Source code for biothings.utils.jsonpatch

# -*- coding: utf-8 -*-
#
# python-json-patch - An implementation of the JSON Patch format
# https://github.com/stefankoegl/python-json-patch
#
# Copyright (c) 2011 Stefan Kögl <[email protected]>
# All rights reserved.
#
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# modification, are permitted provided that the following conditions
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#
# 1. Redistributions of source code must retain the above copyright
#    notice, this list of conditions and the following disclaimer.
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#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
# 3. The name of the author may not be used to endorse or promote products
#    derived from this software without specific prior written permission.
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""" Apply JSON-Patches (RFC 6902) """

from __future__ import unicode_literals

import collections
import copy
import functools
import inspect
import itertools
import json
import sys

try:
    from collections.abc import MutableMapping, MutableSequence
except ImportError:
    from collections import MutableMapping, MutableSequence

from jsonpointer import JsonPointer, JsonPointerException

# Will be parsed by setup.py to determine package metadata
__author__ = 'Stefan Kögl <[email protected]>'
__version__ = '1.13'
__website__ = 'https://github.com/stefankoegl/python-json-patch'
__license__ = 'Modified BSD License'


# pylint: disable=E0611,W0404
if sys.version_info >= (3, 0):
    basestring = (bytes, str)  # pylint: disable=C0103,W0622


[docs]class JsonPatchException(Exception): """Base Json Patch exception"""
[docs]class InvalidJsonPatch(JsonPatchException): """ Raised if an invalid JSON Patch is created """
[docs]class JsonPatchConflict(JsonPatchException): """Raised if patch could not be applied due to conflict situation such as: - attempt to add object key then it already exists; - attempt to operate with nonexistence object key; - attempt to insert value to array at position beyond of it size; - etc. """
[docs]class JsonPatchTestFailed(JsonPatchException, AssertionError): """ A Test operation failed """
[docs]def multidict(ordered_pairs): """Convert duplicate keys values to lists.""" # read all values into lists mdict = collections.defaultdict(list) for key, value in ordered_pairs: mdict[key].append(value) return dict( # unpack lists that have only 1 item (key, values[0] if len(values) == 1 else values) for key, values in mdict.items() )
[docs]def get_loadjson(): """ adds the object_pairs_hook parameter to json.load when possible The "object_pairs_hook" parameter is used to handle duplicate keys when loading a JSON object. This parameter does not exist in Python 2.6. This methods returns an unmodified json.load for Python 2.6 and a partial function with object_pairs_hook set to multidict for Python versions that support the parameter. """ if sys.version_info >= (3, 3): args = inspect.signature(json.load).parameters else: args = inspect.getargspec(json.load).args if 'object_pairs_hook' not in args: return json.load return functools.partial(json.load, object_pairs_hook=multidict)
json.load = get_loadjson()
[docs]def apply_patch(doc, patch, in_place=False, ignore_conflicts=False, verify=False): """Apply list of patches to specified json document. :param doc: Document object. :type doc: dict :param patch: JSON patch as list of dicts or raw JSON-encoded string. :type patch: list or str :param in_place: While :const:`True` patch will modify target document. By default patch will be applied to document copy. :type in_place: bool :param ignore_conflicts: Ignore JsonConflicts errors :type ignore_conflicts: bool :param verify: works with `ignore_conflicts` = True, if errors and `verify` is True (recommanded), make sure the resulting objects is the same as the original one. `ignore_conflicts` and `verify` are used to run patches multiple times and get rif of errors when operations can't be performed multiple times because the object has already been patched This will force `in_place` to False in order the comparison to occur. :type verify: bool :return: Patched document object. :rtype: dict >>> doc = {'foo': 'bar'} >>> patch = [{'op': 'add', 'path': '/baz', 'value': 'qux'}] >>> other = apply_patch(doc, patch) >>> doc is not other True >>> other == {'foo': 'bar', 'baz': 'qux'} True >>> patch = [{'op': 'add', 'path': '/baz', 'value': 'qux'}] >>> apply_patch(doc, patch, in_place=True) == {'foo': 'bar', 'baz': 'qux'} True >>> doc == other True """ if isinstance(patch, basestring): patch = JsonPatch.from_string(patch) else: patch = JsonPatch(patch) return patch.apply(doc, in_place, ignore_conflicts)
