Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/yaml/constructor.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
---|---|
date | Sat, 02 May 2020 07:14:21 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/yaml/constructor.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,748 @@ + +__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