Pydantic#

Subclass of linkml.generators.PydanticGenerator

The pydantic generator is a subclass of - linkml.utils.generator.Generator - linkml.generators.oocodegen.OOCodeGenerator

The default __main__ method - Instantiates the class - Calls serialize()

The serialize method:

Note

This module is heinous. We have mostly copied and pasted the existing linkml.generators.PydanticGenerator and overridden what we need to make this work for NWB, but the source is… a little messy. We will be tidying this up and trying to pull changes upstream, but for now this is just our hacky little secret.

pydantic model LinkML_Meta#

Extra LinkML Metadata stored as a class attribute

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

__init__ uses __pydantic_self__ instead of the more common self for the first arg to allow self as a field name.

Fields:
field tree_root: bool = False#
default_template(pydantic_ver: str = '2', extra_classes: List[Type[BaseModel]] | None = None) → str#

Constructs a default template for pydantic classes based on the version of pydantic

class NWBPydanticGenerator(schema: Union[str, TextIO, linkml_runtime.linkml_model.meta.SchemaDefinition, ForwardRef('Generator')], schemaview: Optional[linkml_runtime.utils.schemaview.SchemaView] = None, format: Optional[str] = None, metadata: bool = <factory>, useuris: Optional[bool] = None, log_level: int = 30, mergeimports: Optional[bool] = <factory>, source_file_date: Optional[str] = None, source_file_size: Optional[int] = None, logger: Optional[logging.Logger] = None, verbose: Optional[bool] = None, output: Optional[str] = None, namespaces: Optional[linkml_runtime.utils.namespaces.Namespaces] = None, directory_output: bool = False, base_dir: str = None, metamodel_name_map: Dict[str, str] = None, importmap: Union[str, Mapping[str, str], NoneType] = None, emit_prefixes: Set[str] = <factory>, metamodel: linkml.utils.schemaloader.SchemaLoader = None, stacktrace: bool = False, template_file: str = None, package: str = 'example', pydantic_version: str = <factory>, allow_extra: bool = <factory>, gen_mixin_inheritance: bool = <factory>, gen_classvars: bool = <factory>, gen_slots: bool = <factory>, genmeta: bool = <factory>, emit_metadata: bool = <factory>, SKIP_ENUM: Tuple[str] = ('FlatDType',), SKIP_SLOTS: Tuple[str] = ('',), SKIP_CLASSES: Tuple[str] = ('',), INJECTED_FIELDS: Tuple[str] = ('hdf5_path: Optional[str] = Field(None, description="The absolute path that this object is stored in an NWB file")', 'object_id: Optional[str] = Field(None, description="Unique UUID for each object")'), split: bool = True, schema_map: Optional[Dict[str, linkml_runtime.linkml_model.meta.SchemaDefinition]] = None, versions: dict = None, **_kwargs)#
SKIP_ENUM: Tuple[str] = ('FlatDType',)#
SKIP_SLOTS: Tuple[str] = ('',)#
SKIP_CLASSES: Tuple[str] = ('',)#
INJECTED_FIELDS: Tuple[str] = ('hdf5_path: Optional[str] = Field(None, description="The absolute path that this object is stored in an NWB file")', 'object_id: Optional[str] = Field(None, description="Unique UUID for each object")')#
split: bool = True#
schema_map: Dict[str, SchemaDefinition] | None = None#
versions: dict = None#

See LinkMLProvider.build() for usage - a list of specific versions to import from

pydantic_version: str = '2'#
sort_classes(clist: List[ClassDefinition], imports: Dict[str, List[str]]) → List[ClassDefinition]#

sort classes such that if C is a child of P then C appears after P in the list

Overridden method include mixin classes

Modified from original to allow for imported classes

get_class_slot_range(slot_range: str, inlined: bool, inlined_as_list: bool) → str#

Monkeypatch to convert Array typed slots and classes into npytyped hints

get_class_isa_plus_mixins(classes: List[ClassDefinition] | None = None) → Dict[str, List[str]]#

Generate the inheritance list for each class from is_a plus mixins

Patched to only get local classes

Returns:

get_predefined_slot_value(slot: SlotDefinition, class_def: ClassDefinition) → str | None#

Modified from base pydantic generator to use already grabbed induced_slot from already-grabbed and modified classes rather than doing a fresh iteration to save time and respect changes already made elsewhere in the serialization routine

Returns:

Dictionary of dictionaries with predefined slot values for each class

serialize() → str#

Generate output in the required format

Parameters:

kwargs – Generator specific parameters

Returns:

Generated output

compile_module(module_path: Path = None, module_name: str = 'test') → module#

Compiles generated python code to a module :return:

compile_python(text_or_fn: str, package_path: Path = None, module_name: str = 'test') → module#

Compile the text or file and return the resulting module @param text_or_fn: Python text or file name that references python file @param package_path: Root package path. If omitted and we’ve got a python file, the package is the containing directory @return: Compiled module