Update app.py

app.py

@@ -24,125 +24,8 @@ def extract_text_from_pdf(pdf_path):
     except Exception as e:
         return f"Error extracting text from PDF: {str(e)}"
 
-# Function to generate PRISMA flow chart SVG
-def generate_prisma_flow_chart(records_db, records_other, duplicates, excluded_screening, excluded_fulltext, included_studies, 
-                              included_meta=None, fulltext_assessed=None):
-    # Calculate values if not provided
-    if fulltext_assessed is None:
-        fulltext_assessed = excluded_fulltext + included_studies
-    
-    records_after_duplicates = records_db + records_other - duplicates
-    
-    # Create SVG content for PRISMA flow chart with improved arrows, spacing, and centered text
-    meta_analysis_section = ''
-    if included_meta is not None:
-        meta_analysis_section = f'''
-        <line x1="400" y1="650" x2="400" y2="690" class="arrow" />
-        <rect x="250" y="690" width="300" height="80" class="box" />
-        <text x="400" y="710" class="box-title">Meta-Analysis</text>
-        <text x="400" y="730">Studies included in quantitative</text>
-        <text x="400" y="750">synthesis (n = {included_meta})</text>
-        '''
-    
-    svg_content = f'''
-    <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 800 900" width="700" height="800">
-        <style>
-            .box {{
-                fill: #f9f9f9;
-                stroke: #333;
-                stroke-width: 2;
-            }}
-            .arrow {{
-                stroke: #333;
-                stroke-width: 2;
-                marker-end: url(#arrowhead);
-            }}
-            text {{
-                font-family: Arial, sans-serif;
-                font-size: 14px;
-                text-anchor: middle;
-                dominant-baseline: middle;
-            }}
-            .box-title {{
-                font-weight: bold;
-                font-size: 16px;
-            }}
-        </style>
-        
-        <defs>
-            <marker id="arrowhead" markerWidth="10" markerHeight="7" refX="9" refY="3.5" orient="auto">
-                <polygon points="0 0, 10 3.5, 0 7" />
-            </marker>
-        </defs>
-        
-        <!-- PRISMA Title -->
-        <text x="400" y="20" style="font-size: 18px; font-weight: bold; text-anchor: middle;">PRISMA Flow Diagram</text>
-        
-        <!-- Identification Section -->
-        <rect x="250" y="60" width="300" height="80" class="box" />
-        <text x="400" y="90" class="box-title">Identification</text>
-        <text x="400" y="110">Records identified through</text>
-        <text x="400" y="125">database searching (n = {records_db})</text>
-        
-        <rect x="550" y="60" width="200" height="80" class="box" />
-        <text x="650" y="90" class="box-title">Additional</text>
-        <text x="650" y="110">Other sources</text>
-        <text x="650" y="125">(n = {records_other})</text>
-        
-        <!-- Arrows -->
-        <line x1="400" y1="140" x2="400" y2="190" class="arrow" />
-        <line x1="650" y1="140" x2="650" y2="165" class="arrow" />
-        <line x1="650" y1="165" x2="400" y2="165" class="arrow" />
-        
-        <!-- Screening Section -->
-        <rect x="250" y="210" width="300" height="80" class="box" />
-        <text x="400" y="240" class="box-title">Screening</text>
-        <text x="400" y="260">Records after duplicates removed</text>
-        <text x="400" y="275">(n = {records_after_duplicates})</text>
-        
-        <line x1="400" y1="290" x2="400" y2="340" class="arrow" />
-        
-        <!-- Title/Abstract Screening Section -->
-        <rect x="250" y="360" width="300" height="80" class="box" />
-        <text x="400" y="390" class="box-title">Title/Abstract Screening</text>
-        <text x="400" y="410">Records screened</text>
-        <text x="400" y="425">(n = {records_after_duplicates})</text>
-        
-        <rect x="550" y="360" width="200" height="80" class="box" />
-        <text x="650" y="390">Records excluded</text>
-        <text x="650" y="410">(n = {excluded_screening})</text>
-        
-        <line x1="400" y1="440" x2="400" y2="490" class="arrow" />
-        <line x1="550" y1="400" x2="600" y2="400" class="arrow" />
-        
-        <!-- Eligibility Section -->
-        <rect x="250" y="510" width="300" height="80" class="box" />
-        <text x="400" y="540" class="box-title">Eligibility</text>
-        <text x="400" y="560">Full-text articles assessed for</text>
-        <text x="400" y="575">eligibility (n = {fulltext_assessed})</text>
-        
-        <rect x="550" y="510" width="200" height="80" class="box" />
-        <text x="650" y="540">Full-text articles excluded,</text>
-        <text x="650" y="555">with reasons (n = {excluded_fulltext})</text>
-        
-        <line x1="400" y1="590" x2="400" y2="640" class="arrow" />
-        <line x1="550" y1="550" x2="600" y2="550" class="arrow" />
-        
-        <!-- Included Section -->
-        <rect x="250" y="660" width="300" height="80" class="box" />
-        <text x="400" y="690" class="box-title">Included</text>
-        <text x="400" y="710">Studies included in qualitative</text>
-        <text x="400" y="725">synthesis (n = {included_studies})</text>
-        
-        <!-- Optional Meta-Analysis Box -->
-        {meta_analysis_section}
-    </svg>
-    '''
-    
-    return svg_content
-
 # Function to interact with OpenAI API for systematic review
-def generate_systematic_review(pdf_files, review_question, prisma_numbers, include_tables=True):
+def generate_systematic_review(pdf_files, review_question, include_tables=True):
     if not api_key:
         return "Please enter your OpenAI API key first."
     
