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galaxy.tool_util.toolbox.views package

Submodules

galaxy.tool_util.toolbox.views.definitions module

class galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum(value)[source]

Bases: str, enum.Enum

An enumeration.

generic = 'generic'
activity = 'activity'
publication = 'publication'
training = 'training'
class galaxy.tool_util.toolbox.views.definitions.ExcludeTool(*, tool_id: str)[source]

Bases: pydantic.main.BaseModel

tool_id: str
class galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex(*, tool_id_regex: str)[source]

Bases: pydantic.main.BaseModel

tool_id_regex: str
class galaxy.tool_util.toolbox.views.definitions.ExcludeTypes(*, types: List[str])[source]

Bases: pydantic.main.BaseModel

types: List[str]
class galaxy.tool_util.toolbox.views.definitions.Tool(*, type: typing_extensions.Literal[tool] = 'tool', id: str)[source]

Bases: pydantic.main.BaseModel

content_type: typing_extensions.Literal[tool]
id: str
class Config[source]

Bases: object

allow_population_by_field_name = True
class galaxy.tool_util.toolbox.views.definitions.Label(*, type: typing_extensions.Literal[label], id: str = None, text: str)[source]

Bases: pydantic.main.BaseModel

content_type: typing_extensions.Literal[label]
id: Optional[str]
text: str
class Config[source]

Bases: object

allow_population_by_field_name = True
class galaxy.tool_util.toolbox.views.definitions.LabelShortcut(*, label: str, content_type: str = 'simple_label')[source]

Bases: pydantic.main.BaseModel

label: str
class galaxy.tool_util.toolbox.views.definitions.Workflow(*, type: typing_extensions.Literal[workflow], id: str)[source]

Bases: pydantic.main.BaseModel

content_type: typing_extensions.Literal[workflow]
id: str
class Config[source]

Bases: object

allow_population_by_field_name = True
class galaxy.tool_util.toolbox.views.definitions.ItemsFrom(*, items_from: str, excludes: List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]] = None, content_type: str = 'items_from')[source]

Bases: pydantic.main.BaseModel

items_from: str
excludes: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]]]
class galaxy.tool_util.toolbox.views.definitions.HasItems[source]

Bases: object

items: Optional[List[Any]]
property items_expanded: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.Section, galaxy.tool_util.toolbox.views.definitions.SectionAlias, galaxy.tool_util.toolbox.views.definitions.Tool, galaxy.tool_util.toolbox.views.definitions.Label, galaxy.tool_util.toolbox.views.definitions.Workflow, galaxy.tool_util.toolbox.views.definitions.ItemsFrom]]]
class galaxy.tool_util.toolbox.views.definitions.Section(*, type: typing_extensions.Literal[section], id: str = None, name: str = None, items: List[Union[galaxy.tool_util.toolbox.views.definitions.Tool, galaxy.tool_util.toolbox.views.definitions.Label, galaxy.tool_util.toolbox.views.definitions.LabelShortcut, galaxy.tool_util.toolbox.views.definitions.Workflow, galaxy.tool_util.toolbox.views.definitions.ItemsFrom]] = None, excludes: List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]] = None)[source]

Bases: pydantic.main.BaseModel, galaxy.tool_util.toolbox.views.definitions.HasItems

content_type: typing_extensions.Literal[section]
id: Optional[str]
name: Optional[str]
items: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.Tool, galaxy.tool_util.toolbox.views.definitions.Label, galaxy.tool_util.toolbox.views.definitions.LabelShortcut, galaxy.tool_util.toolbox.views.definitions.Workflow, galaxy.tool_util.toolbox.views.definitions.ItemsFrom]]]
excludes: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]]]
class Config[source]

Bases: object

allow_population_by_field_name = True
class galaxy.tool_util.toolbox.views.definitions.SectionAlias(*, section: str, excludes: List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]] = None, content_type: str = 'section_alias')[source]

Bases: pydantic.main.BaseModel

section: str
excludes: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]]]
class galaxy.tool_util.toolbox.views.definitions.SectionAliases(*, sections: List[str], excludes: List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]] = None, content_type: str = 'section_aliases')[source]

Bases: pydantic.main.BaseModel

sections: List[str]
excludes: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]]]
class galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView(*, id: str, name: str, description: str = None, type: galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum, items: List[Union[galaxy.tool_util.toolbox.views.definitions.Section, galaxy.tool_util.toolbox.views.definitions.SectionAlias, galaxy.tool_util.toolbox.views.definitions.SectionAliases, galaxy.tool_util.toolbox.views.definitions.Tool, galaxy.tool_util.toolbox.views.definitions.Label, galaxy.tool_util.toolbox.views.definitions.LabelShortcut, galaxy.tool_util.toolbox.views.definitions.Workflow, galaxy.tool_util.toolbox.views.definitions.ItemsFrom]] = None, excludes: List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]] = None)[source]

