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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)

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) → Optional[Dict[str, Any]]

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: Optional[str] = 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[Union[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.

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

Bases: AbstractToolBox

Extend the AbstractToolBox with more Galaxy tooling-specific functionality. Adds dependencies on dependency resolution and tool loading modules, that an abstract description of panels shouldn’t really depend on.

__init__(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view=None, 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.

property sa_session

Returns a SQLAlchemy session

reload_dependency_manager()

load_builtin_converters()

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()

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

Return a dict that includes section’s attributes.

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
    • ExcludeToolRegex
      • ExcludeToolRegex.tool_id_regex
    • ExcludeTypes
      • ExcludeTypes.types
    • Tool
      • Tool.content_type
      • Tool.id
      • Tool.Config
    • Label
      • Label.content_type
      • Label.id
      • Label.text
      • Label.Config
    • LabelShortcut
      • LabelShortcut.label
    • Workflow
      • Workflow.content_type
      • Workflow.id
      • Workflow.Config
    • ItemsFrom
      • ItemsFrom.items_from
      • ItemsFrom.excludes
    • HasItems
      • HasItems.items
      • HasItems.items_expanded
    • Section
      • Section.content_type
      • Section.id
      • Section.name
      • Section.items
      • Section.excludes
      • Section.Config
    • SectionAlias
      • SectionAlias.section
      • SectionAlias.excludes
    • SectionAliases
      • SectionAliases.sections
      • SectionAliases.excludes
    • StaticToolBoxView
      • StaticToolBoxView.id
      • StaticToolBoxView.name
      • StaticToolBoxView.description
      • StaticToolBoxView.view_type
      • StaticToolBoxView.items
      • StaticToolBoxView.excludes
      • StaticToolBoxView.from_dict()
      • StaticToolBoxView.Config
  • 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
    • 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.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)

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) → Optional[Dict[str, Any]]

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: Optional[str] = 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[Union[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.

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

Bases: AbstractToolBox

Extend the AbstractToolBox with more Galaxy tooling-specific functionality. Adds dependencies on dependency resolution and tool loading modules, that an abstract description of panels shouldn’t really depend on.

__init__(config_filenames, tool_root_dir, app, view_sources=None, default_panel_view=None, 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.

property sa_session

Returns a SQLAlchemy session

reload_dependency_manager()

load_builtin_converters()

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()

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

Return a dict that includes section’s attributes.

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[Optional[str], Optional[str]]

replace_tool_for_id(tool_id: str, new_tool) → None

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

remove_tool(tool_id: str) → None

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

get_label(label: str) → Optional[ToolSection]

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) → Optional[int]

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: Optional[str], target_section_name: Optional[str])

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: Union[str, PathLike])

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

galaxy.tool_util.toolbox.tags module

Handle details of tool tagging - perhaps a deprecated feature.

galaxy.tool_util.toolbox.tags.tool_tag_manager(app)

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

class galaxy.tool_util.toolbox.tags.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.tags.NullToolTagManager

Bases: AbstractToolTagManager

reset_tags()

Starting to load tool panels, reset all tags.

handle_tags(tool_id, tool_definition_source)

Parse out tags and persist them.

class galaxy.tool_util.toolbox.tags.PersistentToolTagManager(app)

Bases: AbstractToolTagManager

__init__(app)

reset_tags()

Starting to load tool panels, reset all tags.

handle_tags(tool_id, tool_definition_source)

Parse out tags and persist them.

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)