app.py

#!/usr/bin/env python3
# app.py - Health Reports processing agent (PDF -> cleaned text -> structured JSON)
# nothing
import os
import json
import logging
import re
from pathlib import Path
from typing import List, Dict, Any
from werkzeug.utils import secure_filename
from flask import Flask, request, jsonify
from flask_cors import CORS
from dotenv import load_dotenv
from unstructured.partition.pdf import partition_pdf
from flask import send_from_directory, abort

# Bloatectomy class (as per the source you provided)
from bloatectomy import bloatectomy

# LLM / agent
from langchain_groq import ChatGroq
from langgraph.prebuilt import create_react_agent

# LangGraph imports
from langgraph.graph import StateGraph, START, END
from typing_extensions import TypedDict, NotRequired

# --- Logging ---------------------------------------------------------------
logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s")
logger = logging.getLogger("health-agent")

# --- Environment & config -------------------------------------------------
load_dotenv()
from pathlib import Path
REPORTS_ROOT = Path(os.getenv("REPORTS_ROOT", "reports")).resolve()   # e.g. /app/reports/<patient_id>/<file.pdf>
SSRI_FILE = Path(os.getenv("SSRI_FILE", "app/medicationCategories/SSRI_list.txt")).resolve()
MISC_FILE = Path(os.getenv("MISC_FILE", "app/medicationCategories/MISC_list.txt")).resolve()
GROQ_API_KEY = os.getenv("GROQ_API_KEY", None)
ALLOWED_EXTENSIONS = {"pdf"}
# --- LLM setup -------------------------------------------------------------
llm = ChatGroq(
    model=os.getenv("LLM_MODEL", "meta-llama/llama-4-scout-17b-16e-instruct"),
    temperature=0.0,
    max_tokens=None,
)

# Top-level strict system prompt for report JSON pieces (each node will use a more specific prompt)
NODE_BASE_INSTRUCTIONS = """

You are HealthAI — a clinical assistant producing JSON for downstream processing.

Produce only valid JSON (no extra text). Follow field types exactly. If missing data, return empty strings or empty arrays.

Be conservative: do not assert diagnoses; provide suggestions and ask physician confirmation where needed.

"""

# Build a generic agent and a JSON resolver agent (to fix broken JSON from LLM)
agent = create_react_agent(model=llm, tools=[], prompt=NODE_BASE_INSTRUCTIONS)
agent_json_resolver = create_react_agent(model=llm, tools=[], prompt="""

You are a JSON fixer. Input: a possibly-malformed JSON-like text. Output: valid JSON only (enclosed in triple backticks).

Fix missing quotes, trailing commas, unescaped newlines, stray assistant labels, and ensure schema compliance.

""")

# -------------------- JSON extraction / sanitizer ---------------------------
def extract_json_from_llm_response(raw_response: str) -> dict:
    try:
        # --- 1) Pull out the JSON code-block if present ---
        md = re.search(r"```(?:json)?\s*([\s\S]*?)\s*```", raw_response)
        json_string = md.group(1).strip() if md else raw_response

        # --- 2) Trim to the outermost { … } so we drop any prefix/suffix junk ---
        first, last = json_string.find('{'), json_string.rfind('}')
        if 0 <= first < last:
            json_string = json_string[first:last+1]

        # --- 3) PRE-CLEANUP: remove rogue assistant labels, fix boolean quotes ---
        json_string = re.sub(r'\b\w+\s*{', '{', json_string)
        json_string = re.sub(r'"assistant"\s*:', '', json_string)
        json_string = re.sub(r'\b(false|true)"', r'\1', json_string)

        # --- 4) Escape embedded quotes in long string fields (best-effort) ---
        def _esc(m):
            prefix, body = m.group(1), m.group(2)
            return prefix + body.replace('"', r'\"')
        json_string = re.sub(
            r'("logic"\s*:\s*")([\s\S]+?)(?=",\s*"[A-Za-z_]\w*"\s*:\s*)',
            _esc,
            json_string
        )

        # --- 5) Remove trailing commas before } or ] ---
        json_string = re.sub(r',\s*(?=[}\],])', '', json_string)
        json_string = re.sub(r',\s*,', ',', json_string)

