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'