Removed customization feature for now

app.py

@@ -334,244 +334,248 @@ def load_existing_graph():
         return jsonify({"error": str(e)}), 500
 
 
-@app.route("/api/create_graph", methods=["POST"])
-def create_graph():
-    """Create a new POA graph from text sequences"""
-    try:
-        print("DEBUG: Received create_graph request")
-        data = request.get_json()
-        sequences = data.get("sequences", [])
-
-        print(f"DEBUG: Number of sequences: {len(sequences)}")
-
-        if len(sequences) < 2:
-            return jsonify({"error": "At least 2 sequences are required"}), 400
-
-        print("DEBUG: Creating initial graph")
-        # Create the graph from first sequence
-        graph = TextPOAGraph(sequences[0], label=0)
-        print("DEBUG: Initial graph created")
-
-        # Add remaining sequences
-        for i, sequence in enumerate(sequences[1:], 1):
-            print(f"DEBUG: Adding sequence {i}")
-            alignment = TextSeqGraphAlignment(
-                text=sequence,
-                graph=graph,
-                fastMethod=True,
-                globalAlign=True,
-                matchscore=1,
-                mismatchscore=-2,
-                gap_open=-1,
-            )
-            graph.incorporateSeqAlignment(alignment, sequence, label=i)
-
-        print("DEBUG: All sequences added")
-
-        # Refine the graph with proper domain and model parameters
-        graph.refine_graph(verbose=False, domain="text", model="gpt-4o-mini")
-        print("DEBUG: Graph refined")
-
-        # Convert to JSON format for vis.js
-        nodes = []
-        edges = []
-
-        try:
-            print("DEBUG: Starting to process graph data")
-            # Get consensus nodes for coloring (make it optional)
-            try:
-                consensus_nodes = set(graph.consensus_node_ids)
-                print(f"DEBUG: Consensus nodes: {consensus_nodes}")
-            except Exception as e:
-                print(f"DEBUG: Error getting consensus nodes: {e}")
-                consensus_nodes = set()  # Fallback to empty set if consensus fails
-
-            # Create nodes using the same logic as jsOutput
-            for node in graph.nodeiterator()():
-                title_text = ""
-                if node.sequences:
-                    title_text += f"Sequences: {node.sequences}"
-                if node.variations:
-                    title_text += ";;;".join(
-                        [f"{sequence_id}: {text}" for sequence_id, text in node.variations.items()]
-                    )
-                    title_text = title_text.replace('"', "'")
-
-                # Use the same color logic as jsOutput
-                color = "#ceeab2" if node.ID in consensus_nodes else "#cae0e6"
-
-                node_data = {
-                    "id": node.ID,
-                    "label": f"{node.ID}: {node.text}",
-                    "title": title_text,
-                    "color": color,
-                }
-                nodes.append(node_data)
-
-            print(f"DEBUG: Created {len(nodes)} nodes")
-
-            # Create edges using the same logic as jsOutput
-            for node in graph.nodeiterator()():
-                nodeID = node.ID  # Keep as integer
-                for edge in node.outEdges:
-                    target = edge  # Keep as integer
-                    weight = node.outEdges[edge].weight + 1.5
-                    edge_data = {
-                        "from": nodeID,
-                        "to": target,
-                        "value": weight,
-                        "color": "#cae0e6",
-                        "arrows": "to",
-                    }
-                    edges.append(edge_data)
-
-            print(f"DEBUG: Created {len(edges)} edges")
-        except Exception as e:
-            print(f"DEBUG: Error processing graph data: {e}")
-            return jsonify({"error": f"Error processing graph data: {str(e)}"}), 500
-
-        # Extract text from consensus nodes
-        consensus_text = ""
-        try:
-            consensus_node_texts = []
-            for node in graph.nodeiterator()():
-                if node.ID in consensus_nodes and node.text and node.text.strip():
-                    consensus_node_texts.append(node.text.strip())
-            consensus_text = " ".join(consensus_node_texts)
-        except Exception:
-            consensus_text = ""
-
-        # Check if we should compute consensus using decode_consensus
-        compute_consensus = data.get("compute_consensus", False)
-        if compute_consensus and decode_consensus:
-            try:
-                # Default to "bio" task for new graphs
-                consensus_text = decode_consensus(graph, selection_threshold=0.5, task="bio")
