""" Generate JSONld
"""
import os
from copy import deepcopy
from dataclasses import dataclass
from typing import Any, Optional
import click
from jsonasobj2 import as_json, items, loads
from linkml_runtime.linkml_model.meta import (
ClassDefinition,
ClassDefinitionName,
ElementName,
SchemaDefinition,
SlotDefinition,
SlotDefinitionName,
SubsetDefinition,
SubsetDefinitionName,
TypeDefinition,
TypeDefinitionName,
)
from linkml_runtime.utils.formatutils import camelcase, underscore
from linkml_runtime.utils.yamlutils import YAMLRoot
from linkml import METAMODEL_CONTEXT_URI
from linkml._version import __version__
from linkml.generators.jsonldcontextgen import ContextGenerator
from linkml.utils.generator import Generator, shared_arguments
[docs]@dataclass
class JSONLDGenerator(Generator):
"""
Generates JSON-LD from a Schema
Status: incompletely implemented
Note: this is distinct from
:class:`~linkml.generators.jsonldcontextgen.ContextGenerator`, which generates a JSON-LD context
"""
# ClassVars
generatorname = os.path.basename(__file__)
generatorversion = "0.0.2"
valid_formats = [
"jsonld",
"json",
] # jsonld includes @type and @context. json is pure JSON
uses_schemaloader = True
requires_metamodel = True
file_extension = "jsonld"
# ObjectVars
original_schema: SchemaDefinition = None
"""See https://github.com/linkml/linkml/issues/871"""
context: str = None
"""Path to a JSONLD context file"""
def __post_init__(self) -> None:
self.original_schema = deepcopy(self.schema)
super().__post_init__()
def _add_type(self, node: YAMLRoot) -> dict:
if self.format == "jsonld":
typ = node.__class__.__name__
node = node.__dict__
node["@type"] = typ
return node
def _visit(self, node: Any) -> Optional[Any]:
if isinstance(node, (YAMLRoot, dict)):
if isinstance(node, YAMLRoot):
node = self._add_type(node)
for k, v in list(items(node)):
if v:
new_v = self._visit(v)
if new_v is not None:
node[k] = new_v
elif isinstance(node, list):
for i in range(0, len(node)):
new_v = self._visit(node[i])
if new_v is not None:
node[i] = new_v
elif isinstance(node, set):
for v in list(node):
new_v = self._visit(v)
if new_v is not None:
node.remove(v)
node.add(new_v)
elif isinstance(node, ClassDefinitionName):
return ClassDefinitionName(camelcase(node))
elif isinstance(node, SlotDefinitionName):
return SlotDefinitionName(underscore(node))
elif isinstance(node, TypeDefinitionName):
return TypeDefinitionName(underscore(node))
elif isinstance(node, SubsetDefinitionName):
return SubsetDefinitionName(underscore(node))
elif isinstance(node, ElementName):
return (
ClassDefinitionName(camelcase(node))
if node in self.schema.classes
else (
SlotDefinitionName(underscore(node))
if node in self.schema.slots
else (
SubsetDefinitionName(camelcase(node))
if node in self.schema.subsets
else TypeDefinitionName(underscore(node)) if node in self.schema.types else None
)
)
)
return None
[docs] def adjust_slot(self, slot: SlotDefinition) -> None:
if slot.range in self.schema.classes:
slot.range = ClassDefinitionName(camelcase(slot.range))
elif slot.range in self.schema.slots:
slot.range = SlotDefinitionName(underscore(slot.range))
elif slot.range in self.schema.types:
slot.range = TypeDefinitionName(underscore(slot.range))
slot.slot_uri = self.namespaces.uri_for(slot.slot_uri)
for f in [
"mappings",
"exact_mappings",
"broad_mappings",
"close_mappings",
"narrow_mappings",
"related_mappings",
]:
setattr(slot, f, [self.namespaces.uri_for(v) for v in getattr(slot, f)])
[docs] def visit_class(self, cls: ClassDefinition) -> bool:
self._visit(cls)
cls.class_uri = self.namespaces.uri_for(cls.class_uri)
# Slot usage is a construction artifact
# TODO: Figure out why this is here. It isn't good form to alter a schema that may be used by other things
cls.slot_usage = {}
return False
[docs] def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None:
self._visit(slot)
self.adjust_slot(slot)
[docs] def visit_type(self, typ: TypeDefinition) -> None:
self._visit(typ)
typ.uri = self.namespaces.uri_for(typ.uri)
[docs] def visit_subset(self, ss: SubsetDefinition) -> None:
self._visit(ss)
[docs] def end_schema(self, context: str = None, **_) -> str:
self._add_type(self.schema)
base_prefix = self.default_prefix()
# TODO: fix this, see https://github.com/linkml/linkml/issues/871
# JSON LD adjusts context reference using '@base'. If context is supplied and not a URI, generate an
# absolute URI for it
if context is None and self.format == "jsonld":
# TODO: Once we get pyld running w/ relative contexts, we need to figure out how to generate and add
# the relative (?) context reference below
# model_context = self.schema.source_file.replace('.yaml', '.prefixes.context.jsonld')
# context = [METAMODEL_CONTEXT_URI, f'file://./{model_context}']
# TODO: The _visit function above alters the schema in situ
add_prefixes = ContextGenerator(self.original_schema, model=False, metadata=False).serialize()
add_prefixes_json = loads(add_prefixes)
context = [METAMODEL_CONTEXT_URI, add_prefixes_json["@context"]]
elif isinstance(context, str): # Some of the older code doesn't do multiple contexts
context = [context]
elif isinstance(context, tuple):
context = list(context)
for imp in list(self.loaded.values())[1:]:
context.append(imp[0] + ".context.jsonld")
# Absolute file paths have to have a prefix
for ci in range(0, len(context)):
if isinstance(context[ci], str) and context[ci].startswith(
"/"
): # TODO: how do we deal with absolute DOS paths?
context[ci] = "file://" + context[ci]
if self.format == "jsonld":
self.schema["@context"] = context[0] if len(context) == 1 and not base_prefix else context
if base_prefix:
self.schema["@context"].append({"@base": base_prefix})
# json_obj["@id"] = self.schema.id
out = str(as_json(self.schema, indent=" ")) + "\n"
self.schema = self.original_schema
return out
@shared_arguments(JSONLDGenerator)
@click.command()
@click.option(
"--context",
multiple=True,
help=f"JSONLD context file (default: {METAMODEL_CONTEXT_URI} and <model>.prefixes.context.jsonld)",
)
@click.version_option(__version__, "-V", "--version")
def cli(yamlfile, **kwargs):
"""Generate JSONLD file from LinkML schema.
Status: incomplete
"""
print(JSONLDGenerator(yamlfile, **kwargs).serialize(**kwargs))
if __name__ == "__main__":
cli()