Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/yaml/constructor.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
children |
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--- a/env/lib/python3.7/site-packages/yaml/constructor.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,748 +0,0 @@ - -__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