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.

galaxy.tool_util.toolbox package

API for this module containing functionality related to the toolbox.

class galaxy.tool_util.toolbox.AbstractToolBox(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view='default', save_integrated_tool_panel=True)

Bases: Dictifiable, ManagesIntegratedToolPanelMixin

Abstract container for managing a ToolPanel - containing tools and workflows optionally in labelled sections.

__init__(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view='default', save_integrated_tool_panel=True)

Create a toolbox from the config files named by config_filenames, using tool_root_dir as the base directory for finding individual tool config files.

create_tool(config_file, tool_shed_repository=None, guid=None, **kwds)

create_dynamic_tool(dynamic_tool)

can_load_config_file(config_filename)

tool_tag_manager()

Build a tool tag manager according to app’s configuration and return it.

panel_views() → List[ToolPanelViewModel]

panel_view_dicts() → Dict[str, Dict]

panel_has_tool(tool, panel_view_id)

load_dynamic_tool(dynamic_tool)

load_item(item, tool_path, panel_dict=None, integrated_panel_dict=None, load_panel_dict=True, guid=None, index=None, tool_cache_data_dir=None)

get_shed_config_dict_by_filename(filename) → Dict[str, Any] | None

update_shed_config(shed_conf)

Update the in-memory descriptions of tools and write out the changes to integrated tool panel unless we are just deactivating a tool (since that doesn’t affect that file).

get_section(section_id, new_label=None, create_if_needed=False)

create_section(section_dict)

get_section_for_tool(tool)

add_tool_to_tool_panel_view(tool, view_panel_component)

get_tool(tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None)

Attempt to locate a tool in the tool box. Note that exact only refers to the tool_id, not the tool_version.

has_tool(tool_id: str, tool_version: str | None = None, exact: bool = False)

is_missing_shed_tool(tool_id: str) → bool

Confirm that the tool ID does reference a shed tool and is not installed.

get_loaded_tools_by_lineage(tool_id: str) → list

Get all loaded tools associated by lineage to the tool whose id is tool_id.

tools()

dynamic_confs(include_migrated_tool_conf=False) → List[Dict[str, Any]]

default_shed_tool_conf_dict() → Dict[str, Any]

If set, returns the first shed_tool_conf_dict corresponding to shed_tool_config_file, else the first dynamic conf.

dynamic_conf_filenames()

Return list of dynamic tool configuration filenames (shed_tools). These must be used with various dynamic tool configuration update operations (e.g. with update_shed_config).

get_tool_repository_from_xml_item(elem, path)

load_tool(config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds)

Load a single tool from the file named by config_file and return an instance of Tool.

watch_tool(tool)

add_tool_to_cache(tool, config_file)

load_tool_from_cache(config_file, recover_tool=False)

load_hidden_lib_tool(path)

load_hidden_tool(config_file, **kwds)

Load a hidden tool (in this context meaning one that does not appear in the tool panel) and register it in _tools_by_id.

register_tool(tool)

package_tool(trans, tool_id)

Create a tarball with the tool’s xml, help images, and test data. :param trans: the web transaction :param tool_id: the tool ID from app.toolbox :returns: tuple of tarball filename, success True/False, message/None

reload_tool_by_id(tool_id: str) → Tuple[str | Dict[str, str], str]

Attempt to reload the tool identified by ‘tool_id’, if successful replace the old tool.

remove_tool_by_id(tool_id, remove_from_panel=True)

Attempt to remove the tool identified by ‘tool_id’. Ignores tool lineage - so to remove a tool with potentially multiple versions send remove_from_panel=False and handle the logic of promoting the next newest version of the tool into the panel if needed.

get_sections()

Return section id and name pairs.

Only used by build_tool_panel_section_select_field in tool shed client code.

find_section_id(tool_panel_section_id)

Find the section ID referenced by the key or return ‘’ indicating no such section id.

tool_panel_contents(trans, view=None, **kwds)

Filter tool_panel contents for displaying for user.

get_tool_to_dict(trans, tool, tool_help=False)

Return tool’s to_dict. Use cache if present, store to cache otherwise. Note: The cached tool’s to_dict is specific to the calls from toolbox.

to_dict(trans, in_panel=True, tool_help=False, view=None, **kwds)

Create a dictionary representation of the toolbox. Uses primitive cache for toolbox-specific tool ‘to_dict’s.

to_panel_view(trans, view='default_panel_view', **kwds)

Create a panel view representation of the toolbox. Uses the structure:

{section_id: { section but with .tools=List[all tool ids] }, …}}

class galaxy.tool_util.toolbox.AbstractToolTagManager

Bases: object

abstract reset_tags()

Starting to load tool panels, reset all tags.

abstract handle_tags(tool_id, tool_definition_source)

Parse out tags and persist them.

class galaxy.tool_util.toolbox.panel_item_types(value)

Bases: str, Enum

An enumeration.

