check_isa_schemas updated to new json validator. #591

Author: knirirr

isatools/isajson/validate.py

@@ -14,7 +14,7 @@
 import re
 from io import StringIO
 
-from jsonschema import Draft4Validator, RefResolver, ValidationError
+from jsonschema import Draft4Validator, ValidationError
 
 from isatools.isajson.load import load
 
@@ -548,9 +548,9 @@ def check_isa_schemas(isa_json, investigation_schema_path):
     try:
         with open(investigation_schema_path) as fp:
             investigation_schema = json.load(fp)
-            resolver = RefResolver("file://" + investigation_schema_path, investigation_schema)
-            validator = Draft4Validator(investigation_schema, resolver=resolver)
+            validator = Draft4Validator(investigation_schema)
             validator.validate(isa_json)
+            #jsonschema.validate(instance=isa_json, schema=investigation_schema, cls=jsonschema.Draft4Validator)
     except ValidationError as ve:
         errors.append({"message": "Invalid JSON against ISA-JSON schemas", "supplemental": str(ve), "code": 3})
         log.fatal("(F) The JSON does not validate against the provided ISA-JSON schemas!")

pyproject.toml

@@ -57,6 +57,7 @@ dependencies = [
     "graphene~=3.4.3",
     "graphql-core~=3.2.6",
     "ruff>=0.14.1",
+    "pytest-timeout>=2.4.0",
 ]
 
 [project.optional-dependencies]

tests/validators/test_validators.py

@@ -484,7 +484,6 @@ def test_info_reporting_mtbls1_isatab(self):
             report = isatab.validate(
                 fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR, log_level=self._reporting_level
             )
-            print(report)
             # self.assertIn(
             #     {'supplemental': 'Found 4 study groups in s_MTBLS1.txt',
             #      'code': 5001,