Some tests fixed; one test issue outstanding #591

Author: knirirr

isatools/convert/isatab2cedar.py

@@ -8,9 +8,10 @@
 import os
 from os import listdir
 from os.path import isdir, join
+from pathlib import Path
 from uuid import uuid4
 
-from jsonschema import Draft4Validator
+from jsonschema import Draft4Validator, FormatChecker
 from referencing.jsonschema import DRAFT4
 from referencing import Registry
 
@@ -43,9 +44,21 @@ def createCEDARjson(self, work_dir, json_dir, inv_identifier):
             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)))
-        schema = DRAFT4.create_resource(investigation_schema)
-        registry = Registry.with_resource(investigation_schema['id'], schema)
-        validator = Draft4Validator(investigation_schema, registry=registry)
+
+        resources = []
+        schemas_dir = Path(CEDAR_SCHEMA_PATH)
+        investigation_schema_path = Path(join(CEDAR_SCHEMA_PATH, schema_file))
+
+        for p in sorted(schemas_dir.glob("*.json")):
+            contents = json.loads(p.read_text(encoding="utf-8"))
+            resource = DRAFT4.create_resource(contents)
+            resources.append((p.resolve().as_uri(), resource))
+
+        registry = Registry().with_resources(resources)
+        main_uri = investigation_schema_path.resolve().as_uri()
+        print(registry.contents(main_uri))
+        schema_ref = {"$ref": main_uri, "$schema": "http://json-schema.org/draft-04/schema"}
+        validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
 
         isa_tab = isatab_parser.parse(work_dir)
 

isatools/convert/isatab2json.py

@@ -8,11 +8,12 @@
 import re
 from enum import Enum
 from os.path import join
+from pathlib import Path
 from uuid import uuid4
 
-from jsonschema import Draft4Validator
+from jsonschema import Draft202012Validator, FormatChecker
 from referencing import Registry
-from referencing.jsonschema import DRAFT4
+from referencing.jsonschema import DRAFT202012
 
 from isatools import isatab
 from isatools.io.isatab_parser import parse
@@ -141,10 +142,26 @@ def convert(self, work_dir):
 
             # validate json
             with open(join(SCHEMAS_PATH, INVESTIGATION_SCHEMA)) as json_fp:
-                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)
+                #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)
+
+                resources = []
+                schemas_dir = Path(SCHEMAS_PATH)
+                investigation_schema_path = Path(join(SCHEMAS_PATH, INVESTIGATION_SCHEMA))
+
+                for p in sorted(schemas_dir.glob("*.json")):
+                    contents = json.loads(p.read_text(encoding="utf-8"))
+                    resource = DRAFT202012.create_resource(contents)
+                    resources.append((p.resolve().as_uri(), resource))
+
+                registry = Registry().with_resources(resources)
+                main_uri = investigation_schema_path.resolve().as_uri()
+                print(registry.contents(main_uri))
+                schema_ref = {"$ref": main_uri, "$schema": "https://json-schema.org/draft/2020-12/schema"}
+                validator = Draft202012Validator(schema_ref, registry=registry, format_checker=FormatChecker())
                 validator.validate(isa_json)
 
                 log.info("Conversion finished")

isatools/isajson/validate.py

@@ -13,10 +13,11 @@
 import os
 import re
 from io import StringIO
+from pathlib import Path
 
-from jsonschema import Draft4Validator, ValidationError
+from jsonschema import Draft4Validator, ValidationError, Draft202012Validator, FormatChecker
 from referencing import Registry
-from referencing.jsonschema import DRAFT4
+from referencing.jsonschema import DRAFT4, DRAFT202012
 
 from isatools.isajson.load import load
 
@@ -545,15 +546,27 @@ def check_utf8(fp):
             raise SystemError()
 
 
+
 def check_isa_schemas(isa_json, investigation_schema_path):
     """Used for rule 0003 and 4003"""
     try:
         with open(investigation_schema_path) as fp:
-            investigation_schema = json.load(fp)
-            schema = DRAFT4.create_resource(investigation_schema)
-            registry = Registry.with_resource(investigation_schema['id'], schema)
-            validator = Draft4Validator(investigation_schema, registry=registry)
+            resources = []
+            investigation_schema_path = Path(investigation_schema_path)
+            schemas_dir = investigation_schema_path.parent
+
+            for p in sorted(schemas_dir.glob("*.json")):
+                contents = json.loads(p.read_text(encoding="utf-8"))
+                resource = DRAFT202012.create_resource(contents)
+                resources.append((p.resolve().as_uri(), resource))
+
+            registry = Registry().with_resources(resources)
+            main_uri = investigation_schema_path.resolve().as_uri()
+            print(registry.contents(main_uri))
+            schema_ref = {"$ref": main_uri, "$schema": "https://json-schema.org/draft/2020-12/schema"}
+            validator = Draft202012Validator(schema_ref, registry=registry, format_checker=FormatChecker())
             validator.validate(isa_json)
+
     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!")

isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json

@@ -1,5 +1,5 @@
 {
-  "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json",
+  "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json",
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "ISA Assay JSON Schema",
   "name": "ISA Assay JSON Schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Comment schema - it corresponds to ISA Comment[] construct",
     "name" : "ISA Comment schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Data schema",
     "name" : "ISA Data schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Factor schema",
     "name": "ISA Factor schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Factor Value schema",
     "name": "ISA Factor Value schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA investigation schema",
     "name" : "ISA Investigation schema",

isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json

@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA material attribute schema",
     "name" : "ISA Material Attribute schema",