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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
if start_date is None or end_date is None:
return "Please select both start and end dates.", None, None
# Join MeSH terms for query
query = " AND ".join([f'"{term}"[MeSH Terms]' for term in mesh_terms.split(", ")])
# Format the start and end dates
start_date_str = start_date.strftime("%Y/%m/%d %H:%M:%S")
end_date_str = end_date.strftime("%Y/%m/%d %H:%M:%S")
# 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
# Fetch article details
records = fetch_details(pubmed_ids)
if not records["PubmedArticle"]:
return "No detailed articles found.", None, None
# Compile summaries
markdown_content = compile_summaries(records)
text_content = markdown_content.replace("\n", "\r\n")
# Save files temporarily for download
with open("results.md", "w") as md_file:
md_file.write(markdown_content)
with open("results.txt", "w") as txt_file:
txt_file.write(text_content)
return "Search completed successfully. Download your files below.", "results.md", "results.txt"
# 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)
# Default values for date-time fields
start_date = gr.DateTime(label="Start Date and Time", value=datetime.now())
end_date = gr.DateTime(label="End Date and Time", value=datetime.now())
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_list = terms.split(", ") if terms else []
terms_list.append(term.strip())
return ", ".join(terms_list)
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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