@@ -195,7 +78,6 @@ def generate_systematic_review(pdf_files, review_question, prisma_numbers, inclu
         Include a comprehensive reference list following a specific citation style (APA, Vancouver, etc.). Provide links to source papers when available.
         
         Your response should be formatted in HTML (but avoid showing these tags ```html ```) but generate the content to look like a professional academic paper. Include proper section headers, abstracts, methodology sections, etc. Number all sections like an academic paper. Follow academic journal standards with double spacing, appropriate margins, and consistent formatting throughout.
-        Make sure to include that you conducted a PRISMA flow diagram as part of the methodology section. Reference the PRISMA diagram in your methodology section and explain the numbers used in the diagram.
         """
         
         # Extract text from each PDF
@@ -218,22 +100,8 @@ def generate_systematic_review(pdf_files, review_question, prisma_numbers, inclu
         table_instruction = ""
         if include_tables:
             table_instruction = " Please include important new generated tables in your review."
-        
-        # Add PRISMA flow information
-        prisma_info = f"""
-        Additionally, I have conducted a PRISMA flow diagram with the following data:
-        - Records identified through database searching: {prisma_numbers['records_db']}
-        - Additional records identified through other sources: {prisma_numbers['records_other']}
-        - Records after duplicates removed: {int(prisma_numbers['records_db']) + int(prisma_numbers['records_other']) - int(prisma_numbers['duplicates'])}
-        - Records excluded during title/abstract screening: {prisma_numbers['excluded_screening']}
-        - Full-text articles excluded with reasons: {prisma_numbers['excluded_fulltext']}
-        - Studies included in qualitative synthesis: {prisma_numbers['included_studies']}
-        """
-        
-        if prisma_numbers.get('included_meta') and prisma_numbers['included_meta'].strip():
-            prisma_info += f"- Studies included in quantitative synthesis (meta-analysis): {prisma_numbers['included_meta']}\n"
             
-        user_prompt = f"Please generate a systematic review of the following {len(pdf_files)} papers: {', '.join(pdf_names)}.{table_instruction}\n\nReview Question: {review_question}\n\n{prisma_info}"
+        user_prompt = f"Please generate a systematic review of the following {len(pdf_files)} papers: {', '.join(pdf_names)}.{table_instruction}\n\nReview Question: {review_question}"
         
         # Create the messages for the API call
         messages = [
@@ -253,37 +121,7 @@ def generate_systematic_review(pdf_files, review_question, prisma_numbers, inclu
         # Get the AI response
         review_content = response["choices"][0]["message"]["content"]
         
