Update app.py

app.py

@@ -43,9 +43,18 @@ def pubmed_search(mesh_terms, email, start_date, end_date):
         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")
-    
+    try:
+        # If start_date and end_date are strings, parse them first
+        if isinstance(start_date, str):
+            start_date = datetime.strptime(start_date, "%Y-%m-%d")
+        if isinstance(end_date, str):
+            end_date = datetime.strptime(end_date, "%Y-%m-%d")
+        
+        start_date_str = start_date.strftime("%Y-%m-%d")
+        end_date_str = end_date.strftime("%Y-%m-%d")
+    except ValueError as e:
+        return f"Error processing dates: {str(e)}", None, None
+
     # Join MeSH terms for query
     query = " AND ".join([f'"{term}"[MeSH Terms]' for term in mesh_terms.split(",")])
     
@@ -53,39 +62,84 @@ def pubmed_search(mesh_terms, email, start_date, end_date):
     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)
+
+    # Fetch article details
+    try:
+        records = fetch_details(pubmed_ids)
+    except Exception as e:
+        return f"Error fetching article details: {str(e)}", None, None
+
+    # Compile markdown content
+    markdown_content = compile_summaries(records)
+
+    # Create temporary files
+    timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+    markdown_filename = f"pubmed_results_{timestamp}.md"
+    text_filename = f"pubmed_results_{timestamp}.txt"
+
+    # Save files
+    try:
+        with open(markdown_filename, "w", encoding="utf-8") as f:
+            f.write(markdown_content)
+        with open(text_filename, "w", encoding="utf-8") as f:
+            f.write(markdown_content)
+    except Exception as e:
+        return f"Error saving files: {str(e)}", None, None
+
+    return "Search completed successfully!", markdown_filename, text_filename
+
+# 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
 
 # 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)
+        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)
+        mesh_terms_box = gr.Textbox(
+            label="Added MeSH Terms",
+            interactive=False,
+            lines=2
+        )
     
-    start_date = gr.DateTime(label="Start Date", value="2025-01-01")
-    end_date = gr.DateTime(label="End Date", value="2025-01-07")
-    email_input = gr.Textbox(label="Email", placeholder="Your email (required by PubMed API)", interactive=True)
+    with gr.Row():
+        start_date = gr.Date(label="Start Date", value="2025-01-01")  # Changed from DateTime to Date
+        end_date = gr.Date(label="End Date", value="2025-01-07")      # Changed from DateTime to 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])
+    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()
+app.launch()