TOOL = 'TOOL'

WORKFLOW = 'WORKFLOW'

SECTION = 'SECTION'

LABEL = 'LABEL'

class galaxy.tool_util.toolbox.ToolSection(item=None)

Bases: Dictifiable, HasPanelItems

A group of tools with similar type/purpose that will be displayed as a group in the user interface.

dict_collection_visible_keys = ['id', 'name', 'version', 'description', 'links']

__init__(item=None)

Build a ToolSection from an ElementTree element or a dictionary.

copy(merge_tools=False)

to_dict(trans, link_details=False, tool_help=False, toolbox=None, only_ids=False)

Return a dict that includes section’s attributes.

if only_ids is True, we store only the ids of the section’s tools in section.tools (also full ToolSectionLabel objects in section.tools if any are present)

if only_ids is False, we store the section’s full Tool (and any other) objects in section.elems

panel_items()

Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections).

class galaxy.tool_util.toolbox.ToolSectionLabel(item)

Bases: Dictifiable

A label for a set of tools that can be displayed above groups of tools and sections in the user interface

dict_collection_visible_keys = ['id', 'text', 'version', 'description', 'links']

__init__(item)

Build a ToolSectionLabel from an ElementTree element or a dictionary.

to_dict(**kwds)

Return item dictionary.

