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Delete gradiopubmedapp2.py
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gradiopubmedapp2.py
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import gradio as gr
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import requests
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import pandas as pd
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import io
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from docx import Document
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import tempfile
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API_BASE_URL = "https://pubmed-api-jwfq.onrender.com/search_pubmed"
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global_df = None # Global variable to store search results for export
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def fetch_pubmed_articles(query, max_results=10, page=1, sort_by="Year", filter_journal="All", min_year=None, max_year=None):
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"""
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Fetches PubMed articles and applies sorting and filtering.
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"""
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try:
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url = f"{API_BASE_URL}?query={query}&max_results={max_results}&page={page}"
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response = requests.get(url)
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if response.status_code != 200:
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return f"β οΈ API Error: {response.status_code} - {response.text}", None
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articles = response.json()
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if not articles:
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return "No articles found for this query.", None
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for article in articles:
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try:
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article["Year"] = int(article["Year"])
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except:
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article["Year"] = 0
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# Apply journal filtering
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if filter_journal and filter_journal != "All":
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articles = [a for a in articles if filter_journal.lower() in a['Journal'].lower()]
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# Apply year filtering
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if min_year:
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articles = [a for a in articles if a["Year"] >= int(min_year)]
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if max_year:
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articles = [a for a in articles if a["Year"] <= int(max_year)]
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# Apply sorting
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if sort_by == "Year":
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articles.sort(key=lambda x: x["Year"], reverse=True)
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elif sort_by == "Title":
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articles.sort(key=lambda x: x["Title"])
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elif sort_by == "Journal":
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articles.sort(key=lambda x: x["Journal"])
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# Format results
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formatted_results = []
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for article in articles:
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formatted_results.append(
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f"## π° {article['Title']}\n"
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f"π **<span style='color:blue'>{article['Journal']}</span>** ({article['Year']})\n"
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f"π¨βπ¬ **<span style='color:gray'>{article['Authors']}</span>**\n"
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f"π [Read on PubMed]({article['PubMed_URL']})\n\n"
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f"<details><summary>π **Show Abstract**</summary>\n{article['Abstract']}\n</details>"
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f"\n---\n"
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)
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df = pd.DataFrame(articles)
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return "\n\n".join(formatted_results), df
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except Exception as e:
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return f"β οΈ Error fetching data: {str(e)}", None
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def export_results(df, format_type):
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"""
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Exports search results as a CSV or DOCX file.
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- Returns the file path instead of BytesIO to avoid TypeError in Gradio.
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"""
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if df is None or df.empty:
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return None
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temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=f".{format_type.lower()}")
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temp_file_path = temp_file.name # Store the temporary file path
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if format_type == "CSV":
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df.to_csv(temp_file_path, index=False)
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elif format_type == "DOCX":
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doc = Document()
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doc.add_heading("PubMed Search Results", level=1)
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for _, row in df.iterrows():
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doc.add_heading(row["Title"], level=2)
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doc.add_paragraph(f"π Journal: {row['Journal']} ({row['Year']})")
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doc.add_paragraph(f"π¨βπ¬ Authors: {row['Authors']}")
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doc.add_paragraph(f"π Link: {row['PubMed_URL']}")
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doc.add_paragraph(f"π Abstract: {row['Abstract']}")
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doc.add_paragraph("---")
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doc.save(temp_file_path)
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temp_file.close() # Close the file before returning the path
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return temp_file_path # Return file path instead of BytesIO
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with gr.Blocks() as app:
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gr.Markdown("""
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# π **PubMed Search Tool with Advanced Features**
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## π **How to Use This App**
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1οΈβ£ **Enter a Search Query** *(e.g., "Deep Learning in Psychiatry")*
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2οΈβ£ **Set the Number of Results & Page Number** *(Default: 10 results per page)*
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3οΈβ£ **Choose Sorting Option** *(Year, Title, or Journal - Default: Year)*
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4οΈβ£ **(Optional) Filter by Journal Name** *(e.g., "Nature", "JAMA")*
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5οΈβ£ **(Optional) Filter by Year Range** *(Set min & max year, e.g., 2015 - 2023)*
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6οΈβ£ **Click "π Search" to fetch results**
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7οΈβ£ **Click "π Export as CSV" or "π Export as Word DOCX" to save articles**
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8οΈβ£ **Click "π Show Abstract" under each result to expand full abstract**
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## β οΈ **Important Notes**
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- **Sorting & Filtering can be combined** *(e.g., show only "Nature" articles from 2020-2024, sorted by Title)*
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""")
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with gr.Row():
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query_input = gr.Textbox(label="π Search Query", placeholder="Enter topic (e.g., 'Neural Networks in Psychiatry')", lines=1)
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with gr.Row():
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max_results_input = gr.Slider(1, 50, value=10, step=1, label="π Number of Results per Page")
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page_input = gr.Slider(1, 200, value=1, step=1, label="π Page Number")
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with gr.Row():
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sort_input = gr.Dropdown(choices=["Year", "Title", "Journal"], value="Year", label="π Sort By")
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journal_filter_input = gr.Textbox(label="π― Filter by Journal (Optional)", placeholder="Enter journal name or leave blank")
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with gr.Row():
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min_year_input = gr.Number(label="π
Min Year", value=None)
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max_year_input = gr.Number(label="π
Max Year", value=None)
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with gr.Row():
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search_button = gr.Button("π Search")
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export_csv_button = gr.Button("π Export as CSV")
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export_docx_button = gr.Button("π Export as Word DOCX")
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results_output = gr.HTML()
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export_csv_output = gr.File(label="Download CSV")
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export_docx_output = gr.File(label="Download Word DOCX")
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def search_and_display(query, max_results, page, sort_by, journal_filter, min_year, max_year):
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global global_df
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result_text, df = fetch_pubmed_articles(query, max_results, page, sort_by, journal_filter, min_year, max_year)
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global_df = df
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return result_text
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def export_csv():
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if global_df is not None:
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return export_results(global_df, "CSV")
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def export_docx():
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if global_df is not None:
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return export_results(global_df, "DOCX")
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search_button.click(search_and_display,
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inputs=[query_input, max_results_input, page_input, sort_input, journal_filter_input, min_year_input, max_year_input],
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outputs=results_output)
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export_csv_button.click(export_csv, outputs=export_csv_output)
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export_docx_button.click(export_docx, outputs=export_docx_output)
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if __name__ == "__main__":
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app.launch(inbrowser=True)
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