        # --- 6) Balance braces if obvious excess ---
        ob, cb = json_string.count('{'), json_string.count('}')
        if cb > ob:
            excess = cb - ob
            json_string = json_string.rstrip()[:-excess]

        # --- 7) Escape literal newlines inside strings so json.loads can parse ---
        def _escape_newlines_in_strings(s: str) -> str:
            return re.sub(
                r'"((?:[^"\\]|\\.)*?)"',
                lambda m: '"' + m.group(1).replace('\n', '\\n').replace('\r', '\\r') + '"',
                s,
                flags=re.DOTALL
            )
        json_string = _escape_newlines_in_strings(json_string)

        # Final parse
        return json.loads(json_string)
    except Exception as e:
        logger.error(f"Failed to extract JSON from LLM response: {e}")
        raise

# -------------------- Utility: Bloatectomy wrapper ------------------------
def clean_notes_with_bloatectomy(text: str, style: str = "remov") -> str:
    try:
        b = bloatectomy(text, style=style, output="html")
        tokens = getattr(b, "tokens", None)
        if not tokens:
            return text
        return "\n".join(tokens)
    except Exception:
        logger.exception("Bloatectomy cleaning failed; returning original text")
        return text

# --------------- Utility: medication extraction (adapted) -----------------
def readDrugs_from_file(path: Path):
    try:
        if not path.exists():
            return {}, []
        txt = path.read_text(encoding="utf-8", errors="ignore")
        generics = re.findall(r"^(.*?)\|", txt, re.MULTILINE)
        generics = [g.lower() for g in generics if g]
        lines = [ln.strip().lower() for ln in txt.splitlines() if ln.strip()]
        return dict(zip(generics, lines)), generics
    except Exception:
        logger.exception(f"Failed to read drugs from file: {path}")
        return {}, []

def addToDrugs_line(line: str, drugs_flags: List[int], listing: Dict[str,str], genList: List[str]) -> List[int]:
    try:
        gen_index = {g:i for i,g in enumerate(genList)}
        for generic, pattern_line in listing.items():
            try:
                if re.search(pattern_line, line, re.I):
                    idx = gen_index.get(generic)
                    if idx is not None:
                        drugs_flags[idx] = 1
            except re.error:
                continue
        return drugs_flags
    except Exception:
        logger.exception("Error in addToDrugs_line")
        return drugs_flags

def extract_medications_from_text(text: str) -> List[str]:
    try:
        ssri_map, ssri_generics = readDrugs_from_file(SSRI_FILE)
        misc_map, misc_generics = readDrugs_from_file(MISC_FILE)
        combined_map = {**ssri_map, **misc_map}
        combined_generics = []
        if ssri_generics:
            combined_generics.extend(ssri_generics)
        if misc_generics:
            combined_generics.extend(misc_generics)

        flags = [0]* len(combined_generics)
        meds_found = set()
        for ln in text.splitlines():
            ln = ln.strip()
            if not ln:
                continue
            if combined_map:
                flags = addToDrugs_line(ln, flags, combined_map, combined_generics)
            m = re.search(r"\b(Rx|Drug|Medication|Prescribed|Tablet)\s*[:\-]?\s*([A-Za-z0-9\-\s/\.]+)", ln, re.I)
            if m:
                meds_found.add(m.group(2).strip())
            m2 = re.findall(r"\b([A-Z][a-z0-9\-]{2,}\s*(?:[0-9]{1,4}\s*(?:mg|mcg|g|IU))?)", ln)
            for s in m2:
                if re.search(r"\b(mg|mcg|g|IU)\b", s, re.I):
                    meds_found.add(s.strip())
        for i, f in enumerate(flags):
            if f == 1:
                meds_found.add(combined_generics[i])
        return list(meds_found)
    except Exception:
        logger.exception("Failed to extract medications from text")
        return []

# -------------------- Node prompts --------------------------
PATIENT_NODE_PROMPT = """

You will extract patientDetails from the provided document texts.

Return ONLY JSON with this exact shape:

{ "patientDetails": {"name": "", "age": "", "sex": "", "pid": ""} }

Fill fields using text evidence or leave empty strings.

"""

DOCTOR_NODE_PROMPT = """

You will extract doctorDetails found in the documents.

