RF: json => simplejson

Author: Ben Cipollini

nipype/interfaces/fsl/tests/test_maths.py

@@ -14,12 +14,19 @@
 from nipype.interfaces.base import Undefined
 import nipype.interfaces.fsl.maths as fsl
 from nipype.interfaces.fsl import no_fsl, Info
+from nipype.interfaces.fsl.base import FSLCommand
 
 
-def set_output_type(fsl_output_type=None):
+def set_output_type(fsl_output_type):
     prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
+
     if fsl_output_type is not None:
         os.environ['FSLOUTPUTTYPE'] = fsl_output_type
+    elif 'FSLOUTPUTTYPE' in os.environ:
+        del os.environ['FSLOUTPUTTYPE']
+
+    FSLCommand.set_default_output_type(Info.output_type())
+
     return prev_output_type
 
 def create_files_in_directory():
@@ -500,7 +507,7 @@ def test_tempfilt(fsl_output_type=None):
 
 @skipif(no_fsl)
 def test_all_again():
-    # Rerun tests with all file types
+    # Rerun tests with all output file types
     all_func = [test_binarymaths, test_changedt, test_dilation, test_erosion,
                 test_mask, test_maximage, test_meanimage, test_multimaths,
                 test_smooth, test_tempfilt, test_threshold, test_unarymaths]

nipype/interfaces/io.py

@@ -20,6 +20,7 @@
 from builtins import zip
 from builtins import filter
 from builtins import range
+
 import glob
 import fnmatch
 import string
@@ -2158,7 +2159,7 @@ class JSONFileGrabber(IOBase):
     >>> jsonSource.inputs.in_file = 'jsongrabber.txt'
     >>> res = jsonSource.run()
     >>> pprint.pprint(res.outputs.get())  # doctest: +NORMALIZE_WHITESPACE
-    {'param1': u'exampleStr', 'param2': 4, 'param3': 1.0}
+    {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
 
 
     """
@@ -2167,12 +2168,12 @@ class JSONFileGrabber(IOBase):
     _always_run = True
 
     def _list_outputs(self):
-        import json
+        import simplejson
 
         outputs = {}
         if isdefined(self.inputs.in_file):
             with open(self.inputs.in_file, 'r') as f:
-                data = json.load(f)
+                data = simplejson.load(f)
 
             if not isinstance(data, dict):
                 raise RuntimeError('JSON input has no dictionary structure')
@@ -2269,7 +2270,7 @@ def _process_name(self, name, val):
         return name, val
 
     def _list_outputs(self):
-        import json
+        import simplejson
         import os.path as op
 
         if not isdefined(self.inputs.out_file):
@@ -2287,7 +2288,7 @@ def _list_outputs(self):
             out_dict[key] = val
 
         with open(out_file, 'w') as f:
-            json.dump(out_dict, f)
+            simplejson.dump(out_dict, f)
         outputs = self.output_spec().get()
         outputs['out_file'] = out_file
         return outputs

nipype/interfaces/tests/test_io.py

@@ -373,7 +373,7 @@ def test_freesurfersource():
 
 
 def test_jsonsink():
-    import json
+    import simplejson
     import os
 
     ds = nio.JSONFileSink()
@@ -392,7 +392,7 @@ def test_jsonsink():
     res = js.run()
 
     with open(res.outputs.out_file, 'r') as f:
-        data = json.load(f)
+        data = simplejson.load(f)
     yield assert_true, data == {"contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"}
 
     js = nio.JSONFileSink(infields=['test'], in_dict={'foo': 'var'})
@@ -402,7 +402,7 @@ def test_jsonsink():
     res = js.run()
 
     with open(res.outputs.out_file, 'r') as f:
-        data = json.load(f)
+        data = simplejson.load(f)
     yield assert_true, data == {"test": "testInfields", "contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"}
 
     os.chdir(curdir)

nipype/utils/filemanip.py

@@ -10,7 +10,7 @@
 import gzip
 import hashlib
 from hashlib import md5
-import json
+import simplejson
 import os
 import re
 import shutil
@@ -382,7 +382,7 @@ def save_json(filename, data):
     """
 
     with open(filename, 'w') as fp:
-        json.dump(data, fp, sort_keys=True, indent=4)
+        simplejson.dump(data, fp, sort_keys=True, indent=4)
 
 
 def load_json(filename):
@@ -400,7 +400,7 @@ def load_json(filename):
     """
 
     with open (filename, 'r') as fp:
-        data = json.load(fp)
+        data = simplejson.load(fp)
     return data
 
 def loadcrash(infile, *args):

nipype/utils/nipype2boutiques.py

@@ -15,7 +15,7 @@
 import argparse
 import inspect
 import sys
-import json
+import simplejson
 import tempfile
 
 from nipype.interfaces.base import Interface
@@ -106,7 +106,7 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input
   for input in tool_desc['inputs']:
     del input['tempvalue']
 
-  return json.dumps(tool_desc, indent=4, separators=(',', ': '))
+  return simplejson.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 def get_boutiques_input(inputs,interface,input_name,spec,ignored_template_inputs,verbose,ignore_template_numbers):
   """

nipype/utils/provenance.py

@@ -3,7 +3,7 @@
 from builtins import object
 
 from pickle import dumps
-import json
+import simplejson
 import os
 import getpass
 from socket import getfqdn
@@ -156,8 +156,8 @@ def safe_encode(x, as_literal=True):
                 else:
                     outdict[key] = encoded_value
             if not as_literal:
-                return json.dumps(outdict)
-            return pm.Literal(json.dumps(outdict), pm.XSD['string'])
+                return simplejson.dumps(outdict)
+            return pm.Literal(simplejson.dumps(outdict), pm.XSD['string'])
         if isinstance(x, list):
             try:
                 nptype = np.array(x).dtype
@@ -174,8 +174,8 @@ def safe_encode(x, as_literal=True):
             else:
                 outlist = x
             if not as_literal:
-                return json.dumps(outlist)
-            return pm.Literal(json.dumps(outlist), pm.XSD['string'])
+                return simplejson.dumps(outlist)
+            return pm.Literal(simplejson.dumps(outlist), pm.XSD['string'])
         if not as_literal:
             return dumps(x)
         return pm.Literal(dumps(x), nipype_ns['pickle'])
@@ -393,5 +393,5 @@ def write_provenance(self, filename='provenance', format='turtle'):
                     fp.writelines(self.g.get_provn())
             if format in ['json', 'all']:
                 with open(filename + '.json', 'wt') as fp:
-                    pm.json.dump(self.g, fp, cls=pm.ProvBundle.JSONEncoder)
+                    pm.simplejson.dump(self.g, fp, cls=pm.ProvBundle.JSONEncoder)
         return self.g

requirements.txt

@@ -6,3 +6,4 @@ python-dateutil>=1.5
 nibabel>=2.0.1
 nose>=1.2
 future==0.15.2
+simplejson

tools/github.py

@@ -2,7 +2,7 @@
 standard_library.install_aliases()
 import http.client
 import inspect
-import json
+import simplejson
 import os
 from subprocess import Popen, PIPE
 
@@ -58,7 +58,7 @@ def create_hash_map():
         r1 = conn.getresponse()
         if r1.reason != 'OK':
             raise Exception('HTTP Response  %s:%s' % (r1.status, r1.reason))
-        payload = json.loads(r1.read())
+        payload = simplejson.loads(r1.read())
         for infodict in payload['tree']:
             if infodict['type'] == "blob":
                 hashmap[infodict['sha']] = infodict['path']