def __init__(self, url=None):
if url is None:
url = "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld"
# if set, this falls back to other prefixmappings
self.fallback = True
# NOTE: this is cached
# to clear cache: rm ~/.cachier/.prefixcommons.curie_util.read_remote_jsonld_context
self.set_prefixmap(cu.read_remote_jsonld_context(url))
def __init__(self, url: str = None):
"""
Initialize an instance of PrefixManager.
Parameters
----------
url: str
The URL from which to read a JSON-LD context for prefix mappings
"""
if url is None:
url = "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld"
# NOTE: this is cached
self.set_prefix_map(cu.read_remote_jsonld_context(url))
def __init__(self, url: str = None):
"""
Initialize an instance of PrefixManager.
Parameters
----------
url: str
The URL from which to read a JSON-LD context for prefix mappings
"""
if url:
context = cu.read_remote_jsonld_context(url)
else:
context = get_jsonld_context()
self.set_prefix_map(context)
import logging
import networkx as nx
from typing import List, Set, Dict, Tuple
import rdflib
from rdflib import URIRef, Namespace, RDF, RDFS, OWL
from kgx.utils.rdf_utils import find_category, category_mapping, equals_predicates, property_mapping, predicate_mapping, process_iri, make_curie, is_property_multivalued
from prefixcommons.curie_util import read_remote_jsonld_context
biolink_prefix_map = read_remote_jsonld_context(
'https://biolink.github.io/biolink-model/context.jsonld')
class RdfGraphMixin(object):
"""
A mixin that defines the following methods,
- load_networkx_graph(): template method that all deriving classes should implement
- add_node(): method to add a node from a RDF form to property graph form
- add_node_attribute(): method to add a node attribute from a RDF form to property graph form
- add_edge(): method to add an edge from a RDF form to property graph form
- add_edge_attribute(): method to add an edge attribute from an RDF form to property graph form
"""
# TODO: use OBO IRI from biolink model context once https://github.com/biolink/biolink-model/issues/211 is resolved
OBO = Namespace('http://purl.obolibrary.org/obo/')
OBAN = Namespace(biolink_prefix_map['OBAN'])
PMID = Namespace(biolink_prefix_map['PMID'])
# TODO: double check: is this the correct prefix change? (biolink --> biolinkml)
BIOLINK = Namespace(biolink_prefix_map['biolinkml'])
DEFAULT_EDGE_LABEL = 'related_to'