upgrade to latest schema_salad; misc cleanups

Author: mr-c

cwltool/provenance.py

@@ -934,7 +934,7 @@ def finalize_prov_profile(self, name):
             self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld")
             prov_ids.append(self.provenance_ns[filename + ".jsonld"])
 
-        _logger.debug("[provenance] added provenance: %s", prov_ids)
+        _logger.debug(u"[provenance] added provenance: %s", prov_ids)
         return prov_ids
 
 

cwltool/validate_js.py

@@ -6,15 +6,14 @@
 from typing import (Any, Dict, List, MutableMapping, MutableSequence, Optional,
                     Tuple, Union)
 
-import avro.schema  # always import after schema_salad, never before
 from pkg_resources import resource_stream
 from ruamel.yaml.comments import CommentedMap  # pylint: disable=unused-import
-from schema_salad.sourceline import SourceLine
-from schema_salad.validate import Schema  # pylint: disable=unused-import
-from schema_salad.validate import ValidationException, validate_ex
 from six import string_types
 from typing_extensions import Text  # pylint: disable=unused-import
-# move to a regular typing import when Python 3.3-3.6 is no longer supported
+from schema_salad import avro
+from schema_salad.sourceline import SourceLine
+from schema_salad.validate import Schema  # pylint: disable=unused-import
+from schema_salad.validate import validate_ex
 
 from .expression import scanner as scan_expression
 from .loghandler import _logger
@@ -60,8 +59,8 @@ def get_expressions(tool,             # type: Union[CommentedMap, Any]
         if not isinstance(tool, MutableSequence):
             return []
 
-        return list(itertools.chain(*
-            map(lambda x: get_expressions(x[1], schema.items, SourceLine(tool, x[0])), enumerate(tool))  # type: ignore # https://github.com/python/mypy/issues/4679
+        return list(itertools.chain(
+            *map(lambda x: get_expressions(x[1], schema.items, SourceLine(tool, x[0])), enumerate(tool))  # type: ignore # https://github.com/python/mypy/issues/4679
         ))
 
     elif isinstance(schema, avro.schema.RecordSchema):
@@ -166,7 +165,7 @@ def validate_js_expressions(tool, schema, jshint_options=None):
 
     default_globals = [u"self", u"inputs", u"runtime", u"console"]
 
-    for i, prop in enumerate(reversed(requirements)):
+    for prop in reversed(requirements):
         if prop["class"] == "InlineJavascriptRequirement":
             expression_lib = prop.get("expressionLib", [])
             break

requirements.txt

@@ -2,7 +2,7 @@ requests>=2.4.3
 ruamel.yaml>=0.12.4,<=0.15.77
 rdflib>=4.2.2,<4.3
 shellescape>=3.4.1,<3.5
-schema-salad>=2.7.20180905124720,<3
+schema-salad>=2.7.20181128093206,<3
 typing>=3.5.3; python_version<"3.6"
 pathlib2==2.3.2; python_version<"3"
 prov==1.5.1

setup.py

@@ -53,7 +53,7 @@
           'ruamel.yaml >= 0.12.4, <= 0.15.77',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
-          'schema-salad >= 2.7.20180905124720, < 3',
+          'schema-salad >= 2.7.20181128093206, < 3',
           'mypy-extensions',
           'six >= 1.9.0',  # >= 1.9.0 required by prov
           'psutil',

tests/test_provenance.py

@@ -51,7 +51,7 @@ def folder():
 
 def cwltool(folder, *args):
     load_tool.loaders = {}
-    new_args = ['--no-container', '--provenance', folder]
+    new_args = ['--provenance', folder]
     new_args.extend(args)
     # Run within a temporary directory to not pollute git checkout
     with temp_dir("cwltool-run") as tmp_dir: