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Source code for galaxy.schema

import typing
from copy import deepcopy
from datetime import datetime
from enum import Enum
from typing import (

from pydantic import (
from pydantic.fields import FieldInfo

[docs]class BootstrapAdminUser(BaseModel): id: int = 0 email: Optional[str] = None preferences: Dict[str, str] = {} bootstrap_admin_user: bool = True
[docs] def all_roles(*args) -> list: return []
[docs]class ValueFilterQueryParams(BaseModel): """Allows filtering/querying elements by value like `q=<property>-<operator>&qv=<value>` Multiple `q/qv` queries can be concatenated. """ q: Optional[Union[List[str], str]] = Field( default=None, title="Filter Query", description="Generally a property name to filter by followed by an (often optional) hyphen and operator string.", examples=["create_time-gt"], ) qv: Optional[Union[List[str], str]] = Field( default=None, title="Filter Value", description="The value to filter by.", examples=["2015-01-29"], )
[docs]class PaginationQueryParams(BaseModel): """Used to paginate a the request results by limiting and offsetting.""" offset: Optional[int] = Field( default=0, ge=0, title="Offset", description="Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item", ) limit: Optional[int] = Field( default=None, ge=1, title="Limit", description="The maximum number of items to return.", )
[docs]class FilterQueryParams(ValueFilterQueryParams, PaginationQueryParams): """Contains full filtering options to query elements, paginate and order them.""" order: Optional[str] = Field( default=None, title="Order", description=( "String containing one of the valid ordering attributes followed (optionally) " "by '-asc' or '-dsc' for ascending and descending order respectively. " "Orders can be stacked as a comma-separated list of values." ), examples=["name-dsc,create_time"], )
[docs]class SerializationParams(BaseModel): """Contains common parameters for customizing model serialization.""" view: Optional[str] = Field( default=None, title="View", description=( "The name of the view used to serialize this item. " "This will return a predefined set of attributes of the item." ), examples=["summary"], ) keys: Optional[List[str]] = Field( default=None, title="Keys", description=( "List of keys (name of the attributes) that will be returned in addition " "to the ones included in the `view`." ), ) default_view: Optional[str] = Field( default=None, title="Default View", description="The item view that will be used in case none was specified.", )
[docs]class PdfDocumentType(str, Enum): invocation_report = "invocation_report" page = "page"
[docs]class APIKeyModel(BaseModel): key: str = Field(..., title="Key", description="API key to interact with the Galaxy API") create_time: datetime = Field(..., title="Create Time", description="The time and date this API key was created.")
T = TypeVar("T", bound="BaseModel") # TODO: This is a workaround to make all fields optional. # It should be removed when Python/pydantic supports this feature natively. # https://github.com/pydantic/pydantic/issues/1673
[docs]def partial_model( include: Optional[List[str]] = None, exclude: Optional[List[str]] = None ) -> Callable[[Type[T]], Type[T]]: """Decorator to make all model fields optional""" if exclude is None: exclude = [] @typing.no_type_check # Mypy doesn't understand pydantic's create_model def decorator(model: Type[T]) -> Type[T]: def make_optional(field: FieldInfo, default: Any = None) -> Tuple[Any, FieldInfo]: new = deepcopy(field) new.default = default new.annotation = Optional[field.annotation or Any] return new.annotation, new fields = model.model_fields if include is None: fields = fields.items() else: fields = ((k, v) for k, v in fields.items() if k in include) return create_model( model.__name__, __base__=model, __module__=model.__module__, **{ field_name: make_optional(field_info) for field_name, field_info in fields if exclude is None or field_name not in exclude }, ) return decorator