Subpackages

• galaxy.tool_util.toolbox.filters package
  • FilterFactory
    • FilterFactory.__init__()
    • FilterFactory.build_filters()
    • FilterFactory.build_filter_function()
• galaxy.tool_util.toolbox.lineages package
  • LineageMap
    • LineageMap.__init__()
    • LineageMap.register()
    • LineageMap.get()
  • ToolLineage
    • ToolLineage.lineages_by_id
    • ToolLineage.lock
    • ToolLineage.__init__()
    • ToolLineage.tool_ids
    • ToolLineage.from_tool()
    • ToolLineage.register_version()
    • ToolLineage.get_versions()
    • ToolLineage.get_version_ids()
    • ToolLineage.to_dict()
  • Submodules
  • galaxy.tool_util.toolbox.lineages.factory module
    • LineageMap
      • LineageMap.__init__()
      • LineageMap.register()
      • LineageMap.get()
  • galaxy.tool_util.toolbox.lineages.interface module
    • ToolLineageVersion
      • ToolLineageVersion.__init__()
      • ToolLineageVersion.id_based
      • ToolLineageVersion.to_dict()
    • ToolLineage
      • ToolLineage.lineages_by_id
      • ToolLineage.lock
      • ToolLineage.__init__()
      • ToolLineage.tool_ids
      • ToolLineage.from_tool()
      • ToolLineage.register_version()
      • ToolLineage.get_versions()
      • ToolLineage.get_version_ids()
      • ToolLineage.to_dict()
• galaxy.tool_util.toolbox.views package
  • Submodules
  • galaxy.tool_util.toolbox.views.definitions module
    • StaticToolBoxViewTypeEnum
      • StaticToolBoxViewTypeEnum.generic
      • StaticToolBoxViewTypeEnum.activity
      • StaticToolBoxViewTypeEnum.publication
      • StaticToolBoxViewTypeEnum.training
    • ExcludeTool
      • ExcludeTool.tool_id
      • ExcludeTool.model_config
      • ExcludeTool.model_fields
    • ExcludeToolRegex
      • ExcludeToolRegex.tool_id_regex
      • ExcludeToolRegex.model_config
      • ExcludeToolRegex.model_fields
    • ExcludeTypes
      • ExcludeTypes.types
      • ExcludeTypes.model_config
      • ExcludeTypes.model_fields
    • Tool
      • Tool.content_type
      • Tool.id
      • Tool.model_config
      • Tool.model_fields
    • Label
      • Label.content_type
      • Label.id
      • Label.text
      • Label.model_config
      • Label.model_fields
    • LabelShortcut
      • LabelShortcut.content_type
      • LabelShortcut.label
      • LabelShortcut.model_config
      • LabelShortcut.model_fields
    • Workflow
      • Workflow.content_type
      • Workflow.id
      • Workflow.model_config
      • Workflow.model_fields
    • ItemsFrom
      • ItemsFrom.content_type
      • ItemsFrom.items_from
      • ItemsFrom.excludes
      • ItemsFrom.model_config
      • ItemsFrom.model_fields
    • HasItems
      • HasItems.items
      • HasItems.items_expanded
    • Section
      • Section.content_type
      • Section.id
      • Section.name
      • Section.items
      • Section.excludes
      • Section.model_config
      • Section.model_fields
    • SectionAlias
      • SectionAlias.content_type
      • SectionAlias.section
      • SectionAlias.excludes
      • SectionAlias.model_config
      • SectionAlias.model_fields
    • SectionAliases
      • SectionAliases.content_type
      • SectionAliases.sections
      • SectionAliases.excludes
      • SectionAliases.model_config
      • SectionAliases.model_fields
    • StaticToolBoxView
      • StaticToolBoxView.id
      • StaticToolBoxView.name
      • StaticToolBoxView.description
      • StaticToolBoxView.view_type
      • StaticToolBoxView.items
      • StaticToolBoxView.excludes
      • StaticToolBoxView.from_dict()
      • StaticToolBoxView.model_config
      • StaticToolBoxView.model_fields
  • galaxy.tool_util.toolbox.views.edam module
    • EdamPanelMode
      • EdamPanelMode.merged
      • EdamPanelMode.topics
      • EdamPanelMode.operations
    • EdamToolPanelView
      • EdamToolPanelView.__init__()
      • EdamToolPanelView.apply_view()
      • EdamToolPanelView.to_model()
  • galaxy.tool_util.toolbox.views.interface module
    • ToolPanelViewModelType
      • ToolPanelViewModelType.default_type
      • ToolPanelViewModelType.generic
      • ToolPanelViewModelType.activity
      • ToolPanelViewModelType.ontology
      • ToolPanelViewModelType.publication
      • ToolPanelViewModelType.training
    • ToolPanelViewModel
      • ToolPanelViewModel.id
      • ToolPanelViewModel.model_class
      • ToolPanelViewModel.name
      • ToolPanelViewModel.description
      • ToolPanelViewModel.view_type
      • ToolPanelViewModel.searchable
      • ToolPanelViewModel.model_config
      • ToolPanelViewModel.model_fields
    • ToolBoxRegistry
      • ToolBoxRegistry.has_tool()
      • ToolBoxRegistry.get_tool()
      • ToolBoxRegistry.get_workflow()
      • ToolBoxRegistry.add_tool_to_tool_panel_view()
    • ToolPanelView
      • ToolPanelView.apply_view()
      • ToolPanelView.to_model()
    • walk_loaded_tools()
  • galaxy.tool_util.toolbox.views.sources module
    • StaticToolBoxViewSources
      • StaticToolBoxViewSources.__init__()
      • StaticToolBoxViewSources.view_directories
      • StaticToolBoxViewSources.view_dicts
      • StaticToolBoxViewSources.get_definitions()
    • looks_like_view_source_filename()
  • galaxy.tool_util.toolbox.views.static module
    • build_filter()
    • StaticToolPanelView
      • StaticToolPanelView.__init__()
      • StaticToolPanelView.apply_view()
      • StaticToolPanelView.to_model()

Submodules

galaxy.tool_util.toolbox.base module

class galaxy.tool_util.toolbox.base.ToolConfRepository(tool_shed, name, owner, installed_changeset_revision, changeset_revision, tool_dependencies_installed_or_in_error, repository_path, tool_path)

Bases: _ToolConfRepository

get_tool_relative_path(*args, **kwargs)

class galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl(toolbox: AbstractToolBox)

Bases: ToolBoxRegistry

View of ToolBox provided to ToolPanelView to reason about tools loaded.

__init__(toolbox: AbstractToolBox)

has_tool(tool_id: str) → bool

Return bool indicating if tool with specified id is loaded.

get_tool(tool_id: str)

Return tool with supplied tool id.

get_workflow(id: str)

Return workflow from panel with supplied id.

add_tool_to_tool_panel_view(tool, tool_panel_component) → None

Add tool to the tool panel view component (root or section).

class galaxy.tool_util.toolbox.base.AbstractToolTagManager

Bases: object

abstract reset_tags()

Starting to load tool panels, reset all tags.

abstract handle_tags(tool_id, tool_definition_source)

Parse out tags and persist them.

class galaxy.tool_util.toolbox.base.NullToolTagManager

Bases: AbstractToolTagManager

reset_tags() → None

Starting to load tool panels, reset all tags.

handle_tags(tool_id, tool_definition_source) → None

Parse out tags and persist them.

class galaxy.tool_util.toolbox.base.AbstractToolBox(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view='default', save_integrated_tool_panel=True)

Bases: Dictifiable, ManagesIntegratedToolPanelMixin

Abstract container for managing a ToolPanel - containing tools and workflows optionally in labelled sections.

