type fixes

Author: mr-c

cwltool/builder.py

@@ -10,7 +10,7 @@
 from ruamel.yaml.comments import CommentedMap
 from schema_salad import validate
 from schema_salad.schema import Names, convert_to_dict
-from schema_salad.avro.schema import make_avsc_object
+from schema_salad.avro.schema import make_avsc_object, Schema
 from schema_salad.sourceline import SourceLine
 from six import iteritems, string_types
 from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
@@ -209,7 +209,7 @@ def bind_input(self,
         if isinstance(schema["type"], MutableSequence):
             bound_input = False
             for t in schema["type"]:
-                avsc = None
+                avsc = None  # type: Optional[Schema]
                 if isinstance(t, string_types) and self.names.has_name(t, ""):
                     avsc = self.names.get_name(t, "")
                 elif isinstance(t, MutableMapping) and "name" in t and self.names.has_name(t["name"], ""):

cwltool/command_line_tool.py

@@ -17,6 +17,7 @@
 
 import shellescape
 from schema_salad import validate
+from schema_salad.avro.schema import Schema
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine
 from six import string_types
@@ -612,17 +613,17 @@ def makeWorkflowException(msg):
 
                 if compute_checksum:
                     adjustFileObjs(ret, partial(compute_checksums, fs_access))
-
-            validate.validate_ex(
-                self.names.get_name("outputs_record_schema", ""), ret,
+            expected_schema = cast(Schema, self.names.get_name(
+                "outputs_record_schema", ""))
+            validate.validate_ex(expected_schema, ret,
                 strict=False, logger=_logger_validation_warnings)
             if ret is not None and builder.mutation_manager is not None:
                 adjustFileObjs(ret, builder.mutation_manager.set_generation)
             return ret if ret is not None else {}
         except validate.ValidationException as e:
             raise WorkflowException(
-                "Error validating output record. " + Text(e) + "\n in " +
-                json_dumps(ret, indent=4))
+                "Error validating output record. " + Text(e) + "\n in "
+                + json_dumps(ret, indent=4))
         finally:
             if builder.mutation_manager and readers:
                 for r in readers.values():