1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449
|
import warnings
from collections import OrderedDict
from types import GeneratorType
import numpy as np
import yaml
from . import config, schema, tagged, treeutil, util
from .constants import STSCI_SCHEMA_TAG_BASE, YAML_TAG_PREFIX
from .exceptions import AsdfConversionWarning, AsdfSerializationError
from .extension._serialization_context import BlockAccess
from .tags.core import AsdfObject
from .versioning import _YAML_VERSION, _yaml_base_loader
__all__ = ["custom_tree_to_tagged_tree", "tagged_tree_to_custom_tree"]
_yaml_base_dumper = yaml.CSafeDumper if getattr(yaml, "__with_libyaml__", None) else yaml.SafeDumper
YAML_OMAP_TAG = YAML_TAG_PREFIX + "omap"
# ----------------------------------------------------------------------
# Custom loader/dumpers
class AsdfDumper(_yaml_base_dumper):
"""
A specialized YAML dumper that understands "tagged basic Python
data types" as implemented in the `tagged` module.
"""
def __init__(self, *args, **kwargs):
kwargs["default_flow_style"] = None
super().__init__(*args, **kwargs)
def represent_data(self, data):
node = super().represent_data(data)
tag_name = getattr(data, "_tag", None)
if tag_name is not None:
node.tag = tag_name
return node
_flow_style_map = {"flow": True, "block": False}
def represent_sequence(dumper, sequence):
flow_style = _flow_style_map.get(sequence.flow_style, None)
sequence = sequence.data
return super(AsdfDumper, dumper).represent_sequence(None, sequence, flow_style)
def represent_mapping(dumper, mapping):
flow_style = _flow_style_map.get(mapping.flow_style, None)
node = super(AsdfDumper, dumper).represent_mapping(None, mapping.data, flow_style)
if mapping.property_order:
values = node.value
new_mapping = {}
for key, val in values:
new_mapping[key.value] = (key, val)
new_values = []
for key in mapping.property_order:
if key in mapping:
new_values.append(new_mapping[key])
property_order = set(mapping.property_order)
for key, val in values:
if key.value not in property_order:
new_values.append((key, val))
node.value = new_values
return node
_style_map = {"inline": '"', "folded": ">", "literal": "|"}
def represent_scalar(dumper, value):
style = _style_map.get(value.style, None)
return super(AsdfDumper, dumper).represent_scalar(None, value.data, style)
def represent_ordered_mapping(dumper, tag, data):
# TODO: Again, adjust for preferred flow style, and other stylistic details
# NOTE: For block style this uses the compact omap notation, but for flow style
# it does not.
# TODO: Need to see if I can figure out a mechanism so that classes that
# use this representer can specify which values should use flow style
values = []
node = yaml.SequenceNode(tag, values, flow_style=dumper.default_flow_style)
if dumper.alias_key is not None:
dumper.represented_objects[dumper.alias_key] = node
for key, value in data.items():
key_item = dumper.represent_data(key)
value_item = dumper.represent_data(value)
node_item = yaml.MappingNode(YAML_OMAP_TAG, [(key_item, value_item)], flow_style=False)
values.append(node_item)
return node
def represent_ordereddict(dumper, data):
return represent_ordered_mapping(dumper, YAML_OMAP_TAG, data)
AsdfDumper.add_representer(tagged.TaggedList, represent_sequence)
AsdfDumper.add_representer(tagged.TaggedDict, represent_mapping)
AsdfDumper.add_representer(tagged.TaggedString, represent_scalar)
AsdfDumper.add_representer(OrderedDict, represent_ordereddict)
# ----------------------------------------------------------------------
# Handle numpy scalars
for scalar_type in util._iter_subclasses(np.floating):
AsdfDumper.add_representer(scalar_type, lambda dumper, data: dumper.represent_float(float(data)))
for scalar_type in util._iter_subclasses(np.integer):
AsdfDumper.add_representer(scalar_type, lambda dumper, data: dumper.represent_int(int(data)))
def represent_numpy_str(dumper, data):
# The CSafeDumper implementation will raise an error if it
# doesn't recognize data as a string. The Python SafeDumper
# has no problem with np.str_.
return dumper.represent_str(str(data))
AsdfDumper.add_representer(np.str_, represent_numpy_str)
AsdfDumper.add_representer(np.bytes_, AsdfDumper.represent_binary)
class _IgnoreCustomTagsLoader(_yaml_base_loader):
"""
A specialized YAML loader that ignores tags unknown to the
base (safe) loader. This is used by `asdf.util.load_yaml`
to read the ASDF tree as "basic" objects, ignoring the
custom tags.