__init__(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view='default', save_integrated_tool_panel=True)

Create a toolbox from the config files named by config_filenames, using tool_root_dir as the base directory for finding individual tool config files.

create_tool(config_file, tool_shed_repository=None, guid=None, **kwds)

create_dynamic_tool(dynamic_tool)

can_load_config_file(config_filename)

tool_tag_manager()

Build a tool tag manager according to app’s configuration and return it.

panel_views() → List[ToolPanelViewModel]

panel_view_dicts() → Dict[str, Dict]

panel_has_tool(tool, panel_view_id)

load_dynamic_tool(dynamic_tool)

load_item(item, tool_path, panel_dict=None, integrated_panel_dict=None, load_panel_dict=True, guid=None, index=None, tool_cache_data_dir=None)

get_shed_config_dict_by_filename(filename) → Dict[str, Any] | None

update_shed_config(shed_conf)

Update the in-memory descriptions of tools and write out the changes to integrated tool panel unless we are just deactivating a tool (since that doesn’t affect that file).

get_section(section_id, new_label=None, create_if_needed=False)

create_section(section_dict)

get_section_for_tool(tool)

add_tool_to_tool_panel_view(tool, view_panel_component)

get_tool(tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None)

Attempt to locate a tool in the tool box. Note that exact only refers to the tool_id, not the tool_version.

has_tool(tool_id: str, tool_version: str | None = None, exact: bool = False)

is_missing_shed_tool(tool_id: str) → bool

Confirm that the tool ID does reference a shed tool and is not installed.

get_loaded_tools_by_lineage(tool_id: str) → list

Get all loaded tools associated by lineage to the tool whose id is tool_id.

tools()

dynamic_confs(include_migrated_tool_conf=False) → List[Dict[str, Any]]

default_shed_tool_conf_dict() → Dict[str, Any]

If set, returns the first shed_tool_conf_dict corresponding to shed_tool_config_file, else the first dynamic conf.

dynamic_conf_filenames()

Return list of dynamic tool configuration filenames (shed_tools). These must be used with various dynamic tool configuration update operations (e.g. with update_shed_config).

get_tool_repository_from_xml_item(elem, path)

load_tool(config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds)

Load a single tool from the file named by config_file and return an instance of Tool.

watch_tool(tool)

add_tool_to_cache(tool, config_file)

load_tool_from_cache(config_file, recover_tool=False)

load_hidden_lib_tool(path)

load_hidden_tool(config_file, **kwds)

Load a hidden tool (in this context meaning one that does not appear in the tool panel) and register it in _tools_by_id.

register_tool(tool)

package_tool(trans, tool_id)

Create a tarball with the tool’s xml, help images, and test data. :param trans: the web transaction :param tool_id: the tool ID from app.toolbox :returns: tuple of tarball filename, success True/False, message/None

reload_tool_by_id(tool_id: str) → Tuple[str | Dict[str, str], str]

Attempt to reload the tool identified by ‘tool_id’, if successful replace the old tool.

remove_tool_by_id(tool_id, remove_from_panel=True)

Attempt to remove the tool identified by ‘tool_id’. Ignores tool lineage - so to remove a tool with potentially multiple versions send remove_from_panel=False and handle the logic of promoting the next newest version of the tool into the panel if needed.

get_sections()

Return section id and name pairs.

Only used by build_tool_panel_section_select_field in tool shed client code.

find_section_id(tool_panel_section_id)

Find the section ID referenced by the key or return ‘’ indicating no such section id.

tool_panel_contents(trans, view=None, **kwds)

Filter tool_panel contents for displaying for user.

get_tool_to_dict(trans, tool, tool_help=False)

Return tool’s to_dict. Use cache if present, store to cache otherwise. Note: The cached tool’s to_dict is specific to the calls from toolbox.

to_dict(trans, in_panel=True, tool_help=False, view=None, **kwds)

Create a dictionary representation of the toolbox. Uses primitive cache for toolbox-specific tool ‘to_dict’s.

to_panel_view(trans, view='default_panel_view', **kwds)

Create a panel view representation of the toolbox. Uses the structure:

{section_id: { section but with .tools=List[all tool ids] }, …}}

galaxy.tool_util.toolbox.integrated_panel module

class galaxy.tool_util.toolbox.integrated_panel.ManagesIntegratedToolPanelMixin

Bases: object

galaxy.tool_util.toolbox.panel module

class galaxy.tool_util.toolbox.panel.panel_item_types(value)

Bases: str, Enum

An enumeration.