Bases: pydantic.main.BaseModel, galaxy.tool_util.toolbox.views.definitions.HasItems

id: str
name: str
description: Optional[str]
view_type: galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum
items: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.Section, galaxy.tool_util.toolbox.views.definitions.SectionAlias, galaxy.tool_util.toolbox.views.definitions.SectionAliases, galaxy.tool_util.toolbox.views.definitions.Tool, galaxy.tool_util.toolbox.views.definitions.Label, galaxy.tool_util.toolbox.views.definitions.LabelShortcut, galaxy.tool_util.toolbox.views.definitions.Workflow, galaxy.tool_util.toolbox.views.definitions.ItemsFrom]]]
excludes: Optional[List[Union[galaxy.tool_util.toolbox.views.definitions.ExcludeTool, galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex, galaxy.tool_util.toolbox.views.definitions.ExcludeTypes]]]
static from_dict(as_dict)[source]
class Config[source]

Bases: object

allow_population_by_field_name = True

galaxy.tool_util.toolbox.views.edam module

class galaxy.tool_util.toolbox.views.edam.EdamPanelMode(value)[source]

Bases: str, enum.Enum

An enumeration.

merged = 'merged'
topics = 'topics'
operations = 'operations'
class galaxy.tool_util.toolbox.views.edam.EdamToolPanelView(edam_ontology_path: Optional[str], mode: galaxy.tool_util.toolbox.views.edam.EdamPanelMode = EdamPanelMode.merged)[source]

Bases: galaxy.tool_util.toolbox.views.interface.ToolPanelView

__init__(edam_ontology_path: Optional[str], mode: galaxy.tool_util.toolbox.views.edam.EdamPanelMode = EdamPanelMode.merged)[source]
apply_view(base_tool_panel: galaxy.tool_util.toolbox.panel.ToolPanelElements, toolbox_registry: galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry) → galaxy.tool_util.toolbox.panel.ToolPanelElements[source]

Consume tool panel state and return custom tool panel view.

to_model() → galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel[source]

Convert abstract description to dictionary description to emit via the API.

galaxy.tool_util.toolbox.views.interface module

class galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType(value)[source]

Bases: str, enum.Enum

An enumeration.

default_type = 'default'
generic = 'generic'
activity = 'activity'
ontology = 'ontology'
publication = 'publication'
training = 'training'
class galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel(*, id: str, model_class: str, name: str, description: str = None, view_type: galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType, searchable: bool)[source]

Bases: pydantic.main.BaseModel

A view of ToolPanelView objects serialized for the API.

id: str
model_class: str
name: str
description: Optional[str]
view_type: galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType
searchable: bool
class galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry[source]

Bases: object

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

abstract has_tool(tool_id: str) → bool[source]

Return bool indicating if tool with specified id is loaded.

abstract get_tool(tool_id: str)[source]

Return tool with supplied tool id.

abstract get_workflow(id: str)[source]

Return workflow from panel with supplied id.

abstract add_tool_to_tool_panel_view(tool, tool_panel_component: galaxy.tool_util.toolbox.panel.HasPanelItems) → None[source]

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

class galaxy.tool_util.toolbox.views.interface.ToolPanelView[source]

Bases: object

abstract apply_view(base_tool_panel: galaxy.tool_util.toolbox.panel.ToolPanelElements, toolbox_registry: galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry) → galaxy.tool_util.toolbox.panel.ToolPanelElements[source]

Consume tool panel state and return custom tool panel view.

abstract to_model() → galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel[source]

Convert abstract description to dictionary description to emit via the API.

galaxy.tool_util.toolbox.views.interface.walk_loaded_tools(tool_panel: galaxy.tool_util.toolbox.panel.ToolPanelElements, toolbox_registry: galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry)[source]

galaxy.tool_util.toolbox.views.sources module

class galaxy.tool_util.toolbox.views.sources.StaticToolBoxViewSources(view_directories=None, view_dicts=None)[source]

Bases: object

__init__(view_directories=None, view_dicts=None)[source]
view_directories: List[str]
view_dicts: List[Dict]
get_definitions() → List[galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView][source]
galaxy.tool_util.toolbox.views.sources.looks_like_view_source_filename(filename: str) → bool[source]

galaxy.tool_util.toolbox.views.static module

galaxy.tool_util.toolbox.views.static.build_filter(excludes_)[source]
class galaxy.tool_util.toolbox.views.static.StaticToolPanelView(definition: galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView)[source]

Bases: galaxy.tool_util.toolbox.views.interface.ToolPanelView

__init__(definition: galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView)[source]
apply_view(base_tool_panel: galaxy.tool_util.toolbox.panel.ToolPanelElements, toolbox_registry: galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry) → galaxy.tool_util.toolbox.panel.ToolPanelElements[source]

Consume tool panel state and return custom tool panel view.

to_model() → galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel[source]

Convert abstract description to dictionary description to emit via the API.