"""
def construct_undefined(self, node):
if isinstance(node, yaml.MappingNode):
return self.construct_yaml_map(node)
elif isinstance(node, yaml.SequenceNode):
return self.construct_yaml_seq(node)
elif isinstance(node, yaml.ScalarNode):
return self.construct_scalar(node)
return super().construct_undefined(node)
# pyyaml will invoke the constructor associated with None when a node's
# tag is not explicitly handled by another constructor.
_IgnoreCustomTagsLoader.add_constructor(None, _IgnoreCustomTagsLoader.construct_undefined)
class AsdfLoader(_yaml_base_loader):
"""
A specialized YAML loader that can construct "tagged basic Python
data types" as implemented in the `tagged` module.
"""
def construct_undefined(self, node):
if isinstance(node, yaml.MappingNode):
return self._construct_tagged_mapping(node)
if isinstance(node, yaml.SequenceNode):
return self._construct_tagged_sequence(node)
if isinstance(node, yaml.ScalarNode):
return self._construct_tagged_scalar(node)
return super().construct_undefined(node)
def _construct_tagged_mapping(self, node):
data = tagged.tag_object(node.tag, {})
yield data
data.update(self.construct_mapping(node))
def _construct_tagged_sequence(self, node):
data = tagged.tag_object(node.tag, [])
yield data
data.extend(self.construct_sequence(node))
def _construct_tagged_scalar(self, node):
return tagged.tag_object(node.tag, self.construct_scalar(node))
# Custom omap deserializer that builds an OrderedDict instead
# of a list of tuples. Code is mostly identical to pyyaml's SafeConstructor.
def construct_yaml_omap(self, node):
omap = OrderedDict()
yield omap
if not isinstance(node, yaml.SequenceNode):
msg = "while constructing an ordered map"
raise yaml.constructor.ConstructorError(
msg,
node.start_mark,
f"expected a sequence, but found {node.id}",
node.start_mark,
)
for subnode in node.value:
if not isinstance(subnode, yaml.MappingNode):
msg = "while constructing an ordered map"
raise yaml.constructor.ConstructorError(
msg,
node.start_mark,
f"expected a mapping of length 1, but found {subnode.id}",
subnode.start_mark,
)
if len(subnode.value) != 1:
msg = "while constructing an ordered map"
raise yaml.constructor.ConstructorError(
msg,
node.start_mark,
f"expected a single mapping item, but found {len(subnode.value)} items",
subnode.start_mark,
)
key_node, value_node = subnode.value[0]
key = self.construct_object(key_node)
value = self.construct_object(value_node)
omap[key] = value
# pyyaml will invoke the constructor associated with None when a node's
# tag is not explicitly handled by another constructor.
AsdfLoader.add_constructor(None, AsdfLoader.construct_undefined)
AsdfLoader.add_constructor(YAML_TAG_PREFIX + "omap", AsdfLoader.construct_yaml_omap)
def custom_tree_to_tagged_tree(tree, ctx, _serialization_context=None):
"""
Convert a tree, possibly containing custom data types that aren't
directly representable in YAML, to a tree of basic data types,
annotated with tags.
"""
if _serialization_context is None:
_serialization_context = ctx._create_serialization_context(BlockAccess.WRITE)
extension_manager = _serialization_context.extension_manager
def _convert_obj(obj, converter):
tag = converter.select_tag(obj, _serialization_context)
# if select_tag returns None, converter.to_yaml_tree should return a new
# object which will be handled by a different converter
converters_used = set()
while tag is None:
converters_used.add(converter)
obj = converter.to_yaml_tree(obj, tag, _serialization_context)
try:
converter = extension_manager.get_converter_for_type(type(obj))
except KeyError:
# no converter supports this type, return it as-is
yield obj
return
if converter in converters_used:
msg = "Conversion cycle detected"
raise TypeError(msg)
tag = converter.select_tag(obj, _serialization_context)
_serialization_context.assign_object(obj)
node = converter.to_yaml_tree(obj, tag, _serialization_context)
_serialization_context.assign_blocks()
if isinstance(node, GeneratorType):
generator = node
node = next(generator)
else:
generator = None
if isinstance(node, dict):
tagged_node = tagged.TaggedDict(node, tag)
elif isinstance(node, list):
tagged_node = tagged.TaggedList(node, tag)
elif isinstance(node, str):
tagged_node = tagged.TaggedString(node)
tagged_node._tag = tag
else:
msg = f"Converter returned illegal node type: {util.get_class_name(node)}"
raise TypeError(msg)
_serialization_context._mark_extension_used(converter.extension)
yield tagged_node
if generator is not None:
yield from generator
cfg = config.get_config()
convert_ndarray_subclasses = cfg.convert_unknown_ndarray_subclasses
converters_cache = {}
def _walker(obj):
typ = type(obj)
if typ in converters_cache:
return converters_cache[typ](obj)
if extension_manager.handles_type(typ):
converter = extension_manager.get_converter_for_type(typ)
converters_cache[typ] = lambda obj, _converter=converter: _convert_obj(obj, _converter)
return _convert_obj(obj, converter)
if convert_ndarray_subclasses and isinstance(obj, np.ndarray):
warnings.warn(
f"A ndarray subclass ({type(obj)}) was converted as a ndarray. "
"This behavior will be removed from a future version of ASDF. "
"See https://asdf.readthedocs.io/en/latest/asdf/config.html#convert-unknown-ndarray-subclasses",
AsdfConversionWarning,
)
converter = extension_manager.get_converter_for_type(np.ndarray)
converters_cache[typ] = lambda obj, _converter=converter: _convert_obj(obj, _converter)
return _convert_obj(obj, converter)
