app.py

import os
import io
import json
import csv
import asyncio
import xml.etree.ElementTree as ET
from typing import Any, Dict, Optional, Tuple, Union, List

import httpx
import gradio as gr
import torch
from dotenv import load_dotenv
from loguru import logger
from huggingface_hub import login
from openai import OpenAI
from reportlab.pdfgen import canvas
from transformers import (
    AutoTokenizer,
    AutoModelForSequenceClassification,
    MarianMTModel,
    MarianTokenizer,
)
import pandas as pd
import altair as alt
import spacy
import spacy.cli
import PyPDF2

###############################################################################
#                          1) ENVIRONMENT & LOGGING                           #
###############################################################################

# Ensure spaCy model is downloaded (English Core Web)
try:
    nlp = spacy.load("en_core_web_sm")
except OSError:
    logger.info("Downloading SpaCy 'en_core_web_sm' model...")
    spacy.cli.download("en_core_web_sm")
    nlp = spacy.load("en_core_web_sm")

# Logging
logger.add("error_logs.log", rotation="1 MB", level="ERROR")

# Load environment variables
load_dotenv()
HUGGINGFACE_TOKEN = os.getenv("HF_TOKEN")
OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")  # For BioPortal integration
ENTREZ_EMAIL = os.getenv("ENTREZ_EMAIL")

if not HUGGINGFACE_TOKEN or not OPENAI_API_KEY:
    logger.error("Missing Hugging Face or OpenAI credentials.")
    raise ValueError("Missing credentials for Hugging Face or OpenAI.")

# Warn if BioPortal key is missing
if not BIOPORTAL_API_KEY:
    logger.warning("BIOPORTAL_API_KEY is not set. BioPortal fetch calls will fail.")

# Hugging Face login
login(HUGGINGFACE_TOKEN)

# OpenAI
client = OpenAI(api_key=OPENAI_API_KEY)

# Device: CPU or GPU
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
logger.info(f"Using device: {device}")

###############################################################################
#                 2) HUGGING FACE & TRANSLATION MODEL SETUP                   #
###############################################################################

MODEL_NAME = "mgbam/bert-base-finetuned-mgbam"
try:
    model = AutoModelForSequenceClassification.from_pretrained(
        MODEL_NAME, use_auth_token=HUGGINGFACE_TOKEN
    ).to(device)
    tokenizer = AutoTokenizer.from_pretrained(
        MODEL_NAME, use_auth_token=HUGGINGFACE_TOKEN
    )
except Exception as e:
    logger.error(f"Model load error: {e}")
    raise

try:
    translation_model_name = "Helsinki-NLP/opus-mt-en-fr"
    translation_model = MarianMTModel.from_pretrained(
        translation_model_name, use_auth_token=HUGGINGFACE_TOKEN
    ).to(device)
    translation_tokenizer = MarianTokenizer.from_pretrained(
        translation_model_name, use_auth_token=HUGGINGFACE_TOKEN
    )
except Exception as e:
    logger.error(f"Translation model load error: {e}")
    raise

# Language map for translation
LANGUAGE_MAP: Dict[str, Tuple[str, str]] = {
    "English to French": ("en", "fr"),
    "French to English": ("fr", "en"),
}

###############################################################################
#                         3) API ENDPOINTS & CONSTANTS                        #
###############################################################################

PUBMED_SEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
PUBMED_FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
EUROPE_PMC_BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"
BIOPORTAL_API_BASE = "https://data.bioontology.org"
CROSSREF_API_URL = "https://api.crossref.org/works"

###############################################################################
#                            4) HELPER FUNCTIONS                              #
###############################################################################

def safe_json_parse(text: str) -> Union[Dict[str, Any], None]:
    """Safely parse JSON."""
    try:
        return json.loads(text)
    except json.JSONDecodeError as e:
        logger.error(f"JSON parsing error: {e}")
        return None

def parse_pubmed_xml(xml_data: str) -> List[Dict[str, Any]]:
    """Parse PubMed XML data into a structured list of articles."""
    root = ET.fromstring(xml_data)
    articles = []
    for article in root.findall(".//PubmedArticle"):
        pmid = article.findtext(".//PMID")
        title = article.findtext(".//ArticleTitle")
        abstract = article.findtext(".//AbstractText")
        journal = article.findtext(".//Journal/Title")
        pub_date_elem = article.find(".//JournalIssue/PubDate")
        pub_date = None
        if pub_date_elem is not None:
            year = pub_date_elem.findtext("Year")
            month = pub_date_elem.findtext("Month")
            day = pub_date_elem.findtext("Day")
            if year and month and day:
                pub_date = f"{year}-{month}-{day}"
            else:
                pub_date = year
        articles.append({
            "PMID": pmid,
            "Title": title,
            "Abstract": abstract,
            "Journal": journal,
            "PublicationDate": pub_date,
        })
    return articles

