Merge pull request #44 from HolobiomicsLab/dev

Easier onboarding of Toolomics & Shell MCP multi-client concurrency

Author: Fosowl

README.md

@@ -31,7 +31,19 @@ In this repository, Toolomics:
 
 ## Quick Start
 
-Run Toolomics against a workspace and a port range:
+### Deploy all automatically with default setup for Mimosa-AI
+
+The simplest way is to simply run:
+
+```bash
+./start.sh
+```
+
+This would create a workspace `workspace/` and start all Toolomics MCPs servers enabled using port in the range `5000-5200`.
+
+**Some MCPs server running in docker can take several minutes to start on first run.** 
+
+### Deploy all tools automatically with custom port range and workspace
 
 ```bash
 ./start.sh <min port> <max port> <workspace name>

deploy.py

@@ -510,7 +510,7 @@ def load_config(self) -> Dict[str, dict]:
                                 'enabled': item.get('enabled', True)  # Default to enabled
                             }
                         else:
-                            raise ValueError(f"Can't parse config file: {self.config_path}")
+                            raise ValueError("Can't parse config.json file")
 
                     logger.info(f"Successfully loaded {len(config_dict)} items from config (enabled: {sum(1 for v in config_dict.values() if v.get('enabled'))})")
                     return config_dict
@@ -588,10 +588,12 @@ def save_config(self, config: Dict[str, dict]) -> None:
     def assign_ports(self, server_files: List[Path], compose_files: List[Path] = None,
                      starting_port: int = HOST_PORT_MIN,
                      host_port_min: int = HOST_PORT_MIN,
-                     host_port_max: int = HOST_PORT_MAX) -> Dict[str, dict]:
+                     host_port_max: int = HOST_PORT_MAX,
+                     enable_new: bool = False) -> Dict[str, dict]:
         """
         Assign ports to server files and docker-compose files with proper range management.
-        Preserves enabled status for existing servers, new servers are enabled by default.
+        Preserves enabled status for existing servers, new servers are disabled by default
+        unless enable_new=True is passed (e.g. via --enable-all flag).
         Returns dict mapping path to {"port": int, "enabled": bool}
         """
         config = self.load_config()
@@ -618,12 +620,10 @@ def assign_ports(self, server_files: List[Path], compose_files: List[Path] = Non
                     if next_host_port > host_port_max:
                         raise RuntimeError(f"No available ports in host range ({host_port_min}-{host_port_max}) for server {server_str}")
 
-                config[server_str] = {'port': next_host_port, 'enabled': False}
+                config[server_str] = {'port': next_host_port, 'enabled': enable_new}
                 used_ports.add(next_host_port)
-                logger.info(
-                    f"Assigned host port {next_host_port} to {server_str} "
-                    f"(disabled - edit {self.config_path} to enable)"
-                )
+                status = "enabled" if enable_new else "disabled - edit config to enable"
+                logger.info(f"Assigned host port {next_host_port} to {server_str} ({status})")
                 next_host_port += 1
 
         # Assign ports to docker-compose files
@@ -639,12 +639,10 @@ def assign_ports(self, server_files: List[Path], compose_files: List[Path] = Non
                         if next_host_port > host_port_max:
                             raise RuntimeError(f"No available ports in host range ({host_port_min}-{host_port_max}) for compose {compose_str}")
 
-                    config[compose_str] = {'port': next_host_port, 'enabled': False}
+                    config[compose_str] = {'port': next_host_port, 'enabled': enable_new}
                     used_ports.add(next_host_port)
-                    logger.info(
-                        f"Assigned host port {next_host_port} to {compose_str} "
-                        f"(disabled - edit {self.config_path} to enable)"
-                    )
+                    status = "enabled" if enable_new else "disabled - edit config to enable"
+                    logger.info(f"Assigned host port {next_host_port} to {compose_str} ({status})")
                     next_host_port += 1
 
         self.save_config(config)
@@ -681,7 +679,8 @@ def _signal_handler(self, signum, frame):
 
