Code cleanup for dangling file pointer investigation

datablock.py

@@ -24,7 +24,6 @@
 )
 from dxtbx.serialize import load
 from dxtbx.serialize.filename import resolve_path
-from dxtbx.serialize.load import _decode_dict
 from dxtbx.util import get_url_scheme
 
 try:
@@ -1502,7 +1501,7 @@ def from_dict(obj, check_format=True, directory=None):
     def from_json(string, check_format=True, directory=None):
         """Decode a datablock from JSON string."""
         return DataBlockFactory.from_dict(
-            json.loads(string, object_hook=_decode_dict),
+            json.loads(string),
             check_format=check_format,
             directory=directory,
         )

model/experiment_list.py

@@ -1,14 +1,9 @@
-from __future__ import absolute_import, division, print_function
-
 import copy
-import errno
 import json
 import os
-from builtins import range
+import pickle
 
 import pkg_resources
-import six
-import six.moves.cPickle as pickle
 
 from dxtbx.datablock import (
     BeamComparison,
@@ -34,7 +29,6 @@
 from dxtbx.sequence_filenames import template_image_range
 from dxtbx.serialize import xds
 from dxtbx.serialize.filename import resolve_path
-from dxtbx.serialize.load import _decode_dict
 from dxtbx.util import get_url_scheme
 
 try:
@@ -174,10 +168,7 @@ def _load_pickle_path(self, imageset_data, param):
         filename = resolve_path(imageset_data[param], directory=self._directory)
         if self._check_format and filename:
             with open(filename, "rb") as fh:
-                if six.PY3:
-                    return filename, pickle.load(fh, encoding="bytes")
-                else:
-                    return filename, pickle.load(fh)
+                return filename, pickle.load(fh, encoding="bytes")
 
         return filename or "", None
 
@@ -475,7 +466,7 @@ def _experimentlist_from_file(filename, directory=None):
     filename = resolve_path(filename, directory=directory)
     try:
         with open(filename, "r") as infile:
-            return json.load(infile, object_hook=_decode_dict)
+            return json.load(infile)
     except IOError:
         raise IOError("unable to read file, %s" % filename)
 
@@ -687,7 +678,7 @@ def from_dict(obj, check_format=True, directory=None):
     def from_json(text, check_format=True, directory=None):
         """Load an experiment list from JSON."""
         return ExperimentListFactory.from_dict(
-            json.loads(text, object_hook=_decode_dict),
+            json.loads(text),
             check_format=check_format,
             directory=directory,
         )
@@ -737,10 +728,8 @@ def from_serialized_format(filename, check_format=True):
         # First try as a JSON file
         try:
             return ExperimentListFactory.from_json_file(filename, check_format)
-        except IOError as e:
-            # In an ideal Python 3 world this would be much more simply FileNotFoundError, PermissionError
-            if e.errno in (errno.ENOENT, errno.EACCES):
-                raise
+        except (FileNotFoundError, PermissionError):
+            raise
         except Exception:
             pass
 

newsfragments/316.misc

@@ -0,0 +1 @@
+Code cleanup as part of a dangling filepointer investigation

serialize/load.py

@@ -1,48 +1,11 @@
-from __future__ import absolute_import, division, print_function
-
 import json
 import os
-
-import six
+import warnings
 
 from dxtbx.model.crystal import CrystalFactory
 from dxtbx.serialize.imageset import imageset_from_dict
 
 
-def _decode_list(data):
-    """Decode a list to str from unicode."""
-    if six.PY3:
-        return data
-    rv = []
-    for item in data:
-        if isinstance(item, six.text_type):
-            item = item.encode("utf-8")
-        elif isinstance(item, list):
-            item = _decode_list(item)
-        elif isinstance(item, dict):
-            item = _decode_dict(item)
-        rv.append(item)
-    return rv
-
-
-def _decode_dict(data):
-    """Decode a dict to str from unicode."""
-    if six.PY3:
-        return data
-    rv = {}
-    for key, value in data.items():
-        if isinstance(key, six.text_type):
-            key = key.encode("utf-8")
-        if isinstance(value, six.text_type):
-            value = value.encode("utf-8")
-        elif isinstance(value, list):
-            value = _decode_list(value)
-        elif isinstance(value, dict):
-            value = _decode_dict(value)
-        rv[key] = value
-    return rv
-
-
 def imageset_from_string(string, directory=None):
     """Load the string and return the models.
 
@@ -53,10 +16,14 @@ def imageset_from_string(string, directory=None):
         The models
 
     """
-    return imageset_from_dict(
-        json.loads(string, object_hook=_decode_dict), directory=directory
+    warnings.warn(
+        "This function is deprecated and will be removed in the next release",
+        DeprecationWarning,
+        stacklevel=2,
     )
 
+    return imageset_from_dict(json.loads(string), directory=directory)
+
 
 def imageset(filename):
     """Load the given JSON file.
@@ -72,7 +39,7 @@ def imageset(filename):
     filename = os.path.abspath(filename)
     directory = os.path.dirname(filename)
     with open(filename, "r") as infile:
-        return imageset_from_string(infile.read(), directory=directory)
+        return imageset_from_dict(json.load(infile), directory=directory)
 
 
 def datablock(filename, check_format=True):
@@ -112,7 +79,7 @@ def crystal(infile):
 
 
 def experiment_list(infile, check_format=True):
-    """Load an experiment list from a serialzied format."""
+    """Load an experiment list from a serialized format."""
     # Resolve recursive import
     from dxtbx.model.experiment_list import ExperimentListFactory