/usr/lib/python3/dist-packages/asdf/asdf.py is in python3-asdf 1.2.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 | # Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, unicode_literals, print_function
import datetime
import copy
import io
import re
import numpy as np
from .extern import semver
from . import block
from . import constants
from . import extension
from . import generic_io
from . import reference
from . import schema
from . import treeutil
from . import util
from . import version
from . import versioning
from . import yamlutil
from .tags.core import AsdfObject, Software, HistoryEntry
def get_asdf_library_info():
"""
Get information about asdf to include in the asdf_library entry
in the Tree.
"""
return Software({
'name': 'asdf',
'version': version.version,
'homepage': 'http://github.com/spacetelescope/asdf',
'author': 'Space Telescope Science Institute'
})
class AsdfFile(versioning.VersionedMixin):
"""
The main class that represents a ASDF file.
"""
def __init__(self, tree=None, uri=None, extensions=None, version=None):
"""
Parameters
----------
tree : dict or AsdfFile, optional
The main tree data in the ASDF file. Must conform to the
ASDF schema.
uri : str, optional
The URI for this ASDF file. Used to resolve relative
references against. If not provided, will be
automatically determined from the associated file object,
if possible and if created from `AsdfFile.open`.
extensions : list of AsdfExtension
A list of extensions to the ASDF to support when reading
and writing ASDF files. See `asdftypes.AsdfExtension` for
more information.
version : str, optional
The ASDF version to use when writing out. If not
provided, it will write out in the latest version
supported by asdf.
"""
if extensions is None or extensions == []:
self._extensions = extension._builtin_extension_list
else:
if isinstance(extensions, extension.AsdfExtensionList):
self._extensions = extensions
else:
if not isinstance(extensions, list):
extensions = [extensions]
extensions.insert(0, extension.BuiltinExtension())
self._extensions = extension.AsdfExtensionList(extensions)
self._fd = None
self._external_asdf_by_uri = {}
self._blocks = block.BlockManager(self)
self._uri = None
if tree is None:
self.tree = {}
elif isinstance(tree, AsdfFile):
if self._extensions != tree._extensions:
raise ValueError(
"Can not copy AsdfFile and change active extensions")
self._uri = tree.uri
# Set directly to self._tree (bypassing property), since
# we can assume the other AsdfFile is already valid.
self._tree = tree.tree
self.run_modifying_hook('copy_to_new_asdf', validate=False)
self.find_references()
else:
self.tree = tree
self.find_references()
if uri is not None:
self._uri = uri
self._comments = []
if version is not None:
self.version = version
def __enter__(self):
return self
def __exit__(self, type, value, traceback):
if self._fd:
# This is ok to always do because GenericFile knows
# whether it "owns" the file and should close it.
self._fd.__exit__(type, value, traceback)
self._fd = None
for external in self._external_asdf_by_uri.values():
external.__exit__(type, value, traceback)
self._external_asdf_by_uri.clear()
self._blocks.close()
@property
def file_format_version(self):
if self._file_format_version is None:
return semver.parse(self.versionspec['FILE_FORMAT'])
else:
return self._file_format_version
def close(self):
"""
Close the file handles associated with the `AsdfFile`.
"""
if self._fd:
# This is ok to always do because GenericFile knows
# whether it "owns" the file and should close it.
self._fd.close()
self._fd = None
for external in self._external_asdf_by_uri.values():
external.close()
self._external_asdf_by_uri.clear()
self._blocks.close()
def copy(self):
return self.__class__(
copy.deepcopy(self._tree),
self._uri,
self._extensions
)
__copy__ = __deepcopy__ = copy
@property
def uri(self):
"""
Get the URI associated with the `AsdfFile`.
In many cases, it is automatically determined from the file
handle used to read or write the file.
"""
if self._uri is not None:
return self._uri
if self._fd is not None:
return self._fd._uri
return None
@property
def tag_to_schema_resolver(self):
return self._extensions.tag_to_schema_resolver
@property
def url_mapping(self):
return self._extensions.url_mapping
@property
def type_index(self):
return self._extensions.type_index
def resolve_uri(self, uri):
"""
Resolve a (possibly relative) URI against the URI of this ASDF
file. May be overridden by base classes to change how URIs
are resolved. This does not apply any `uri_mapping` that was
passed to the constructor.
