LinkML Generators

The LinkML generator will “generate” LinkML schemas from LinkML.

While this may sound redundant, it can be useful to perform transformations as a part of generation

Docs

Command Line

gen-linkml

gen-linkml [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-o, --output <output>

Name of JSON or YAML file to be created

--materialize-patterns, --no-materialize-patterns

Materialize structured patterns as patterns

Default:

True

--materialize-attributes, --no-materialize-attributes

Materialize induced slots as attributes

Default:

True

--materialize, --no-materialize

Materialize both, induced slots as attributes and structured patterns as patterns

Default:

True

-f, --format <format>

Output format

Default:

'json'

Options:

json | yaml

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

Code

class linkml.generators.linkmlgen.LinkmlGenerator(schema: str | ~typing.TextIO | ~linkml_runtime.linkml_model.meta.SchemaDefinition | ~linkml.utils.generator.Generator | ~pathlib.Path, schemaview: ~linkml_runtime.utils.schemaview.SchemaView | None = None, format: str | None = None, metadata: bool = True, useuris: bool | None = None, log_level: int | None = 30, mergeimports: bool | None = True, source_file_date: str | None = None, source_file_size: int | None = None, logger: ~logging.Logger | None = None, verbose: bool | None = None, output: str | None = None, namespaces: ~linkml_runtime.utils.namespaces.Namespaces | None = None, directory_output: bool = False, base_dir: str = None, metamodel_name_map: ~typing.Dict[str, str] = None, importmap: str | ~typing.Mapping[str, str] | None = None, emit_prefixes: ~typing.Set[str] = <factory>, metamodel: ~linkml.utils.schemaloader.SchemaLoader = None, stacktrace: bool = False, include: str | ~pathlib.Path | ~linkml_runtime.linkml_model.meta.SchemaDefinition | None = None, materialize_attributes: bool = False, materialize_patterns: bool = False, **_kwargs)

This generator provides a direct conversion of a LinkML schema into json, optionally merging imports and unrolling induced slots into attributes

generatorname: ClassVar[str] = 'linkmlgen.py'

Name of the generator. Override with os.path.basename(__file__)

generatorversion: ClassVar[str] = '1.0.0'

Version of the generator. Consider deprecating and instead use overall linkml version

materialize_attributes: bool = False

materialize_classes() → None

Materialize class slots from schema as attributes, in place

materialize_patterns: bool = False

requires_metamodel: ClassVar[bool] = False

Generator queries an instance of the metamodel

serialize(output: str = None, **kwargs) → str

Generate output in the required format

Parameters:

kwargs – Generator specific parameters

Returns:

Generated output

uses_schemaloader: ClassVar[bool] = False

Old-style generator that uses the SchemaLoader and visitor pattern

valid_formats: ClassVar[List[str]] = ['json', 'yaml']

Allowed formats - first format is default