Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.toolbox.views.interface

from abc import abstractmethod
from enum import Enum
from typing import Optional

from pydantic import (
    BaseModel,
    ConfigDict,
)

from ..panel import (
    HasPanelItems,
    panel_item_types,
    ToolPanelElements,
)


class ToolPanelViewModelType(str, Enum):
    default_type = "default"
    generic = "generic"
    activity = "activity"
    ontology = "ontology"
    publication = "publication"
    training = "training"


class ToolPanelViewModel(BaseModel):
    """A view of ToolPanelView objects serialized for the API."""

    id: str
    model_class: str
    name: str
    description: Optional[str] = None
    view_type: ToolPanelViewModelType
    searchable: bool  # Allow for more dynamic views that don't plug into fixed search indicies in the future...
    model_config = ConfigDict(protected_namespaces=())


class ToolBoxRegistry:
    """View of ToolBox provided to ToolPanelView to reason about tools loaded."""

    @abstractmethod
    def has_tool(self, tool_id: str) -> bool:
        """Return bool indicating if tool with specified id is loaded."""

    @abstractmethod
    def get_tool(self, tool_id: str):
        """Return tool with supplied tool id."""

    @abstractmethod
    def get_workflow(self, id: str):
        """Return workflow from panel with supplied id."""

    @abstractmethod
    def add_tool_to_tool_panel_view(self, tool, tool_panel_component: HasPanelItems) -> None:
        """Add tool to the tool panel view component (root or section)."""


class ToolPanelView:
    @abstractmethod
    def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
        """Consume tool panel state and return custom tool panel view."""

    @abstractmethod
    def to_model(self) -> ToolPanelViewModel:
        """Convert abstract description to dictionary description to emit via the API."""


def walk_loaded_tools(tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry):
    for key, item_type, val in tool_panel.panel_items_iter():
        if item_type == panel_item_types.TOOL:
            tool_id = key.replace("tool_", "", 1)
            if toolbox_registry.has_tool(tool_id):
                yield (tool_id, key, val, val.name)
        elif item_type == panel_item_types.SECTION:
            for section_key, section_item_type, section_val in val.panel_items_iter():
                if section_item_type == panel_item_types.TOOL:
                    tool_id = section_key.replace("tool_", "", 1)
                    if toolbox_registry.has_tool(tool_id):
                        yield (tool_id, key, section_val, val.name)