Parameters
----------
uri : str
An absolute or relative URI to resolve against the URI of
this ASDF file.
Returns
-------
uri : str
The resolved URI.
"""
return generic_io.resolve_uri(self.uri, uri)
def open_external(self, uri, do_not_fill_defaults=False):
"""
Open an external ASDF file, from the given (possibly relative)
URI. There is a cache (internal to this ASDF file) that ensures
each external ASDF file is loaded only once.
Parameters
----------
uri : str
An absolute or relative URI to resolve against the URI of
this ASDF file.
do_not_fill_defaults : bool, optional
When `True`, do not fill in missing default values.
Returns
-------
asdffile : AsdfFile
The external ASDF file.
"""
# For a cache key, we want to ignore the "fragment" part.
base_uri = util.get_base_uri(uri)
resolved_uri = self.resolve_uri(base_uri)
# A uri like "#" should resolve back to ourself. In that case,
# just return `self`.
if resolved_uri == '' or resolved_uri == self.uri:
return self
asdffile = self._external_asdf_by_uri.get(resolved_uri)
if asdffile is None:
asdffile = self.open(
resolved_uri,
do_not_fill_defaults=do_not_fill_defaults)
self._external_asdf_by_uri[resolved_uri] = asdffile
return asdffile
@property
def tree(self):
"""
Get/set the tree of data in the ASDF file.
When set, the tree will be validated against the ASDF schema.
"""
return self._tree
@tree.setter
def tree(self, tree):
asdf_object = AsdfObject(tree)
self._validate(asdf_object)
self._tree = asdf_object
@property
def comments(self):
"""
Get the comments after the header, before the tree.
"""
return self._comments
def _validate(self, tree):
tagged_tree = yamlutil.custom_tree_to_tagged_tree(
tree, self)
schema.validate(tagged_tree, self)
def validate(self):
"""
Validate the current state of the tree against the ASDF schema.
"""
self._validate(self._tree)
def make_reference(self, path=[]):
"""
Make a new reference to a part of this file's tree, that can be
assigned as a reference to another tree.
Parameters
----------
path : list of str and int, optional
The parts of the path pointing to an item in this tree.
If omitted, points to the root of the tree.
Returns
-------
reference : reference.Reference
A reference object.
Examples
--------
For the given AsdfFile ``ff``, add an external reference to the data in
an external file::
>>> import asdf
>>> flat = asdf.open("http://stsci.edu/reference_files/flat.asdf") # doctest: +SKIP
>>> ff.tree['flat_field'] = flat.make_reference(['data']) # doctest: +SKIP
"""
return reference.make_reference(self, path)
@property
def blocks(self):
"""
Get the block manager associated with the `AsdfFile`.
"""
return self._blocks
def set_array_storage(self, arr, array_storage):
"""
Set the block type to use for the given array data.
Parameters
----------
arr : numpy.ndarray
The array to set. If multiple views of the array are in
the tree, only the most recent block type setting will be
used, since all views share a single block.
array_storage : str
Must be one of:
- ``internal``: The default. The array data will be
stored in a binary block in the same ASDF file.
- ``external``: Store the data in a binary block in a
separate ASDF file.
- ``inline``: Store the data as YAML inline in the tree.
"""
block = self.blocks[arr]
self.blocks.set_array_storage(block, array_storage)
def get_array_storage(self, arr):
"""
Get the block type for the given array data.
Parameters
----------
arr : numpy.ndarray
"""
return self.blocks[arr].array_storage
def set_array_compression(self, arr, compression):
"""
Set the compression to use for the given array data.
Parameters
----------
arr : numpy.ndarray
The array to set. If multiple views of the array are in
the tree, only the most recent compression setting will be
used, since all views share a single block.
array_compression : str or None
Must be one of:
- ``zlib``: Use zlib compression
- ``bzp2``: Use bzip2 compression
- ``''`` or `None`: no compression
"""
self.blocks[arr].compression = compression
def get_array_compression(self, arr):
"""
Get the compression type for the given array data.
