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Source code for galaxy.tool_util.toolbox.views.definitions
from enum import Enum
from typing import (
Any,
cast,
List,
Optional,
Union,
)
from pydantic import (
BaseModel,
ConfigDict,
Field,
)
from typing_extensions import (
Annotated,
Literal,
)
[docs]class StaticToolBoxViewTypeEnum(str, Enum):
generic = "generic"
activity = "activity"
publication = "publication"
training = "training"
Exclusions = Union[
ExcludeTool,
ExcludeToolRegex,
ExcludeTypes,
]
OptionalExclusionList = Annotated[Optional[List[Exclusions]], Field(None)]
[docs]class Tool(BaseModel):
content_type: Literal["tool"] = Field("tool", alias="type")
id: str
model_config = ConfigDict(populate_by_name=True)
[docs]class Label(BaseModel):
content_type: Literal["label"] = Field(alias="type", default="label")
id: Optional[str] = None
text: str
model_config = ConfigDict(populate_by_name=True)
[docs]class LabelShortcut(BaseModel):
content_type: Literal["simple_label"] = "simple_label"
label: str
[docs]class Workflow(BaseModel):
content_type: Literal["workflow"] = Field(alias="type", default="workflow")
id: str
model_config = ConfigDict(populate_by_name=True)
[docs]class ItemsFrom(BaseModel):
content_type: Literal["items_from"] = "items_from"
items_from: str
excludes: OptionalExclusionList
SectionContent = Union[
Tool,
Label,
LabelShortcut,
Workflow,
ItemsFrom,
]
[docs]class HasItems:
items: Optional[List[Any]]
@property
def items_expanded(self) -> Optional[List["ExpandedRootContent"]]:
if self.items is None:
return None
# replace SectionAliases with individual SectionAlias objects
# replace LabelShortcuts with Labels
items: List[ExpandedRootContent] = []
for item in self.items:
item = cast(RootContent, item)
if isinstance(item, SectionAliases):
for section in item.sections:
section_alias = SectionAlias(
section=section,
excludes=item.excludes,
)
items.append(section_alias)
elif isinstance(item, LabelShortcut):
new_item = Label(
id=None,
text=item.label,
content_type="label",
)
items.append(new_item)
else:
items.append(item)
return items
[docs]class Section(BaseModel, HasItems):
content_type: Literal["section"] = Field(alias="type")
id: Optional[str] = None
name: Optional[str] = None
items: Optional[List[SectionContent]] = None
excludes: OptionalExclusionList
model_config = ConfigDict(populate_by_name=True)
[docs]class SectionAlias(BaseModel):
content_type: Literal["section_alias"] = "section_alias"
section: str
excludes: OptionalExclusionList = None
[docs]class SectionAliases(BaseModel):
content_type: Literal["section_aliases"] = "section_aliases"
sections: List[str]
excludes: OptionalExclusionList = None
RootContent = Union[
Section,
SectionAlias,
SectionAliases,
Tool,
Label,
LabelShortcut,
Workflow,
ItemsFrom,
]
ExpandedRootContent = Union[
Section,
SectionAlias,
Tool,
Label,
Workflow,
ItemsFrom,
]
[docs]class StaticToolBoxView(BaseModel, HasItems):
id: str
name: str
description: Optional[str] = None
view_type: StaticToolBoxViewTypeEnum = Field(alias="type")
items: Optional[List[RootContent]] = None # if empty, use integrated tool panel
excludes: OptionalExclusionList
model_config = ConfigDict(populate_by_name=True)