Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/yaml/constructor.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
---|---|
date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
children |
line wrap: on
line source
__all__ = [ 'BaseConstructor', 'SafeConstructor', 'FullConstructor', 'UnsafeConstructor', 'Constructor', 'ConstructorError' ] from .error import * from .nodes import * import collections.abc, datetime, base64, binascii, re, sys, types class ConstructorError(MarkedYAMLError): pass class BaseConstructor: yaml_constructors = {} yaml_multi_constructors = {} def __init__(self): self.constructed_objects = {} self.recursive_objects = {} self.state_generators = [] self.deep_construct = False def check_data(self): # If there are more documents available? return self.check_node() def check_state_key(self, key): """Block special attributes/methods from being set in a newly created object, to prevent user-controlled methods from being called during deserialization""" if self.get_state_keys_blacklist_regexp().match(key): raise ConstructorError(None, None, "blacklisted key '%s' in instance state found" % (key,), None) def get_data(self): # Construct and return the next document. if self.check_node(): return self.construct_document(self.get_node()) def get_single_data(self): # Ensure that the stream contains a single document and construct it. node = self.get_single_node() if node is not None: return self.construct_document(node) return None def construct_document(self, node): data = self.construct_object(node) while self.state_generators: state_generators = self.state_generators self.state_generators = [] for generator in state_generators: for dummy in generator: pass self.constructed_objects = {} self.recursive_objects = {} self.deep_construct = False return data def construct_object(self, node, deep=False): if node in self.constructed_objects: return self.constructed_objects[node] if deep: old_deep = self.deep_construct self.deep_construct = True if node in self.recursive_objects: raise ConstructorError(None, None, "found unconstructable recursive node", node.start_mark) self.recursive_objects[node] = None constructor = None tag_suffix = None if node.tag in self.yaml_constructors: constructor = self.yaml_constructors[node.tag] else: for tag_prefix in self.yaml_multi_constructors: if tag_prefix is not None and node.tag.startswith(tag_prefix): tag_suffix = node.tag[len(tag_prefix):] constructor = self.yaml_multi_constructors[tag_prefix] break else: if None in self.yaml_multi_constructors: tag_suffix = node.tag constructor = self.yaml_multi_constructors[None] elif None in self.yaml_constructors: constructor = self.yaml_constructors[None] elif isinstance(node, ScalarNode): constructor = self.__class__.construct_scalar elif isinstance(node, SequenceNode): constructor = self.__class__.construct_sequence elif isinstance(node, MappingNode): constructor = self.__class__.construct_mapping if tag_suffix is None: data = constructor(self, node) else: data = constructor(self, tag_suffix, node) if isinstance(data, types.GeneratorType): generator = data data = next(generator) if self.deep_construct: for dummy in generator: pass else: self.state_generators.append(generator) self.constructed_objects[node] = data del self.recursive_objects[node] if deep: self.deep_construct = old_deep return data def construct_scalar(self, node): if not isinstance(node, ScalarNode): raise ConstructorError(None, None, "expected a scalar node, but found %s" % node.id, node.start_mark) return node.value def construct_sequence(self, node, deep=False): if not isinstance(node, SequenceNode): raise ConstructorError(None, None, "expected a sequence node, but found %s" % node.id, node.start_mark) return [self.construct_object(child, deep=deep) for child in node.value] def construct_mapping(self, node, deep=False): if not isinstance(node, MappingNode): raise ConstructorError(None, None, "expected a mapping node, but found %s" % node.id, node.start_mark) mapping = {} for key_node, value_node in node.value: key = self.construct_object(key_node, deep=deep) if not isinstance(key, collections.abc.Hashable): raise ConstructorError("while constructing a mapping", node.start_mark, "found unhashable key", key_node.start_mark) value = self.construct_object(value_node, deep=deep) mapping[key] = value return mapping def construct_pairs(self, node, deep=False): if not isinstance(node, MappingNode): raise ConstructorError(None, None, "expected a mapping node, but found %s" % node.id, node.start_mark) pairs = [] for key_node, value_node in node.value: key = self.construct_object(key_node, deep=deep) value = self.construct_object(value_node, deep=deep) pairs.append((key, value)) return pairs @classmethod def add_constructor(cls, tag, constructor): if not 'yaml_constructors' in cls.