Test speed fixed but can't validate JSON again. #591

Author: knirirr

isatools/convert/isatab2cedar.py

@@ -10,9 +10,11 @@
 from os.path import isdir, join
 from uuid import uuid4
 
-from jsonschema import Draft4Validator, RefResolver
-from jsonschema.exceptions import ValidationError
+from jsonschema import Draft4Validator
+from referencing.jsonschema import DRAFT4
+from referencing import Registry
 
+from jsonschema.exceptions import ValidationError
 from isatools.io import isatab_parser
 
 __author__ = "agbeltran"
@@ -38,10 +40,12 @@ def createCEDARjson(self, work_dir, json_dir, inv_identifier):
         log.info("Converting ISA to CEDAR model for {}".format(work_dir))
         schema_file = "investigation_template.json"
         with open(join(CEDAR_SCHEMA_PATH, schema_file)) as json_fp:
-            schema = json.load(json_fp)
-        if schema is None:
+            investigation_schema = json.load(json_fp)
+        if investigation_schema is None:
             raise IOError("Could not load schema from {}".format(join(CEDAR_SCHEMA_PATH, schema_file)))
-        validator = Draft4Validator(schema)
+        schema = DRAFT4.create_resource(investigation_schema)
+        registry = Registry.with_resource(investigation_schema['id'], schema)
+        validator = Draft4Validator(investigation_schema, registry=registry)
 
         isa_tab = isatab_parser.parse(work_dir)
 

isatools/convert/isatab2json.py

@@ -10,7 +10,9 @@
 from os.path import join
 from uuid import uuid4
 
-from jsonschema import Draft4Validator, RefResolver
+from jsonschema import Draft4Validator
+from referencing import Registry
+from referencing.jsonschema import DRAFT4
 
 from isatools import isatab
 from isatools.io.isatab_parser import parse
@@ -139,8 +141,10 @@ def convert(self, work_dir):
 
             # validate json
             with open(join(SCHEMAS_PATH, INVESTIGATION_SCHEMA)) as json_fp:
-                schema = json.load(json_fp)
-                validator = Draft4Validator(schema)
+                investigation_schema = json.load(json_fp)
+                schema = DRAFT4.create_resource(investigation_schema)
+                registry = Registry.with_resource(investigation_schema['id'], schema)
+                validator = Draft4Validator(investigation_schema, registry=registry)
                 validator.validate(isa_json)
 
                 log.info("Conversion finished")

isatools/isajson/validate.py

@@ -15,6 +15,8 @@
 from io import StringIO
 
 from jsonschema import Draft4Validator, ValidationError
+from referencing import Registry
+from referencing.jsonschema import DRAFT4
 
 from isatools.isajson.load import load
 
@@ -548,9 +550,10 @@ def check_isa_schemas(isa_json, investigation_schema_path):
     try:
         with open(investigation_schema_path) as fp:
             investigation_schema = json.load(fp)
-            validator = Draft4Validator(investigation_schema)
+            schema = DRAFT4.create_resource(investigation_schema)
+            registry = Registry.with_resource(investigation_schema['id'], schema)
+            validator = Draft4Validator(investigation_schema, registry=registry)
             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!")