remove jsonschema version constrain (#287)

* remove jsonschema version constrain

* Use referencing library

* Fix lint

* Fix lint

* update schema validatoin code

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
     # This 'graphviz' is equivalent to `conda install python-graphviz` or
     # `sudo apt install python3-graphviz` ONLY.
     "graphviz",
-    "jsonschema<4.18", # temporarily downgrade due to severe performance regression
+    "jsonschema",
     "pyyaml",
     "requests",
     "mergedeep",
@@ -42,7 +42,8 @@ dependencies = [
     "toil[cwl]",
     "fastapi",
     "python-jose",
-    "uvicorn"
+    "uvicorn",
+    "referencing"
 ]
 
 [project.readme]

src/sophios/schemas/wic_schema.py

@@ -5,7 +5,9 @@
 
 import networkx as nx
 import graphviz
-from jsonschema import RefResolver, Draft202012Validator
+from jsonschema import Draft202012Validator
+from referencing import Registry, Resource
+from referencing.jsonschema import DRAFT202012
 import yaml
 
 import sophios
@@ -680,7 +682,6 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str
 
     schema = wic_main_schema(tools_cwl, yml_stems, schema_store, hypothesis)
     schema_store[schema['$id']] = schema
-    schema_store['wic_tag'] = wic_tag_schema(hypothesis)
     if write_to_disk:
         with open('autogenerated/schemas/wic.json', mode='w', encoding='utf-8') as f:
             f.write(json.dumps(schema, indent=2))
@@ -696,7 +697,11 @@ 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)
+    schema_store_resource: Resource = Resource(contents=schema_store, specification=DRAFT202012)  # type: ignore
+    registry: Registry = Registry().with_resource(uri="wic_schema_store", resource=schema_store_resource)
+    wic_tag_schema_resource: Resource = Resource(contents=wic_tag_schema(
+        hypothesis), specification=DRAFT202012)  # type: ignore
+    registry = registry.with_resource(uri="wic_tag", resource=wic_tag_schema_resource)
     """ 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 +712,5 @@ 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)
+    validator = Draft202012Validator(schema, registry=registry)
     return validator