Fix MCP server communication: remove line limit and improve JSON parsing

- Remove {:line, 1024} port option that was truncating long JSON responses
- Rewrite collect_response to handle binary data instead of line-based data
- Add extract_json_messages function to properly parse complete JSON from mixed stdout
- Filter out log messages while preserving complete JSON responses
- Add timeouts to all GenServer calls to prevent blocking
- This fixes the 'unexpected end of input at position 1024' JSON decode errors

lib/agent_coordinator/mcp_server_manager.ex

@@ -27,35 +27,35 @@ defmodule AgentCoordinator.MCPServerManager do
   Get all tools from all managed servers plus Agent Coordinator tools
   """
   def get_unified_tools do
-    GenServer.call(__MODULE__, :get_unified_tools)
+    GenServer.call(__MODULE__, :get_unified_tools, 60_000)
   end
 
   @doc """
   Route a tool call to the appropriate server
   """
   def route_tool_call(tool_name, arguments, agent_context) do
-    GenServer.call(__MODULE__, {:route_tool_call, tool_name, arguments, agent_context})
+    GenServer.call(__MODULE__, {:route_tool_call, tool_name, arguments, agent_context}, 60_000)
   end
 
   @doc """
   Get status of all managed servers
   """
   def get_server_status do
-    GenServer.call(__MODULE__, :get_server_status)
+    GenServer.call(__MODULE__, :get_server_status, 15_000)
   end
 
   @doc """
   Restart a specific server
   """
   def restart_server(server_name) do
-    GenServer.call(__MODULE__, {:restart_server, server_name})
+    GenServer.call(__MODULE__, {:restart_server, server_name}, 30_000)
   end
 
   @doc """
   Refresh tool registry by re-discovering tools from all servers
   """
   def refresh_tools do
-    GenServer.call(__MODULE__, :refresh_tools)
+    GenServer.call(__MODULE__, :refresh_tools, 60_000)
   end
 
   # Server callbacks
@@ -432,7 +432,6 @@ defmodule AgentCoordinator.MCPServerManager do
     port_options = [
       :binary,
       :stream,
-      {:line, 1024},
       {:env, env_list},
       :exit_status,
       :hide
@@ -567,6 +566,13 @@ defmodule AgentCoordinator.MCPServerManager do
     # Collect full response by reading multiple lines if needed
     response_data = collect_response(server_info.port, "", 30_000)
 
+    cond do
+      # Check if we got any response data
+      response_data == "" ->
+        {:error, "No response received from server #{server_info.name}"}
+        
+      # Try to decode JSON response
+      true ->
         case Jason.decode(response_data) do
           {:ok, response} -> {:ok, response}
           {:error, %Jason.DecodeError{} = error} ->
@@ -577,22 +583,23 @@ defmodule AgentCoordinator.MCPServerManager do
             {:error, "JSON decode error: #{inspect(reason)}"}
         end
     end
+  end
 
   defp collect_response(port, acc, timeout) do
     receive do
-      {^port, {:data, {_eol, response_line}}} ->
-        # Accumulate the response line
-        new_acc = acc <> response_line
+      {^port, {:data, data}} ->
+        # Accumulate binary data
+        new_acc = acc <> data
         
-        # Check if we have a complete JSON object
-        case Jason.decode(new_acc) do
-          {:ok, _} ->
-            # Successfully decoded, return the complete response
-            new_acc
+        # Try to extract complete JSON messages from the accumulated data
+        case extract_json_messages(new_acc) do
+          {json_message, _remaining} when json_message != nil ->
+            # We found a complete JSON message, return it
+            json_message
             
-          {:error, _} ->
-            # Not complete yet, continue collecting
-            collect_response(port, new_acc, timeout)
+          {nil, remaining} ->
+            # No complete JSON message yet, continue collecting
+            collect_response(port, remaining, timeout)
         end
 