[docs]def reapply_patch(doc, patch): """Apply or (safely) re-apply patch to doc""" return apply_patch(doc,patch,ignore_conflicts=True, verify=True)
[docs]def make_patch(src, dst): """Generates patch by comparing of two document objects. Actually is a proxy to :meth:`JsonPatch.from_diff` method. :param src: Data source document object. :type src: dict :param dst: Data source document object. :type dst: dict >>> src = {'foo': 'bar', 'numbers': [1, 3, 4, 8]} >>> dst = {'baz': 'qux', 'numbers': [1, 4, 7]} >>> patch = make_patch(src, dst) >>> new = patch.apply(src) >>> new == dst True """ return JsonPatch.from_diff(src, dst)
[docs]class JsonPatch(object): """A JSON Patch is a list of Patch Operations. >>> patch = JsonPatch([ ... {'op': 'add', 'path': '/foo', 'value': 'bar'}, ... {'op': 'add', 'path': '/baz', 'value': [1, 2, 3]}, ... {'op': 'remove', 'path': '/baz/1'}, ... {'op': 'test', 'path': '/baz', 'value': [1, 3]}, ... {'op': 'replace', 'path': '/baz/0', 'value': 42}, ... {'op': 'remove', 'path': '/baz/1'}, ... ]) >>> doc = {} >>> result = patch.apply(doc) >>> expected = {'foo': 'bar', 'baz': [42]} >>> result == expected True JsonPatch object is iterable, so you could easily access to each patch statement in loop: >>> lpatch = list(patch) >>> expected = {'op': 'add', 'path': '/foo', 'value': 'bar'} >>> lpatch[0] == expected True >>> lpatch == patch.patch True Also JsonPatch could be converted directly to :class:`bool` if it contains any operation statements: >>> bool(patch) True >>> bool(JsonPatch([])) False This behavior is very handy with :func:`make_patch` to write more readable code: >>> old = {'foo': 'bar', 'numbers': [1, 3, 4, 8]} >>> new = {'baz': 'qux', 'numbers': [1, 4, 7]} >>> patch = make_patch(old, new) >>> if patch: ... # document have changed, do something useful ... patch.apply(old) #doctest: +ELLIPSIS {...} """ def __init__(self, patch): self.patch = patch self.operations = { 'remove': RemoveOperation, 'add': AddOperation, 'replace': ReplaceOperation, 'move': MoveOperation, 'test': TestOperation, 'copy': CopyOperation, } def __str__(self): """str(self) -> self.to_string()""" return self.to_string() def __bool__(self): return bool(self.patch) __nonzero__ = __bool__ def __iter__(self): return iter(self.patch) def __hash__(self): return hash(tuple(self._ops)) def __eq__(self, other): if not isinstance(other, JsonPatch): return False return self._ops == other._ops def __ne__(self, other): return not(self == other)
[docs] @classmethod def from_string(cls, patch_str): """Creates JsonPatch instance from string source. :param patch_str: JSON patch as raw string. :type patch_str: str :return: :class:`JsonPatch` instance. """ patch = json.loads(patch_str) return cls(patch)
[docs] @classmethod def from_diff(cls, src, dst): """Creates JsonPatch instance based on comparing of two document objects. Json patch would be created for `src` argument against `dst` one. :param src: Data source document object. :type src: dict :param dst: Data source document object. :type dst: dict :return: :class:`JsonPatch` instance. >>> src = {'foo': 'bar', 'numbers': [1, 3, 4, 8]} >>> dst = {'baz': 'qux', 'numbers': [1, 4, 7]} >>> patch = JsonPatch.from_diff(src, dst) >>> new = patch.apply(src) >>> new == dst True """ def compare_values(path, value, other): if value == other: return if isinstance(value, MutableMapping) and \ isinstance(other, MutableMapping): for operation in compare_dicts(path, value, other): yield operation elif isinstance(value, MutableSequence) and \ isinstance(other, MutableSequence): for operation in compare_lists(path, value, other): yield operation else: ptr = JsonPointer.from_parts(path) yield {'op': 'replace', 'path': ptr.path, 'value': other} def compare_dicts(path, src, dst): for key in src: if key not in dst: ptr = JsonPointer.from_parts(path + [key]) yield {'op': 'remove', 'path': ptr.path} continue current = path + [key] for operation in compare_values(current, src[key], dst[key]): yield operation for key in dst: if key not in src: ptr = JsonPointer.from_parts(path + [key]) yield {'op': 'add', 'path': ptr.path, 'value': dst[key]} def compare_lists(path, src, dst): return _compare_lists(path, src, dst) return cls(list(compare_values([], src, dst)))
