Detect when an abstract class is used but doesn't have a concrete subtype.

Author: Peter Amstutz

schema_salad/schema.py

@@ -417,6 +417,10 @@ def extend_and_specialize(items, loader):
                     add_dictlist(extended_by, ex, ex_types[t["name"]])
                     add_dictlist(extended_by, avro_name(ex), ex_types[ex])
 
+    for t in n:
+        if t.get("abstract") and t["name"] not in extended_by:
+            raise validate.ValidationException("%s is abstract but missing a concrete subtype" % t["name"])
+
     for t in n:
         if "fields" in t:
             t["fields"] = replace_type(t["fields"], extended_by, loader, set())

tests/test_examples.py

@@ -20,11 +20,11 @@ def test_schemas(self):
             "edam:has_format": "edam:format_1915"
         }, "")
 
-        self.assertEqual(ra, {
+        self.assertEqual({
             "$schemas": ["tests/EDAM.owl"],
             "$namespaces": {"edam": "http://edamontology.org/"},
             'http://edamontology.org/has_format': 'http://edamontology.org/format_1915'
-        })
+        }, ra)
 
     # def test_domain(self):
     #     l = schema_salad.ref_resolver.Loader({})
@@ -46,9 +46,12 @@ def test_schemas(self):
     #     })
 
     def test_self_validate(self):
-        schema_salad.main.main(argsl=["schema_salad/metaschema/metaschema.yml"])
-        schema_salad.main.main(argsl=["schema_salad/metaschema/metaschema.yml",
-                                     "schema_salad/metaschema/metaschema.yml"])
+        self.assertEqual(0, schema_salad.main.main(argsl=["schema_salad/metaschema/metaschema.yml"]))
+        self.assertEqual(0, schema_salad.main.main(argsl=["schema_salad/metaschema/metaschema.yml",
+                                     "schema_salad/metaschema/metaschema.yml"]))
+
+    def test_avro_regression(self):
+        self.assertEqual(0, schema_salad.main.main(argsl=["tests/Process.yml"]))
 
     def test_jsonld_ctx(self):
         ldr, _, _, _ = schema_salad.schema.load_schema({