Update app.py

app.py

@@ -24,6 +24,112 @@ 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 HTML
+def generate_prisma_flow_chart():
+    # Placeholder values for the PRISMA flow chart (as per the provided image)
+    records_db = 0  # Records from databases
+    records_other = 0  # Records from other sources
+    duplicates_removed = 0  # After duplicates removed
+    records_screened = 0  # Records screened
+    records_excluded_screening = 0  # Records excluded during screening
+    reports_sought = 0  # Reports sought for retrieval
+    reports_not_retrieved = 0  # Reports not retrieved
+    reports_assessed = 0  # Reports assessed for eligibility
+    reports_excluded_eligibility = 0  # Reports excluded during eligibility
+    studies_included = 0  # Studies included in review
+
+    # HTML and CSS for PRISMA flow chart
+    prisma_html = f"""
+    <div class="prisma-flowchart" style="margin: 40px 0; font-family: 'Times New Roman', Times, serif; font-size: 14px;">
+        <h3 style="text-align: center; margin-bottom: 20px;">PRISMA Flow Diagram</h3>
+        <div style="display: flex; justify-content: space-between;">
+            <!-- Left Side: Database Search -->
+            <div style="width: 45%;">
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Identification of new studies via databases and registers<br>
+                    Records identified from:<br>
+                    Databases (n = {records_db})<br>
+                    Registers (n = 0)
+                </div>
+                <div style="text-align: center; margin: 10px 0;">↓</div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Records removed before screening:<br>
+                    Duplicate records (n = 0)<br>
+                    Records marked as ineligible by automation tools (n = 0)<br>
+                    Records removed for other reasons (n = 0)
+                </div>
+                <div style="text-align: center; margin: 10px 0;">↓</div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Records screened (n = {records_screened})
+                </div>
+                <div style="display: flex; justify-content: space-between; align-items: center;">
+                    <div style="width: 50%; text-align: center; margin: 10px 0;">↓</div>
+                    <div style="width: 50%; background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                        Records excluded (n = {records_excluded_screening})
+                    </div>
+                </div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Reports sought for retrieval (n = {reports_sought})
+                </div>
+                <div style="display: flex; justify-content: space-between; align-items: center;">
+                    <div style="width: 50%; text-align: center; margin: 10px 0;">↓</div>
+                    <div style="width: 50%; background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                        Reports not retrieved (n = {reports_not_retrieved})
+                    </div>
+                </div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Reports assessed for eligibility (n = {reports_assessed})
+                </div>
+                <div style="display: flex; justify-content: space-between; align-items: center;">
+                    <div style="width: 50%; text-align: center; margin: 10px 0;">↓</div>
+                    <div style="width: 50%; background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                        Reports excluded:<br>
+                        Reason 1 (n = NA)<br>
+                        Reason 2 (n = NA)
+                    </div>
+                </div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    New studies included in review (n = {studies_included})<br>
+                    Reports of new studies (n = 0)
+                </div>
+            </div>
+
+            <!-- Right Side: Other Methods -->
+            <div style="width: 45%;">
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Identification of new studies via other methods<br>
+                    Records identified from:<br>
+                    Websites (n = 0)<br>
+                    Organisations (n = 0)<br>
+                    Citation searching (n = 0)
+                </div>
+                <div style="text-align: center; margin: 10px 0;">↓</div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Reports sought for retrieval (n = {reports_sought})
+                </div>
+                <div style="display: flex; justify-content: space-between; align-items: center;">
+                    <div style="width: 50%; text-align: center; margin: 10px 0;">↓</div>
+                    <div style="width: 50%; background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                        Reports not retrieved (n = {reports_not_retrieved})
+                    </div>
+                </div>
+                <div style="background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                    Reports assessed for eligibility (n = {reports_assessed})
+                </div>
+                <div style="display: flex; justify-content: space-between; align-items: center;">
+                    <div style="width: 50%; text-align: center; margin: 10px 0;">↓</div>
+                    <div style="width: 50%; background-color: #f0f0f0; padding: 10px; border: 1px solid #ccc; text-align: center;">
+                        Reports excluded:<br>
+                        Reason 1 (n = NA)<br>
+                        Reason 2 (n = NA)
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+    """
+    return prisma_html
+
 # Function to interact with OpenAI API for systematic review
 def generate_systematic_review(pdf_files, review_question, include_tables=True):
     if not api_key:
@@ -39,7 +145,7 @@ def generate_systematic_review(pdf_files, review_question, include_tables=True):
         openai.api_key = api_key
         
         # Create the system message with systematic review guidelines
-        system_prompt = """You are an expert academic assistant. Create a systematic review using academic research paper formatting. The Systematic Review must be in great details. Structure it using these steps:
+        system_prompt = """You are an expert academic assistant. Create a systematic review using academic research paper formatting. The Systematic Review must be in great detail. Structure it using these steps:
         
         Step 1: Identify a Research Field
         The first step in writing a systematic review paper is to identify a research field. This involves selecting a specific area of study that you are interested in and want to explore further.
@@ -121,6 +227,15 @@ def generate_systematic_review(pdf_files, review_question, include_tables=True):
         # Get the AI response
         review_content = response["choices"][0]["message"]["content"]
         
+        # Generate PRISMA flow chart
+        prisma_flow_chart = generate_prisma_flow_chart()
+        
+        # Insert PRISMA flow chart into the review content (after the methodology section, assuming section 3 is methodology)
+        review_content = review_content.replace(
+            '<h2>4. Results</h2>',
+            '<h2>4. Results</h2>\n' + prisma_flow_chart
+        )
+        
         # Apply professional academic paper styling
         styled_html = f"""
         <!DOCTYPE html>
@@ -449,6 +564,7 @@ with gr.Blocks(css=custom_css) as demo:
         - Upload papers that are related to the same research topic or field
         - Be specific in your review question to get more focused results
         - The generated review will follow a systematic structure including research field identification, data extraction, analysis, and conclusions
+        - A PRISMA flow chart will be included in the review to visualize the study selection process
         - The more papers you upload, the more comprehensive the review will be
         - The review will be formatted as a professional academic paper with proper sections and citations
         """)