Source code for allensdk.core.json_utilities

# Allen Institute Software License - This software license is the 2-clause BSD
# license plus a third clause that prohibits redistribution for commercial
# purposes without further permission.
#
# Copyright 2015-2016. Allen Institute. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Redistributions for commercial purposes are not permitted without the
# Allen Institute's written permission.
# For purposes of this license, commercial purposes is the incorporation of the
# Allen Institute's software into anything for which you will charge fees or
# other compensation. Contact terms@alleninstitute.org for commercial licensing
# opportunities.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
import numpy as np
import simplejson as json
import math
import re
import logging

ju_logger = logging.getLogger(__name__)

try:
    import urllib.request as urllib_request
except ImportError:
    import urllib2 as urllib_request
try:
    from urllib.parse import urlparse
except ImportError:
    import urlparse


[docs]def read(file_name): """ Shortcut reading JSON from a file. """ with open(file_name, 'rb') as f: json_string = f.read().decode('utf-8') if len(json_string)==0: # If empty file json_string='{}' # Create a string that will give an empty JSON object instead of an error json_obj = json.loads(json_string) return json_obj
[docs]def write(file_name, obj): """ Shortcut for writing JSON to a file. This also takes care of serializing numpy and data types. """ with open(file_name, 'wb') as f: try: f.write(write_string(obj)) # Python 2.7 except TypeError: f.write(bytes(write_string(obj), 'utf-8')) # Python 3
[docs]def write_string(obj): """ Shortcut for writing JSON to a string. This also takes care of serializing numpy and data types. """ return json.dumps(obj, indent=2, ignore_nan=True, default=json_handler, iterable_as_array=True)
[docs]def read_url(url, method='POST'): if method == 'GET': return read_url_get(url) elif method == 'POST': return read_url_post(url) else: raise Exception('Unknown request method: (%s)' % method)
[docs]def read_url_get(url): '''Transform a JSON contained in a file into an equivalent nested python dict. Parameters ---------- url : string where to get the json. Returns ------- dict Python version of the input Note: if the input is a bare array or literal, for example, the output will be of the corresponding type. ''' response = urllib_request.urlopen(url) json_string = response.read().decode('utf-8') return json.loads(json_string)
[docs]def read_url_post(url): '''Transform a JSON contained in a file into an equivalent nested python dict. Parameters ---------- url : string where to get the json. Returns ------- dict Python version of the input Note: if the input is a bare array or literal, for example, the output will be of the corresponding type. ''' urlp = urlparse.urlparse(url) main_url = urlparse.urlunsplit( (urlp.scheme, urlp.netloc, urlp.path, '', '')) data = json.dumps(dict(urlparse.parse_qsl(urlp.query))) handler = urllib_request.HTTPHandler() opener = urllib_request.build_opener(handler) request = urllib_request.Request(main_url, data) request.add_header("Content-Type", 'application/json') request.get_method = lambda: 'POST' try: response = opener.open(request) except Exception as e: response = e if response.code == 200: json_string = response.read() else: json_string = response.read() return json.loads(json_string)
[docs]def json_handler(obj): """ Used by write_json convert a few non-standard types to things that the json package can handle. """ if hasattr(obj, 'to_dict'): return obj.to_dict() elif isinstance(obj, np.ndarray): return obj.tolist() elif (isinstance(obj, np.float64) or isinstance(obj, np.float32) or isinstance(obj, np.float16)): return float(obj) elif (isinstance(obj, np.int64) or isinstance(obj, np.int32) or isinstance(obj, np.int16) or isinstance(obj, np.int8) or isinstance(obj, np.uint64) or isinstance(obj, np.uint32) or isinstance(obj, np.uint16) or isinstance(obj, np.uint8)): return long(obj) elif (isinstance(obj, np.bool) or isinstance(obj, np.bool_)): return bool(obj) elif hasattr(obj, 'isoformat'): return obj.isoformat() else: raise TypeError( 'Object of type %s with value of %s is not JSON serializable' % (type(obj), repr(obj)))
[docs]class JsonComments(object): _oneline_comment = re.compile(r"\/\/.*$", re.MULTILINE) _multiline_comment_start = re.compile(r"\/\*", re.MULTILINE | re.DOTALL) _multiline_comment_end = re.compile(r"\*\/", re.MULTILINE | re.DOTALL) _blank_line = re.compile(r"\n?^\s*$", re.MULTILINE) _carriage_return = re.compile(r"\r$", re.MULTILINE) @classmethod
[docs] def read_string(cls, json_string): json_string_no_comments = cls.remove_comments(json_string) return json.loads(json_string_no_comments)
@classmethod
[docs] def read_file(cls, file_name): try: with open(file_name) as f: json_string = f.read() json_object = cls.read_string(json_string) return json_object except ValueError: ju_logger.error( "Could not load json object from file: %s" % (file_name)) raise
@classmethod
[docs] def remove_comments(cls, json_string): '''Strip single and multiline javascript-style comments. Parameters ---------- json : string Json string with javascript-style comments. Returns ------- string Copy of the input with comments removed. Note: A JSON decoder MAY accept and ignore comments. ''' json_string = JsonComments._oneline_comment.sub('', json_string) json_string = JsonComments._carriage_return.sub('', json_string) json_string = JsonComments.remove_multiline_comments(json_string) json_string = JsonComments._blank_line.sub('', json_string) return json_string
@classmethod
[docs] def remove_multiline_comments(cls, json_string): '''Rebuild input without substrings matching /*...*/. Parameters ---------- json_string : string may or may not contain multiline comments. Returns ------- string Copy of the input without the comments. ''' new_json = [] start_iter = JsonComments._multiline_comment_start.finditer( json_string) json_slice_start = 0 for comment_start in start_iter: json_slice_end = comment_start.start() new_json.append(json_string[json_slice_start:json_slice_end]) search_start = comment_start.end() comment_end = JsonComments._multiline_comment_end.search(json_string[ search_start:]) if comment_end is None: break else: json_slice_start = search_start + comment_end.end() new_json.append(json_string[json_slice_start:]) return ''.join(new_json)