"""
The Serena Model Context Protocol (MCP) Server
"""

import json
import multiprocessing
import os
import platform
import subprocess
import sys
from collections.abc import Callable, Iterator, Sequence
from contextlib import contextmanager
from logging import Logger
from typing import TYPE_CHECKING, Optional, TypeVar

import webview
from sensai.util import logging
from sensai.util.logging import LogTime
from sensai.util.string import dict_string

from interprompt.jinja_template import JinjaTemplate
from serena import serena_version
from serena.analytics import RegisteredTokenCountEstimator, ToolUsageStats
from serena.config.context_mode import SerenaAgentContext, SerenaAgentMode
from serena.config.serena_config import (
    LanguageBackend,
    ModeSelectionDefinition,
    NamedToolInclusionDefinition,
    RegisteredProject,
    SerenaConfig,
    SerenaPaths,
    ToolInclusionDefinition,
)
from serena.dashboard import SerenaDashboardAPI, SerenaDashboardViewer
from serena.ls_manager import LanguageServerManager
from serena.project import MemoriesManager, Project
from serena.prompt_factory import SerenaPromptFactory
from serena.task_executor import TaskExecutor
from serena.tools import (
    ActivateProjectTool,
    GetCurrentConfigTool,
    OpenDashboardTool,
    ReadMemoryTool,
    ReplaceContentTool,
    Tool,
    ToolMarker,
    ToolRegistry,
)
from serena.util.gui import system_has_usable_display
from serena.util.inspection import iter_subclasses
from serena.util.logging import MemoryLogHandler
from solidlsp.ls_config import Language

if TYPE_CHECKING:
    from serena.gui_log_viewer import GuiLogViewer

log = logging.getLogger(__name__)
TTool = TypeVar("TTool", bound="Tool")
T = TypeVar("T")
SUCCESS_RESULT = "OK"


class ProjectNotFoundError(Exception):
    pass


class AvailableTools:
    """
    Represents the set of available/exposed tools of a SerenaAgent.
    """

    def __init__(self, tools: list[Tool]):
        """
        :param tools: the list of available tools
        """
        self.tools = tools
        self.tool_names = sorted([tool.get_name_from_cls() for tool in tools])
        """
        the list of available tool names, sorted alphabetically
        """
        self._tool_name_set = set(self.tool_names)
        self.tool_marker_names = set()
        for marker_class in iter_subclasses(ToolMarker):
            for tool in tools:
                if isinstance(tool, marker_class):
                    self.tool_marker_names.add(marker_class.__name__)

    def __len__(self) -> int:
        return len(self.tools)

    def contains_tool_name(self, tool_name: str) -> bool:
        return tool_name in self._tool_name_set

    def contains_tool_class(self, tool_class: type[Tool]) -> bool:
        return self.contains_tool_name(tool_class.get_name_from_cls())


class ToolSet:
    """
    Represents a set of tools by their names.
    """

    LEGACY_TOOL_NAME_MAPPING = {"replace_regex": ReplaceContentTool.get_name_from_cls()}
    """
    maps legacy tool names to their new names for backward compatibility
    """

    def __init__(self, tool_names: set[str]) -> None:
        self._tool_names = tool_names

    def __len__(self) -> int:
        return len(self._tool_names)

    @classmethod
    def default(cls) -> "ToolSet":
        """
        :return: the default tool set, which contains all tools that are enabled by default
        """
        from serena.tools import ToolRegistry

        return cls(set(ToolRegistry().get_tool_names_default_enabled()))

    def apply(self, *tool_inclusion_definitions: "ToolInclusionDefinition") -> "ToolSet":
        """
        Applies one or more tool inclusion definitions to this tool set,
        resulting in a new tool set.

        :param tool_inclusion_definitions: the definitions to apply
        :return: a new tool set with the definitions applied
        """
        from serena.tools import ToolRegistry

        def get_updated_tool_name(tool_name: str) -> str:
            """Retrieves the updated tool name if the provided tool name is deprecated, logging a warning."""
            if tool_name in self.LEGACY_TOOL_NAME_MAPPING:
                new_tool_name = self.LEGACY_TOOL_NAME_MAPPING[tool_name]
                log.warning("Tool name '%s' is deprecated, please use '%s' instead", tool_name, new_tool_name)
                return new_tool_name
            return tool_name