[docs] def to_string(self): """Returns patch set as JSON string.""" return json.dumps(self.patch)
@property def _ops(self): return tuple(map(self._get_operation, self.patch))
[docs] def apply(self, orig_obj, in_place=False, ignore_conflicts=False, verify=False): """Applies the patch to given object. :param obj: Document object. :type obj: dict :param in_place: Tweaks way how patch would be applied - directly to specified `obj` or to his copy. :type in_place: bool :type ignore_conflicts: Ignore JsonConflicts errors :type verify: works with `ignore_conflicts` = True, if errors and `verify` is True (recommanded), make sure the resulting objects is the same as the original one. `ignore_conflicts` and `verify` are used to run patches multiple times and get rif of errors when operations can't be performed multiple times because the object has already been patched :return: Modified `obj`. """ if verify: in_place = False if not in_place: obj = copy.deepcopy(orig_obj) else: obj = orig_obj got_conflicts = False for operation in self._ops: try: obj = operation.apply(obj) except JsonPatchConflict as e: if ignore_conflicts: got_conflicts = True else: raise # it you're gonna ignore conflicts you'll have to make # sure the resulting document is the same as the passed-one # (patch run mutiple times) if got_conflicts and verify: assert obj == orig_obj, "Resulting object is different from original but got conflict errors, this is not good..." return obj
def _get_operation(self, operation): if 'op' not in operation: raise InvalidJsonPatch("Operation does not contain 'op' member") op = operation['op'] if not isinstance(op, basestring): raise InvalidJsonPatch("Operation must be a string") if op not in self.operations: raise InvalidJsonPatch("Unknown operation {0!r}".format(op)) cls = self.operations[op] return cls(operation)
[docs]class PatchOperation(object): """A single operation inside a JSON Patch.""" def __init__(self, operation): self.location = operation['path'] self.pointer = JsonPointer(self.location) self.operation = operation
[docs] def apply(self, obj): """Abstract method that applies patch operation to specified object.""" raise NotImplementedError('should implement patch operation.')
def __hash__(self): return hash(frozenset(self.operation.items())) def __eq__(self, other): if not isinstance(other, PatchOperation): return False return self.operation == other.operation def __ne__(self, other): return not(self == other)
[docs]class RemoveOperation(PatchOperation): """Removes an object property or an array element."""
[docs] def apply(self, obj): subobj, part = self.pointer.to_last(obj) try: del subobj[part] except (KeyError, IndexError) as ex: msg = "can't remove non-existent object '{0}'".format(part) raise JsonPatchConflict(msg) return obj
[docs]class AddOperation(PatchOperation): """Adds an object property or an array element."""
[docs] def apply(self, obj): try: value = self.operation["value"] except KeyError as ex: raise InvalidJsonPatch( "The operation does not contain a 'value' member") subobj, part = self.pointer.to_last(obj) if isinstance(subobj, MutableSequence): if part == '-': subobj.append(value) # pylint: disable=E1103 elif part > len(subobj) or part < 0: raise JsonPatchConflict("can't insert outside of list") else: subobj.insert(part, value) # pylint: disable=E1103 elif isinstance(subobj, MutableMapping): if part is None: obj = value # we're replacing the root else: subobj[part] = value else: raise TypeError("invalid document type {0}".format(type(subobj))) return obj
[docs]class ReplaceOperation(PatchOperation): """Replaces an object property or an array element by new value."""
[docs] def apply(self, obj): try: value = self.operation["value"] except KeyError as ex: raise InvalidJsonPatch( "The operation does not contain a 'value' member") subobj, part = self.pointer.to_last(obj) if part is None: return value if isinstance(subobj, MutableSequence): if part > len(subobj) or part < 0: raise JsonPatchConflict("can't replace outside of list") elif isinstance(subobj, MutableMapping): if not part in subobj: msg = "can't replace non-existent object '{0}'".format(part) raise JsonPatchConflict(msg) else: raise TypeError("invalid document type {0}".format(type(subobj))) subobj[part] = value return obj
[docs]class MoveOperation(PatchOperation): """Moves an object property or an array element to new location."""