Return ONLY JSON with this exact shape:

{ "doctorDetails": {"referredBy": ""} }

"""

TEST_REPORT_NODE_PROMPT = """

You will extract per-test structured results from the documents.

Return ONLY JSON with this exact shape:

{

 "reports": [

   {

     "testName": "",

     "dateReported": "",

     "timeReported": "",

     "abnormalFindings": [

       {"investigation": "", "result": 0, "unit": "", "status": "", "referenceValue": ""}

     ],

     "interpretation": "",

     "trends": []

   }

 ]

}

- Include only findings that are outside reference ranges OR explicitly called 'abnormal' in the report.

- For result numeric parsing, prefer numeric values; if not numeric, keep original string.

- Use statuses: Low, High, Borderline, Positive, Negative, Normal.

"""

ANALYSIS_NODE_PROMPT = """

You will create an overallAnalysis based on the extracted reports (the agent will give you the 'reports' JSON).

Return ONLY JSON:

{ "overallAnalysis": { "summary": "", "recommendations": "", "longTermTrends": "",""risk_prediction": "","drug_interaction": "" } }

Be conservative, evidence-based, and suggest follow-up steps for physicians.

"""

CONDITION_LOOP_NODE_PROMPT = """

Validation and condition node:

Input: partial JSON (patientDetails, doctorDetails, reports, overallAnalysis).

Task: Check required keys exist and that each report has at least testName and abnormalFindings list.

Return ONLY JSON:

{ "valid": true, "missing": [] }

If missing fields, list keys in 'missing'. Do NOT modify content.

"""

# -------------------- Node helpers -------------------------
def call_node_agent(node_prompt: str, payload: dict) -> dict:
    """

    Call the generic agent with a targeted node prompt and the payload.

    Tries to parse JSON. If parsing fails, uses the JSON resolver agent once.

    """
    try:
        content = {
            "prompt": node_prompt,
            "payload": payload
        }
        resp = agent.invoke({"messages": [{"role": "user", "content": json.dumps(content)}]})

        # Extract raw text from AIMessage or other response types
        raw = None
        if isinstance(resp, str):
            raw = resp
        elif hasattr(resp, "content"):  # AIMessage or similar
            raw = resp.content
        elif isinstance(resp, dict):
            msgs = resp.get("messages")
            if msgs:
                last_msg = msgs[-1]
                if isinstance(last_msg, str):
                    raw = last_msg
                elif hasattr(last_msg, "content"):
                    raw = last_msg.content
                elif isinstance(last_msg, dict):
                    raw = last_msg.get("content", "")
                else:
                    raw = str(last_msg)
            else:
                raw = json.dumps(resp)
        else:
            raw = str(resp)

        parsed = extract_json_from_llm_response(raw)
        return parsed

    except Exception as e:
        logger.warning("Node agent JSON parse failed: %s. Attempting JSON resolver.", e)
        try:
            resolver_prompt = f"Fix this JSON. Input:\n```json\n{raw}\n```\nReturn valid JSON only."
            r = agent_json_resolver.invoke({"messages": [{"role": "user", "content": resolver_prompt}]})

            rtxt = None
            if isinstance(r, str):
                rtxt = r
            elif hasattr(r, "content"):
                rtxt = r.content
            elif isinstance(r, dict):
                msgs = r.get("messages")
                if msgs:
                    last_msg = msgs[-1]
                    if isinstance(last_msg, str):
                        rtxt = last_msg
                    elif hasattr(last_msg, "content"):
                        rtxt = last_msg.content
                    elif isinstance(last_msg, dict):
                        rtxt = last_msg.get("content", "")
                    else:
                        rtxt = str(last_msg)
                else:
                    rtxt = json.dumps(r)
            else:
                rtxt = str(r)

            corrected = extract_json_from_llm_response(rtxt)
            return corrected
        except Exception as e2:
            logger.exception("JSON resolver also failed: %s", e2)
            return {}

# -------------------- Define LangGraph State schema -------------------------
class State(TypedDict):
    patient_meta: NotRequired[Dict[str, Any]]
    patient_id: str
    documents: List[Dict[str, Any]]
    medications: List[str]
    patientDetails: NotRequired[Dict[str, Any]]
    doctorDetails: NotRequired[Dict[str, Any]]
    reports: NotRequired[List[Dict[str, Any]]]
    overallAnalysis: NotRequired[Dict[str, Any]]
    valid: NotRequired[bool]
    missing: NotRequired[List[str]]

