Source code for linkml.generators.rdfgen

"""
YAML Schema to RDF Generator

Generate a JSON LD representation of the model

"""

import os
import urllib.parse as urlparse
from copy import deepcopy
from dataclasses import dataclass

import click
from rdflib import Graph
from rdflib.plugin import Parser as rdflib_Parser
from rdflib.plugin import plugins as rdflib_plugins

from linkml import LOCAL_METAMODEL_LDCONTEXT_FILE
from linkml._version import __version__
from linkml.generators.jsonldgen import JSONLDGenerator
from linkml.utils.generator import Generator, shared_arguments
from linkml_runtime.linkml_model import SchemaDefinition
from linkml_runtime.utils.rdf_canonicalize import canonicalize_rdf_graph




@dataclass
class RDFGenerator(Generator):
    # ClassVars
    generatorname = os.path.basename(__file__)
    generatorversion = "0.1.1"
    # TODO: we leave ttl as default for backwards compatibility but nt is
    # recommended, see https://github.com/linkml/linkml/issues/163
    valid_formats = ["ttl"] + sorted([x.name for x in rdflib_plugins(None, rdflib_Parser) if "/" not in str(x.name)])
    visit_all_class_slots = False
    uses_schemaloader = True

    # ObjectVars
    emit_metadata: bool = False
    context: list[str] = None
    original_schema: SchemaDefinition = None
    """See https://github.com/linkml/linkml/issues/871"""

    def __post_init__(self):
        self.original_schema = deepcopy(self.schema)
        super().__post_init__()

    def _data(self, g: Graph) -> str:
        fmt = "turtle" if self.format == "ttl" else self.format
        return canonicalize_rdf_graph(g, output_format=fmt)



    def end_schema(self, output: str | None = None, context: str = None, **_) -> str:
        gen = JSONLDGenerator(
            self.original_schema,
            format=JSONLDGenerator.valid_formats[0],
            metadata=self.emit_metadata,
            importmap=self.importmap,
            metamodel_context=LOCAL_METAMODEL_LDCONTEXT_FILE,
        )
        # Iterate over permissible text strings making them URI compatible
        for e in gen.schema.enums.values():
            for pv in e.permissible_values.values():
                pv.text = urlparse.quote(pv.text)
        jsonld_str = gen.serialize(context=context)

        graph = Graph()
        graph.parse(
            data=jsonld_str,
            format="json-ld",
            base=str(self.namespaces._base),
            prefix=True,
        )
        if output:
            out = self._data(graph)
            with open(output, "w", encoding="UTF-8") as outf:
                outf.write(out)
            return out

        return self._data(graph)




@shared_arguments(RDFGenerator)
@click.command(name="rdf")
@click.option("-o", "--output", help="Output file name")
@click.option(
    "--context",
    default=[LOCAL_METAMODEL_LDCONTEXT_FILE],
    show_default=True,
    multiple=True,
    help="JSONLD context file (default: vendored meta.context.jsonld)",
)
@click.version_option(__version__, "-V", "--version")
def cli(yamlfile, **kwargs):
    """Generate an RDF representation of a LinkML model"""
    print(RDFGenerator(yamlfile, **kwargs).serialize(**kwargs))


if __name__ == "__main__":
    cli()