     def deploy(self, skip_docker: bool = False, starting_port: int = HOST_PORT_MIN,
                                                 host_port_min: int = HOST_PORT_MIN,
-                                                host_port_max: int = HOST_PORT_MAX):
+                                                host_port_max: int = HOST_PORT_MAX,
+                                                enable_all: bool = False):
         """Deploy all MCP servers and Docker services"""
         if not self.mcp_dir.exists():
             raise FileNotFoundError(f"MCP directory {self.mcp_dir} does not exist")
@@ -692,7 +691,7 @@ def deploy(self, skip_docker: bool = False, starting_port: int = HOST_PORT_MIN,
 
         # Assign ports to all services
         logger.info("Assigning ports to all services...")
-        port_config = self.config_manager.assign_ports(server_files, compose_files, starting_port, host_port_min, host_port_max)
+        port_config = self.config_manager.assign_ports(server_files, compose_files, starting_port, host_port_min, host_port_max, enable_new=enable_all)
 
         # Start Docker services
         if not skip_docker:
@@ -757,18 +756,15 @@ def _deploy_docker_services(self, compose_files: List[Path], port_config: Dict[s
 
         # Save config if any ports were reassigned
         if config_updated:
-            logger.info(f"Updating {self.config_manager.config_path} with new port assignments")
+            logger.info("Updating config.json with new port assignments")
             self.config_manager.save_config(port_config)
 
         if started_count > 0:
             logger.info(f"Started {started_count} Docker services ({disabled_count} disabled)")
             logger.info("Waiting for Docker services to start...")
             time.sleep(3)
         elif disabled_count > 0:
-            logger.info(
-                f"⚠️ All {disabled_count} Docker services are disabled. "
-                f"Change {self.config_manager.config_path} to enable them."
-            )
+            logger.info(f"⚠️ All {disabled_count} Docker services are disabled. Change config.json to enable.")
 
     def _deploy_mcp_servers(self, server_files: List[Path], port_config: Dict[str, dict],
                           host_port_min: int = HOST_PORT_MIN, host_port_max: int = HOST_PORT_MAX):
@@ -820,15 +816,12 @@ def _deploy_mcp_servers(self, server_files: List[Path], port_config: Dict[str, d
 
         # Save config if any ports were reassigned
         if config_updated:
-            logger.info(f"Updating {self.config_manager.config_path} with new port assignments")
+            logger.info("Updating config.json with new port assignments")
             self.config_manager.save_config(port_config)
 
         logger.info(f"Started {started_count} MCP servers ({disabled_count} disabled)")
         if started_count == 0:
-            raise Exception(
-                f"⚠️ No MCP server enabled. Change {self.config_manager.config_path} "
-                "and select MCP servers to enable."
-            )
+            raise Exception("⚠️ No MCP server enabled, change config.json and select MCP servers to enable.")
 
 def main():
     parser = argparse.ArgumentParser(description="Deploy MCP servers with centralized workspace file management")
@@ -839,6 +832,7 @@ def main():
     parser.add_argument("--host_port_min", type=int, default=HOST_PORT_MIN, help="Minimum port for port assignment range.")
     parser.add_argument("--host_port_max", type=int, default=HOST_PORT_MAX, help="Maximum port for port assignment range.")
     parser.add_argument("--no-docker", action="store_true", help="Skip Docker services")
+    parser.add_argument("--enable-all", action="store_true", help="Enable all newly discovered MCP servers immediately (skip manual config editing)")
     parser.add_argument("--verbose", "-v", action="store_true", help="Enable verbose logging")
 
     args = parser.parse_args()
@@ -856,12 +850,13 @@ def main():
             skip_docker=args.no_docker,
             starting_port=args.starting_port,
             host_port_min=args.host_port_min,
-            host_port_max=args.host_port_max
+            host_port_max=args.host_port_max,
+            enable_all=args.enable_all
         )
 
     except Exception as e:
         logger.error(f"Deployment failed: {e}")
         sys.exit(1)
 
 if __name__ == "__main__":
-    main()
+    main()