        registry = ToolRegistry()
        tool_names = set(self._tool_names)
        for definition in tool_inclusion_definitions:
            if definition.is_fixed_tool_set():
                tool_names = set()
                for fixed_tool in definition.fixed_tools:
                    fixed_tool = get_updated_tool_name(fixed_tool)
                    if not registry.is_valid_tool_name(fixed_tool):
                        raise ValueError(f"Invalid tool name '{fixed_tool}' provided for fixed tool set")
                    tool_names.add(fixed_tool)
                log.info(f"{definition} defined a fixed tool set with {len(tool_names)} tools: {', '.join(tool_names)}")
            else:
                included_tools = []
                excluded_tools = []
                for included_tool in definition.included_optional_tools:
                    included_tool = get_updated_tool_name(included_tool)
                    if not registry.is_valid_tool_name(included_tool):
                        raise ValueError(f"Invalid tool name '{included_tool}' provided for inclusion")
                    if included_tool not in tool_names:
                        tool_names.add(included_tool)
                        included_tools.append(included_tool)
                for excluded_tool in definition.excluded_tools:
                    excluded_tool = get_updated_tool_name(excluded_tool)
                    if not registry.is_valid_tool_name(excluded_tool):
                        raise ValueError(f"Invalid tool name '{excluded_tool}' provided for exclusion")
                    if excluded_tool in tool_names:
                        tool_names.remove(excluded_tool)
                        excluded_tools.append(excluded_tool)
                if included_tools:
                    log.info(f"{definition} included {len(included_tools)} tools: {', '.join(included_tools)}")
                if excluded_tools:
                    log.info(f"{definition} excluded {len(excluded_tools)} tools: {', '.join(excluded_tools)}")
        return ToolSet(tool_names)

    def without_editing_tools(self) -> "ToolSet":
        """
        :return: a new tool set that excludes all tools that can edit
        """
        from serena.tools import ToolRegistry

        registry = ToolRegistry()
        tool_names = set(self._tool_names)
        for tool_name in self._tool_names:
            if registry.get_tool_class_by_name(tool_name).can_edit():
                tool_names.remove(tool_name)
        return ToolSet(tool_names)

    def get_tool_names(self) -> set[str]:
        """
        Returns the names of the tools that are currently included in the tool set.
        """
        return self._tool_names

    def includes_name(self, tool_name: str) -> bool:
        return tool_name in self._tool_names

    def to_available_tools(self, all_tools: dict[type[Tool], Tool]) -> AvailableTools:
        return AvailableTools([t for t in all_tools.values() if self.includes_name(t.get_name())])


class ActiveModes:
    def __init__(self) -> None:
        self._base_modes: Sequence[str] | None = None
        self._default_modes: Sequence[str] | None = None
        self._active_mode_names: Sequence[str] | None = []
        self._active_modes: Sequence[SerenaAgentMode] | None = []

    def apply(self, mode_selection: ModeSelectionDefinition) -> None:
        # invalidate active modes
        self._active_mode_names = None
        self._active_modes = None

        # apply overrides
        log.debug("Applying mode selection: default_modes=%s, base_modes=%s", mode_selection.default_modes, mode_selection.base_modes)
        if mode_selection.base_modes is not None:
            self._base_modes = mode_selection.base_modes
        if mode_selection.default_modes is not None:
            self._default_modes = mode_selection.default_modes
        log.debug("Current mode selection: base_modes=%s, default_modes=%s", self._base_modes, self._default_modes)

    def get_mode_names(self) -> Sequence[str]:
        if self._active_mode_names is not None:
            return self._active_mode_names
        active_mode_names: set[str] = set()
        if self._base_modes is not None:
            active_mode_names.update(self._base_modes)
        if self._default_modes is not None:
            active_mode_names.update(self._default_modes)
        self._active_mode_names = sorted(active_mode_names)
        log.info("Active modes: %s", self._active_mode_names)
        return self._active_mode_names

    def get_modes(self) -> Sequence[SerenaAgentMode]:
        if self._active_modes is not None:
            return self._active_modes
        self._active_modes = []
        for mode_name in self.get_mode_names():
            mode = SerenaAgentMode.load(mode_name)
            self._active_modes.append(mode)
        return self._active_modes

    # TODO: apply caching like in get_modes
    def get_default_modes(self) -> Sequence[SerenaAgentMode]:
        return [SerenaAgentMode.load(mode_name) for mode_name in self._default_modes or []]

    def get_base_modes(self) -> Sequence[SerenaAgentMode]:
        return [SerenaAgentMode.load(mode_name) for mode_name in self._base_modes or []]


class SerenaAgent:
    def __init__(
        self,
        project: str | None = None,
        project_activation_callback: Callable[[], None] | None = None,
        serena_config: SerenaConfig | None = None,
        context: SerenaAgentContext | None = None,
        modes: ModeSelectionDefinition | None = None,
        memory_log_handler: MemoryLogHandler | None = None,
    ):
        """
        :param project: the project to load immediately or None to not load any project; may be a path to the project or a name of
            an already registered project;
        :param project_activation_callback: a callback function to be called when a project is activated.
        :param serena_config: the Serena configuration or None to read the configuration from the default location.
        :param context: the context in which the agent is operating, None for default context.
            The context may adjust prompts, tool availability, and tool descriptions.
        :param modes: list of modes in which the agent is operating (they will be combined), None for default modes.
            The modes may adjust prompts, tool availability, and tool descriptions.
        :param memory_log_handler: a MemoryLogHandler instance from which to read log messages; if None, a new one will be created
            if necessary.
        """
        # obtain serena configuration using the decoupled factory function
        self.serena_config = serena_config or SerenaConfig.from_config_file()

