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import gradio as gr
from Bio import Entrez
from datetime import datetime
import os
# Function to fetch PubMed articles
def fetch_pubmed(query, email, start_date, end_date, max_results=100):
Entrez.email = email
handle = Entrez.esearch(
db="pubmed",
term=query,
retmax=max_results,
sort="pub_date",
mindate=start_date,
maxdate=end_date,
datetype="pdat"
)
results = Entrez.read(handle)
handle.close()
ids = results["IdList"]
return ids
# Function to fetch article details
def fetch_details(pubmed_ids):
handle = Entrez.efetch(db="pubmed", id=",".join(pubmed_ids), retmode="xml")
records = Entrez.read(handle)
handle.close()
return records
# Function to compile Markdown content
def compile_summaries(records):
content = "# PubMed Search Results\n\n"
for record in records["PubmedArticle"]:
title = record["MedlineCitation"]["Article"]["ArticleTitle"]
abstract = record["MedlineCitation"]["Article"].get("Abstract", {}).get("AbstractText", ["No abstract available."])[0]
url = f'https://pubmed.ncbi.nlm.nih.gov/{record["MedlineCitation"]["PMID"]}/'
content += f"## [{title}]({url})\n\n{abstract}\n\n"
return content
# Main function for the Gradio interface
def pubmed_search(mesh_terms, email, start_date, end_date):
if not mesh_terms or not email:
return "Please provide MeSH terms and email.", None, None
# Convert date objects to string format
start_date_str = start_date.strftime("%Y-%m-%d")
end_date_str = end_date.strftime("%Y-%m-%d")
# Join MeSH terms for query
query = " AND ".join([f'"{term}"[MeSH Terms]' for term in mesh_terms.split(",")])
# Fetch PubMed IDs
pubmed_ids = fetch_pubmed(query, email, start_date_str, end_date_str)
if not pubmed_ids:
return "No articles found for the given search terms and date range.", None, None
# (Keep the rest of the function unchanged)
# Gradio interface components
with gr.Blocks() as app:
gr.Markdown("# PubMed Search Tool for Thyroid AI Research")
with gr.Row():
mesh_term_input = gr.Textbox(label="Enter a MeSH Term", placeholder="e.g., thyroid", interactive=True)
add_button = gr.Button("Add MeSH Term")
mesh_terms_box = gr.Textbox(label="Added MeSH Terms", interactive=False, lines=2)
start_date = gr.Date(label="Start Date", value="2025-01-01")
end_date = gr.Date(label="End Date", value="2025-01-07")
email_input = gr.Textbox(label="Email", placeholder="Your email (required by PubMed API)", interactive=True)
search_button = gr.Button("Search PubMed")
status_output = gr.Textbox(label="Status")
markdown_file = gr.File(label="Markdown File", interactive=False)
text_file = gr.File(label="Text File", interactive=False)
# Logic for adding MeSH terms
def add_mesh_term(term, terms):
if term.strip():
terms = terms.split(",") if terms else []
terms.append(term.strip())
return ", ".join(terms)
return terms
# Bind functions to interface
add_button.click(fn=add_mesh_term, inputs=[mesh_term_input, mesh_terms_box], outputs=mesh_terms_box)
search_button.click(fn=pubmed_search, inputs=[mesh_terms_box, email_input, start_date, end_date], outputs=[status_output, markdown_file, text_file])
# Launch app
app.launch()
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