-        # Generate PRISMA flow chart SVG
-        prisma_svg = generate_prisma_flow_chart(
-            int(prisma_numbers['records_db']),
-            int(prisma_numbers['records_other']),
-            int(prisma_numbers['duplicates']),
-            int(prisma_numbers['excluded_screening']),
-            int(prisma_numbers['excluded_fulltext']),
-            int(prisma_numbers['included_studies']),
-            int(prisma_numbers['included_meta']) if prisma_numbers.get('included_meta') and prisma_numbers['included_meta'].strip() else None
-        )
-        
-        # Find a suitable place to insert the PRISMA flow chart
-        prisma_html = f'''
-        <div class="prisma-flow-chart">
-            <h3>Figure 1: PRISMA Flow Diagram</h3>
-            {prisma_svg}
-        </div>
-        '''
-        
-        if "<h2>3. Methodology" in review_content:
-            parts = review_content.split("<h2>3. Methodology", 1)
-            if len(parts) > 1:
-                next_section = parts[1].find("<h2>")
-                if next_section > -1:
-                    review_content = parts[0] + "<h2>3. Methodology" + parts[1][:next_section] + prisma_html + parts[1][next_section:]
-                else:
-                    review_content = parts[0] + "<h2>3. Methodology" + parts[1] + prisma_html
-        else:
-            insert_pos = review_content.find("<h2>4.") if "<h2>4." in review_content else len(review_content) - 100
-            review_content = review_content[:insert_pos] + prisma_html + review_content[insert_pos:]
-        
+        # Apply professional academic paper styling
         styled_html = f"""
         <!DOCTYPE html>
         <html lang="en">
@@ -292,6 +130,7 @@ def generate_systematic_review(pdf_files, review_question, prisma_numbers, inclu
             <meta name="viewport" content="width=device-width, initial-scale=1.0">
             <title>Systematic Review</title>
             <style>
+                /* Academic Paper Styling */
                 body {{
                     font-family: 'Times New Roman', Times, serif;
                     line-height: 1.6;
@@ -405,13 +244,6 @@ def generate_systematic_review(pdf_files, review_question, prisma_numbers, inclu
                     font-size: 12px;
                     color: #777;
                 }}
-                .prisma-flow-chart {{
-                    margin: 30px 0;
-                    text-align: center;
-                }}
-                .prisma-flow-chart h3 {{
-                    margin-bottom: 15px;
-                }}
                 @media print {{
                     body {{
                         background-color: white;
@@ -449,9 +281,9 @@ def save_uploaded_files(files):
     saved_paths = []
     for file in files:
         if file is not None:
+            # Create a temporary file
             with tempfile.NamedTemporaryFile(delete=False, suffix=".pdf") as tmp_file:
-                with open(file, "rb") as src_file:
-                    tmp_file.write(src_file.read())
+                tmp_file.write(file)
                 saved_paths.append(tmp_file.name)
     
     return saved_paths
@@ -461,9 +293,11 @@ def create_html_download_link(html_content):
     if not html_content or "<div style=\"color: red; padding: 20px;" in html_content or "Please upload at least one PDF file" in html_content:
         return None
     
+    # Create timestamp for the filename
     timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
     filename = f"systematic_review_{timestamp}.html"
     
+    # Encode the HTML content for download
     b64_html = base64.b64encode(html_content.encode()).decode()
     download_link = f'<a href="data:text/html;base64,{b64_html}" download="{filename}" class="download-button">Download HTML</a>'
     