def explain_clinical_results(results: str) -> str:
    """Generate a clinical explanation from raw results."""
    try:
        response = client.chat.completions.create(
            model="gpt-3.5-turbo",
            messages=[{"role": "user", "content": f"Explain the clinical test results:\n{results}"}],
            max_tokens=500,
            temperature=0.7,
        )
        return response.choices[0].message.content.strip()
    except Exception as e:
        logger.error(f"Explanation error: {e}")
        return "Failed to generate explanation."

###############################################################################
#                           6) CORE FUNCTIONS                                 #
###############################################################################

def summarize_text(text: str) -> str:
    """OpenAI GPT-3.5 summarization."""
    if not text.strip():
        return "No text provided for summarization."
    try:
        response = client.chat.completions.create(
            model="gpt-3.5-turbo",
            messages=[{"role": "user", "content": f"Summarize this clinical data:\n{text}"}],
            max_tokens=200,
            temperature=0.7,
        )
        return response.choices[0].message.content.strip()
    except Exception as e:
        logger.error(f"Summarization error: {e}")
        return "Summarization failed."

def generate_report(text: str, filename: str = "clinical_report.pdf") -> Optional[str]:
    """Generate a professional PDF report from the text."""
    try:
        if not text.strip():
            logger.warning("No text provided for the report.")
        c = canvas.Canvas(filename)
        c.drawString(100, 750, "Clinical Research Report")
        lines = text.split("\n")
        y = 730
        for line in lines:
            if y < 50:
                c.showPage()
                y = 750
            c.drawString(100, y, line)
            y -= 15
        c.save()
        logger.info(f"Report generated: {filename}")
        return filename
    except Exception as e:
        logger.error(f"Report generation error: {e}")
        return None

def visualize_predictions(predictions: Dict[str, float]) -> alt.Chart:
    """Simple Altair bar chart to visualize classification probabilities."""
    data = pd.DataFrame(list(predictions.items()), columns=["Label", "Probability"])
    chart = (
        alt.Chart(data)
        .mark_bar()
        .encode(
            x=alt.X("Label:N", sort=None),
            y="Probability:Q",
            tooltip=["Label", "Probability"],
        )
        .properties(title="Prediction Probabilities", width=500, height=300)
    )
    return chart

###############################################################################
#                     7) BUILDING THE GRADIO APP                           #
###############################################################################

with gr.Blocks() as demo:
    gr.Markdown("# 🏥 AI-Driven Clinical Assistant")
    gr.Markdown("""
**Highlights**:  
- **Summarize** clinical text (OpenAI GPT-3.5)  
- **Explain** clinical test results and trial outcomes  
- **Generate** professional PDF reports  
""")

    text_input = gr.Textbox(label="Input Text", lines=5, placeholder="Enter clinical text or test results...")
    action = gr.Radio(
        [
            "Summarize",
            "Explain Clinical Results",
            "Generate Report",
        ],
        label="Select an Action",
    )

    output_text = gr.Textbox(label="Output", lines=8)
    output_file = gr.File(label="Generated File")

    submit_btn = gr.Button("Submit")

    async def handle_action(
        action: str,
        txt: str,
        report_fn: str
    ) -> Tuple[Optional[str], Optional[str]]:
        """Handle clinical actions based on the user's selection."""
        try:
            combined_text = txt.strip()

            if action == "Summarize":
                summary = summarize_text(combined_text)
                return summary, None

            elif action == "Explain Clinical Results":
                explanation = explain_clinical_results(combined_text)
                return explanation, None

            elif action == "Generate Report":
                path = generate_report(combined_text, report_fn)
                msg = f"Report generated: {path}" if path else "Report generation failed."
                return msg, path

            return "Invalid action.", None
        except Exception as e:
            logger.error(f"Exception: {e}")
            return f"Error: {str(e)}", None

    submit_btn.click(
        fn=handle_action,
        inputs=[action, text_input, report_filename_input],
        outputs=[output_text, output_file],
    )

# Launch the Gradio interface
demo.launch(server_name="0.0.0.0", server_port=7860, share=True)