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Source code for galaxy.schema.fields

import inspect
import re
from typing import Optional

from pydantic import (

ENCODED_DATABASE_ID_PATTERN = re.compile('f?[0-9a-f]+')

[docs]class EncodedDatabaseIdField(str): """ Encoded Database ID validation. """ @classmethod def __get_validators__(cls): # one or more validators may be yielded which will be called in the # order to validate the input, each validator will receive as an input # the value returned from the previous validator yield cls.validate @classmethod def __modify_schema__(cls, field_schema): # __modify_schema__ should mutate the dict it receives in place, # the returned value will be ignored field_schema.update( min_length=16, pattern='[0-9a-fA-F]+', examples=['0123456789ABCDEF'], )
[docs] @classmethod def validate(cls, v): if not isinstance(v, str): raise TypeError('String required') if v.startswith("F"): # Library Folder ids start with an additional "F" len_v = len(v) - 1 else: len_v = len(v) if len_v % ENCODED_ID_LENGTH_MULTIPLE: raise ValueError('Invalid id length, must be multiple of 16') m = ENCODED_DATABASE_ID_PATTERN.fullmatch(v.lower()) if not m: raise ValueError('Invalid characters in encoded ID') return cls(v)
def __repr__(self): return f'EncodedDatabaseID ({super().__repr__()})'
[docs]def ModelClassField(class_name: str) -> str: """Represents a database model class name annotated as a constant pydantic Field. :param class_name: The name of the database class. :return: A constant pydantic Field with default annotations for model classes. """ return Field( class_name, title="Model class", description="The name of the database model class.", const=True, # Make this field constant )
[docs]def OrderParamField(default_order: str) -> Optional[str]: return Field( default=default_order, 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." ), example="name-dsc,create_time", )
[docs]def optional(*fields): """Decorator function used to modify a pydantic model's fields to all be optional. Alternatively, you can also pass the field names that should be made optional as arguments to the decorator. Taken from https://github.com/samuelcolvin/pydantic/issues/1223#issuecomment-775363074 """ def dec(_cls): for field in fields: _cls.__fields__[field].required = False return _cls if fields and inspect.isclass(fields[0]) and issubclass(fields[0], BaseModel): cls = fields[0] fields = cls.__fields__ return dec(cls) return dec