deprecate REFResolver

pyproject.toml

@@ -50,7 +50,8 @@ dependencies = [
     "parse>=1.20.0",
     "click",
     "docstring-parser",
-    "packaging"  # Issue 903
+    "packaging",  # Issue 903
+    "referencing",
 ]
 
 

src/neuroconv/tools/yaml_conversion_specification/_yaml_conversion_specification.py

@@ -1,11 +1,11 @@
-import sys
 from importlib import import_module
 from pathlib import Path
 from typing import Optional
 
 import click
-from jsonschema import RefResolver, validate
+from jsonschema import validate
 from pydantic import DirectoryPath, FilePath
+from referencing import Registry, Resource
 
 from ...nwbconverter import NWBConverter
 from ...utils import dict_deep_update, load_dict_from_file
@@ -79,12 +79,30 @@ def run_conversion_from_yaml(
         output_folder_path = Path(output_folder_path)
     specification = load_dict_from_file(file_path=specification_file_path)
     schema_folder = Path(__file__).parent.parent.parent / "schemas"
+
+    # Load all required schemas
     specification_schema = load_dict_from_file(file_path=schema_folder / "yaml_conversion_specification_schema.json")
-    sys_uri_base = "file:/" if sys.platform.startswith("win32") else "file://"
+    metadata_schema = load_dict_from_file(file_path=schema_folder / "metadata_schema.json")
+
+    # Create registry and add schemas starting with the metadata schema
+    registry = Registry().with_resource(
+        "metadata_schema.json", Resource.from_contents(metadata_schema)  # Base name without './'
+    )
+
+    # Then add the specification schema with the metadata schema reference
+    registry = registry.with_resource(
+        "yaml_conversion_specification_schema.json",  # This will be the base URI
+        Resource.from_contents(specification_schema),
+    )
+
+    # Also add with relative path since that's how it's referenced
+    registry = registry.with_resource("./metadata_schema.json", Resource.from_contents(metadata_schema))
+
+    # Validate using the registry
     validate(
         instance=specification,
         schema=specification_schema,
-        resolver=RefResolver(base_uri=sys_uri_base + str(schema_folder) + "/", referrer=specification_schema),
+        registry=registry,
     )
 
     global_metadata = specification.get("metadata", dict())

tests/test_on_data/test_yaml/test_yaml_conversion_specification.py

@@ -1,12 +1,12 @@
-import sys
 import unittest
 from datetime import datetime
 from pathlib import Path
 
 import pytest
 from hdmf.testing import TestCase
-from jsonschema import RefResolver, validate
+from jsonschema import validate
 from pynwb import NWBHDF5IO
+from referencing import Registry, Resource
 
 from neuroconv import run_conversion_from_yaml
 from neuroconv.utils import load_dict_from_file
@@ -27,16 +27,24 @@
 def test_validate_example_specifications(fname):
     path_to_test_yml_files = Path(__file__).parent / "conversion_specifications"
     schema_folder = path_to_test_yml_files.parent.parent.parent.parent / "src" / "neuroconv" / "schemas"
+
+    # Load schemas
     specification_schema = load_dict_from_file(file_path=schema_folder / "yaml_conversion_specification_schema.json")
-    sys_uri_base = "file://"
-    if sys.platform.startswith("win32"):
-        sys_uri_base = "file:/"
+    metadata_schema = load_dict_from_file(file_path=schema_folder / "metadata_schema.json")
+
+    # Create registry and add schemas
+    registry = (
+        Registry()
+        .with_resource("metadata_schema.json", Resource.from_contents(metadata_schema))
+        .with_resource("yaml_conversion_specification_schema.json", Resource.from_contents(specification_schema))
+        .with_resource("./metadata_schema.json", Resource.from_contents(metadata_schema))
+    )
 
     yaml_file_path = path_to_test_yml_files / fname
     validate(
         instance=load_dict_from_file(file_path=yaml_file_path),
-        schema=load_dict_from_file(file_path=schema_folder / "yaml_conversion_specification_schema.json"),
-        resolver=RefResolver(base_uri=sys_uri_base + str(schema_folder) + "/", referrer=specification_schema),
+        schema=specification_schema,
+        registry=registry,
     )