# -------------------- Node implementations as LangGraph nodes -------------------------
def patient_details_node(state: State) -> dict:
    payload = {
        "patient_meta": state.get("patient_meta", {}),
        "documents": state.get("documents", []),
        "medications": state.get("medications", [])
    }
    logger.info("Running patient_details_node")
    out = call_node_agent(PATIENT_NODE_PROMPT, payload)
    return {"patientDetails": out.get("patientDetails", {}) if isinstance(out, dict) else {}}

def doctor_details_node(state: State) -> dict:
    payload = {
        "documents": state.get("documents", []),
        "medications": state.get("medications", [])
    }
    logger.info("Running doctor_details_node")
    out = call_node_agent(DOCTOR_NODE_PROMPT, payload)
    return {"doctorDetails": out.get("doctorDetails", {}) if isinstance(out, dict) else {}}

def test_report_node(state: State) -> dict:
    payload = {
        "documents": state.get("documents", []),
        "medications": state.get("medications", [])
    }
    logger.info("Running test_report_node")
    out = call_node_agent(TEST_REPORT_NODE_PROMPT, payload)
    return {"reports": out.get("reports", []) if isinstance(out, dict) else []}

def analysis_node(state: State) -> dict:
    payload = {
        "patientDetails": state.get("patientDetails", {}),
        "doctorDetails": state.get("doctorDetails", {}),
        "reports": state.get("reports", []),
        "medications": state.get("medications", [])
    }
    logger.info("Running analysis_node")
    out = call_node_agent(ANALYSIS_NODE_PROMPT, payload)
    return {"overallAnalysis": out.get("overallAnalysis", {}) if isinstance(out, dict) else {}}

def condition_loop_node(state: State) -> dict:
    payload = {
        "patientDetails": state.get("patientDetails", {}),
        "doctorDetails": state.get("doctorDetails", {}),
        "reports": state.get("reports", []),
        "overallAnalysis": state.get("overallAnalysis", {})
    }
    logger.info("Running condition_loop_node (validation)")
    out = call_node_agent(CONDITION_LOOP_NODE_PROMPT, payload)
    if isinstance(out, dict) and "valid" in out:
        return {"valid": bool(out.get("valid")), "missing": out.get("missing", [])}
    missing = []
    if not state.get("patientDetails"):
        missing.append("patientDetails")
    if not state.get("reports"):
        missing.append("reports")
    return {"valid": len(missing) == 0, "missing": missing}

# -------------------- Build LangGraph StateGraph -------------------------
graph_builder = StateGraph(State)

graph_builder.add_node("patient_details", patient_details_node)
graph_builder.add_node("doctor_details", doctor_details_node)
graph_builder.add_node("test_report", test_report_node)
graph_builder.add_node("analysis", analysis_node)
graph_builder.add_node("condition_loop", condition_loop_node)

graph_builder.add_edge(START, "patient_details")
graph_builder.add_edge("patient_details", "doctor_details")
graph_builder.add_edge("doctor_details", "test_report")
graph_builder.add_edge("test_report", "analysis")
graph_builder.add_edge("analysis", "condition_loop")
graph_builder.add_edge("condition_loop", END)

graph = graph_builder.compile()

# -------------------- Flask app & endpoints -------------------------------
# -------------------- Flask app & endpoints -------------------------------
BASE_DIR = Path(__file__).resolve().parent
static_folder = BASE_DIR / "static"
app = Flask(__name__, static_folder=str(static_folder), static_url_path="/static")
CORS(app)  # dev convenience; lock down in production

# serve frontend root
@app.route("/", methods=["GET"])
def serve_frontend():
    try:
        return app.send_static_file("frontend.html")
    except Exception as e:
        logger.error(f"Failed to serve frontend.html: {e}")
        return "<h3>frontend.html not found in static/ — drop your frontend.html there.</h3>", 404

