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galaxy.tools.toolbox package

API for this module containing functionality related to the toolbox.

class galaxy.tools.toolbox.AbstractToolBox(config_filenames, tool_root_dir, app)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.tools.toolbox.integrated_panel.ManagesIntegratedToolPanelMixin

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

__init__(config_filenames, tool_root_dir, app)

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.

handle_panel_update(section_dict)

Extension-point for Galaxy-app specific reload logic.

This abstract representation of the toolbox shouldn’t have details about interacting with the rest of the Galaxy app or message queues, etc….

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

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

get_shed_config_dict_by_filename(filename, default=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_integrated_section_for_tool(tool)

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

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, tool_version=None, exact=False)

is_missing_shed_tool(tool_id)

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

get_tool_id(tool_id)

Take a tool id - potentially from a different Galaxy instance or that is no longer loaded - and find the closest match to the currently loaded tools (using get_tool for inexact matches which currently returns the oldest tool shed installed tool with the same short id).

get_loaded_tools_by_lineage(tool_id)

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

tools()

dynamic_confs(include_migrated_tool_conf=False)

dynamic_conf_filenames(include_migrated_tool_conf=False)

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(item, path)

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

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

add_tool_to_cache(tool, config_file)

load_tool_from_cache(config_file)

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)

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()

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, **kwds)

Filter tool_panel contents for displaying for user.

get_tool_to_dict(trans, tool)

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, **kwds)

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

class galaxy.tools.toolbox.BaseGalaxyToolBox(config_filenames, tool_root_dir, app)

Bases: galaxy.tools.toolbox.base.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)

sa_session

Returns a SQLAlchemy session

reload_dependency_manager()

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

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.tools.toolbox.panel.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']

__init__(item=None)

Build a ToolSection from an ElementTree element or a dictionary.

copy()

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

Return a dict that includes section’s attributes.

panel_items()

class galaxy.tools.toolbox.ToolSectionLabel(item)

Bases: galaxy.util.dictifiable.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']

__init__(item)

Build a ToolSectionLabel from an ElementTree element or a dictionary.

to_dict(**kwds)

Subpackages

• galaxy.tools.toolbox.filters package
• galaxy.tools.toolbox.lineages package
  • Submodules
  • galaxy.tools.toolbox.lineages.factory module
  • galaxy.tools.toolbox.lineages.interface module
  • galaxy.tools.toolbox.lineages.stock module
  • galaxy.tools.toolbox.lineages.tool_shed module

Submodules

galaxy.tools.toolbox.base module

class galaxy.tools.toolbox.base.AbstractToolBox(config_filenames, tool_root_dir, app)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.tools.toolbox.integrated_panel.ManagesIntegratedToolPanelMixin

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

__init__(config_filenames, tool_root_dir, app)

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.

handle_panel_update(section_dict)

Extension-point for Galaxy-app specific reload logic.

This abstract representation of the toolbox shouldn’t have details about interacting with the rest of the Galaxy app or message queues, etc….

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

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

get_shed_config_dict_by_filename(filename, default=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_integrated_section_for_tool(tool)

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

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, tool_version=None, exact=False)

is_missing_shed_tool(tool_id)

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

get_tool_id(tool_id)

Take a tool id - potentially from a different Galaxy instance or that is no longer loaded - and find the closest match to the currently loaded tools (using get_tool for inexact matches which currently returns the oldest tool shed installed tool with the same short id).

get_loaded_tools_by_lineage(tool_id)

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

tools()

dynamic_confs(include_migrated_tool_conf=False)

dynamic_conf_filenames(include_migrated_tool_conf=False)

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(item, path)

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

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

add_tool_to_cache(tool, config_file)

load_tool_from_cache(config_file)

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)

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()

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, **kwds)

Filter tool_panel contents for displaying for user.

get_tool_to_dict(trans, tool)

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, **kwds)

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

class galaxy.tools.toolbox.base.BaseGalaxyToolBox(config_filenames, tool_root_dir, app)

Bases: galaxy.tools.toolbox.base.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)

sa_session

Returns a SQLAlchemy session

reload_dependency_manager()

galaxy.tools.toolbox.cache module

galaxy.tools.toolbox.integrated_panel module

class galaxy.tools.toolbox.integrated_panel.ManagesIntegratedToolPanelMixin

Bases: object

galaxy.tools.toolbox.panel module

class galaxy.tools.toolbox.panel.HasPanelItems

Bases: object

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.tools.toolbox.panel.ToolSection(item=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.tools.toolbox.panel.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']

__init__(item=None)

Build a ToolSection from an ElementTree element or a dictionary.

copy()

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

Return a dict that includes section’s attributes.

panel_items()

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

Bases: galaxy.util.dictifiable.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']

__init__(item)

Build a ToolSectionLabel from an ElementTree element or a dictionary.

to_dict(**kwds)

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

Bases: galaxy.util.odict.odict, galaxy.tools.toolbox.panel.HasPanelItems

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

update_or_append(index, key, value)

has_tool_with_id(tool_id)

replace_tool(previous_tool_id, new_tool_id, tool)

index_of_tool_id(tool_id)

insert_tool(index, tool)

get_tool_with_id(tool_id)

append_tool(tool)

stub_tool(key)

stub_workflow(key)

stub_label(key)

append_section(key, section_elems)

panel_items()

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

galaxy.tools.toolbox.parser.get_toolbox_parser(config_filename)

galaxy.tools.toolbox.tags module

Handle details of tool tagging - perhaps a deprecated feature.

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

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

class galaxy.tools.toolbox.tags.AbstractToolTagManager

Bases: object

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.tools.toolbox.tags.NullToolTagManager

Bases: galaxy.tools.toolbox.tags.AbstractToolTagManager

reset_tags()

handle_tags(tool_id, tool_definition_source)

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

Bases: galaxy.tools.toolbox.tags.AbstractToolTagManager

__init__(app)

reset_tags()

handle_tags(tool_id, tool_definition_source)

galaxy.tools.toolbox.watcher module

galaxy.tools.toolbox.watcher.get_observer_class(config_value, default, monitor_what_str)

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

galaxy.tools.toolbox.watcher.get_tool_data_dir_watcher(tool_data_tables, config)

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

class galaxy.tools.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.tools.toolbox.watcher.NullToolConfWatcher

Bases: object

start()

shutdown()

monitor(conf_path)

watch_file(tool_file, tool_id)

class galaxy.tools.toolbox.watcher.ToolWatcher(toolbox, observer_class)

Bases: object

__init__(toolbox, observer_class)

start()

shutdown()

monitor(dir)

watch_file(tool_file, tool_id)

watch_directory(tool_dir, callback)

class galaxy.tools.toolbox.watcher.ToolDataWatcher(observer_class, tool_data_tables)

Bases: object

__init__(observer_class, tool_data_tables)

start()

shutdown()

monitor(dir)

watch_directory(tool_data_dir)

class galaxy.tools.toolbox.watcher.LocFileEventHandler(loc_watcher)

Bases: watchdog.events.FileSystemEventHandler

__init__(loc_watcher)

on_any_event(event)

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

Bases: watchdog.events.FileSystemEventHandler

__init__(tool_watcher)

on_any_event(event)

class galaxy.tools.toolbox.watcher.NullWatcher

Bases: object

start()

shutdown()

watch_file(tool_file, tool_id)

watch_directory(tool_dir, callback=None)