Add validation of ome_tif_fields.json

src/ingest_validation_tests/ome_tiff_field_validator.py

@@ -9,6 +9,7 @@
 
 import tifffile
 import xmlschema
+from jsonschema import validate
 from ingest_validation_tools.plugin_validator import Validator
 
 
@@ -107,7 +108,15 @@ class OmeTiffFieldValidator(Validator):
     def collect_errors(self, **kwargs) -> List[Optional[str]]:
         cfg_path = Path(__file__).parent / "ome_tiff_fields.json"
         cfg_list = json.loads(cfg_path.read_text())
-        # TODO: need a jsonschema test of cfg_list here
+        cfg_schema_path = Path(__file__).parent / "ome_tiff_fields_schema.json"
+        schema = json.loads(cfg_schema_path.read_text())
+        try:
+            pprint(cfg_list)
+            pprint(schema)
+            validate(cfg_list, schema)
+        except Exception as excp:
+            raise RuntimeError(f"Configuration error: {cfg_path}"
+                               f" does not satisfy schema {cfg_schema_path}")
         all_tests = {}
         for test_set in cfg_list:
             if re.fullmatch(test_set["re"], self.assay_type):

src/ingest_validation_tests/ome_tiff_fields_schema.json

@@ -0,0 +1,47 @@
+{
+  "$schema": "http://json-schema.org/schema#",
+  "$id": "http://schemata.hubmapconsortium.org/ome_tiff_fields_schema_schema.json",
+  "title": "ome-tiff fields schema",
+  "description": "schema for the definitions file of required ome-tiff fields",
+  "allOf":[{"$ref": "#/definitions/file_info"}],
+  "definitions": {
+    "file_info_record": {
+      "type": "object",
+      "properties": {
+	"re": {
+	  "type": "string",
+	  "description": "regular expression for assay types"
+	},
+	"fields": {
+	  "type": "object",
+	  "additionalProperties": {
+	    "oneOf": [
+	      {
+		"type": "object",
+		"properties": {
+		  "dtype": {"enum": ["integer", "float"]}
+		},
+		"required": ["dtype"]
+	      },
+	      {
+		"type": "object",
+		"properties": {
+		  "dtype": {"enum": ["categorical"]},
+		  "allowed_values": {
+		    "type": "array",
+		    "items": {"type": "string"}
+		  }
+		},
+		"required": ["dtype", "allowed_values"]
+	      }
+	    ]
+	  }
+	}
+      }
+    },
+    "file_info": {
+      "type":  "array",
+      "items": {"$ref": "#/definitions/file_info_record"}
+    }
+  }
+}