__dict__: cls.yaml_constructors = cls.yaml_constructors.copy() cls.yaml_constructors[tag] = constructor @classmethod def add_multi_constructor(cls, tag_prefix, multi_constructor): if not 'yaml_multi_constructors' in cls.__dict__: cls.yaml_multi_constructors = cls.yaml_multi_constructors.copy() cls.yaml_multi_constructors[tag_prefix] = multi_constructor class SafeConstructor(BaseConstructor): def construct_scalar(self, node): if isinstance(node, MappingNode): for key_node, value_node in node.value: if key_node.tag == 'tag:yaml.org,2002:value': return self.construct_scalar(value_node) return super().construct_scalar(node) def flatten_mapping(self, node): merge = [] index = 0 while index < len(node.value): key_node, value_node = node.value[index] if key_node.tag == 'tag:yaml.org,2002:merge': del node.value[index] if isinstance(value_node, MappingNode): self.flatten_mapping(value_node) merge.extend(value_node.value) elif isinstance(value_node, SequenceNode): submerge = [] for subnode in value_node.value: if not isinstance(subnode, MappingNode): raise ConstructorError("while constructing a mapping", node.start_mark, "expected a mapping for merging, but found %s" % subnode.id, subnode.start_mark) self.flatten_mapping(subnode) submerge.append(subnode.value) submerge.reverse() for value in submerge: merge.extend(value) else: raise ConstructorError("while constructing a mapping", node.start_mark, "expected a mapping or list of mappings for merging, but found %s" % value_node.id, value_node.start_mark) elif key_node.tag == 'tag:yaml.org,2002:value': key_node.tag = 'tag:yaml.org,2002:str' index += 1 else: index += 1 if merge: node.value = merge + node.value def construct_mapping(self, node, deep=False): if isinstance(node, MappingNode): self.flatten_mapping(node) return super().construct_mapping(node, deep=deep) def construct_yaml_null(self, node): self.construct_scalar(node) return None bool_values = { 'yes': True, 'no': False, 'true': True, 'false': False, 'on': True, 'off': False, } def construct_yaml_bool(self, node): value = self.construct_scalar(node) return self.bool_values[value.lower()] def construct_yaml_int(self, node): value = self.construct_scalar(node) value = value.replace('_', '') sign = +1 if value[0] == '-': sign = -1 if value[0] in '+-': value = value[1:] if value == '0': return 0 elif value.startswith('0b'): return sign*int(value[2:], 2) elif value.startswith('0x'): return sign*int(value[2:], 16) elif value[0] == '0': return sign*int(value, 8) elif ':' in value: digits = [int(part) for part in value.split(':')] digits.reverse() base = 1 value = 0 for digit in digits: value += digit*base base *= 60 return sign*value else: return sign*int(value) inf_value = 1e300 while inf_value != inf_value*inf_value: inf_value *= inf_value nan_value = -inf_value/inf_value # Trying to make a quiet NaN (like C99). def construct_yaml_float(self, node): value = self.construct_scalar(node) value = value.replace('_', '').lower() sign = +1 if value[0] == '-': sign = -1 if value[0] in '+-': value = value[1:] if value == '.inf': return sign*self.inf_value elif value == '.nan': return self.nan_value elif ':' in value: digits = [float(part) for part in value.split(':')] digits.reverse() base = 1 value = 0.0 for digit in digits: value += digit*base base *= 60 return sign*value else: return sign*float(value) def construct_yaml_binary(self, node): try: value = self.construct_scalar(node).encode('ascii') except UnicodeEncodeError as exc: raise ConstructorError(None, None, "failed to convert base64 data into ascii: %s" % exc, node.start_mark) try: if hasattr(base64, 'decodebytes'): return base64.decodebytes(value) else: return base64.decodestring(value) except binascii.Error as exc: raise ConstructorError(None, None, "failed to decode base64 data: %s" % exc, node.start_mark) timestamp_regexp = re.compile( r'''^(?P<year>[0-9][0-9][0-9][0-9]) -(?P<month>[0-9][0-9]?) -(?P<day>[0-9][0-9]?) (?:(?:[Tt]|[ \t]+) (?P<hour>[0-9][0-9]?) :(?P<minute>[0-9][0-9]) :(?P<second>[0-9][0-9]) (?:\.