converters_cache[typ] = lambda obj: obj
return obj
return treeutil.walk_and_modify(
tree,
_walker,
# Walk the tree in preorder, so that extensions can return
# container nodes with unserialized children.
postorder=False,
_context=ctx._tree_modification_context,
)
def tagged_tree_to_custom_tree(tree, ctx, force_raw_types=False, _serialization_context=None):
"""
Convert a tree containing only basic data types, annotated with
tags, to a tree containing custom data types.
"""
if _serialization_context is None:
_serialization_context = ctx._create_serialization_context(BlockAccess.READ)
extension_manager = _serialization_context.extension_manager
def _walker(node):
if force_raw_types:
return node
tag = getattr(node, "_tag", None)
if tag is None:
return node
if extension_manager.handles_tag(tag):
converter = extension_manager.get_converter_for_tag(tag)
obj = converter.from_yaml_tree(node.data, tag, _serialization_context)
_serialization_context.assign_object(obj)
_serialization_context.assign_blocks()
_serialization_context._mark_extension_used(converter.extension)
return obj
if not ctx._ignore_unrecognized_tag:
warnings.warn(
f"{tag} is not recognized, converting to raw Python data structure",
AsdfConversionWarning,
)
return node
return treeutil.walk_and_modify(
tree,
_walker,
# Walk the tree in postorder, so that extensions receive
# container nodes with children already deserialized.
postorder=True,
_context=ctx._tree_modification_context,
)
def load_tree(stream):
"""
Load YAML, returning a tree of objects.
Parameters
----------
stream : readable file-like object
Stream containing the raw YAML content.
"""
# The following call to yaml.load is safe because we're
# using a loader that inherits from pyyaml's SafeLoader.
return yaml.load(stream, Loader=AsdfLoader) # noqa: S506
def dump_tree(tree, fd, ctx, tree_finalizer=None, _serialization_context=None):
"""
Dump a tree of objects, possibly containing custom types, to YAML.
Parameters
----------
tree : object
Tree of objects, possibly containing custom data types.
fd : asdf.generic_io.GenericFile
A file object to dump the serialized YAML to.
ctx : Context
The writing context.
tree_finalizer : callable, optional
Callback that receives the tagged tree before it is validated
and defaults are removed. `asdf.AsdfFile` uses this to update
extension metadata on the tagged tree before it is fully
serialized to YAML.
"""
# The _serialization_context parameter allows AsdfFile to track
# what extensions were used when converting the tree's custom
# types. In 3.0, it will be passed as the `ctx` instead of the
# AsdfFile itself.
if type(tree) is not AsdfObject:
msg = "Root node of ASDF tree must be of type AsdfObject"
raise TypeError(msg)
tags = {"!": STSCI_SCHEMA_TAG_BASE + "/"}
tree = custom_tree_to_tagged_tree(tree, ctx, _serialization_context=_serialization_context)
if tree_finalizer is not None:
tree_finalizer(tree)
schema.validate(tree, ctx)
# add yaml %TAG definitions from extensions
if _serialization_context:
for ext in _serialization_context._extensions_used:
for key, val in ext.yaml_tag_handles.items():
if key not in tags:
tags[key] = val
try:
yaml.dump_all(
[tree],
stream=fd,
Dumper=AsdfDumper,
explicit_start=True,
explicit_end=True,
version=_YAML_VERSION,
allow_unicode=True,
encoding="utf-8",
tags=tags,
)
except yaml.representer.RepresenterError as err:
if len(err.args) < 2:
raise err
# inspect the exception arguments to determine what object failed
obj = err.args[1]
msg = (
f"Object of type[{type(obj)}] is not serializable by asdf. "
"Please convert the object to a supported type or implement "
"a Converter for this type to allow the tree to be serialized."
)
raise AsdfSerializationError(msg, obj) from err
|