Upload 3 files

app.py

@@ -1,27 +1,15 @@
-import os
 import sys
-from generate_markdown import load_llm_model, generate_markdown, sanitize_markdown
 from generate_mindmap import generate_mindmap
 import gradio as gr
 import subprocess
 
-def generate(file):
-    print(f"Generating mindmap for {file.name}")
-    unformatted_markdown = True
-    summary = "This is a summary of the research paper"
-    mindmap_markdown = generate_markdown(llm, file)
-    print('mindmap_markdown:', mindmap_markdown)
-    
-    while unformatted_markdown:
-        if mindmap_markdown.startswith("#") and '-' in mindmap_markdown:
-            unformatted_markdown = False
-            mindmap_svg, mindmap_pdf = generate_mindmap(mindmap_markdown)
-        else:
-            unformatted_markdown = True
-            mindmap_markdown = sanitize_markdown(llm, mindmap_markdown)
-    
-    print("Mindmap generated successfully")
-    return summary, mindmap_markdown, mindmap_svg, mindmap_svg, mindmap_pdf, mindmap_pdf
+def generate(mindmap_markdown):
+    mindmap_svg, mindmap_pdf = generate_mindmap(mindmap_markdown)
+    with open(mindmap_svg, 'wb') as f:
+        svg_mindmap = f.read()
+    with open(mindmap_pdf, 'wb') as f:
+        pdf_mindmap = f.read
+    return svg_mindmap, pdf_mindmap
 
 theme = gr.themes.Soft(
     primary_hue="purple",
@@ -32,47 +20,15 @@ theme = gr.themes.Soft(
 
 with gr.Blocks(theme=theme, title="Binary Biology") as app:
     with gr.Row():
-        file = gr.File(file_count='single', label='Upload Research Paper PDF file', file_types=['.pdf'])
         with gr.Column():
-            submit = gr.Button(value='Submit')
-            clear = gr.ClearButton(value='Clear')
-    
-    with gr.Row():
-        summary = gr.TextArea(label='Summary', lines=5, interactive=False, show_copy_button=True)
-        markdown_mindmap = gr.Textbox(label='Mindmap', lines=5, interactive=False, show_copy_button=True)
-    
-    with gr.Row():
-        with gr.Column():
-            svg_mindmap = gr.File(label='Graphical SVG Mindmap', interactive=False)
-            download_svg_mindmap = gr.File(label='Download SVG Mindmap', interactive=False)
-        
+            mindmap_markdown = gr.Textbox(label="Mindmap Markdown", placeholder="Enter the markdown for the mindmap", lines=10)
+            generate_mindmap = gr.Button(value="Generate Mindmap")
         with gr.Column():
-            pdf_mindmap = gr.File(label='Graphical PDF Mindmap', interactive=False)
-            download_pdf_mindmap = gr.File(label='Download PDF Mindmap', interactive=False)
-
-    submit.click(
-        generate,
-        inputs=[file],
-        outputs=[summary, markdown_mindmap, svg_mindmap, download_svg_mindmap, pdf_mindmap, download_pdf_mindmap],
-        scroll_to_output=True,
-        show_progress='minimal',
-        queue=True,
-    )
-    
-    clear.click(
-        lambda: (None, None, None, None, None, None),
-        inputs=[file],
-        outputs=[summary, markdown_mindmap, svg_mindmap, download_svg_mindmap, pdf_mindmap, download_pdf_mindmap]
-    )
+            svg_mindmap = gr.TextArea(label="SVG Mindmap", placeholder="The SVG representation of the mindmap", lines=10, readonly=True)
+            pdf_mindmap = gr.TextArea(label="PDF Mindmap", placeholder="The PDF representation of the mindmap", lines=10, readonly=True)
+    generate_mindmap.click(generate, inputs=[mindmap_markdown], outputs=[svg_mindmap, pdf_mindmap])
 
 if __name__ == "__main__":
-    try:
-        env = os.environ.copy()
-        env["CMAKE_ARGS"] = "-DGGML_BLAS=ON -DGGML_BLAS_VENDOR=OpenBLAS"
-        subprocess.run(["pip", "install", "llama-cpp-python"], env=env)
-    except Exception as e:
-        print(f"Failed to install llama-cpp-python: {e}")
-    
     try:
         subprocess.run(['apt', 'install', '-y', 'graphviz'])
         print("Graphviz installed successfully")
@@ -83,8 +39,5 @@ if __name__ == "__main__":
         except:
             print("Graphviz installation failed")
             sys.exit(1)
-    
     print("Graphviz loaded successfully")
-    llm = load_llm_model()
-    print("Model loaded successfully")
-    app.queue(default_concurrency_limit=1).launch(show_error=True)
+    app.queue(default_concurrency_limit=25).launch(show_error=True)