        # propagate configuration to other components
        self.serena_config.propagate_settings()

        # project-specific instances, which will be initialized upon project activation
        self._active_project: Project | None = None

        # determine registered project to be activated (if any)
        registered_project_to_activate: RegisteredProject | None = (
            self.serena_config.get_registered_project(project, autoregister=True) if project is not None else None
        )

        # dashboard URL (set when dashboard is started)
        self._dashboard_url: str | None = None

        # adjust log level
        serena_log_level = self.serena_config.log_level
        if Logger.root.level != serena_log_level:
            log.info(f"Changing the root logger level to {serena_log_level}")
            Logger.root.setLevel(serena_log_level)

        def get_memory_log_handler() -> MemoryLogHandler:
            nonlocal memory_log_handler
            if memory_log_handler is None:
                memory_log_handler = MemoryLogHandler(level=serena_log_level)
                Logger.root.addHandler(memory_log_handler)
            return memory_log_handler

        # open GUI log window if enabled
        self._gui_log_viewer: Optional["GuiLogViewer"] = None
        if self.serena_config.gui_log_window:
            log.info("Opening GUI window")
            if platform.system() == "Darwin":
                log.warning("GUI log window is not supported on macOS")
            else:
                # even importing on macOS may fail if tkinter dependencies are unavailable (depends on Python interpreter installation
                # which uv used as a base, unfortunately)
                from serena.gui_log_viewer import GuiLogViewer

                self._gui_log_viewer = GuiLogViewer("dashboard", title="Serena Logs", memory_log_handler=get_memory_log_handler())
                self._gui_log_viewer.start()
        else:
            log.debug("GUI window is disabled")

        # set the agent context
        if context is None:
            context = SerenaAgentContext.load_default()
        self._context = context

        # instantiate all tool classes
        self._all_tools: dict[type[Tool], Tool] = {tool_class: tool_class(self) for tool_class in ToolRegistry().get_all_tool_classes()}
        tool_names = [tool.get_name_from_cls() for tool in self._all_tools.values()]

        # If GUI log window is enabled, set the tool names for highlighting
        if self._gui_log_viewer is not None:
            self._gui_log_viewer.set_tool_names(tool_names)

        token_count_estimator = RegisteredTokenCountEstimator[self.serena_config.token_count_estimator]
        log.info(f"Will record tool usage statistics with token count estimator: {token_count_estimator.name}.")
        self._tool_usage_stats = ToolUsageStats(token_count_estimator)

        # log fundamental information
        log.info(
            f"Starting Serena server (version={serena_version()}, process id={os.getpid()}, parent process id={os.getppid()}; "
            f"language backend={self.serena_config.language_backend.name}); Python version={platform.python_version()}, platform={platform.platform()}"
        )
        log.info("Configuration file: %s", self.serena_config.config_file_path)
        log.info("Available projects: {}".format(", ".join(self.serena_config.project_names)))
        log.info(f"Loaded tools ({len(self._all_tools)}): {', '.join([tool.get_name_from_cls() for tool in self._all_tools.values()])}")

        self._check_shell_settings()

        # determine the effective language backend for this session.
        # If a startup project is provided and has a per-project override, use it; otherwise use the global config.
        # Since we don't want to change the toolset after startup, the language backend cannot be changed within a running Serena session
        self._language_backend = self.serena_config.language_backend
        if registered_project_to_activate is not None and registered_project_to_activate.project_config.language_backend is not None:
            self._language_backend = registered_project_to_activate.project_config.language_backend
            log.info(f"Using language backend as configured in project.yml: {self._language_backend.name}")
        else:
            log.info(f"Using language backend from global configuration: {self._language_backend.name}")

        # create executor for starting the language server and running tools in another thread
        # This executor is used to achieve linear task execution
        self._task_executor = TaskExecutor("SerenaAgentTaskExecutor")

        # Initialize the prompt factory
        self.prompt_factory = SerenaPromptFactory()
        self._project_activation_callback = project_activation_callback

        # activate the given project (if any), also updating the active modes
        # Note: We cannot update the active tools yet, because the base toolset has not been computed yet
        #       (and its computation depends on the active project)
        self._active_modes: ActiveModes
        self._mode_overrides = modes
        if project is not None:
            try:
                self.activate_project_from_path_or_name(project, update_active_modes=False, update_active_tools=False)
            except Exception as e:
                log.error(f"Error activating project '{project}' at startup: {e}", exc_info=e)
        self._update_active_modes()