-            except Exception as e:
-                print(f"DEBUG: Error computing consensus with decode_consensus: {e}")
-                # Keep the original consensus text if decode_consensus fails
-
-        # Get original sequences
-        try:
-            raw_sequences = graph._seqs if hasattr(graph, "_seqs") else []
-            # Process sequences: join with spaces and remove "||"
-            original_sequences = []
-            for seq in raw_sequences:
-                if isinstance(seq, list):
-                    # Join list elements with spaces
-                    processed_seq = " ".join(str(item) for item in seq)
-                else:
-                    processed_seq = str(seq)
-                # Remove "||" characters
-                processed_seq = processed_seq.replace("||", "")
-                original_sequences.append(processed_seq)
-        except Exception:
-            original_sequences = []
-
-        print("DEBUG: Returning success response")
-        return jsonify(
-            {
-                "success": True,
-                "nodes": nodes,
-                "edges": edges,
-                "num_sequences": len(sequences),
-                "num_nodes": len(nodes),
-                "num_edges": len(edges),
-                "original_sequences": original_sequences,
-                "consensus_text": consensus_text,
-            }
-        )
-
-    except Exception as e:
-        print(f"DEBUG: Main exception in create_graph: {e}")
-        return jsonify({"error": str(e)}), 500
-
-
-@app.route("/api/save_graph", methods=["POST"])
-def save_graph():
-    """Save a POA graph to a pickle file"""
-    try:
-        data = request.get_json()
-        sequences = data.get("sequences", [])
-        filename = data.get("filename", "graph.pkl")
-
-        if len(sequences) < 2:
-            return jsonify({"error": "At least 2 sequences are required"}), 400
-
-        # Create the graph
-        graph = TextPOAGraph(sequences[0], label=0)
-
-        # Add remaining sequences
-        for i, sequence in enumerate(sequences[1:], 1):
-            alignment = TextSeqGraphAlignment(
-                text=sequence,
-                graph=graph,
-                fastMethod=True,
-                globalAlign=True,
-                matchscore=1,
-                mismatchscore=-2,
-                gap_open=-1,
-            )
-            graph.incorporateSeqAlignment(alignment, sequence, label=i)
-
-        # Refine the graph
-        graph.refine_graph(verbose=False)
-
-        # Save to pickle file
-        graph.save_to_pickle(filename)
-
-        return jsonify(
-            {"success": True, "filename": filename, "message": f"Graph saved to {filename}"}
-        )
-
-    except Exception as e:
-        return jsonify({"error": str(e)}), 500
-
-
-@app.route("/api/graph_info", methods=["POST"])
-def graph_info():
-    """Get information about a graph without creating the full visualization"""
-    try:
-        data = request.get_json()
-        sequences = data.get("sequences", [])
-
-        if len(sequences) < 2:
-            return jsonify({"error": "At least 2 sequences are required"}), 400
-
-        # Create the graph
-        graph = TextPOAGraph(sequences[0], label=0)
-
-        # Add remaining sequences
-        for i, sequence in enumerate(sequences[1:], 1):
-            alignment = TextSeqGraphAlignment(
-                text=sequence,
-                graph=graph,
-                fastMethod=True,
-                globalAlign=True,
-                matchscore=1,
-                mismatchscore=-2,
-                gap_open=-1,
-            )
-            graph.incorporateSeqAlignment(alignment, sequence, label=i)
-
-        # Refine the graph
-        graph.refine_graph(verbose=False)
-
-        # Get consensus response
-        consensus_text = graph.consensus_response()
-
-        return jsonify(
-            {
-                "success": True,
-                "num_sequences": len(sequences),
-                "num_nodes": graph._nnodes,
-                "consensus_text": consensus_text,
-                "consensus_node_ids": graph.consensus_node_ids,
-            }
-        )
-
-    except Exception as e:
-        return jsonify({"error": str(e)}), 500
+# ============================================================================
+# COMMENTED OUT: Create New Graph Feature - Disabled per user request
+# ============================================================================
+
+# @app.route("/api/create_graph", methods=["POST"])
+# def create_graph():
+#     """Create a new POA graph from text sequences"""
+#     try:
+#         print("DEBUG: Received create_graph request")