       {^port, {:exit_status, status}} ->
@@ -606,6 +613,93 @@ defmodule AgentCoordinator.MCPServerManager do
     end
   end
 
+  # Extract complete JSON messages from accumulated binary data
+  defp extract_json_messages(data) do
+    lines = String.split(data, "\n", trim: false)
+    
+    # Process each line to find JSON messages and skip log messages
+    {json_lines, _remaining_data} = extract_json_from_lines(lines, [])
+    
+    case json_lines do
+      [] ->
+        # No complete JSON found, return the last partial line if any
+        last_line = List.last(lines) || ""
+        if String.trim(last_line) != "" and not String.ends_with?(data, "\n") do
+          {nil, last_line}
+        else
+          {nil, ""}
+        end
+        
+      _ ->
+        # Join all JSON lines and try to parse
+        json_data = Enum.join(json_lines, "\n")
+        
+        case Jason.decode(json_data) do
+          {:ok, _} ->
+            # Valid JSON found
+            {json_data, ""}
+            
+          {:error, _} ->
+            # Invalid JSON, might be incomplete
+            {nil, data}
+        end
+    end
+  end
+
+  defp extract_json_from_lines([], acc), do: {Enum.reverse(acc), ""}
+  
+  defp extract_json_from_lines([line], acc) do
+    # This is the last line, it might be incomplete
+    trimmed = String.trim(line)
+    
+    cond do
+      trimmed == "" ->
+        {Enum.reverse(acc), ""}
+        
+      # Skip log messages
+      Regex.match?(~r/^\d{4}-\d{2}-\d{2}\s+\d{2}:\d{2}:\d{2}/, trimmed) ->
+        {Enum.reverse(acc), ""}
+        
+      Regex.match?(~r/^\d{2}:\d{2}:\d{2}\.\d+\s+\[(info|warning|error|debug)\]/, trimmed) ->
+        {Enum.reverse(acc), ""}
+        
+      # Check if this looks like JSON
+      String.starts_with?(trimmed, ["{"]) ->
+        {Enum.reverse([line | acc]), ""}
+        
+      true ->
+        # Non-JSON line, might be incomplete
+        {Enum.reverse(acc), line}
+    end
+  end
+  
+  defp extract_json_from_lines([line | rest], acc) do
+    trimmed = String.trim(line)
+    
+    cond do
+      trimmed == "" ->
+        extract_json_from_lines(rest, acc)
+        
+      # Skip log messages
+      Regex.match?(~r/^\d{4}-\d{2}-\d{2}\s+\d{2}:\d{2}:\d{2}/, trimmed) ->
+        Logger.debug("Skipping log message from MCP server: #{trimmed}")
+        extract_json_from_lines(rest, acc)
+        
+      Regex.match?(~r/^\d{2}:\d{2}:\d{2}\.\d+\s+\[(info|warning|error|debug)\]/, trimmed) ->
+        Logger.debug("Skipping log message from MCP server: #{trimmed}")
+        extract_json_from_lines(rest, acc)
+        
+      # Check if this looks like JSON
+      String.starts_with?(trimmed, ["{"]) ->
+        extract_json_from_lines(rest, [line | acc])
+        
+      true ->
+        # Skip non-JSON lines
+        Logger.debug("Skipping non-JSON line from MCP server: #{trimmed}")
+        extract_json_from_lines(rest, acc)
+    end
+  end
+
   defp refresh_tool_registry(state) do
     new_registry =
       Enum.reduce(state.servers, %{}, fn {name, server_info}, acc ->

lib/agent_coordinator/unified_mcp_server.ex

@@ -26,7 +26,7 @@ defmodule AgentCoordinator.UnifiedMCPServer do
   Handle MCP request from GitHub Copilot
   """
   def handle_mcp_request(request) do
-    GenServer.call(__MODULE__, {:handle_request, request})
+    GenServer.call(__MODULE__, {:handle_request, request}, 60_000)
   end
 
   # Server callbacks