        # determine the base toolset defining the set of exposed tools (which e.g. the MCP shall see),
        self._base_toolset = self._create_base_toolset(
            self.serena_config, self._language_backend, self._context, self._active_modes, self._active_project
        )
        self._exposed_tools = self._base_toolset.to_available_tools(self._all_tools)
        log.info(f"Number of exposed tools: {len(self._exposed_tools)}. Exposed tools: {self._exposed_tools.tool_names}")

        # update the active tools (considering the active project, if any)
        self._active_tools: AvailableTools
        self._update_active_tools()

        # start the dashboard (web frontend), registering its log handler
        # should be the last thing to happen in the initialization since the dashboard
        # may access various parts of the agent
        if self.serena_config.web_dashboard:
            self._dashboard_thread, port = SerenaDashboardAPI(
                get_memory_log_handler(), tool_names, agent=self, tool_usage_stats=self._tool_usage_stats
            ).run_in_thread(host=self.serena_config.web_dashboard_listen_address)
            dashboard_host = self.serena_config.web_dashboard_listen_address
            if dashboard_host == "0.0.0.0":
                dashboard_host = "localhost"
            dashboard_url = f"http://{dashboard_host}:{port}/dashboard/index.html"
            self._dashboard_url = dashboard_url
            log.info("Serena web dashboard started at %s", dashboard_url)
            self._start_dashboard_viewer(minimized=not self.serena_config.web_dashboard_open_on_launch)
            # inform the GUI window (if any)
            if self._gui_log_viewer is not None:
                self._gui_log_viewer.set_dashboard_url(dashboard_url)

    @classmethod
    def _create_base_toolset(
        cls,
        serena_config: SerenaConfig,
        language_backend: LanguageBackend,
        context: SerenaAgentContext,
        modes: ActiveModes,
        project: Project | None,
    ) -> ToolSet:
        """
        Determines the base toolset defining the set of exposed tools (which e.g. the MCP shall see).
        It depends on ...
           * dashboard availability/opening on launch
           * Serena config
           * the context (which is fixed for the session)
           * the optional tools enabled by initial modes
           * single-project mode reductions (if applicable)
           * JetBrains mode
        """
        # determine whether to include the OpenDashboardTool based on the Serena configuration
        tool_inclusion_definitions: list[ToolInclusionDefinition] = []
        if serena_config.web_dashboard and not serena_config.web_dashboard_open_on_launch and not serena_config.gui_log_window:
            tool_inclusion_definitions.append(
                NamedToolInclusionDefinition(name="OpenDashboard", included_optional_tools=[OpenDashboardTool.get_name_from_cls()])
            )

        # consider Serena configuration and the active context
        tool_inclusion_definitions.append(serena_config)
        tool_inclusion_definitions.append(context)

        # consider modes
        # Since modes can be dynamically turned on and off, we don't include their definitions directly,
        # For the initially active dynamic modes, we make sure that the tools they enable are included.
        for mode in modes.get_default_modes():
            tool_inclusion_definitions.append(
                NamedToolInclusionDefinition(
                    name=f"InitialDynamicModeInclusions[{mode.name}]", included_optional_tools=mode.included_optional_tools
                )
            )
        # For the base modes, we also apply the tool exclusions, since they apply throughout the entire session
        for base_mode in modes.get_base_modes():
            tool_inclusion_definitions.append(
                NamedToolInclusionDefinition(
                    name=f"BaseMode[{base_mode.name}]",
                    included_optional_tools=base_mode.included_optional_tools,
                    excluded_tools=base_mode.excluded_tools,
                )
            )

        # When in a single-project context, the agent is assumed to work on a single project, and we thus
        # want to apply that project's tool exclusions/inclusions from the get-go, limiting the set
        # of tools that will be exposed to the client.
        # Furthermore, we disable tools that are only relevant for project activation.
        # So if the project exists, we apply all the aforementioned exclusions.
        if context.single_project and project is not None:
            log.info(
                "Applying tool inclusion/exclusion definitions for single-project context based on project '%s'",
                project.project_name,
            )
            tool_inclusion_definitions.append(
                NamedToolInclusionDefinition(
                    name="SingleProjectExclusions",
                    excluded_tools=[ActivateProjectTool.get_name_from_cls(), GetCurrentConfigTool.get_name_from_cls()],
                )
            )
            tool_inclusion_definitions.append(project.project_config)

        # enabled the internal 'jetbrains' mode for the JetBrains backend
        if language_backend == LanguageBackend.JETBRAINS:
            tool_inclusion_definitions.append(SerenaAgentMode.from_name_internal("jetbrains"))

        # compute the resulting tool set
        base_toolset = ToolSet.default().apply(*tool_inclusion_definitions)
        log.info(f"Number of exposed tools: {len(base_toolset)}")
        return base_toolset

    def get_language_backend(self) -> LanguageBackend:
        return self._language_backend

    def get_current_tasks(self) -> list[TaskExecutor.TaskInfo]:
        """
        Gets the list of tasks currently running or queued for execution.
        The function returns a list of thread-safe TaskInfo objects (specifically created for the caller).

