see Evidence below._"

    # Sources list
    src_lines = [f"[{i}] {c['citation']}" for i, c in enumerate(ctx[:use_n], 1)]
    sources_md = "Sources:\n" + "\n".join(src_lines)
    if answer:
        a = answer.strip()
        if not a.lower().startswith("answer:"):
            answer = f"Answer: {a}"

    dur = time.time() - start
    status = f"{ONLINE_BADGE}  Done in {dur:.1f}s (conf={conf:.2f})."
    return evidence_md, answer, sources_md, status

def save_feedback(question, rating, note, answer_shown):
    fpath = LOGS_DIR / "feedback.csv"
    new = not fpath.exists()
    with fpath.open("a", newline="", encoding="utf-8") as f:
        w = csv.writer(f)
        if new:
            w.writerow(["timestamp","question","rating","note","answer_shown"])
        w.writerow([time.strftime("%Y-%m-%d %H:%M:%S"), question, rating, note, "yes" if answer_shown else "no"])
    return "Feedback saved. Thank you!"

APP_CSS = """
:root{
  --app-font: system-ui, -apple-system, "Segoe UI", Roboto, Helvetica, Arial,
              "Apple Color Emoji","Segoe UI Emoji";
}
body, .gradio-container { font-family: var(--app-font) !important; }
/* make reading nicer */
.gr-markdown { font-size: 16px; line-height: 1.6; }
.gr-markdown h2 { font-size: 18px; margin-top: 0.6rem; }
.gr-textbox textarea { font-size: 16px; }
"""

with gr.Blocks(title="Clinician Q&A", theme="soft", css=APP_CSS) as demo:
    gr.Markdown(f"## Clinician Q&A   {'&nbsp;&nbsp;'+ONLINE_BADGE if ONLINE_BADGE else ''}")
    with gr.Row():
        with gr.Column(scale=1):
            q = gr.Textbox(label="Ask a question", placeholder="e.g., When can confidentiality be broken?")
            do_gen = gr.Checkbox(value=cfg["generator"]["enabled_default"], label="Use LLM")
            mode = gr.Radio(choices=["standard","quick"], value=cfg["ui"].get("performance_mode","standard"), label="Performance mode")
            run = gr.Button("Answer", variant="primary")
            rating = gr.Radio(choices=["Helpful","Not sure","Incorrect"], label="Feedback", value=None)
            note = gr.Textbox(label="Add a note (optional)")
            submit = gr.Button("Submit feedback")
            status = gr.Markdown("Ready.")
        with gr.Column(scale=1):
            ans = gr.Markdown(label="Answer")
            ev = gr.Markdown(label="Evidence")
            src = gr.Markdown(label="Sources")

    run.click(app_infer, inputs=[q, do_gen, mode], outputs=[ ans,ev,src, status])
    submit.click(lambda question, r, n, a: save_feedback(question, r, n, bool(a and a.strip())),
                 inputs=[q, rating, note, ans], outputs=[status])

# if __name__ == "__main__":
#     # Bind to localhost only; opens a browser tab automatically.
#     demo.launch(server_name="127.0.0.1", server_port=7860, inbrowser=True, show_error=True)

if __name__ == "__main__":
    # In cloud (HF Spaces), bind to 0.0.0.0 and respect PORT if provided.
    port = int(os.getenv("PORT", "7860"))
    host = "0.0.0.0"
    demo.queue(max_size=32).launch(server_name=host, server_port=port, show_error=True)