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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

An enumeration.

generic = 'generic'¶

activity = 'activity'¶

publication = 'publication'¶

training = 'training'¶

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

Bases: BaseModel

tool_id: str¶

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

Bases: BaseModel

tool_id_regex: str¶

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

Bases: BaseModel

types: List[str]¶

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

Bases: 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: 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: BaseModel

label: str¶

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

Bases: 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[ExcludeTool, ExcludeToolRegex, ExcludeTypes]] = None, content_type: str = 'items_from')[source]¶

Bases: BaseModel

items_from: str¶

excludes: Optional[List[Union[ExcludeTool, ExcludeToolRegex, ExcludeTypes]]]¶

class galaxy.tool_util.toolbox.views.definitions.HasItems[source]¶

Bases: object

items: Optional[List[Any]]¶

property items_expanded: Optional[List[Union[Section, SectionAlias, Tool, Label, Workflow, ItemsFrom]]]¶

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

Bases: BaseModel, HasItems

content_type: typing_extensions.Literal[section]¶

id: Optional[str]¶

name: Optional[str]¶

items: Optional[List[Union[Tool, Label, LabelShortcut, Workflow, ItemsFrom]]]¶

excludes: Optional[List[Union[ExcludeTool, ExcludeToolRegex, 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[ExcludeTool, ExcludeToolRegex, ExcludeTypes]] = None, content_type: str = 'section_alias')[source]¶

Bases: BaseModel

section: str¶

excludes: Optional[List[Union[ExcludeTool, ExcludeToolRegex, ExcludeTypes]]]¶

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

Bases: BaseModel

sections: List[str]¶

excludes: Optional[List[Union[ExcludeTool, ExcludeToolRegex, ExcludeTypes]]]¶

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

Bases: BaseModel, HasItems

id: str¶

name: str¶

description: Optional[str]¶

view_type: StaticToolBoxViewTypeEnum¶

items: Optional[List[Union[Section, SectionAlias, SectionAliases, Tool, Label, LabelShortcut, Workflow, ItemsFrom]]]¶

excludes: Optional[List[Union[ExcludeTool, ExcludeToolRegex, 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

An enumeration.

merged = 'merged'¶

topics = 'topics'¶

operations = 'operations'¶

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

Bases: ToolPanelView

__init__(edam_ontology_path: Optional[str], mode: EdamPanelMode = EdamPanelMode.merged)[source]¶

apply_view(base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) → ToolPanelElements[source]¶: Consume tool panel state and return custom tool panel view.

to_model() → 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

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: ToolPanelViewModelType, searchable: bool)[source]¶

Bases: BaseModel

A view of ToolPanelView objects serialized for the API.

id: str¶

model_class: str¶

name: str¶

description: Optional[str]¶

view_type: 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: 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: ToolPanelElements, toolbox_registry: ToolBoxRegistry) → ToolPanelElements[source]¶: Consume tool panel state and return custom tool panel view.

abstract to_model() → ToolPanelViewModel[source]¶: Convert abstract description to dictionary description to emit via the API.

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

Bases: ToolPanelView

__init__(definition: StaticToolBoxView)[source]¶

apply_view(base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) → ToolPanelElements[source]¶: Consume tool panel state and return custom tool panel view.

to_model() → ToolPanelViewModel[source]¶: Convert abstract description to dictionary description to emit via the API.