Code#

MetaModel#

See Datamodel docs for full documentation

class linkml_runtime.linkml_model.meta.SchemaDefinition(*args, _if_missing: Optional[Callable[[JsonObj, str], Tuple[bool, Any]]] = None, **kwargs)[source]#

A collection of definitions that make up a schema or a data model.

class linkml_runtime.linkml_model.meta.ClassDefinition(*args, _if_missing: Optional[Callable[[JsonObj, str], Tuple[bool, Any]]] = None, **kwargs)[source]#

an element whose instances are complex objects that may have slot-value assignments

class linkml_runtime.linkml_model.meta.SlotDefinition(*args, _if_missing: Optional[Callable[[JsonObj, str], Tuple[bool, Any]]] = None, **kwargs)[source]#

an element that describes how instances are related to other instances

Generators#

Code for various generators for schema definitions

class linkml.generators.jsonschemagen.JsonSchemaGenerator(schema: ~typing.Union[str, ~typing.TextIO, ~linkml_runtime.linkml_model.meta.SchemaDefinition, ~linkml.utils.generator.Generator], schemaview: ~typing.Optional[~linkml_runtime.utils.schemaview.SchemaView] = None, format: ~typing.Optional[str] = None, metadata: bool = <factory>, useuris: ~typing.Optional[bool] = None, log_level: int = 30, mergeimports: ~typing.Optional[bool] = <factory>, source_file_date: ~typing.Optional[str] = None, source_file_size: ~typing.Optional[int] = None, logger: ~typing.Optional[~logging.Logger] = None, verbose: ~typing.Optional[bool] = None, output: ~typing.Optional[str] = None, namespaces: ~typing.Optional[~linkml_runtime.utils.namespaces.Namespaces] = None, directory_output: bool = False, base_dir: ~typing.Optional[str] = None, metamodel_name_map: ~typing.Optional[~typing.Dict[str, str]] = None, importmap: ~typing.Optional[~typing.Union[str, ~typing.Mapping[str, str]]] = None, emit_prefixes: ~typing.Set[str] = <factory>, metamodel: ~typing.Optional[~linkml.utils.schemaloader.SchemaLoader] = None, stacktrace: bool = False, topClass: ~typing.Optional[str] = None, not_closed: ~typing.Optional[bool] = <factory>, indent: int = 4, inline: bool = False, top_class: ~typing.Optional[~linkml_runtime.linkml_model.meta.ClassDefinitionName] = None, include_range_class_descendants: bool = <factory>, top_level_schema: ~typing.Optional[~linkml.generators.jsonschemagen.JsonSchema] = None, **_kwargs)[source]#

Generates JSONSchema documents from a LinkML SchemaDefinition

  • Each linkml class generates a schema

  • inheritance hierarchies are rolled-down from ancestors

  • Composition not yet implemented

  • Enumerations treated as strings

  • Foreign key references are treated as semantics-free strings

serialize(**kwargs) → str[source]#

Generate output in the required format

Parameters:

kwargs – Generater specific parameters

Returns:

Generated output

class linkml.generators.yamlgen.YAMLGenerator(schema: ~typing.Union[str, ~typing.TextIO, ~linkml_runtime.linkml_model.meta.SchemaDefinition, ~linkml.utils.generator.Generator], schemaview: ~typing.Optional[~linkml_runtime.utils.schemaview.SchemaView] = None, format: ~typing.Optional[str] = None, metadata: bool = <factory>, useuris: ~typing.Optional[bool] = None, log_level: int = 30, mergeimports: ~typing.Optional[bool] = <factory>, source_file_date: ~typing.Optional[str] = None, source_file_size: ~typing.Optional[int] = None, logger: ~typing.Optional[~logging.Logger] = None, verbose: ~typing.Optional[bool] = None, output: ~typing.Optional[str] = None, namespaces: ~typing.Optional[~linkml_runtime.utils.namespaces.Namespaces] = None, directory_output: bool = False, base_dir: ~typing.Optional[str] = None, metamodel_name_map: ~typing.Optional[~typing.Dict[str, str]] = None, importmap: ~typing.Optional[~typing.Union[str, ~typing.Mapping[str, str]]] = None, emit_prefixes: ~typing.Set[str] = <factory>, metamodel: ~typing.Optional[~linkml.utils.schemaloader.SchemaLoader] = None, stacktrace: bool = False, validateonly: bool = <factory>, **_kwargs)[source]#

A generator that produces a schema as a YAML Document

serialize(validateonly: bool = False, **kwargs) → str[source]#

Generate output in the required format

Parameters:

kwargs – Generater specific parameters

Returns:

Generated output

Loaders and Dumpers#

class linkml_runtime.dumpers.json_dumper.JSONDumper[source]#
dump(element: Union[BaseModel, YAMLRoot], to_file: str, contexts: Optional[Union[str, dict, JsonObj, List[Union[str, dict, JsonObj]]]] = None, **kwargs) → None[source]#

Write element as json to to_file :param element: LinkML object to be serialized as YAML :param to_file: file to write to :param contexts: JSON-LD context(s) in the form of:

  • file name

  • URL

  • JSON String

  • dict

  • JSON Object

  • A list containing elements of any type named above

dumps(element: Union[BaseModel, YAMLRoot], contexts: Optional[Union[str, dict, JsonObj, List[Union[str, dict, JsonObj]]]] = None, inject_type=True) → str[source]#

Return element as a JSON or a JSON-LD string :param element: LinkML object to be emitted :param contexts: JSON-LD context(s) in the form of:

  • file name

  • URL

  • JSON String

  • dict

  • JSON Object

  • A list containing elements of any type named above

Parameters:

inject_type – if True (default), add a @type at the top level

Returns:

JSON Object representing the element

class linkml_runtime.loaders.JSONLoader[source]#
loads(source: str, target_class: Type[Union[BaseModel, YAMLRoot]], *, metadata: Optional[FileInfo] = None, **_) → Union[BaseModel, YAMLRoot]#

Load source as a string :param source: source :param target_class: destination class :param metadata: metadata about the source :param _: extensions :return: instance of taarget_class

Schema Utils#

class linkml_runtime.utils.schemaview.SchemaView(schema: Union[str, Path, SchemaDefinition], importmap: Optional[Mapping[str, str]] = None, merge_imports: bool = False)[source]#

A SchemaView provides a virtual schema layered on top of a schema plus its import closure

Most operations are parameterized by imports. If this is set to True (default), then the full import closure is considered when answering

This class utilizes caching for efficient lookup operations.

TODO: decide how to use this in conjunction with the existing schemaloader, which injects into the schema rather than providing dynamic methods.

See:

Utils#

Utilities