Create app.py

app.py

@@ -0,0 +1,102 @@
+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
+    
+    # Join MeSH terms for query
+    query = " AND ".join([f'"{term}"[MeSH Terms]' for term in mesh_terms])
+    
+    # Fetch PubMed IDs
+    pubmed_ids = fetch_pubmed(query, email, start_date, end_date)
+    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)
+    
+    start_date = gr.Date(label="Start Date")
+    end_date = gr.Date(label="End Date")
+    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()