cleanups

Author: mr-c

cwltool/provenance.py

@@ -4,7 +4,6 @@
 import copy
 import datetime
 import hashlib
-import io
 import logging
 import os
 import os.path
@@ -15,10 +14,10 @@
 import uuid
 from collections import OrderedDict
 from getpass import getuser
-from io import open
+from io import BytesIO, FileIO, TextIOWrapper, open
 from socket import getfqdn
-from typing import (IO, Any, Callable, Dict, List, MutableMapping, Optional,
-                    Set, Tuple, Union, cast)
+from typing import (IO, Any, Callable, Dict, List, Generator, MutableMapping,
+                    Optional, Set, Tuple, Union, cast)
 
 import prov.model as provM
 import six
@@ -149,7 +148,7 @@ def _whoami():
     return (username, fullname)
 
 
-class WritableBagFile(io.FileIO):
+class WritableBagFile(FileIO):
     """Writes files in research object."""
 
     def __init__(self, research_object, rel_path):
@@ -209,7 +208,7 @@ def readable(self):
 
     def truncate(self, size=None):
         # type: (Optional[int]) -> int
-        # FIXME: This breaks contract io.IOBase,
+        # FIXME: This breaks contract IOBase,
         # as it means we would have to recalculate the hash
         if size is not None:
             raise IOError("WritableBagFile can't truncate")
@@ -680,7 +679,7 @@ def declare_directory(self, value):  # type: (MutableMapping) -> ProvEntity
     def declare_string(self, value):
         # type: (Union[Text, str]) -> Tuple[ProvEntity,Text]
         """Save as string in UTF-8."""
-        byte_s = io.BytesIO(str(value).encode(ENCODING))
+        byte_s = BytesIO(str(value).encode(ENCODING))
         data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN)
         checksum = posixpath.basename(data_file)
         # FIXME: Don't naively assume add_data_file uses hash in filename!
@@ -716,7 +715,7 @@ def declare_artefact(self, value):
 
         if isinstance(value, bytes):
             # If we got here then we must be in Python 3
-            byte_s = io.BytesIO(value)
+            byte_s = BytesIO(value)
             data_file = self.research_object.add_data_file(byte_s)
             # FIXME: Don't naively assume add_data_file uses hash in filename!
             data_id = "data:%s" % posixpath.split(data_file)[1]
@@ -1051,13 +1050,13 @@ def write_bag_file(self, path, encoding=ENCODING):
         # type: (Text, Optional[str]) -> IO
         """Write the bag file into our research object."""
         # For some reason below throws BlockingIOError
-        #fp = io.BufferedWriter(WritableBagFile(self, path))
+        #fp = BufferedWriter(WritableBagFile(self, path))
         bag_file = cast(IO, WritableBagFile(self, path))
         if encoding:
             # encoding: match Tag-File-Character-Encoding: UTF-8
             # newline: ensure LF also on Windows
             return cast(IO,
-                        io.TextIOWrapper(bag_file, encoding=encoding, newline="\n"))
+                        TextIOWrapper(bag_file, encoding=encoding, newline="\n"))
         return bag_file
 
     def add_tagfile(self, path, when=None):
@@ -1505,7 +1504,7 @@ def jdefault(o):
             rel_path = posixpath.join(_posix_path(WORKFLOW), "primary-output.json")
         else:
             rel_path = posixpath.join(_posix_path(WORKFLOW), "primary-job.json")
-        j = json.dumps(copied, indent=4, ensure_ascii=False, default=jdefault)
+        j = json_dumps(copied, indent=4, ensure_ascii=False, default=jdefault)
         with self.write_bag_file(rel_path) as file_path:
             file_path.write(j + u"\n")
         _logger.debug(u"[provenance] Generated customised job file: %s",

tests/test_provenance.py

@@ -13,8 +13,7 @@
 import arcp
 import pytest
 from rdflib import Graph, Literal, Namespace, URIRef
-from rdflib.namespace import DC, DCTERMS, FOAF, RDF, RDFS, SKOS, XSD
-from six import StringIO
+from rdflib.namespace import DC, DCTERMS, RDF
 from six.moves import urllib
 
 import bagit
@@ -25,15 +24,6 @@
 from cwltool.utils import onWindows
 
 from .util import get_data
-import bagit
-import posixpath
-import ntpath
-from six.moves import urllib
-from rdflib import Namespace, URIRef, Graph, Literal
-from rdflib.namespace import RDF,RDFS,SKOS,DCTERMS,FOAF,XSD,DC
-import arcp
-import json
-from hashlib import sha1
 
 # RDF namespaces we'll query for later
 ORE = Namespace("http://www.openarchives.org/ore/terms/")