Remove explicit calls to validate_links since it is folded into resolve_all().

Author: Peter Amstutz

schema_salad/main.py

@@ -98,8 +98,16 @@ def main(argsl=None):  # type: (List[str]) -> int
     if not urlparse.urlparse(schema_uri)[0]:
         schema_uri = "file://" + os.path.abspath(schema_uri)
     schema_raw_doc = metaschema_loader.fetch(schema_uri)
-    schema_doc, schema_metadata = metaschema_loader.resolve_all(
-        schema_raw_doc, schema_uri)
+
+    try:
+        schema_doc, schema_metadata = metaschema_loader.resolve_all(
+            schema_raw_doc, schema_uri)
+    except (validate.ValidationException) as e:
+        _logger.error("Schema `%s` failed link checking:\n%s",
+                      args.schema, e, exc_info=(e if args.debug else False))
+        _logger.debug("Index is %s", metaschema_loader.idx.keys())
+        _logger.debug("Vocabulary is %s", metaschema_loader.vocab.keys())
+        return 1
 
     # Optionally print the schema after ref resolution
     if not args.document and args.print_pre:
@@ -110,16 +118,6 @@ def main(argsl=None):  # type: (List[str]) -> int
         print(json.dumps(metaschema_loader.idx.keys(), indent=4))
         return 0
 
-    # Validate links in the schema document
-    # try:
-    #     metaschema_loader.validate_links(schema_doc)
-    # except (validate.ValidationException) as e:
-    #     _logger.error("Schema `%s` failed link checking:\n%s",
-    #                   args.schema, e, exc_info=(e if args.debug else False))
-    #     _logger.debug("Index is %s", metaschema_loader.idx.keys())
-    #     _logger.debug("Vocabulary is %s", metaschema_loader.vocab.keys())
-    #     return 1
-
     # Validate the schema document against the metaschema
     try:
         schema.validate_doc(metaschema_names, schema_doc,
@@ -196,16 +194,6 @@ def main(argsl=None):  # type: (List[str]) -> int
         print(json.dumps(document_loader.idx.keys(), indent=4))
         return 0
 
-    # Validate links in the target document
-    # try:
-    #     document_loader.validate_links(document)
-    # except (validate.ValidationException) as e:
-    #     _logger.error("Document `%s` failed link checking:\n%s",
-    #                   args.document, e, exc_info=(e if args.debug else False))
-    #     _logger.debug("Index is %s", json.dumps(
-    #         document_loader.idx.keys(), indent=4))
-    #     return 1
-
     # Validate the schema document against the metaschema
     try:
         schema.validate_doc(avsc_names, document,

schema_salad/ref_resolver.py

@@ -239,7 +239,7 @@ def add_context(self, newcontext, baseuri=""):
         _logger.debug("vocab_fields is %s", self.vocab_fields)
         _logger.debug("vocab is %s", self.vocab)
 
-    def resolve_ref(self, ref, base_url=None, toplevel=True):
+    def resolve_ref(self, ref, base_url=None, checklinks=True):
         # type: (Union[Dict[str, Any], str, unicode], Union[str, unicode], bool) -> Tuple[Union[Dict[str, Any], str, unicode], Dict[str, Any]]
         base_url = base_url or 'file://%s/' % os.path.abspath('.')
 
@@ -301,7 +301,7 @@ def resolve_ref(self, ref, base_url=None, toplevel=True):
             doc = self.fetch(doc_url)
 
         # Recursively expand urls and resolve directives
-        obj, metadata = self.resolve_all(doc if doc else obj, doc_url, toplevel=toplevel)
+        obj, metadata = self.resolve_all(doc if doc else obj, doc_url, checklinks=checklinks)
 
         # Requested reference should be in the index now, otherwise it's a bad
         # reference
@@ -322,7 +322,7 @@ def resolve_ref(self, ref, base_url=None, toplevel=True):
         except TypeError:
             return obj, metadata
 
-    def resolve_all(self, document, base_url, file_base=None, toplevel=True):
+    def resolve_all(self, document, base_url, file_base=None, checklinks=True):
         # type: (Any, Union[str, unicode], Union[str, unicode], bool) -> Tuple[Any, Dict[str, Any]]
         loader = self
         metadata = {}  # type: Dict[str, Any]
@@ -332,7 +332,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
         if isinstance(document, dict):
             # Handle $import and $include
             if ('$import' in document or '$include' in document):
-                return self.resolve_ref(document, base_url=file_base, toplevel=toplevel)
+                return self.resolve_ref(document, base_url=file_base, checklinks=checklinks)
         elif isinstance(document, list):
             pass
         else:
@@ -368,7 +368,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
             if "$graph" in document:
                 metadata = _copy_dict_without_key(document, "$graph")
                 document = document["$graph"]
-                metadata, _ = loader.resolve_all(metadata, base_url, file_base=file_base, toplevel=False)
+                metadata, _ = loader.resolve_all(metadata, base_url, file_base=file_base, checklinks=False)
 
         if isinstance(document, dict):
             for idmapField in loader.idmap:
@@ -433,7 +433,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
             try:
                 for key, val in document.items():
                     document[key], _ = loader.resolve_all(
-                        val, base_url, file_base=file_base, toplevel=False)
+                        val, base_url, file_base=file_base, checklinks=False)
             except validate.ValidationException as v:
                 _logger.debug("loader is %s", id(loader))
                 raise validate.ValidationException("(%s) (%s) Validation error in field %s:\n%s" % (
@@ -445,7 +445,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
                 while i < len(document):
                     val = document[i]
                     if isinstance(val, dict) and "$import" in val:
-                        l, _ = loader.resolve_ref(val, base_url=file_base, toplevel=False)
+                        l, _ = loader.resolve_ref(val, base_url=file_base, checklinks=False)
                         if isinstance(l, list):
                             del document[i]
                             for item in aslist(l):
@@ -456,7 +456,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
                             i += 1
                     else:
                         document[i], _ = loader.resolve_all(
-                            val, base_url, file_base=file_base, toplevel=False)
+                            val, base_url, file_base=file_base, checklinks=False)
                         i += 1
             except validate.ValidationException as v:
                 raise validate.ValidationException("(%s) (%s) Validation error in position %i:\n%s" % (
@@ -469,7 +469,7 @@ def resolve_all(self, document, base_url, file_base=None, toplevel=True):
                             metadata[identifer], base_url, scoped=True)
                         loader.idx[metadata[identifer]] = document
 
-        if toplevel:
+        if checklinks:
             self.validate_links(document, "")
 
         return document, metadata

setup.py

@@ -41,7 +41,7 @@
 extras_require = {}               # TODO: to be removed when the above is added
 
 setup(name='schema-salad',
-      version='1.11',
+      version='1.12',
       description='Schema Annotations for Linked Avro Data (SALAD)',
       long_description=open(README).read(),
       author='Common workflow language working group',

tests/test_examples.py

@@ -166,7 +166,7 @@ def test_examples(self):
                 "schema_salad/metaschema/%s_schema.yml" % a)
             with open("schema_salad/metaschema/%s_src.yml" % a) as src_fp:
                 src = ldr.resolve_all(
-                    yaml.load(src_fp, Loader=SafeLoader), "", toplevel=False)[0]
+                    yaml.load(src_fp, Loader=SafeLoader), "", checklinks=False)[0]
             with open("schema_salad/metaschema/%s_proc.yml" % a) as src_proc:
                 proc = yaml.load(src_proc, Loader=SafeLoader)
             self.assertEqual(proc, src)