TOOL = 'TOOL'

WORKFLOW = 'WORKFLOW'

SECTION = 'SECTION'

LABEL = 'LABEL'

class galaxy.tool_util.toolbox.panel.HasPanelItems

Bases: object

abstract panel_items()

Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections).

panel_items_iter()

Iterate through panel items each represented as a tuple of (panel_key, panel_type, panel_content).

class galaxy.tool_util.toolbox.panel.ToolSection(item=None)

Bases: Dictifiable, HasPanelItems

A group of tools with similar type/purpose that will be displayed as a group in the user interface.

dict_collection_visible_keys = ['id', 'name', 'version', 'description', 'links']

__init__(item=None)

Build a ToolSection from an ElementTree element or a dictionary.

copy(merge_tools=False)

to_dict(trans, link_details=False, tool_help=False, toolbox=None, only_ids=False)

Return a dict that includes section’s attributes.

if only_ids is True, we store only the ids of the section’s tools in section.tools (also full ToolSectionLabel objects in section.tools if any are present)

if only_ids is False, we store the section’s full Tool (and any other) objects in section.elems

panel_items()

Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections).

class galaxy.tool_util.toolbox.panel.ToolSectionLabel(item)

Bases: Dictifiable

A label for a set of tools that can be displayed above groups of tools and sections in the user interface

dict_collection_visible_keys = ['id', 'text', 'version', 'description', 'links']

__init__(item)

Build a ToolSectionLabel from an ElementTree element or a dictionary.

to_dict(**kwds)

Return item dictionary.

class galaxy.tool_util.toolbox.panel.ToolPanelElements(dict=None)

Bases: odict, HasPanelItems

Represents an ordered dictionary of tool entries - abstraction used both by tool panel itself (normal and integrated) and its sections.

record_section_for_tool_id(tool_id: str, key: str, val: str)

get_section_for_tool_id(tool_id: str) → Tuple[str | None, str | None]

replace_tool_for_id(tool_id: str, new_tool) → None

get_or_create_section(sec_id: str, sec_nm: str, description: str | None = None, links: Dict[str, str] | None = None) → ToolSection

remove_tool(tool_id: str) → None

update_or_append(index: int, key: str, value) → None

get_label(label: str) → ToolSection | None

has_tool_with_id(tool_id: str) → bool

replace_tool(previous_tool_id: str, new_tool_id: str, tool) → None

index_of_tool_id(tool_id: str) → int | None

insert_tool(index: int, tool) → None

get_tool_with_id(tool_id: str)

append_tool(tool) → None

stub_tool(key: str) → None

stub_workflow(key: str) → None

stub_label(key: str) → None

append_section(key: str, section: ToolSection) → None

panel_items()

Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections).

walk_sections()

closest_section(target_section_id: str | None, target_section_name: str | None)

apply_filter(f)

copy() → ToolPanelElements

has_item_recursive(item)

Check panel and section elements for supplied item.

galaxy.tool_util.toolbox.parser module

This module is used to parse tool_conf files.

These files define tool lists, sections, labels, etc… the elements of the Galaxy tool panel.

galaxy.tool_util.toolbox.parser.get_toolbox_parser(config_filename: str | PathLike)

galaxy.tool_util.toolbox.parser.ensure_tool_conf_item(xml_or_item)

galaxy.tool_util.toolbox.tags module

galaxy.tool_util.toolbox.watcher module

galaxy.tool_util.toolbox.watcher.get_tool_conf_watcher(reload_callback, tool_cache=None)

galaxy.tool_util.toolbox.watcher.get_tool_watcher(toolbox, config)

class galaxy.tool_util.toolbox.watcher.ToolFileEventHandler(tool_watcher)

Bases: FileSystemEventHandler

__init__(tool_watcher)

on_any_event(event)

Catch-all event handler.

Parameters:

event (FileSystemEvent) – The event object representing the file system event.

class galaxy.tool_util.toolbox.watcher.ToolConfWatcher(reload_callback, tool_cache=None)

Bases: object

__init__(reload_callback, tool_cache=None)

start()

shutdown()

check()

Check for changes in self.paths or self.cache and call the event handler.

monitor(path)

watch_file(tool_conf_file)

class galaxy.tool_util.toolbox.watcher.ToolWatcher(observer_class, event_handler_class, toolbox)

Bases: BaseWatcher

__init__(observer_class, event_handler_class, toolbox)

watch_file(tool_file, tool_id)

watch_directory(tool_dir, callback)