[docs] def apply(self, obj): try: from_ptr = JsonPointer(self.operation['from']) except KeyError as ex: raise InvalidJsonPatch( "The operation does not contain a 'from' member") subobj, part = from_ptr.to_last(obj) try: value = subobj[part] except (KeyError, IndexError) as ex: raise JsonPatchConflict(str(ex)) # If source and target are equal, this is a no-op if self.pointer == from_ptr: return obj if isinstance(subobj, MutableMapping) and \ self.pointer.contains(from_ptr): raise JsonPatchConflict('Cannot move values into its own children') obj = RemoveOperation({ 'op': 'remove', 'path': self.operation['from'] }).apply(obj) obj = AddOperation({ 'op': 'add', 'path': self.location, 'value': value }).apply(obj) return obj
[docs]class TestOperation(PatchOperation): """Test value by specified location."""
[docs] def apply(self, obj): try: subobj, part = self.pointer.to_last(obj) if part is None: val = subobj else: val = self.pointer.walk(subobj, part) except JsonPointerException as ex: raise JsonPatchTestFailed(str(ex)) try: value = self.operation['value'] except KeyError as ex: raise InvalidJsonPatch( "The operation does not contain a 'value' member") if val != value: msg = '{0} ({1}) is not equal to tested value {2} ({3})' raise JsonPatchTestFailed(msg.format(val, type(val), value, type(value))) return obj
[docs]class CopyOperation(PatchOperation): """ Copies an object property or an array element to a new location """
[docs] def apply(self, obj): try: from_ptr = JsonPointer(self.operation['from']) except KeyError as ex: raise InvalidJsonPatch( "The operation does not contain a 'from' member") subobj, part = from_ptr.to_last(obj) try: value = copy.deepcopy(subobj[part]) except (KeyError, IndexError) as ex: raise JsonPatchConflict(str(ex)) obj = AddOperation({ 'op': 'add', 'path': self.location, 'value': value }).apply(obj) return obj
def _compare_lists(path, src, dst): """Compares two lists objects and return JSON patch about.""" return _optimize(_compare(path, src, dst, *_split_by_common_seq(src, dst))) def _longest_common_subseq(src, dst): """Returns pair of ranges of longest common subsequence for the `src` and `dst` lists. >>> src = [1, 2, 3, 4] >>> dst = [0, 1, 2, 3, 5] >>> # The longest common subsequence for these lists is [1, 2, 3] ... # which is located at (0, 3) index range for src list and (1, 4) for ... # dst one. Tuple of these ranges we should get back. ... assert ((0, 3), (1, 4)) == _longest_common_subseq(src, dst) """ lsrc, ldst = len(src), len(dst) drange = list(range(ldst)) matrix = [[0] * ldst for _ in range(lsrc)] z = 0 # length of the longest subsequence range_src, range_dst = None, None for i, j in itertools.product(range(lsrc), drange): if src[i] == dst[j]: if i == 0 or j == 0: matrix[i][j] = 1 else: matrix[i][j] = matrix[i-1][j-1] + 1 if matrix[i][j] > z: z = matrix[i][j] if matrix[i][j] == z: range_src = (i-z+1, i+1) range_dst = (j-z+1, j+1) else: matrix[i][j] = 0 return range_src, range_dst def _split_by_common_seq(src, dst, bx=(0, -1), by=(0, -1)): """Recursively splits the `dst` list onto two parts: left and right. The left part contains differences on left from common subsequence, same as the right part by for other side. To easily understand the process let's take two lists: [0, 1, 2, 3] as `src` and [1, 2, 4, 5] for `dst`. If we've tried to generate the binary tree where nodes are common subsequence for both lists, leaves on the left side are subsequence for `src` list and leaves on the right one for `dst`, our tree would looks like:: [1, 2] / \ [0] [] / \ [3] [4, 5] This function generate the similar structure as flat tree, but without nodes with common subsequences - since we're don't need them - only with left and right leaves:: [] / \ [0] [] / \ [3] [4, 5] The `bx` is the absolute range for currently processed subsequence of `src` list. The `by` means the same, but for the `dst` list. """ # Prevent useless comparisons in future bx = bx if bx[0] != bx[1] else None by = by if by[0] != by[1] else None if not src: return [None, by] elif not dst: return [bx, None] # note that these ranges are relative for processed sublists x, y = _longest_common_subseq(src, dst) if x is None or y is None: # no more any common subsequence return [bx, by] return [_split_by_common_seq(src[:x[0]], dst[:y[0]], (bx[0], bx[0] + x[0]), (by[0], by[0] + y[0])), _split_by_common_seq(src[x[1]:], dst[y[1]:], (bx[0] + x[1], bx[0] + len(src)), (by[0] + y[1], by[0] + len(dst)))] def _compare(path, src, dst, left, right): """Same as :func:`_compare_with_shift` but strips emitted `shift` value.""" for op, _ in _compare_with_shift(path, src, dst, left, right, 0): yield op def _compare_with_shift(path, src, dst, left, right, shift): """Recursively compares differences from `left` and `right` sides from common subsequences. The `shift` parameter is used to store index shift which caused by ``add`` and ``remove`` operations. Yields JSON patch operations and list index shift. """ if isinstance(left, MutableSequence): for item, shift in _compare_with_shift(path, src, dst, *left, shift=shift): yield item, shift elif left is not None: for item, shift in _compare_left(path, src, left, shift): yield item, shift if isinstance(right, MutableSequence): for item, shift in _compare_with_shift(path, src, dst, *right, shift=shift): yield item, shift elif right is not None: for item, shift in _compare_right(path, dst, right, shift): yield item, shift def _compare_left(path, src, left, shift): """Yields JSON patch ``remove`` operations for elements that are only exists in the `src` list.""" start, end = left if end == -1: end = len(src) # we need to `remove` elements from list tail to not deal with index shift for idx in reversed(range(start + shift, end + shift)): ptr = JsonPointer.from_parts(path + [str(idx)]) yield ( {'op': 'remove', # yes, there should be any value field, but we'll use it # to apply `move` optimization a bit later and will remove # it in _optimize function. 'value': src[idx - shift], 'path': ptr.path, }, shift - 1 ) shift -= 1 def _compare_right(path, dst, right, shift): """Yields JSON patch ``add`` operations for elements that are only exists in the `dst` list""" start, end = right if end == -1: end = len(dst) for idx in range(start, end): ptr = JsonPointer.from_parts(path + [str(idx)]) yield ( {'op': 'add', 'path': ptr.path, 'value': dst[idx]}, shift + 1 ) shift += 1 def _optimize(operations): """Optimizes operations which was produced by lists comparison. Actually it does two kinds of optimizations: 1. Seeks pair of ``remove`` and ``add`` operations against the same path and replaces them with ``replace`` operation. 2. Seeks pair of ``remove`` and ``add`` operations for the same value and replaces them with ``move`` operation. """ result = [] ops_by_path = {} ops_by_value = {} add_remove = set(['add', 'remove']) for item in operations: # could we apply "move" optimization for dict values? hashable_value = not isinstance(item['value'], (MutableMapping, MutableSequence)) if item['path'] in ops_by_path: _optimize_using_replace(ops_by_path[item['path']], item) continue if hashable_value and item['value'] in ops_by_value: prev_item = ops_by_value[item['value']] # ensure that we processing pair of add-remove ops if set([item['op'], prev_item['op']]) == add_remove: _optimize_using_move(prev_item, item) ops_by_value.pop(item['value']) continue result.append(item) ops_by_path[item['path']] = item if hashable_value: ops_by_value[item['value']] = item # cleanup ops_by_path.clear() ops_by_value.clear() for item in result: if item['op'] == 'remove': item.pop('value') # strip our hack yield item def _optimize_using_replace(prev, cur): """Optimises by replacing ``add``/``remove`` with ``replace`` on same path For nested strucures, tries to recurse replacement, see #36 """ prev['op'] = 'replace' if cur['op'] == 'add': # make recursive patch patch = make_patch(prev['value'], cur['value']) if len(patch.patch) == 1 and patch.patch[0]['op'] != 'remove': prev['path'] = prev['path'] + patch.patch[0]['path'] prev['value'] = patch.patch[0]['value'] else: prev['value'] = cur['value'] def _optimize_using_move(prev_item, item): """Optimises JSON patch by using ``move`` operation instead of ``remove` and ``add`` against the different paths but for the same value.""" prev_item['op'] = 'move' move_from, move_to = [ (item['path'], prev_item['path']), (prev_item['path'], item['path']), ][item['op'] == 'add'] if item['op'] == 'add': # first was remove then add prev_item['from'] = move_from prev_item['path'] = move_to else: # first was add then remove head, move_from = move_from.rsplit('/', 1) # since add operation was first it incremented # overall index shift value. we have to fix this move_from = int(move_from) - 1 prev_item['from'] = head + '/%d' % move_from prev_item['path'] = move_to