@@ -472,32 +306,39 @@ def create_html_download_link(html_content):
 # Add CSS styling for the Gradio interface
 custom_css = """
 <style>
-    .gradio-container {{
+    /* Main UI */
+    .gradio-container {
         font-family: 'Arial', sans-serif;
         background-color: #f9f9f9;
-    }}
-    h1 {{
+    }
+    
+    /* Header */
+    h1 {
         font-size: 28px;
         color: #333;
         margin-bottom: 20px;
         text-align: center;
         padding-bottom: 10px;
         border-bottom: 2px solid #4a00e0;
-    }}
-    #generate_button {{
+    }
+    
+    /* Primary Button */
+    #generate_button {
         background: linear-gradient(135deg, #4a00e0 0%, #8e2de2 100%);
         color: white;
         font-weight: bold;
         padding: 10px 20px;
         border-radius: 5px;
         transition: all 0.3s ease;
-    }}
-    #generate_button:hover {{
+    }
+    #generate_button:hover {
         background: linear-gradient(135deg, #5b10f1 0%, #9f3ef3 100%);
         transform: translateY(-2px);
         box-shadow: 0 4px 8px rgba(0,0,0,0.1);
-    }}
-    #api_key_button {{
+    }
+    
+    /* API Key Button */
+    #api_key_button {
         background: linear-gradient(135deg, #68d391 0%, #48bb78 100%);
         color: white;
         font-weight: bold;
@@ -505,44 +346,56 @@ custom_css = """
         padding: 10px 20px;
         border-radius: 5px;
         transition: all 0.3s ease;
-    }}
-    #api_key_button:hover {{
+    }
+    #api_key_button:hover {
         background: linear-gradient(135deg, #38a169 0%, #68d391 100%);
         transform: translateY(-2px);
         box-shadow: 0 4px 8px rgba(0,0,0,0.1);
-    }}
-    .input-container {{
+    }
+    
+    /* Form Elements */
+    .input-container {
         background-color: white;
         padding: 20px;
         border-radius: 8px;
         box-shadow: 0 2px 10px rgba(0,0,0,0.05);
         margin-bottom: 20px;
-    }}
-    label {{
+    }
+    
+    /* Labels */
+    label {
         font-weight: 600;
         color: #555;
         margin-bottom: 8px;
-    }}
-    .accordion {{
+    }
+    
+    /* Instructions Accordion */
+    .accordion {
         background-color: white;
         border: 1px solid #e0e0e0;
         border-radius: 8px;
         margin-bottom: 20px;
-    }}
-    .output-container {{
+    }
+    
+    /* Output Container */
+    .output-container {
         background-color: white;
         padding: 15px;
         border-radius: 8px;
         box-shadow: 0 2px 10px rgba(0,0,0,0.05);
-    }}
-    .file-upload {{
+    }
+    
+    /* File Upload Area */
+    .file-upload {
         border: 2px dashed #ccc;
         border-radius: 5px;
         padding: 20px;
         text-align: center;
         margin-bottom: 20px;
-    }}
-    .download-button {{
+    }
+    
+    /* Download Button */
+    .download-button {
         display: inline-block;
         background: linear-gradient(135deg, #4a00e0 0%, #8e2de2 100%);
         color: white;
@@ -552,46 +405,35 @@ custom_css = """
         text-decoration: none;
         margin-bottom: 10px;
         transition: all 0.3s ease;
-    }}
-    .download-button:hover {{
+    }
+    .download-button:hover {
         background: linear-gradient(135deg, #5b10f1 0%, #9f3ef3 100%);
         transform: translateY(-2px);
         box-shadow: 0 4px 8px rgba(0,0,0,0.1);
-    }}
-    #download-container {{
+    }
+    
+    /* Download Container */
+    #download-container {
         display: flex;
         justify-content: center;
         margin: 20px 0;
         padding: 15px;
         background-color: #f5f5f5;
         border-radius: 8px;
-    }}
-    .prisma-section {{
-        background-color: white;
-        padding: 20px;
-        border-radius: 8px;
-        box-shadow: 0 2px 10px rgba(0,0,0,0.05);
-        margin-bottom: 20px;
-    }}
-    .prisma-form {{
-        display: grid;
-        grid-template-columns: 1fr 1fr;
-        gap: 15px;
-    }}
-    @media screen and (max-width: 768px) {{
-        .gradio-container {{
+    }
+    
+    /* Responsive adjustments */
+    @media screen and (max-width: 768px) {
+        .gradio-container {
             padding: 10px;
-        }}
-        .prisma-form {{
-            grid-template-columns: 1fr;
-        }}
-    }}
+        }
+    }
 </style>
 """
 
 # Gradio UI Layout with improved styling
 with gr.Blocks(css=custom_css) as demo:
-    gr.Markdown("# Systematic Review Generator with PRISMA Flow Chart")
+    gr.Markdown("# Systematic Review Generator for Research Papers")
     
     with gr.Accordion("How to Use This App", open=False):
         gr.Markdown(""" 
@@ -599,15 +441,9 @@ with gr.Blocks(css=custom_css) as demo:
         1. Enter your OpenAI API key in the field below and click "Set API Key"
         2. Upload multiple PDF research papers (2 or more recommended)
         3. Enter your review question or topic
-        4. Fill in the PRISMA flow chart information (numbers at each stage of your review)
-        5. Check the "Include Tables" option if you want the review to include comparison tables
-        6. Click "Generate Systematic Review" to start the process
-        7. After generation, you can download the review as HTML
-        
-        ### PRISMA Flow Chart:
-        - The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagram shows the flow of information through the different phases of your systematic review
-        - Fill in the numbers for each stage to generate an accurate diagram
-        - The diagram will be embedded in your systematic review
+        4. Check the "Include Tables" option if you want the review to include comparison tables
+        5. Click "Generate Systematic Review" to start the process
+        6. After generation, you can download the review as HTML
         