+#         data = request.get_json()
+#         sequences = data.get("sequences", [])
+#
+#         print(f"DEBUG: Number of sequences: {len(sequences)}")
+#
+#         if len(sequences) < 2:
+#             return jsonify({"error": "At least 2 sequences are required"}), 400
+#
+#         print("DEBUG: Creating initial graph")
+#         # Create the graph from first sequence
+#         graph = TextPOAGraph(sequences[0], label=0)
+#         print("DEBUG: Initial graph created")
+#
+#         # Add remaining sequences
+#         for i, sequence in enumerate(sequences[1:], 1):
+#             print(f"DEBUG: Adding sequence {i}")
+#             alignment = TextSeqGraphAlignment(
+#                 text=sequence,
+#                 graph=graph,
+#                 fastMethod=True,
+#                 globalAlign=True,
+#                 matchscore=1,
+#                 mismatchscore=-2,
+#                 gap_open=-1,
+#             )
+#             graph.incorporateSeqAlignment(alignment, sequence, label=i)
+#
+#         print("DEBUG: All sequences added")
+#
+#         # Refine the graph with proper domain and model parameters
+#         graph.refine_graph(verbose=False, domain="text", model="gpt-4o-mini")
+#         print("DEBUG: Graph refined")
+#
+#         # Convert to JSON format for vis.js
+#         nodes = []
+#         edges = []
+#
+#         try:
+#             print("DEBUG: Starting to process graph data")
+#             # Get consensus nodes for coloring (make it optional)
+#             try:
+#                 consensus_nodes = set(graph.consensus_node_ids)
+#                 print(f"DEBUG: Consensus nodes: {consensus_nodes}")
+#             except Exception as e:
+#                 print(f"DEBUG: Error getting consensus nodes: {e}")
+#                 consensus_nodes = set()  # Fallback to empty set if consensus fails
+#
+#             # Create nodes using the same logic as jsOutput
+#             for node in graph.nodeiterator()():
+#                 title_text = ""
+#                 if node.sequences:
+#                     title_text += f"Sequences: {node.sequences}"
+#                 if node.variations:
+#                     title_text += ";;;".join(
+#                         [f"{sequence_id}: {text}" for sequence_id, text in node.variations.items()]
+#                     )
+#                     title_text = title_text.replace('"', "'")
+#
+#                 # Use the same color logic as jsOutput
+#                 color = "#ceeab2" if node.ID in consensus_nodes else "#cae0e6"
+#
+#                 node_data = {
+#                     "id": node.ID,
+#                     "label": f"{node.ID}: {node.text}",
+#                     "title": title_text,
+#                     "color": color,
+#                 }
+#                 nodes.append(node_data)
+#
+#             print(f"DEBUG: Created {len(nodes)} nodes")
+#
+#             # Create edges using the same logic as jsOutput
+#             for node in graph.nodeiterator()():
+#                 nodeID = node.ID  # Keep as integer
+#                 for edge in node.outEdges:
+#                     target = edge  # Keep as integer
+#                     weight = node.outEdges[edge].weight + 1.5
+#                     edge_data = {
+#                         "from": nodeID,
+#                         "to": target,
+#                         "value": weight,
+#                         "color": "#cae0e6",
+#                         "arrows": "to",
+#                     }
+#                     edges.append(edge_data)
+#
+#             print(f"DEBUG: Created {len(edges)} edges")
+#         except Exception as e:
+#             print(f"DEBUG: Error processing graph data: {e}")
+#             return jsonify({"error": f"Error processing graph data: {str(e)}"}), 500
+#
+#         # Extract text from consensus nodes
+#         consensus_text = ""
+#         try:
+#             consensus_node_texts = []
+#             for node in graph.nodeiterator()():
+#                 if node.ID in consensus_nodes and node.text and node.text.strip():
+#                     consensus_node_texts.append(node.text.strip())
+#             consensus_text = " ".join(consensus_node_texts)
+#         except Exception:
+#             consensus_text = ""
+#
+#         # Check if we should compute consensus using decode_consensus
+#         compute_consensus = data.get("compute_consensus", False)
+#         if compute_consensus and decode_consensus:
+#             try:
+#                 # Default to "bio" task for new graphs
+#                 consensus_text = decode_consensus(graph, selection_threshold=0.5, task="bio")
+#             except Exception as e:
+#                 print(f"DEBUG: Error computing consensus with decode_consensus: {e}")