        :return: the list of tasks in the execution order (running task first)
        """
        return self._task_executor.get_current_tasks()

    def get_last_executed_task(self) -> TaskExecutor.TaskInfo | None:
        """
        Gets the last executed task.

        :return: the last executed task info or None if no task has been executed yet
        """
        return self._task_executor.get_last_executed_task()

    def get_language_server_manager(self) -> LanguageServerManager | None:
        if self._active_project is not None:
            return self._active_project.language_server_manager
        return None

    def get_language_server_manager_or_raise(self) -> LanguageServerManager:
        active_project = self.get_active_project_or_raise()
        return active_project.get_language_server_manager_or_raise()

    def get_log_inspection_instructions(self) -> str:
        if self.serena_config.web_dashboard:
            return f"Live logs can be inspected via the dashboard at {self.get_dashboard_url()}"
        else:
            log_path = SerenaPaths().last_returned_log_file_path
            if log_path is not None:
                return f"Find the current log file here: {log_path}"
            else:
                return "Unfortunately, logs are not available. We recommend enabling the web dashboard/logging in general."

    def get_context(self) -> SerenaAgentContext:
        return self._context

    def get_tool_description_override(self, tool_name: str) -> str | None:
        return self._context.tool_description_overrides.get(tool_name, None)

    def _check_shell_settings(self) -> None:
        # On Windows, Claude Code sets COMSPEC to Git-Bash (often even with a path containing spaces),
        # which causes all sorts of trouble, preventing language servers from being launched correctly.
        # So we make sure that COMSPEC is unset if it has been set to bash specifically.
        if platform.system() == "Windows":
            comspec = os.environ.get("COMSPEC", "")
            if "bash" in comspec:
                os.environ["COMSPEC"] = ""  # force use of default shell
                log.info("Adjusting COMSPEC environment variable to use the default shell instead of '%s'", comspec)

    def record_tool_usage(self, input_kwargs: dict, tool_result: str | dict, tool: Tool) -> None:
        """
        Record the usage of a tool with the given input and output strings if tool usage statistics recording is enabled.
        """
        tool_name = tool.get_name()
        input_str = str(input_kwargs)
        output_str = str(tool_result)
        log.debug(f"Recording tool usage for tool '{tool_name}'")
        self._tool_usage_stats.record_tool_usage(tool_name, input_str, output_str)

    def get_dashboard_url(self) -> str | None:
        """
        :return: the URL of the web dashboard, or None if the dashboard is not running
        """
        return self._dashboard_url

    @staticmethod
    def _start_dashboard_viewer_process_function(url: str, minimized: bool) -> None:
        """
        Main function of the subprocess for starting the dashboard viewer
        """
        try:
            SerenaDashboardViewer(url, start_minimized=minimized).run()
        except webview.errors.WebViewException as e:
            log.warning(f"Could not open Serena Dashboard viewer. Cause:\n{e}")
            # Fall back to opening the browser window if the window was supposed to be shown directly
            if not minimized:
                SerenaAgent._open_dashboard_in_browser(url)

    def _start_dashboard_viewer(self, minimized: bool) -> None:
        """
        Starts the dashboard viewer (in a separate process) or, if the current platform does not support it,
        opens the dashboard in the default web browser.

        :param minimized: whether the dashboard viewer should be started minimized (if supported on the current platform).
            If the viewer is not supported on the current platform, then this controls whether to open the browser window.
        """
        if not system_has_usable_display():
            log.info("Not starting the Serena dashboard viewer because no usable display was detected.")
            return

        url = self.get_dashboard_url()
        assert url is not None
        if SerenaDashboardViewer.is_current_platform_supported():
            process = multiprocessing.Process(target=self._start_dashboard_viewer_process_function, args=(url, minimized), daemon=True)
            process.start()
        else:
            log.info("Not starting Serena dashboard viewer because the current platform does not support it; using browser-based fallback")
            if not minimized:
                self._open_dashboard_in_browser(url)

    def open_dashboard(self) -> bool:
        """
        Opens the Serena dashboard (for on-demand usage as triggered by the user, e.g. via a tool)

        :return: True if the dashboard was opened, False if it could not be opened
        """
        if self._dashboard_url is None:
            raise Exception("Dashboard is not running.")

