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

import logging
import re
from typing import Optional

from .definitions import (
from .interface import (
from ..panel import (

log = logging.getLogger(__name__)

[docs]def build_filter(excludes_): excludes = excludes_ or [] def filter_function(panel_key, panel_value): for exclude in excludes: if panel_key.startswith("tool_"): if isinstance(exclude, ExcludeTool): if panel_value.id == exclude.tool_id: return False if panel_value.old_id == exclude.tool_id: return False if isinstance(exclude, ExcludeToolRegex): if re.match(exclude.tool_id_regex, panel_value.id): return False if re.match(exclude.tool_id_regex, panel_value.old_id): return False if isinstance(exclude, ExcludeTypes): if panel_key.startswith("label_") and "label" in exclude.types: return False if panel_key.startswith("tool_") and "tool" in exclude.types: return False if panel_key.startswith("workflow_") and "workflow" in exclude.types: return False return True return filter_function
[docs]class StaticToolPanelView(ToolPanelView): _definition: StaticToolBoxView
[docs] def __init__(self, definition: StaticToolBoxView): self._definition = definition
[docs] def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements: def apply_filter(definition, elems): excludes = self._all_excludes(definition) if excludes: elems.apply_filter(build_filter(excludes)) def definition_with_items_to_panel(definition, allow_sections: bool = True, items=None): new_panel = ToolPanelElements() if items is None: items = definition.items_expanded for element in items: if element.content_type == "section": assert allow_sections section_def: Section = element section: ToolSection assert section_def.id is not None or section_def.name is not None if element.items: panel = definition_with_items_to_panel(section_def, allow_sections=False) section = ToolSection() if section_def.name is not None: name = section_def.name else: assert section_def.id is not None name = section_def.id section.name = name if section_def.id is not None: section.id = section_def.id else: # TODO: there has to be tool shed code to do this in a consistent way... where is it? section.id = name.replace(" ", "-").lower() section.elems = panel else: closest_section = base_tool_panel.closest_section(section_def.id, section_def.name) if closest_section is None: log.warning(f"Failed to find matching section for (id, name) = ({section_def.id}, {section_def.name})") continue section = closest_section.copy() if section_def.id is not None: section.id = section_def.id if section_def.name is not None: section.name = section_def.name apply_filter(section_def, section.elems) new_panel.append_section(section.id, section) elif element.content_type == "section_alias": assert allow_sections closest_section = base_tool_panel.closest_section(element.section, element.section) if closest_section is None: log.warning(f"Failed to find matching section for (id, name) = ({element.section}, {element.section})") continue section = closest_section.copy() apply_filter(element, section.elems) new_panel.append_section(section.id, section) elif element.content_type == "label": as_dict = { "id": element.id or element.text.lower().replace(" ", "-"), "text": element.text, "type": "label", } label = ToolSectionLabel(as_dict) key = f"label_{label.id}" new_panel[key] = label elif element.content_type == "tool": tool_id = element.id if not toolbox_registry.has_tool(tool_id): log.warning(f"Failed to find tool_id {tool_id} from parent toolbox, cannot load into panel view") continue tool = toolbox_registry.get_tool(tool_id) toolbox_registry.add_tool_to_tool_panel_view(tool, new_panel) elif element.content_type == "workflow": workflow_def: Workflow = element workflow = toolbox_registry.get_workflow(element.id) panel_id = f"workflow_{workflow_def.id}" new_panel[panel_id] = workflow elif element.content_type == "items_from": closest_section = base_tool_panel.closest_section(element.items_from, element.items_from) if closest_section is None: log.warning(f"Failed to find matching section for (id, name) = ({element.items_from}, None)") continue elems = closest_section.elems.copy() apply_filter(element, elems) for key, item in elems.items(): new_panel[key] = item else: raise AssertionError("Unknown static toolbox configuration element encountered.") excludes = self._all_excludes(definition) if excludes: new_panel.apply_filter(build_filter(excludes)) return new_panel root_defintion = self._definition root_items = root_defintion.items_expanded if root_items is None: root_items = [] # No items found, use base tool panel and apply filters to that... for (_, panel_type, panel_value) in base_tool_panel.panel_items_iter(): item: Optional[ExpandedRootContent] = None if panel_type == panel_item_types.TOOL: item = Tool( id=panel_value.id, ) elif panel_type == panel_item_types.SECTION: item = SectionAlias( section=panel_value.id, ) elif panel_type == panel_item_types.LABEL: item = Label( id=panel_value.id, text=panel_value.text, ) elif panel_type == panel_item_types.WORKFLOW: item = Workflow( id=panel_value.id, ) if item is None: raise Exception("Unknown panel item type encountered.") root_items.append(item) return definition_with_items_to_panel(root_defintion, items=root_items)
def _all_excludes(self, has_excludes): excludes = has_excludes.excludes or [] if has_excludes != self._definition and self._definition.excludes: excludes.extend(self._definition.excludes) return excludes
[docs] def to_model(self) -> ToolPanelViewModel: model_id = self._definition.id name = self._definition.name description = self._definition.description view_type = ToolPanelViewModelType[self._definition.view_type.value] model_class = self.__class__.__name__ return ToolPanelViewModel( id=model_id, name=name, description=description, model_class=model_class, view_type=view_type, searchable=True, )