@app.route("/process_reports", methods=["POST"])
def process_reports():
    try:
        data = request.get_json(force=True)
    except Exception as e:
        logger.error(f"Failed to parse JSON request: {e}")
        return jsonify({"error": "Invalid JSON request"}), 400

    patient_id = data.get("patient_id")
    filenames = data.get("filenames", [])
    extra_patient_meta = data.get("patientDetails", {})

    if not patient_id or not filenames:
        return jsonify({"error": "missing patient_id or filenames"}), 400

    patient_folder = REPORTS_ROOT / str(patient_id)
    if not patient_folder.exists() or not patient_folder.is_dir():
        return jsonify({"error": f"patient folder not found: {patient_folder}"}), 404

    documents = []
    combined_text_parts = []

    for fname in filenames:
        file_path = patient_folder / fname
        if not file_path.exists():
            logger.warning("file not found: %s", file_path)
            continue
        try:
            elements = partition_pdf(filename=str(file_path))
            page_text = "\n".join([el.text for el in elements if hasattr(el, "text") and el.text])
        except Exception:
            logger.exception(f"Failed to parse PDF {file_path}")
            page_text = ""
        try:
            cleaned = clean_notes_with_bloatectomy(page_text, style="remov")
        except Exception:
            logger.exception("Failed to clean notes with bloatectomy")
            cleaned = page_text
        documents.append({
            "filename": fname,
            "raw_text": page_text,
            "cleaned_text": cleaned
        })
        combined_text_parts.append(cleaned)

    if not documents:
        return jsonify({"error": "no valid documents found"}), 400

    combined_text = "\n\n".join(combined_text_parts)
    try:
        meds = extract_medications_from_text(combined_text)
    except Exception:
        logger.exception("Failed to extract medications")
        meds = []

    initial_state = {
        "patient_meta": extra_patient_meta,
        "patient_id": patient_id,
        "documents": documents,
        "medications": meds
    }

    try:
        result_state = graph.invoke(initial_state)

        # Validate and fill placeholders if needed
        if not result_state.get("valid", True):
            missing = result_state.get("missing", [])
            logger.info(f"Validation failed; missing keys: {missing}")
            if "patientDetails" in missing:
                result_state["patientDetails"] = extra_patient_meta or {"name": "", "age": "", "sex": "", "pid": patient_id}
            if "reports" in missing:
                result_state["reports"] = []
            # Re-run analysis node to keep overallAnalysis consistent
            result_state.update(analysis_node(result_state))
            # Re-validate
            cond = condition_loop_node(result_state)
            result_state.update(cond)

        safe_response = {
            "patientDetails": result_state.get("patientDetails", {"name": "", "age": "", "sex": "", "pid": patient_id}),
            "doctorDetails": result_state.get("doctorDetails", {"referredBy": ""}),
            "reports": result_state.get("reports", []),
            "overallAnalysis": result_state.get("overallAnalysis", {"summary": "", "recommendations": "", "longTermTrends": ""}),
            "_pre_extracted_medications": result_state.get("medications", []),
            "_validation": {
                "valid": result_state.get("valid", True),
                "missing": result_state.get("missing", [])
            }
        }
        return jsonify(safe_response), 200

    except Exception as e:
        logger.exception("Node pipeline failed")
        return jsonify({"error": "Node pipeline failed", "detail": str(e)}), 500


import mimetypes
import requests
import contextlib
from pathlib import Path

REMOTE_UPLOAD_URL = "https://webashalarforml-patient-bot.hf.space/upload_reports"
REMOTE_UPLOAD_HEADERS = {
    # optional headers used by your curl example; update/remove as required
    "Origin": "https://webashalarforml-patient-bot.hf.space",
    "Accept": "*/*",
    "User-Agent": "PatientReportsUploader/1.0"
    }

@app.route("/upload_reports", methods=["POST"])
def upload_reports():
    """

    Upload one or more files for a patient (same behavior as before).

    After saving locally under REPORTS_ROOT/<patient_id>, if files were saved

    this will POST the same files and patient_id to REMOTE_UPLOAD_URL and

    include the remote response in the returned JSON.