+#                 # Keep the original consensus text if decode_consensus fails
+#
+#         # Get original sequences
+#         try:
+#             raw_sequences = graph._seqs if hasattr(graph, "_seqs") else []
+#             # Process sequences: join with spaces and remove "||"
+#             original_sequences = []
+#             for seq in raw_sequences:
+#                 if isinstance(seq, list):
+#                     # Join list elements with spaces
+#                     processed_seq = " ".join(str(item) for item in seq)
+#                 else:
+#                     processed_seq = str(seq)
+#                 # Remove "||" characters
+#                 processed_seq = processed_seq.replace("||", "")
+#                 original_sequences.append(processed_seq)
+#         except Exception:
+#             original_sequences = []
+#
+#         print("DEBUG: Returning success response")
+#         return jsonify(
+#             {
+#                 "success": True,
+#                 "nodes": nodes,
+#                 "edges": edges,
+#                 "num_sequences": len(sequences),
+#                 "num_nodes": len(nodes),
+#                 "num_edges": len(edges),
+#                 "original_sequences": original_sequences,
+#                 "consensus_text": consensus_text,
+#             }
+#         )
+#
+#     except Exception as e:
+#         print(f"DEBUG: Main exception in create_graph: {e}")
+#         return jsonify({"error": str(e)}), 500
+
+
+# @app.route("/api/save_graph", methods=["POST"])
+# def save_graph():
+#     """Save a POA graph to a pickle file"""
+#     try:
+#         data = request.get_json()
+#         sequences = data.get("sequences", [])
+#         filename = data.get("filename", "graph.pkl")
+#
+#         if len(sequences) < 2:
+#             return jsonify({"error": "At least 2 sequences are required"}), 400
+#
+#         # Create the graph
+#         graph = TextPOAGraph(sequences[0], label=0)
+#
+#         # Add remaining sequences
+#         for i, sequence in enumerate(sequences[1:], 1):
+#             alignment = TextSeqGraphAlignment(
+#                 text=sequence,
+#                 graph=graph,
+#                 fastMethod=True,
+#                 globalAlign=True,
+#                 matchscore=1,
+#                 mismatchscore=-2,
+#                 gap_open=-1,
+#             )
+#             graph.incorporateSeqAlignment(alignment, sequence, label=i)
+#
+#         # Refine the graph
+#         graph.refine_graph(verbose=False)
+#
+#         # Save to pickle file
+#         graph.save_to_pickle(filename)
+#
+#         return jsonify(
+#             {"success": True, "filename": filename, "message": f"Graph saved to {filename}"}
+#         )
+#
+#     except Exception as e:
+#         return jsonify({"error": str(e)}), 500
+
+
+# @app.route("/api/graph_info", methods=["POST"])
+# def graph_info():
+#     """Get information about a graph without creating the full visualization"""
+#     try:
+#         data = request.get_json()
+#         sequences = data.get("sequences", [])
+#
+#         if len(sequences) < 2:
+#             return jsonify({"error": "At least 2 sequences are required"}), 400
+#
+#         # Create the graph
+#         graph = TextPOAGraph(sequences[0], label=0)
+#
+#         # Add remaining sequences
+#         for i, sequence in enumerate(sequences[1:], 1):
+#             alignment = TextSeqGraphAlignment(
+#                 text=sequence,
+#                 graph=graph,
+#                 fastMethod=True,
+#                 globalAlign=True,
+#                 matchscore=1,
+#                 mismatchscore=-2,
+#                 gap_open=-1,
+#             )
+#             graph.incorporateSeqAlignment(alignment, sequence, label=i)
+#
+#         # Refine the graph
+#         graph.refine_graph(verbose=False)
+#
+#         # Get consensus response
+#         consensus_text = graph.consensus_response()
+#
+#         return jsonify(
+#             {
+#                 "success": True,
+#                 "num_sequences": len(sequences),
+#                 "num_nodes": graph._nnodes,
+#                 "consensus_text": consensus_text,
+#                 "consensus_node_ids": graph.consensus_node_ids,
+#             }
+#         )
+#
+#     except Exception as e:
+#         return jsonify({"error": str(e)}), 500
 
 
 if __name__ == "__main__":
@@ -581,4 +585,4 @@ if __name__ == "__main__":
     print(f"Repository root: {REPO_ROOT}")
     print(f"Serving static files from: {os.path.join(REPO_ROOT, 'web_interface')}")
     print(f"Open http://localhost:{port} in your browser")
-    app.run(debug=False, host="0.0.0.0", port=port)
+    app.run(debug=False, host="0.0.0.0", port=port)