app.py

import gradio as gr
import pandas as pd
from Bio import Entrez
import requests

import os 

HF_API = os.getenv('HF_API')
# Function to search PubMed for articles
def search_pubmed(query, retmax):
    Entrez.email = 'example@example.com'
    handle = Entrez.esearch(db="pubmed", term=query, retmax=retmax)
    record = Entrez.read(handle)
    handle.close()
    idlist = record['IdList']
    handle = Entrez.efetch(db="pubmed", id=idlist, retmode="xml")
    articles = Entrez.read(handle)['PubmedArticle']
    handle.close()
    article_list = []
    for article in articles:
        article_dict = {
            'PMID': str(article['MedlineCitation']['PMID']),
            'Authors': ' '.join([author['LastName'] + ' ' + author.get('Initials', '')
                                 for author in article['MedlineCitation']['Article']['AuthorList']]),
            'Title': article['MedlineCitation']['Article']['ArticleTitle'],
            'Abstract': article['MedlineCitation']['Article'].get('Abstract', {}).get('AbstractText', [None])[0]
        }
        article_list.append(article_dict)
    return pd.DataFrame(article_list)

# Function to summarize articles using Hugging Face's API
def summarize_with_huggingface(model, selected_articles):
    API_URL = f"https://api-inference.huggingface.co/models/{model}"
    # Your Hugging Face API key
    API_KEY = HF_API 
    headers = {"Authorization": f"Bearer {API_KEY}"}
    # Prepare the text to summarize: concatenate all abstracts
    print(type(selected_articles))
    print(selected_articles.to_dict(orient='records'))
    text_to_summarize = " ".join(
        [f"PMID: {article['PMID']}. Authors: {article['Authors']}. Title: {article['Title']}. Abstract: {article['Abstract']}." 
         for article in selected_articles.to_dict(orient='records')]
    )
    # Define the payload
    payload = {
        "inputs": text_to_summarize,
        "parameters": {"max_length": 300}  # Adjust as needed
    }
    # Make the POST request to the Hugging Face API
    response = requests.post(API_URL, headers=headers, json=payload)
    response.raise_for_status()  # Raise an HTTPError if the HTTP request returned an unsuccessful status code
    # The API returns a list of dictionaries. We extract the summary from the first one.
    return response.json()[0]['generated_text']


    

import gradio as gr
from Bio import Entrez

# Always tell NCBI who you are
Entrez.email = "your.email@example.com"


def process_query(keywords, top_k):
    articles = search_pubmed(keywords, top_k)
    # Convert each article from a dictionary to a list of values in the correct order
    articles_for_display = [[article['pmid'], article['authors'], article['title'], article['abstract']] for article in articles]
    return articles_for_display


def summarize_articles(indices, articles_for_display):
    # Convert indices to a list of integers
    selected_indices = [int(index.strip()) for index in indices.split(',') if index.strip().isdigit()]
    # Convert the DataFrame to a list of dictionaries
    articles_list = articles_for_display.to_dict(orient='records')
    # Select articles based on the provided indices
    selected_articles = [articles_list[index] for index in selected_indices]
    # Generate the summary
    summary = summarize_with_huggingface(selected_articles)
    return summary

# Gradio interface
with gr.Blocks() as demo:
    gr.Markdown("### PubMed Article Summarizer")
    model_input = gr.Textbox(label="Enter the model to use", value="h2oai/h2ogpt-4096-llama2-7b-chat")
    query_input = gr.Textbox(label="Query Keywords")
    retmax_input = gr.Slider(minimum=1, maximum=20, value=5, step=1, label="Number of articles")
    search_button = gr.Button("Search")
    output_table = gr.Dataframe(headers=["PMID", "Authors", "Title","Abstract" ])
    summarize_button = gr.Button("Summarize")
    summary_output = gr.Textbox()

    def update_output_table(query, retmax):
        df = search_pubmed(query, retmax)
#        output_table.update(value=df)
        return df
    search_button.click(update_output_table, inputs=[query_input, retmax_input], outputs=output_table)
    summarize_button.click(fn=summarize_with_huggingface, inputs=[model_input, output_table], outputs=summary_output)

demo.launch(debug=True)

if False:
    with gr.Blocks() as demo:
        gr.Markdown("### PubMed Article Summarizer")
        with gr.Row():
            query_input = gr.Textbox(label="Query Keywords")
            top_k_input = gr.Slider(minimum=1, maximum=20, value=5,  step=1, label="Top K Results")
        search_button = gr.Button("Search")
        output_table = gr.Dataframe(headers=["Title", "Authors", "Abstract", "PMID"])
        indices_input = gr.Textbox(label="Enter indices of articles to summarize (comma-separated)")
        summarize_button = gr.Button("Summarize Selected Articles")
        summary_output = gr.Textbox(label="Summary")
    
        search_button.click(
            fn=process_query,
            inputs=[query_input, top_k_input],
            outputs=output_table
        )
    
        summarize_button.click(
            fn=summarize_articles,
            inputs=[indices_input, output_table],
            outputs=summary_output
        )
    
    demo.launch(debug=True)