        if not system_has_usable_display():
            log.warning("Not opening the Serena web dashboard because no usable display was detected.")
            return False

        self._open_dashboard_in_browser(self._dashboard_url)
        return True

    @staticmethod
    def _open_dashboard_in_browser(url: str) -> None:
        # Use a subprocess to avoid any output from webbrowser.open being written to stdout
        subprocess.Popen(
            [sys.executable, "-c", f"import webbrowser; webbrowser.open({url!r})"],
            stdin=subprocess.DEVNULL,
            stdout=subprocess.DEVNULL,
            stderr=subprocess.DEVNULL,
            start_new_session=False,
        )

    def get_exposed_tool_instances(self) -> list["Tool"]:
        """
        :return: the tool instances which are exposed (e.g. to the MCP client).
            Note that the set of exposed tools is fixed for the session, as
            clients don't react to changes in the set of tools, so this is the superset
            of tools that can be offered during the session.
            If a client should attempt to use a tool that is dynamically disabled
            (e.g. because a project is activated that disables it), it will receive an error.
        """
        return list(self._exposed_tools.tools)

    def get_active_project(self) -> Project | None:
        """
        :return: the active project or None if no project is active
        """
        return self._active_project

    def get_active_project_or_raise(self) -> Project:
        """
        :return: the active project or raises an exception if no project is active
        """
        project = self.get_active_project()
        if project is None:
            raise ValueError("No active project. Please activate a project first.")
        return project

    def set_modes(self, mode_names: list[str]) -> None:
        """
        Set the current mode configurations.

        :param mode_names: List of mode names or paths to use
        """
        self._mode_overrides = ModeSelectionDefinition(default_modes=mode_names)
        self._update_active_modes()
        self._update_active_tools()

        log.info(f"Set modes to {[mode.name for mode in self.get_active_modes()]}")

    def get_active_modes(self) -> list[SerenaAgentMode]:
        """
        :return: the list of active modes
        """
        return list(self._active_modes.get_modes())

    def _format_prompt(self, prompt_template: str) -> str:
        template = JinjaTemplate(prompt_template)
        return template.render(available_tools=self._exposed_tools.tool_names, available_markers=self._exposed_tools.tool_marker_names)

    def create_system_prompt(self) -> str:
        available_tools = self._active_tools
        available_markers = available_tools.tool_marker_names
        global_memories = MemoriesManager(
            serena_data_folder=None, read_only_memory_patterns=self.serena_config.read_only_memory_patterns
        ).list_global_memories()
        global_memories_str = dict_string(global_memories.to_dict()) if len(global_memories) > 0 else ""
        log.info("Generating system prompt with available_tools=(see active tools), available_markers=%s", available_markers)
        system_prompt = self.prompt_factory.create_system_prompt(
            context_system_prompt=self._format_prompt(self._context.prompt),
            mode_system_prompts=[self._format_prompt(mode.prompt) for mode in self.get_active_modes()],
            available_tools=available_tools.tool_names,
            available_markers=available_markers,
            global_memories_list=global_memories_str,
        )

        # If a project is active at startup, append its activation message
        if self._active_project is not None:
            system_prompt += "\n\n" + self.get_project_activation_message()

        log.info("System prompt:\n%s", system_prompt)
        return system_prompt

    def get_project_activation_message(self) -> str:
        """
        :return: a message providing information about the project upon activation (e.g. programming language, memories, initial prompt)
        :raise: AssertionError if no project is active
        """
        proj = self._active_project
        assert proj is not None, "A project must be active before calling this."
        if proj.is_newly_created:
            msg = f"Created and activated a new project with name '{proj.project_name}' at {proj.project_root}. "
        else:
            msg = f"The project with name '{proj.project_name}' at {proj.project_root} is activated."
        if self._language_backend == LanguageBackend.LSP:
            languages_str = ", ".join([lang.value for lang in proj.project_config.languages])
            msg += f"\nProgramming languages: {languages_str}."
        msg += "File encoding: {proj.project_config.encoding}."

        include_memories = self._active_tools.contains_tool_class(ReadMemoryTool)
        if include_memories:
            project_memories = proj.memories_manager.list_project_memories()
            if project_memories:
                msg += (
                    f"\n{json.dumps(project_memories.to_dict())}\n"
                    + "Use the `read_memory` tool to read these memories later if they are relevant to the task."
                )
        if proj.project_config.initial_prompt:
            msg += f"\nAdditional project-specific instructions:\n {proj.project_config.initial_prompt}"
        return msg

    def _update_active_modes(self) -> None:
        """
        Updates the active modes based on the Serena configuration, the active project configuration (if any),
        and mode overrides (if any).
        """
        self._active_modes = ActiveModes()
        self._active_modes.apply(self.serena_config)
        if self._active_project:
            self._active_modes.apply(self._active_project.project_config)
        if self._mode_overrides:
            self._active_modes.apply(self._mode_overrides)

    def _update_active_tools(self) -> None:
        """
        Updates the active tools based on the active modes and the active project.
        The base tool set already takes the Serena configuration and the context into account
        (as well as many other aspects, such as JetBrains mode).
        """
        # apply modes
        tool_set = self._base_toolset.apply(*self._active_modes.get_modes())