(?P<fraction>[0-9]*))? (?:[ \t]*(?P<tz>Z|(?P<tz_sign>[-+])(?P<tz_hour>[0-9][0-9]?) (?::(?P<tz_minute>[0-9][0-9]))?))?)?$''', re.X) def construct_yaml_timestamp(self, node): value = self.construct_scalar(node) match = self.timestamp_regexp.match(node.value) values = match.groupdict() year = int(values['year']) month = int(values['month']) day = int(values['day']) if not values['hour']: return datetime.date(year, month, day) hour = int(values['hour']) minute = int(values['minute']) second = int(values['second']) fraction = 0 tzinfo = None if values['fraction']: fraction = values['fraction'][:6] while len(fraction) < 6: fraction += '0' fraction = int(fraction) if values['tz_sign']: tz_hour = int(values['tz_hour']) tz_minute = int(values['tz_minute'] or 0) delta = datetime.timedelta(hours=tz_hour, minutes=tz_minute) if values['tz_sign'] == '-': delta = -delta tzinfo = datetime.timezone(delta) elif values['tz']: tzinfo = datetime.timezone.utc return datetime.datetime(year, month, day, hour, minute, second, fraction, tzinfo=tzinfo) def construct_yaml_omap(self, node): # Note: we do not check for duplicate keys, because it's too # CPU-expensive. omap = [] yield omap if not isinstance(node, SequenceNode): raise ConstructorError("while constructing an ordered map", node.start_mark, "expected a sequence, but found %s" % node.id, node.start_mark) for subnode in node.value: if not isinstance(subnode, MappingNode): raise ConstructorError("while constructing an ordered map", node.start_mark, "expected a mapping of length 1, but found %s" % subnode.id, subnode.start_mark) if len(subnode.value) != 1: raise ConstructorError("while constructing an ordered map", node.start_mark, "expected a single mapping item, but found %d items" % len(subnode.value), subnode.start_mark) key_node, value_node = subnode.value[0] key = self.construct_object(key_node) value = self.construct_object(value_node) omap.append((key, value)) def construct_yaml_pairs(self, node): # Note: the same code as `construct_yaml_omap`. pairs = [] yield pairs if not isinstance(node, SequenceNode): raise ConstructorError("while constructing pairs", node.start_mark, "expected a sequence, but found %s" % node.id, node.start_mark) for subnode in node.value: if not isinstance(subnode, MappingNode): raise ConstructorError("while constructing pairs", node.start_mark, "expected a mapping of length 1, but found %s" % subnode.id, subnode.start_mark) if len(subnode.value) != 1: raise ConstructorError("while constructing pairs", node.start_mark, "expected a single mapping item, but found %d items" % len(subnode.value), subnode.start_mark) key_node, value_node = subnode.value[0] key = self.construct_object(key_node) value = self.construct_object(value_node) pairs.append((key, value)) def construct_yaml_set(self, node): data = set() yield data value = self.construct_mapping(node) data.update(value) def construct_yaml_str(self, node): return self.construct_scalar(node) def construct_yaml_seq(self, node): data = [] yield data data.extend(self.construct_sequence(node)) def construct_yaml_map(self, node): data = {} yield data value = self.construct_mapping(node) data.update(value) def construct_yaml_object(self, node, cls): data = cls.__new__(cls) yield data if hasattr(data, '__setstate__'): state = self.construct_mapping(node, deep=True) data.__setstate__(state) else: state = self.construct_mapping(node) data.__dict__.update(state) def construct_undefined(self, node): raise ConstructorError(None, None, "could not determine a constructor for the tag %r" % node.tag, node.start_mark) SafeConstructor.add_constructor( 'tag:yaml.org,2002:null', SafeConstructor.construct_yaml_null) SafeConstructor.add_constructor( 'tag:yaml.org,2002:bool', SafeConstructor.construct_yaml_bool) SafeConstructor.add_constructor( 'tag:yaml.org,2002:int', SafeConstructor.construct_yaml_int) SafeConstructor.add_constructor( 'tag:yaml.org,2002:float', SafeConstructor.construct_yaml_float) SafeConstructor.add_constructor( 'tag:yaml.org,2002:binary', SafeConstructor.construct_yaml_binary) SafeConstructor.add_constructor( 'tag:yaml.org,2002:timestamp', SafeConstructor.construct_yaml_timestamp) SafeConstructor.add_constructor( 'tag:yaml.org,2002:omap', SafeConstructor.construct_yaml_omap) SafeConstructor.add_constructor( 'tag:yaml.org,2002:pairs', SafeConstructor.construct_yaml_pairs) SafeConstructor.add_constructor( 'tag:yaml.org,2002:set', SafeConstructor.construct_yaml_set) SafeConstructor.add_constructor( 'tag:yaml.org,2002:str', SafeConstructor.construct_yaml_str) SafeConstructor.add_constructor( 'tag:yaml.org,2002:seq', SafeConstructor.construct_yaml_seq) SafeConstructor.add_constructor( 'tag:yaml.org,2002:map', SafeConstructor.construct_yaml_map) SafeConstructor.add_constructor(None, SafeConstructor.construct_undefined) class FullConstructor(SafeConstructor): # 'extend' is blacklisted because it is used by # construct_python_object_apply to add `listitems` to a newly generate # python instance def get_state_keys_blacklist(self): return ['^extend$', '^__.