Source code for linkml.generators.jsonldgen

""" Generate JSONld

"""
import os
from copy import deepcopy
from typing import Any, Optional

import click
from jsonasobj2 import as_json, items, loads

from linkml import METAMODEL_CONTEXT_URI
from linkml_runtime.linkml_model.meta import ClassDefinitionName, SlotDefinitionName, TypeDefinitionName, \
    ElementName, SlotDefinition, ClassDefinition, TypeDefinition, SubsetDefinitionName, SubsetDefinition
from linkml_runtime.utils.formatutils import camelcase, underscore

from linkml.generators.jsonldcontextgen import ContextGenerator
from linkml.utils.generator import Generator, shared_arguments
from linkml_runtime.utils.yamlutils import YAMLRoot


[docs]class JSONLDGenerator(Generator): generatorname = os.path.basename(__file__) generatorversion = "0.0.2" valid_formats = ['jsonld', 'json'] # jsonld includes @type and @context. json is pure JSON def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) self.original_schema = deepcopy(self.schema) 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, **_) -> None: self._add_type(self.schema) base_prefix = self.default_prefix() # 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 print(as_json(self.schema, indent=" ")) self.schema = self.original_schema
@shared_arguments(JSONLDGenerator) @click.command() @click.option("--context", multiple=True, help=f"JSONLD context file (default: {METAMODEL_CONTEXT_URI} and <model>.prefixes.context.jsonld)") def cli(yamlfile, **kwargs): """ Generate JSONLD file from biolink schema """ print(JSONLDGenerator(yamlfile, **kwargs).serialize(**kwargs)) if __name__ == '__main__': cli()