"""
YAML Schema to RDF Generator
Generate a JSON LD representation of the model
"""
import os
import urllib.parse as urlparse
from dataclasses import dataclass
from typing import List, Optional
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 METAMODEL_CONTEXT_URI
from linkml._version import __version__
from linkml.generators.jsonldgen import JSONLDGenerator
from linkml.utils.generator import Generator, shared_arguments
[docs]@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
def _data(self, g: Graph) -> str:
return g.serialize(format="turtle" if self.format == "ttl" else self.format)
[docs] def end_schema(self, output: Optional[str] = None, context: str = None, **_) -> None:
gen = JSONLDGenerator(
self,
format=JSONLDGenerator.valid_formats[0],
metadata=self.emit_metadata,
importmap=self.importmap,
)
# 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:
with open(output, "w", encoding="UTF-8") as outf:
outf.write(self._data(graph))
else:
print(self._data(graph))
@shared_arguments(RDFGenerator)
@click.command()
@click.option("-o", "--output", help="Output file name")
@click.option(
"--context",
default=[METAMODEL_CONTEXT_URI],
show_default=True,
multiple=True,
help=f"JSONLD context file (default: {METAMODEL_CONTEXT_URI})",
)
@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()