Use referencing library

pyproject.toml

@@ -42,7 +42,8 @@ dependencies = [
     "toil[cwl]",
     "fastapi",
     "python-jose",
-    "uvicorn"
+    "uvicorn",
+    "referencing"
 ]
 
 [project.readme]

src/sophios/schemas/wic_schema.py

@@ -5,7 +5,8 @@
 
 import networkx as nx
 import graphviz
-from jsonschema import RefResolver, Draft202012Validator
+from jsonschema import Draft202012Validator
+import referencing
 import yaml
 
 import sophios
@@ -696,7 +697,7 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str
     # The $ref tag refers to URIs defined in $id tags, NOT relative paths on
     # the local filesystem! We need to create a global mapping between ids and schemas
     # i.e. schema_store.
-    resolver = RefResolver.from_schema(schema, store=schema_store)
+    registry = referencing.Registry(retrieve=lambda uri: schema_store.get(uri))
     """ Use check_schema to 'first verify that the provided schema is
     itself valid, since not doing so can lead to less obvious error
     messages and fail in less obvious or consistent ways.'
@@ -707,5 +708,5 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str
     # try temporarily commenting this line out to generate the schema anyway.
     # Then, in any yml file, the very first line should show a "schema stack trace"
     Draft202012Validator.check_schema(schema)
-    validator = Draft202012Validator(schema, resolver=resolver)
-    return validator
+    validator = Draft202012Validator(schema, registry=registry)
+    return validator