         ### Tips for Best Results:
         - Upload papers that are related to the same research topic or field
@@ -629,30 +465,14 @@ with gr.Blocks(css=custom_css) as demo:
     with gr.Row(elem_classes="input-container"):
         with gr.Column():
             gr.Markdown("### Upload Research Papers")
-            pdf_files = gr.File(label="Upload PDF Research Papers", file_count="multiple", file_types=[".pdf"], elem_classes="file-upload")
+            pdf_files = gr.File(label="Upload PDF Research Papers", file_count="multiple", type="binary", elem_classes="file-upload")
             review_question = gr.Textbox(
                 label="Review Question or Topic", 
                 value="Please generate a systematic review of the following papers.",
                 placeholder="e.g., What are the effects of mindfulness meditation on stress reduction?"
             )
             include_tables = gr.Checkbox(label="Include Comparison Tables", value=True)
-    
-    # PRISMA Flow Chart inputs
-    with gr.Row(elem_classes="prisma-section"):
-        with gr.Column():
-            gr.Markdown("### PRISMA Flow Chart Information")
-            gr.Markdown("Enter the numbers for each stage of your systematic review process:")
-            
-            with gr.Row(elem_classes="prisma-form"):
-                prisma_records_db = gr.Textbox(label="Records from database searching", value="100", placeholder="e.g., 100")
-                prisma_records_other = gr.Textbox(label="Records from other sources", value="20", placeholder="e.g., 20")
-                prisma_duplicates = gr.Textbox(label="Duplicates removed", value="15", placeholder="e.g., 15")
-                prisma_excluded_screening = gr.Textbox(label="Records excluded at screening", value="60", placeholder="e.g., 60")
-                prisma_excluded_fulltext = gr.Textbox(label="Full-text articles excluded", value="30", placeholder="e.g., 30")
-                prisma_included_studies = gr.Textbox(label="Studies included in synthesis", value="15", placeholder="e.g., 15")
-                prisma_included_meta = gr.Textbox(label="Studies in meta-analysis (optional)", value="10", placeholder="e.g., 10")
-                
-            generate_button = gr.Button("Generate Systematic Review", elem_id="generate_button")
+            generate_button = gr.Button("Generate Systematic Review", elem_id="generate_button", size="large")
     
     # Download link container
     download_html_output = gr.HTML(label="Download Options")
@@ -665,10 +485,7 @@ with gr.Blocks(css=custom_css) as demo:
     api_key_button.click(set_api_key, inputs=[api_key_input], outputs=[api_key_output])
     
     # Generate systematic review
-    def process_files_and_generate_review(files, question, include_tables, 
-                                           records_db, records_other, duplicates, 
-                                           excluded_screening, excluded_fulltext, 
-                                           included_studies, included_meta):
+    def process_files_and_generate_review(files, question, include_tables):
         if not files:
             return ("""
             <div style="padding: 20px; border: 1px solid #e0e0e0; border-radius: 5px; background-color: #f9f9f9;">
@@ -683,35 +500,24 @@ with gr.Blocks(css=custom_css) as demo:
         # Show loading message
         loading_message = """
         <div style="padding: 20px; text-align: center;">
-            <h3>Generating Systematic Review with PRISMA Flow Chart...</h3>
+            <h3>Generating Systematic Review...</h3>
             <p>This may take a few minutes depending on the number and size of papers.</p>
             <div style="width: 100%; height: 4px; background-color: #f0f0f0; margin: 20px 0; border-radius: 2px; overflow: hidden;">
                 <div style="width: 30%; height: 100%; background: linear-gradient(90deg, #4a00e0, #8e2de2); animation: progress 2s infinite linear;"></div>
             </div>
             <style>
-                @keyframes progress {{
-                    0% {{ margin-left: -30%; }}
-                    100% {{ margin-left: 100%; }}
-                }}
+                @keyframes progress {
+                    0% { margin-left: -30%; }
+                    100% { margin-left: 100%; }
+                }
             </style>
         </div>
         """
         
         yield loading_message, ""
         
-        # Collect PRISMA flow chart data
-        prisma_numbers = {
-            'records_db': records_db,
-            'records_other': records_other,
-            'duplicates': duplicates,
-            'excluded_screening': excluded_screening,
-            'excluded_fulltext': excluded_fulltext,
-            'included_studies': included_studies,
-            'included_meta': included_meta
-        }
-        
-        # Generate review with PRISMA flow chart
-        review = generate_systematic_review(saved_paths, question, prisma_numbers, include_tables)
+        # Generate review
+        review = generate_systematic_review(saved_paths, question, include_tables)
         
         # Create HTML download link
         html_link = create_html_download_link(review)
@@ -737,13 +543,10 @@ with gr.Blocks(css=custom_css) as demo:
     
     generate_button.click(
         process_files_and_generate_review, 
-        inputs=[pdf_files, review_question, include_tables, 
-                prisma_records_db, prisma_records_other, prisma_duplicates, 
-                prisma_excluded_screening, prisma_excluded_fulltext, 
-                prisma_included_studies, prisma_included_meta], 
+        inputs=[pdf_files, review_question, include_tables], 
         outputs=[review_output, download_html_output]
     )
 
 # Launch the app
 if __name__ == "__main__":
-    demo.launch()
+    demo.launch(share=True)