*__$'] def get_state_keys_blacklist_regexp(self): if not hasattr(self, 'state_keys_blacklist_regexp'): self.state_keys_blacklist_regexp = re.compile('(' + '|'.join(self.get_state_keys_blacklist()) + ')') return self.state_keys_blacklist_regexp def construct_python_str(self, node): return self.construct_scalar(node) def construct_python_unicode(self, node): return self.construct_scalar(node) def construct_python_bytes(self, node): try: value = self.construct_scalar(node).encode('ascii') except UnicodeEncodeError as exc: raise ConstructorError(None, None, "failed to convert base64 data into ascii: %s" % exc, node.start_mark) try: if hasattr(base64, 'decodebytes'): return base64.decodebytes(value) else: return base64.decodestring(value) except binascii.Error as exc: raise ConstructorError(None, None, "failed to decode base64 data: %s" % exc, node.start_mark) def construct_python_long(self, node): return self.construct_yaml_int(node) def construct_python_complex(self, node): return complex(self.construct_scalar(node)) def construct_python_tuple(self, node): return tuple(self.construct_sequence(node)) def find_python_module(self, name, mark, unsafe=False): if not name: raise ConstructorError("while constructing a Python module", mark, "expected non-empty name appended to the tag", mark) if unsafe: try: __import__(name) except ImportError as exc: raise ConstructorError("while constructing a Python module", mark, "cannot find module %r (%s)" % (name, exc), mark) if name not in sys.modules: raise ConstructorError("while constructing a Python module", mark, "module %r is not imported" % name, mark) return sys.modules[name] def find_python_name(self, name, mark, unsafe=False): if not name: raise ConstructorError("while constructing a Python object", mark, "expected non-empty name appended to the tag", mark) if '.' in name: module_name, object_name = name.rsplit('.', 1) else: module_name = 'builtins' object_name = name if unsafe: try: __import__(module_name) except ImportError as exc: raise ConstructorError("while constructing a Python object", mark, "cannot find module %r (%s)" % (module_name, exc), mark) if module_name not in sys.modules: raise ConstructorError("while constructing a Python object", mark, "module %r is not imported" % module_name, mark) module = sys.modules[module_name] if not hasattr(module, object_name): raise ConstructorError("while constructing a Python object", mark, "cannot find %r in the module %r" % (object_name, module.__name__), mark) return getattr(module, object_name) def construct_python_name(self, suffix, node): value = self.construct_scalar(node) if value: raise ConstructorError("while constructing a Python name", node.start_mark, "expected the empty value, but found %r" % value, node.start_mark) return self.find_python_name(suffix, node.start_mark) def construct_python_module(self, suffix, node): value = self.construct_scalar(node) if value: raise ConstructorError("while constructing a Python module", node.start_mark, "expected the empty value, but found %r" % value, node.start_mark) return self.find_python_module(suffix, node.start_mark) def make_python_instance(self, suffix, node, args=None, kwds=None, newobj=False, unsafe=False): if not args: args = [] if not kwds: kwds = {} cls = self.find_python_name(suffix, node.start_mark) if not (unsafe or isinstance(cls, type)): raise ConstructorError("while constructing a Python instance", node.start_mark, "expected a class, but found %r" % type(cls), node.start_mark) if newobj and isinstance(cls, type): return cls.__new__(cls, *args, **kwds) else: return cls(*args, **kwds) def set_python_instance_state(self, instance, state, unsafe=False): if hasattr(instance, '__setstate__'): instance.