Simplify more code

Author: cthoyt

kgx/config.py

@@ -1,4 +1,5 @@
 import importlib
+from functools import lru_cache
 from typing import Dict, Any, Optional
 import sys
 from os import path
@@ -10,12 +11,13 @@
 import json
 import logging
 
+import curies
 from kgx.graph.base_graph import BaseGraph
 
 config: Optional[Dict[str, Any]] = None
 logger: Optional[logging.Logger] = None
 graph_store_class: Optional[BaseGraph] = None
-jsonld_context_map: Dict = {}
+jsonld_context_map: Dict[str, Dict[str, str]] = {}
 
 CONFIG_FILENAME = path.join(path.dirname(path.abspath(__file__)), "config.yml")
 
@@ -41,6 +43,13 @@ def get_config(filename: str = CONFIG_FILENAME) -> Dict:
     return config
 
 
+@lru_cache
+def get_converter(name: str = "biolink") -> curies.Converter:
+    """Get contents of a JSON-LD context."""
+    filepath = config["jsonld-context"][name]  # type: ignore
+    return curies.load_jsonld_context(filepath)
+
+
 def get_jsonld_context(name: str = "biolink"):
     """
     Get contents of a JSON-LD context.
@@ -55,19 +64,8 @@ def get_jsonld_context(name: str = "biolink"):
     if name in jsonld_context_map:
         content = jsonld_context_map[name]
     else:
-        filepath = config["jsonld-context"][name]  # type: ignore
-        if filepath.startswith("http"):
-            try:
-                content = requests.get(filepath).json()
-            except ConnectionError:
-                raise Exception(f"Unable to download JSON-LD context from {filepath}")
-        else:
-            if path.exists(filepath):
-                content = json.load(open(filepath))
-
-        if "@context" in content:
-            content = content["@context"]
-            jsonld_context_map[name] = content
+        converter = get_converter(name)
+        jsonld_context_map[name] = converter.bimap
     return content
 
 

kgx/config.yml

@@ -18,6 +18,6 @@ logging:
   format: '[%(name)s][%(filename)s][%(funcName)20s] %(levelname)s: %(message)s'
 
 jsonld-context:
-  biolink: https://raw.githubusercontent.com/biolink/biolink-model/2.2.5/context.jsonld
+  biolink: https://raw.githubusercontent.com/biolink/biolink-model/v4.0.0/project/jsonld/biolink_model.context.jsonld
   monarch_context: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/monarch_context.jsonld
-  obo_context: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/obo_context.jsonld
+  obo_context: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/obo_context.jsonld

kgx/utils/kgx_utils.py

@@ -23,7 +23,12 @@
 import numpy as np
 import curies
 
-from kgx.config import get_logger, get_jsonld_context, get_biolink_model_schema
+from kgx.config import (
+    get_logger,
+    get_jsonld_context,
+    get_biolink_model_schema,
+    get_converter,
+)
 from kgx.graph.base_graph import BaseGraph
 
 curie_lookup_service = None
@@ -220,12 +225,9 @@ def format_biolink_slots(s: str) -> str:
         return f"biolink:{formatted}"
 
 
-MONARCH_CONVERTER = curies.load_prefix_map(get_jsonld_context("monarch_context"))
-OBO_CONVERTER = curies.load_prefix_map(get_jsonld_context("obo_context"))
-DEFAULT_CONVERTER = curies.chain([
-    MONARCH_CONVERTER,
-    OBO_CONVERTER
-])
+MONARCH_CONVERTER = get_converter("monarch_context")
+OBO_CONVERTER = get_converter("obo_context")
+DEFAULT_CONVERTER = curies.chain([MONARCH_CONVERTER, OBO_CONVERTER])
 
 
 def _resolve_converter(prefix_maps: Optional[List[Dict[str, str]]] = None) -> curies.Converter:

tests/unit/__init__.py

@@ -1,4 +1,3 @@
-import docker
 import pytest
 from neo4j import GraphDatabase
 
@@ -17,6 +16,8 @@ def check_container():
     is currently running.
     """
     try:
+        import docker
+
         client = docker.from_env()
         status = False
         try: