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| import gradio as gr | |
| import requests | |
| import pandas as pd | |
| import io | |
| from docx import Document | |
| import tempfile | |
| import os | |
| os.system("pip install python-docx") | |
| API_BASE_URL = "https://pubmed-api-jwfq.onrender.com/search_pubmed" | |
| global_df = None # Global variable to store search results for export | |
| def fetch_pubmed_articles(query, max_results=10, page=1, sort_by="Year", filter_journal="All", min_year=None, max_year=None): | |
| """ | |
| Fetches PubMed articles and applies sorting and filtering. | |
| """ | |
| try: | |
| url = f"{API_BASE_URL}?query={query}&max_results={max_results}&page={page}" | |
| response = requests.get(url) | |
| if response.status_code != 200: | |
| return f"⚠️ API Error: {response.status_code} - {response.text}", None | |
| articles = response.json() | |
| if not articles: | |
| return "No articles found for this query.", None | |
| for article in articles: | |
| try: | |
| article["Year"] = int(article["Year"]) | |
| except: | |
| article["Year"] = 0 | |
| # Apply journal filtering | |
| if filter_journal and filter_journal != "All": | |
| articles = [a for a in articles if filter_journal.lower() in a['Journal'].lower()] | |
| # Apply year filtering | |
| if min_year: | |
| articles = [a for a in articles if a["Year"] >= int(min_year)] | |
| if max_year: | |
| articles = [a for a in articles if a["Year"] <= int(max_year)] | |
| # Apply sorting | |
| if sort_by == "Year": | |
| articles.sort(key=lambda x: x["Year"], reverse=True) | |
| elif sort_by == "Title": | |
| articles.sort(key=lambda x: x["Title"]) | |
| elif sort_by == "Journal": | |
| articles.sort(key=lambda x: x["Journal"]) | |
| # Format results | |
| formatted_results = [] | |
| for article in articles: | |
| formatted_results.append( | |
| f"## 📰 {article['Title']}\n" | |
| f"📖 **<span style='color:blue'>{article['Journal']}</span>** ({article['Year']})\n" | |
| f"👨🔬 **<span style='color:gray'>{article['Authors']}</span>**\n" | |
| f"🔗 [Read on PubMed]({article['PubMed_URL']})\n\n" | |
| f"<details><summary>📄 **Show Abstract**</summary>\n{article['Abstract']}\n</details>" | |
| f"\n---\n" | |
| ) | |
| df = pd.DataFrame(articles) | |
| return "\n\n".join(formatted_results), df | |
| except Exception as e: | |
| return f"⚠️ Error fetching data: {str(e)}", None | |
| def export_results(df, format_type): | |
| """ | |
| Exports search results as a CSV or DOCX file. | |
| - Returns the file path instead of BytesIO to avoid TypeError in Gradio. | |
| """ | |
| if df is None or df.empty: | |
| return None | |
| temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=f".{format_type.lower()}") | |
| temp_file_path = temp_file.name # Store the temporary file path | |
| if format_type == "CSV": | |
| df.to_csv(temp_file_path, index=False) | |
| elif format_type == "DOCX": | |
| doc = Document() | |
| doc.add_heading("PubMed Search Results", level=1) | |
| for _, row in df.iterrows(): | |
| doc.add_heading(row["Title"], level=2) | |
| doc.add_paragraph(f"📖 Journal: {row['Journal']} ({row['Year']})") | |
| doc.add_paragraph(f"👨🔬 Authors: {row['Authors']}") | |
| doc.add_paragraph(f"🔗 Link: {row['PubMed_URL']}") | |
| doc.add_paragraph(f"📄 Abstract: {row['Abstract']}") | |
| doc.add_paragraph("---") | |
| doc.save(temp_file_path) | |
| temp_file.close() # Close the file before returning the path | |
| return temp_file_path # Return file path instead of BytesIO | |
| with gr.Blocks() as app: | |
| gr.Markdown(""" | |
| # 🔍 **PubMed Search Tool with Advanced Features** | |
| ## 📖 **How to Use This App** | |
| 1️⃣ **Enter a Search Query** *(e.g., "Deep Learning in Psychiatry")* | |
| 2️⃣ **Set the Number of Results & Page Number** *(Default: 10 results per page)* | |
| 3️⃣ **Choose Sorting Option** *(Year, Title, or Journal - Default: Year)* | |
| 4️⃣ **(Optional) Filter by Journal Name** *(e.g., "Nature", "JAMA")* | |
| 5️⃣ **(Optional) Filter by Year Range** *(Set min & max year, e.g., 2015 - 2023)* | |
| 6️⃣ **Click "🔍 Search" to fetch results** | |
| 7️⃣ **Click "📂 Export as CSV" or "📄 Export as Word DOCX" to save articles** | |
| 8️⃣ **Click "📄 Show Abstract" under each result to expand full abstract** | |
| ## ⚠️ **Important Notes** | |
| - **Sorting & Filtering can be combined** *(e.g., show only "Nature" articles from 2020-2024, sorted by Title)* | |
| """) | |
| with gr.Row(): | |
| query_input = gr.Textbox(label="🔎 Search Query", placeholder="Enter topic (e.g., 'Neural Networks in Psychiatry')", lines=1) | |
| with gr.Row(): | |
| max_results_input = gr.Slider(1, 50, value=10, step=1, label="📄 Number of Results per Page") | |
| page_input = gr.Slider(1, 200, value=1, step=1, label="📄 Page Number") | |
| with gr.Row(): | |
| sort_input = gr.Dropdown(choices=["Year", "Title", "Journal"], value="Year", label="🔄 Sort By") | |
| journal_filter_input = gr.Textbox(label="🎯 Filter by Journal (Optional)", placeholder="Enter journal name or leave blank") | |
| with gr.Row(): | |
| min_year_input = gr.Number(label="📅 Min Year", value=None) | |
| max_year_input = gr.Number(label="📅 Max Year", value=None) | |
| with gr.Row(): | |
| search_button = gr.Button("🔍 Search") | |
| export_csv_button = gr.Button("📂 Export as CSV") | |
| export_docx_button = gr.Button("📄 Export as Word DOCX") | |
| results_output = gr.HTML() | |
| export_csv_output = gr.File(label="Download CSV") | |
| export_docx_output = gr.File(label="Download Word DOCX") | |
| def search_and_display(query, max_results, page, sort_by, journal_filter, min_year, max_year): | |
| global global_df | |
| result_text, df = fetch_pubmed_articles(query, max_results, page, sort_by, journal_filter, min_year, max_year) | |
| global_df = df | |
| return result_text | |
| def export_csv(): | |
| if global_df is not None: | |
| return export_results(global_df, "CSV") | |
| def export_docx(): | |
| if global_df is not None: | |
| return export_results(global_df, "DOCX") | |
| search_button.click(search_and_display, | |
| inputs=[query_input, max_results_input, page_input, sort_input, journal_filter_input, min_year_input, max_year_input], | |
| outputs=results_output) | |
| export_csv_button.click(export_csv, outputs=export_csv_output) | |
| export_docx_button.click(export_docx, outputs=export_docx_output) | |
| if __name__ == "__main__": | |
| app.launch(inbrowser=True) | |