generate_mindmap.py

@@ -30,64 +30,48 @@ generated_colors = set()
 def generate_random_color():
     """Generate a random color that hasn't been generated before."""
     while True:
-        # Generate a random color in hex format
         color = "#{:02x}{:02x}{:02x}".format(random.randint(128, 255), random.randint(128, 255), random.randint(128, 255))
-        # If the color is not in the set, it's unique
         if color not in generated_colors:
-            generated_colors.add(color)  # Add the color to the set of generated colors
-            return color  # Return the unique color
+            generated_colors.add(color)
+            return color
         else:
-            continue  # Try again
+            continue
 
 def brighten_color(color, factor=0.15):
     """Brighten the color by a certain factor (default 10%)"""
-    # Remove the '#' symbol
     color = color.lstrip('#')
-    
-    # Convert hex to RGB
     r, g, b = [int(color[i:i+2], 16) for i in (0, 2, 4)]
-    
-    # Increase each component by the factor, but clamp to 255
     r = min(255, int(r * (1 + factor)))
     g = min(255, int(g * (1 + factor)))
     b = min(255, int(b * (1 + factor)))
-    
-    # Convert back to hex
     return "#{:02x}{:02x}{:02x}".format(r, g, b)
 
 def add_nodes_to_graph(graph, node, parent_id=None, font_size=9, parent_color=None):
     node_id = str(id(node))
     title = node['title']
     if parent_color is None:
-        node_color = "#ADD8E6"  # Light Blue for the main heading
-        border_color = "#000000"  # Dark Blue border for the main heading
+        node_color = "#ADD8E6"
+        border_color = "#000000"
         parent_color = "#ADD8E6"
     elif parent_color == "#ADD8E6":
         node_color = generate_random_color()
         border_color = "#808080"
         parent_color = node_color
     else:
-        # Child node and its descendants with the same random color
         node_color = brighten_color(parent_color, factor=0.15)
         border_color = "#808080"
-    # Check for markdown links
     url_match = re.search(r'\[(.*?)\]\((.*?)\)', title)
     if url_match:
         prefix_text = title[:url_match.start()].strip()
         display_text = url_match.group(1)
         url = url_match.group(2)
-        
         label = f'{prefix_text} {display_text}'
         graph.node(node_id, label=label, shape="box", style="rounded,filled", color=border_color, fontcolor="black", fillcolor=node_color, href=url, tooltip=title, fontsize=str(font_size))
     else:
         graph.node(node_id, title, shape="box", style="rounded,filled", color=border_color, fontcolor="black", fillcolor=node_color, tooltip=title, fontsize=str(font_size))
-    
     if parent_id:
         graph.edge(parent_id, node_id)
-
-    # Recurse to children, passing down color for the child and its descendants
     for child in node.get('children', []):
-        # Assign a random color to each child node (no inheritance from parent)
         add_nodes_to_graph(graph, child, node_id, font_size=max(8, font_size - 1), parent_color=parent_color)
 
 def generate_mindmap_pdf(svg_file):
@@ -105,9 +89,7 @@ def generate_mindmap_svg(md_text):
     graph.attr('node', fontname="Arial", fontsize="9")
     add_nodes_to_graph(graph, mindmap_dict)
     svg_content = graph.pipe(format='svg').decode('utf-8')
-    # Replace %3 with the sanitized filename in the SVG content
     svg_content = svg_content.replace("%3", root_title)
-    # Save the modified SVG content to a file
     with open(output_filename, 'w') as f:
         f.write(svg_content)
     return output_filename

requirements.txt

@@ -1,9 +1,3 @@
 gradio==5.5.0
-langchain==0.3.7
-langchain-community==0.3.7
 graphviz==0.20.3
-llama-cpp-python==0.3.1
-pypdf==5.1.0
-llama-cpp-agent==0.2.35
-huggingface-hub==0.26.2
 cairosvg==2.7.1