    """
    try:
        patient_id = request.form.get("patient_id") or request.args.get("patient_id")
        if not patient_id:
            return jsonify({"error": "patient_id form field required"}), 400

        uploaded_files = request.files.getlist("files")
        if not uploaded_files:
            single = request.files.get("file")
            if single:
                uploaded_files = [single]

        if not uploaded_files:
            return jsonify({"error": "no files uploaded (use form field 'files')"}), 400

        patient_folder = REPORTS_ROOT / str(patient_id)
        patient_folder.mkdir(parents=True, exist_ok=True)

        saved = []
        skipped = []

        for file_storage in uploaded_files:
            orig_name = getattr(file_storage, "filename", "") or ""
            filename = secure_filename(orig_name)
            if not filename:
                skipped.append({"filename": orig_name, "reason": "invalid filename"})
                continue

            ext = filename.rsplit(".", 1)[1].lower() if "." in filename else ""
            if ext not in ALLOWED_EXTENSIONS:
                skipped.append({"filename": filename, "reason": f"extension '{ext}' not allowed"})
                continue

            dest = patient_folder / filename
            if dest.exists():
                base, dot, extension = filename.rpartition(".")
                base = base or filename
                i = 1
                while True:
                    candidate = f"{base}__{i}.{extension}" if extension else f"{base}__{i}"
                    dest = patient_folder / candidate
                    if not dest.exists():
                        filename = candidate
                        break
                    i += 1

            try:
                file_storage.save(str(dest))
                saved.append(filename)
            except Exception as e:
                logger.exception("Failed to save uploaded file %s: %s", filename, e)
                skipped.append({"filename": filename, "reason": f"save failed: {e}"})

        # ---- POST to remote app if we saved any files ----
        remote_result = None
        if saved:
            saved_paths = [patient_folder / name for name in saved]
            # Use ExitStack to ensure all file handles are closed after request
            with contextlib.ExitStack() as stack:
                files_payload = []
                for p in saved_paths:
                    # guess content type, fallback to octet-stream
                    ctype, _ = mimetypes.guess_type(str(p))
                    fh = stack.enter_context(open(p, "rb"))
                    files_payload.append(("files", (p.name, fh, ctype or "application/octet-stream")))

                try:
                    resp = requests.post(
                        REMOTE_UPLOAD_URL,
                        files=files_payload,
                        data={"patient_id": str(patient_id)},
                        headers=REMOTE_UPLOAD_HEADERS,
                        timeout=60  # adjust if needed
                    )
                    # keep remote status and a short snippet of body for debugging
                    remote_result = {
                        "status_code": resp.status_code,
                        "ok": resp.ok,
                        "body_snippet": resp.text[:200]  # don't bloat response
                    }
                except Exception as e:
                    logger.exception("Failed to POST files to remote app: %s", e)
                    remote_result = {"error": str(e)}

        return jsonify({
            "patient_id": str(patient_id),
            "saved": saved,
            "skipped": skipped,
            "patient_folder": str(patient_folder),
            "remote": remote_result
        }), 200

    except Exception as exc:
        logger.exception("Upload failed: %s", exc)
        return jsonify({"error": "upload failed", "detail": str(exc)}), 500

@app.route("/<patient_id>/<filename>")
def serve_report(patient_id, filename):
    """

    Serve a specific uploaded PDF (or other allowed file) for a patient.

    URL format: /<patient_id>/<filename>

    Example:   /p14562/report1.pdf

    """
    try:
        patient_folder = REPORTS_ROOT / str(patient_id)

        if not patient_folder.exists():
            abort(404, description=f"Patient folder not found: {patient_id}")

        # security check: only allow files with allowed extensions
        ext = filename.rsplit(".", 1)[-1].lower() if "." in filename else ""
        if ext not in ALLOWED_EXTENSIONS:
            abort(403, description=f"Extension '{ext}' not allowed")

        return send_from_directory(
            directory=str(patient_folder),
            path=filename,
            as_attachment=False  # set True if you want download instead of inline view
        )

    except Exception as e:
        logger.exception("Failed to serve file %s/%s: %s", patient_id, filename, e)
        abort(500, description=f"Failed to serve file: {e}")

@app.route("/ping", methods=["GET"])
def ping():
    return jsonify({"status": "ok"})

if __name__ == "__main__":
    port = int(os.getenv("PORT", 7860))
    app.run(host="0.0.0.0", port=port, debug=True)