        # apply active project configuration (if any)
        if self._active_project is not None:
            tool_set = tool_set.apply(self._active_project.project_config)
            if self._active_project.project_config.read_only:
                tool_set = tool_set.without_editing_tools()

        self._active_tools = tool_set.to_available_tools(self._all_tools)
        log.info(f"Active tools ({len(self._active_tools)}): {', '.join(self._active_tools.tool_names)}")

        # check if a tool was activated that is not in the exposed tool set and issue a warning if so
        active_tools_not_exposed = set(self._active_tools.tool_names) - set(self._exposed_tools.tool_names)
        if active_tools_not_exposed:
            log.warning(
                "The following active tools are not in the exposed tool set and thus won't be available to clients:\n"
                f"{active_tools_not_exposed}\n"
                "Consider adjusting your configuration to include these tools if you want to use them."
            )

    def issue_task(
        self, task: Callable[[], T], name: str | None = None, logged: bool = True, timeout: float | None = None
    ) -> TaskExecutor.Task[T]:
        """
        Issue a task to the executor for asynchronous execution.
        It is ensured that tasks are executed in the order they are issued, one after another.

        :param task: the task to execute
        :param name: the name of the task for logging purposes; if None, use the task function's name
        :param logged: whether to log management of the task; if False, only errors will be logged
        :param timeout: the maximum time to wait for task completion in seconds, or None to wait indefinitely
        :return: the task object, through which the task's future result can be accessed
        """
        return self._task_executor.issue_task(task, name=name, logged=logged, timeout=timeout)

    def execute_task(self, task: Callable[[], T], name: str | None = None, logged: bool = True, timeout: float | None = None) -> T:
        """
        Executes the given task synchronously via the agent's task executor.
        This is useful for tasks that need to be executed immediately and whose results are needed right away.

        :param task: the task to execute
        :param name: the name of the task for logging purposes; if None, use the task function's name
        :param logged: whether to log management of the task; if False, only errors will be logged
        :param timeout: the maximum time to wait for task completion in seconds, or None to wait indefinitely
        :return: the result of the task execution
        """
        return self._task_executor.execute_task(task, name=name, logged=logged, timeout=timeout)

    def is_using_language_server(self) -> bool:
        """
        :return: whether this agent uses language server-based code analysis
        """
        return self._language_backend == LanguageBackend.LSP

    def _activate_project(self, project: Project, update_active_modes: bool = True, update_active_tools: bool = True) -> None:
        log.info(f"Activating {project.project_name} at {project.project_root}")

        # Check if the project requires a different language backend than the one initialized at startup
        project_backend = project.project_config.language_backend
        if project_backend is not None and project_backend != self._language_backend:
            raise ValueError(
                f"Cannot activate project '{project.project_name}': it requires the {project_backend.value} backend, "
                f"but this session was initialized with {self._language_backend.value}. "
                f"Workarounds: (1) Use project activation at startup via the --project flag, "
                f"(2) Configure one MCP server per backend in your client."
            )

        # shut down the previously active project to release its language server processes
        if self._active_project is not None:
            log.info(f"Shutting down previously active project '{self._active_project.project_name}' before switching")
            self._active_project.shutdown()

        self._active_project = project
        project.set_agent(self)

        if update_active_modes:
            self._update_active_modes()

        if update_active_tools:
            self._update_active_tools()

        def init_language_server_manager() -> None:
            # start the language server
            with LogTime("Language server initialization", logger=log):
                self.reset_language_server_manager()

        # initialize the language server in the background (if in language server mode)
        if self.get_language_backend().is_lsp():
            self.issue_task(init_language_server_manager)

        if self._project_activation_callback is not None:
            self._project_activation_callback()

    def activate_project_from_path_or_name(
        self, project_root_or_name: str, update_active_modes: bool = True, update_active_tools: bool = True
    ) -> Project:
        """
        Activate a project from a path or a name.
        If the project was already registered, it will just be activated.
        If the argument is a path at which no Serena project previously existed, the project will be created beforehand.
        Raises ProjectNotFoundError if the project could neither be found nor created.
        """
        project_instance: Project | None = self.serena_config.get_project(project_root_or_name)
        if project_instance is not None:
            log.info(f"Found registered project '{project_instance.project_name}' at path {project_instance.project_root}")
        elif os.path.isdir(project_root_or_name):
            project_instance = self.serena_config.add_project_from_path(project_root_or_name)
            log.info(f"Added new project {project_instance.project_name} for path {project_instance.project_root}")

        if project_instance is None:
            raise ProjectNotFoundError(
                f"Project '{project_root_or_name}' not found: Not a valid project name or directory. "
                f"Existing project names: {self.serena_config.project_names}"
            )

        self._activate_project(project_instance, update_active_modes=update_active_modes, update_active_tools=update_active_tools)

        return project_instance

    def get_active_tool_names(self) -> list[str]:
        """
        :return: the list of names of the active tools for the current project, sorted alphabetically
        """
        return self._active_tools.tool_names

