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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)[source]
Bases:
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)[source]
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.
- tool_tag_manager()[source]
Build a tool tag manager according to app’s configuration and return it.
- panel_views() List[ToolPanelViewModel] [source]
- 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)[source]
- update_shed_config(shed_conf)[source]
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_tool(tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None)[source]
Attempt to locate a tool in the tool box. Note that exact only refers to the tool_id, not the tool_version.
- is_missing_shed_tool(tool_id: str) bool [source]
Confirm that the tool ID does reference a shed tool and is not installed.
- get_loaded_tools_by_lineage(tool_id: str) list [source]
Get all loaded tools associated by lineage to the tool whose id is tool_id.
- default_shed_tool_conf_dict() Dict[str, Any] [source]
If set, returns the first shed_tool_conf_dict corresponding to shed_tool_config_file, else the first dynamic conf.
- dynamic_conf_filenames()[source]
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).
- load_tool(config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds)[source]
Load a single tool from the file named by config_file and return an instance of Tool.
Load a hidden tool (in this context meaning one that does not appear in the tool panel) and register it in _tools_by_id.
- package_tool(trans, tool_id)[source]
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] [source]
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)[source]
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()[source]
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)[source]
Find the section ID referenced by the key or return ‘’ indicating no such section id.
- tool_panel_contents(trans, view=None, **kwds)[source]
Filter tool_panel contents for displaying for user.
- get_tool_to_dict(trans, tool, tool_help=False)[source]
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.
- class galaxy.tool_util.toolbox.panel_item_types(value)[source]
-
An enumeration.
- TOOL = 'TOOL'
- WORKFLOW = 'WORKFLOW'
- SECTION = 'SECTION'
- LABEL = 'LABEL'
- class galaxy.tool_util.toolbox.ToolSection(item=None)[source]
Bases:
UsesDictVisibleKeys
,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']
- to_dict(trans, link_details=False, tool_help=False, toolbox=None, only_ids=False)[source]
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
- class galaxy.tool_util.toolbox.ToolSectionLabel(item)[source]
Bases:
UsesDictVisibleKeys
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']
Subpackages
- galaxy.tool_util.toolbox.filters package
- galaxy.tool_util.toolbox.lineages package
- galaxy.tool_util.toolbox.views package
- Submodules
- galaxy.tool_util.toolbox.views.definitions module
- galaxy.tool_util.toolbox.views.edam module
- galaxy.tool_util.toolbox.views.interface module
- galaxy.tool_util.toolbox.views.sources module
- galaxy.tool_util.toolbox.views.static module
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)[source]
Bases:
_ToolConfRepository
- class galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl(toolbox: AbstractToolBox)[source]
Bases:
ToolBoxRegistry
View of ToolBox provided to ToolPanelView to reason about tools loaded.
- __init__(toolbox: AbstractToolBox)[source]
- class galaxy.tool_util.toolbox.base.NullToolTagManager[source]
Bases:
AbstractToolTagManager
- 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)[source]
Bases:
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)[source]
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.
- tool_tag_manager()[source]
Build a tool tag manager according to app’s configuration and return it.
- panel_views() List[ToolPanelViewModel] [source]
- 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)[source]
- update_shed_config(shed_conf)[source]
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_tool(tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None)[source]
Attempt to locate a tool in the tool box. Note that exact only refers to the tool_id, not the tool_version.
- is_missing_shed_tool(tool_id: str) bool [source]
Confirm that the tool ID does reference a shed tool and is not installed.
- get_loaded_tools_by_lineage(tool_id: str) list [source]
Get all loaded tools associated by lineage to the tool whose id is tool_id.
- default_shed_tool_conf_dict() Dict[str, Any] [source]
If set, returns the first shed_tool_conf_dict corresponding to shed_tool_config_file, else the first dynamic conf.
- dynamic_conf_filenames()[source]
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).
- load_tool(config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds)[source]
Load a single tool from the file named by config_file and return an instance of Tool.
Load a hidden tool (in this context meaning one that does not appear in the tool panel) and register it in _tools_by_id.
- package_tool(trans, tool_id)[source]
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] [source]
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)[source]
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()[source]
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)[source]
Find the section ID referenced by the key or return ‘’ indicating no such section id.
- tool_panel_contents(trans, view=None, **kwds)[source]
Filter tool_panel contents for displaying for user.
- get_tool_to_dict(trans, tool, tool_help=False)[source]
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.
galaxy.tool_util.toolbox.integrated_panel module
galaxy.tool_util.toolbox.panel module
- class galaxy.tool_util.toolbox.panel.panel_item_types(value)[source]
-
An enumeration.
- TOOL = 'TOOL'
- WORKFLOW = 'WORKFLOW'
- SECTION = 'SECTION'
- LABEL = 'LABEL'
- class galaxy.tool_util.toolbox.panel.HasPanelItems[source]
Bases:
object
- class galaxy.tool_util.toolbox.panel.ToolSection(item=None)[source]
Bases:
UsesDictVisibleKeys
,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']
- to_dict(trans, link_details=False, tool_help=False, toolbox=None, only_ids=False)[source]
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
- class galaxy.tool_util.toolbox.panel.ToolSectionLabel(item)[source]
Bases:
UsesDictVisibleKeys
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']
- class galaxy.tool_util.toolbox.panel.ToolPanelElements(dict=None)[source]
Bases:
odict
,HasPanelItems
Represents an ordered dictionary of tool entries - abstraction used both by tool panel itself (normal and integrated) and its sections.
- get_or_create_section(sec_id: str, sec_nm: str, description: str | None = None, links: Dict[str, str] | None = None) ToolSection [source]
- get_label(label: str) ToolSection | None [source]
- append_section(key: str, section: ToolSection) None [source]
- panel_items()[source]
Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections).
- copy() ToolPanelElements [source]
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.watcher module
- class galaxy.tool_util.toolbox.watcher.ToolFileEventHandler(tool_watcher)[source]
Bases:
FileSystemEventHandler