Merge branch 'update-build-process' into 2.x

tests/config.py

@@ -5,12 +5,12 @@
 from jsonschema import Draft202012Validator
 import re
 
-root_dir = Path(__file__).parent.parent
-schema_dir = root_dir / "schema"
-test_dir = root_dir / "tests"
-examples_dir = root_dir / "examples"
-vrs_source_path = schema_dir / "vrs" / "vrs-source.yaml"
-vrs_jsons_path = schema_dir / "vrs" / "json"
+root_path = Path(__file__).parent.parent
+schema_path = root_path / "schema"
+test_path = root_path / "tests"
+examples_path = root_path / "examples"
+vrs_source_path = schema_path / "vrs" / "vrs-source.yaml"
+vrs_jsons_path = schema_path / "vrs" / "json"
 
 
 ga4gh_re = re.compile(r'.*\/ga4gh\/schema\/([\w\-\.]+)\/[\w\.]+\/(.*)$')
@@ -22,25 +22,25 @@ def retrieve_rel_ref(ga4gh_ref: str):
         raise ValueError(f'ga4gh_ref {ga4gh_ref} is not a root GA4GH reference')
     schema_module = ga4gh_match.group(1)
     local_path = ga4gh_match.group(2)
-    resolved_path = (schema_dir / schema_module / local_path).resolve()
+    resolved_path = (schema_path / schema_module / local_path).resolve()
     schema = json.loads(resolved_path.read_text())
     return Resource.from_contents(schema)
 
 
-vrs_js_registry = Registry(retrieve=retrieve_rel_ref)
-vrs_js = dict()
-vrs_validator = dict()
+js_registry = Registry(retrieve=retrieve_rel_ref)
+js_def = dict()
+validator = dict()
 
-for schema_path in vrs_jsons_path.glob('*'):
+for schema_path in schema_path.glob('*/json/*'):
     content = json.loads(schema_path.read_text())
     schema_uri = schema_path.as_uri()
     content['id'] = schema_uri
     schema_resource = Resource(contents=content, specification=DRAFT202012)
-    vrs_js[schema_path.stem] = content
-    vrs_schemas = vrs_js_registry.with_resources([
+    js_def[schema_path.stem] = content
+    js_registry = js_registry.with_resources([
         (schema_path.name, schema_resource),
         (schema_uri, schema_resource)
     ])
 
-for cls in vrs_js:
-    vrs_validator[cls] = Draft202012Validator(vrs_js[cls], registry=vrs_js_registry)
+for cls in js_def:
+    validator[cls] = Draft202012Validator(js_def[cls], registry=js_registry)

tests/test_basic.py

@@ -3,7 +3,7 @@
 import jsonschema as js
 from ga4gh.gks.metaschema.tools.source_proc import YamlSchemaProcessor
 
-from config import vrs_source_path, vrs_validator
+from config import vrs_source_path, validator
 
 # Is the YAML parseable?
 p = YamlSchemaProcessor(vrs_source_path)
@@ -38,7 +38,7 @@ def test_simple_sequence_location():
         'end': [None, 150],
         'type': 'SequenceLocation'
     }
-    vrs_validator['SequenceLocation'].validate(sl)
+    validator['SequenceLocation'].validate(sl)
 
     a = {
         'location': sl,
@@ -49,4 +49,4 @@ def test_simple_sequence_location():
         },
         'type': 'Allele'
     }
-    vrs_validator['Allele'].validate(a)
+    validator['Allele'].validate(a)

tests/test_examples.py

@@ -1,24 +1,16 @@
-from config import test_dir, examples_dir
+from config import test_path, examples_path
 import yaml
-from config import vrs_validator
-
-
-def get_validator(schema_file, schema_class):
-    validator = globals()[f'{schema_file}_validator'][schema_class]
-    return validator
+from config import validator
 
 
 def test_examples():
-    with open(test_dir / 'test_definitions.yaml') as def_file:
+    with open(test_path / 'test_definitions.yaml') as def_file:
         test_spec = yaml.safe_load(def_file)
     for test in test_spec['tests']:
-        with open(examples_dir / test['test_file']) as datafile:
+        with open(examples_path / test['test_file']) as datafile:
             data = yaml.safe_load(datafile)
-        validator = get_validator(
-            test['schema'],
-            test['definition']
-        )
+        class_validator = validator[test['definition']]
         try:
-            assert validator.validate(data) is None
+            assert class_validator.validate(data) is None
         except AssertionError as e:
             raise AssertionError(f"AssertionError in {test['test_file']}: {e}")