__setstate__(state) else: slotstate = {} if isinstance(state, tuple) and len(state) == 2: state, slotstate = state if hasattr(instance, '__dict__'): if not unsafe and state: for key in state.keys(): self.check_state_key(key) instance.__dict__.update(state) elif state: slotstate.update(state) for key, value in slotstate.items(): if not unsafe: self.check_state_key(key) setattr(instance, key, value) def construct_python_object(self, suffix, node): # Format: # !!python/object:module.name { ... state ... } instance = self.make_python_instance(suffix, node, newobj=True) yield instance deep = hasattr(instance, '__setstate__') state = self.construct_mapping(node, deep=deep) self.set_python_instance_state(instance, state) def construct_python_object_apply(self, suffix, node, newobj=False): # Format: # !!python/object/apply # (or !!python/object/new) # args: [ ... arguments ... ] # kwds: { ... keywords ... } # state: ... state ... # listitems: [ ... listitems ... ] # dictitems: { ... dictitems ... } # or short format: # !!python/object/apply [ ... arguments ... ] # The difference between !!python/object/apply and !!python/object/new # is how an object is created, check make_python_instance for details. if isinstance(node, SequenceNode): args = self.construct_sequence(node, deep=True) kwds = {} state = {} listitems = [] dictitems = {} else: value = self.construct_mapping(node, deep=True) args = value.get('args', []) kwds = value.get('kwds', {}) state = value.get('state', {}) listitems = value.get('listitems', []) dictitems = value.get('dictitems', {}) instance = self.make_python_instance(suffix, node, args, kwds, newobj) if state: self.set_python_instance_state(instance, state) if listitems: instance.extend(listitems) if dictitems: for key in dictitems: instance[key] = dictitems[key] return instance def construct_python_object_new(self, suffix, node): return self.construct_python_object_apply(suffix, node, newobj=True) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/none', FullConstructor.construct_yaml_null) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/bool', FullConstructor.construct_yaml_bool) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/str', FullConstructor.construct_python_str) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/unicode', FullConstructor.construct_python_unicode) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/bytes', FullConstructor.construct_python_bytes) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/int', FullConstructor.construct_yaml_int) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/long', FullConstructor.construct_python_long) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/float', FullConstructor.construct_yaml_float) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/complex', FullConstructor.construct_python_complex) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/list', FullConstructor.construct_yaml_seq) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/tuple', FullConstructor.construct_python_tuple) FullConstructor.add_constructor( 'tag:yaml.org,2002:python/dict', FullConstructor.construct_yaml_map) FullConstructor.add_multi_constructor( 'tag:yaml.org,2002:python/name:', FullConstructor.construct_python_name) FullConstructor.add_multi_constructor( 'tag:yaml.org,2002:python/module:', FullConstructor.construct_python_module) FullConstructor.add_multi_constructor( 'tag:yaml.org,2002:python/object:', FullConstructor.construct_python_object) FullConstructor.add_multi_constructor( 'tag:yaml.org,2002:python/object/new:', FullConstructor.construct_python_object_new) class UnsafeConstructor(FullConstructor): def find_python_module(self, name, mark): return super(UnsafeConstructor, self).find_python_module(name, mark, unsafe=True) def find_python_name(self, name, mark): return super(UnsafeConstructor, self).find_python_name(name, mark, unsafe=True) def make_python_instance(self, suffix, node, args=None, kwds=None, newobj=False): return super(UnsafeConstructor, self).make_python_instance( suffix, node, args, kwds, newobj, unsafe=True) def set_python_instance_state(self, instance, state): return super(UnsafeConstructor, self).set_python_instance_state( instance, state, unsafe=True) UnsafeConstructor.add_multi_constructor( 'tag:yaml.org,2002:python/object/apply:', UnsafeConstructor.construct_python_object_apply) # Constructor is same as UnsafeConstructor. Need to leave this in place in case # people have extended it directly. class Constructor(UnsafeConstructor): pass