    def tool_is_active(self, tool_name: str) -> bool:
        """
        :param tool_class: the name of the tool to check
        :return: True if the tool is active, False otherwise
        """
        return self._active_tools.contains_tool_name(tool_name)

    def get_current_config_overview(self) -> str:
        """
        :return: a string overview of the current configuration, including the active and available configuration options
        """
        result_str = "Current configuration:\n"
        result_str += f"Serena version: {serena_version()}\n"
        result_str += f"Loglevel: {self.serena_config.log_level}, trace_lsp_communication={self.serena_config.trace_lsp_communication}\n"
        if self._active_project is not None:
            result_str += f"Active project: {self._active_project.project_name}\n"
        else:
            result_str += "No active project\n"
        result_str += f"Language backend: {self._language_backend.value}"
        if self._active_project and self._active_project.project_config.language_backend is not None:
            result_str += " (project override)"
        result_str += f" (global default: {self.serena_config.language_backend.value})\n"
        result_str += "Available projects:\n" + "\n".join(list(self.serena_config.project_names)) + "\n"
        result_str += f"Active context: {self._context.name}\n"

        # Active modes
        active_mode_names = [mode.name for mode in self.get_active_modes()]
        result_str += "Active modes: {}\n".format(", ".join(active_mode_names)) + "\n"

        # Available but not active modes
        all_available_modes = SerenaAgentMode.list_registered_mode_names()
        inactive_modes = [mode for mode in all_available_modes if mode not in active_mode_names]
        if inactive_modes:
            result_str += "Available but not active modes: {}\n".format(", ".join(inactive_modes)) + "\n"

        # Active tools
        result_str += "Active tools (after all exclusions from the project, context, and modes):\n"
        active_tool_names = self.get_active_tool_names()
        # print the tool names in chunks
        chunk_size = 4
        for i in range(0, len(active_tool_names), chunk_size):
            chunk = active_tool_names[i : i + chunk_size]
            result_str += "  " + ", ".join(chunk) + "\n"

        # Available but not active tools
        all_tool_names = sorted([tool.get_name_from_cls() for tool in self._all_tools.values()])
        inactive_tool_names = [tool for tool in all_tool_names if tool not in active_tool_names]
        if inactive_tool_names:
            result_str += "Available but not active tools:\n"
            for i in range(0, len(inactive_tool_names), chunk_size):
                chunk = inactive_tool_names[i : i + chunk_size]
                result_str += "  " + ", ".join(chunk) + "\n"

        return result_str

    def reset_language_server_manager(self) -> None:
        """
        Starts/resets the language server manager for the current project
        """
        self.get_active_project_or_raise().create_language_server_manager()

    def add_language(self, language: Language) -> None:
        """
        Adds a new language to the active project, spawning the respective language server and updating the project configuration.
        The addition is scheduled via the agent's task executor and executed synchronously, i.e. the method returns
        when the addition is complete.

        :param language: the language to add
        """
        self.execute_task(lambda: self.get_active_project_or_raise().add_language(language), name=f"AddLanguage:{language.value}")

    def remove_language(self, language: Language) -> None:
        """
        Removes a language from the active project, shutting down the respective language server and updating the project configuration.
        The removal is scheduled via the agent's task executor and executed asynchronously.

        :param language: the language to remove
        """
        self.issue_task(lambda: self.get_active_project_or_raise().remove_language(language), name=f"RemoveLanguage:{language.value}")

    def get_tool(self, tool_class: type[TTool]) -> TTool:
        return self._all_tools[tool_class]  # type: ignore

    def print_tool_overview(self) -> None:
        ToolRegistry().print_tool_overview(self._active_tools.tools)

    def __del__(self) -> None:
        self.shutdown()

    def shutdown(self, timeout: float = 2.0) -> None:
        """
        Shuts down the agent, freeing resources and stopping background tasks.
        """
        # guard against __del__ being called on a partially constructed instance
        if not hasattr(self, "_active_project"):
            return
        log.info("SerenaAgent is shutting down ...")
        if self._active_project is not None:
            self._active_project.shutdown(timeout=timeout)
            self._active_project = None
        if self._gui_log_viewer:
            log.info("Stopping the GUI log window ...")
            self._gui_log_viewer.stop()
            self._gui_log_viewer = None

    def get_tool_by_name(self, tool_name: str) -> Tool:
        tool_class = ToolRegistry().get_tool_class_by_name(tool_name)
        return self.get_tool(tool_class)

    def get_active_lsp_languages(self) -> list[Language]:
        ls_manager = self.get_language_server_manager()
        if ls_manager is None:
            return []
        return ls_manager.get_active_languages()

    @contextmanager
    def active_project_context(self, project: Project) -> Iterator[None]:
        """
        Context manager for temporarily setting/overriding the active project

        :param project: the project to be active
        """
        original_project = self._active_project
        self._active_project = project
        try:
            yield
        finally:
            self._active_project = original_project