Parameters
----------
arr : numpy.ndarray
Returns
-------
compression : str or None
"""
return self.blocks[arr].compression
@classmethod
def _parse_header_line(cls, line):
"""
Parses the header line in a ASDF file to obtain the ASDF version.
"""
parts = line.split()
if len(parts) != 2 or parts[0] != constants.ASDF_MAGIC:
raise ValueError("Does not appear to be a ASDF file.")
try:
version = semver.parse(parts[1].decode('ascii'))
except ValueError:
raise ValueError(
"Unparseable version in ASDF file: {0}".format(parts[1]))
return version
@classmethod
def _parse_comment_section(cls, content):
"""
Parses the comment section, between the header line and the
Tree or first block.
"""
comments = []
lines = content.splitlines()
for line in lines:
if not line.startswith(b'#'):
raise ValueError("Invalid content between header and tree")
comments.append(line[1:].strip())
return comments
@classmethod
def _find_asdf_version_in_comments(cls, comments):
for comment in comments:
parts = comment.split()
if len(parts) == 2 and parts[0] == constants.ASDF_STANDARD_COMMENT:
try:
version = semver.parse(parts[1].decode('ascii'))
except ValueError:
pass
else:
return version
return None
@classmethod
def _open_impl(cls, self, fd, uri=None, mode='r',
validate_checksums=False,
do_not_fill_defaults=False,
_get_yaml_content=False):
fd = generic_io.get_file(fd, mode=mode, uri=uri)
self._fd = fd
try:
header_line = fd.read_until(b'\r?\n', 2, "newline", include=True)
except ValueError:
raise ValueError("Does not appear to be a ASDF file.")
self._file_format_version = cls._parse_header_line(header_line)
self.version = self._file_format_version
comment_section = fd.read_until(
b'(%YAML)|(' + constants.BLOCK_MAGIC + b')', 5,
"start of content", include=False, exception=False)
self._comments = cls._parse_comment_section(comment_section)
version = cls._find_asdf_version_in_comments(self._comments)
if version is not None:
self.version = version
yaml_token = fd.read(4)
yaml_content = b''
tree = {}
has_blocks = False
if yaml_token == b'%YAM':
reader = fd.reader_until(
constants.YAML_END_MARKER_REGEX, 7, 'End of YAML marker',
include=True, initial_content=yaml_token)
if _get_yaml_content:
yaml_content = reader.read()
else:
# We parse the YAML content into basic data structures
# now, but we don't do anything special with it until
# after the blocks have been read
tree = yamlutil.load_tree(reader, self)
has_blocks = fd.seek_until(constants.BLOCK_MAGIC, 4, include=True)
elif yaml_token == constants.BLOCK_MAGIC:
has_blocks = True
elif yaml_token != b'':
raise IOError("ASDF file appears to contain garbage after header.")
# For testing: just return the raw YAML content
if _get_yaml_content:
fd.close()
return yaml_content
if has_blocks:
self._blocks.read_internal_blocks(
fd, past_magic=True, validate_checksums=validate_checksums)
self._blocks.read_block_index(fd, self)
tree = reference.find_references(tree, self)
if not do_not_fill_defaults:
schema.fill_defaults(tree, self)
self._validate(tree)
tree = yamlutil.tagged_tree_to_custom_tree(tree, self)
self._tree = tree
self.run_hook('post_read')
return self
@classmethod
def open(cls, fd, uri=None, mode='r',
validate_checksums=False,
extensions=None,
do_not_fill_defaults=False):
"""
Open an existing ASDF file.
Parameters
----------
fd : string or file-like object
May be a string ``file`` or ``http`` URI, or a Python
file-like object.
uri : string, optional
The URI of the file. Only required if the URI can not be
automatically determined from `fd`.
mode : string, optional
The mode to open the file in. Must be ``r`` (default) or
``rw``.
validate_checksums : bool, optional
If `True`, validate the blocks against their checksums.
Requires reading the entire file, so disabled by default.
extensions : list of AsdfExtension
A list of extensions to the ASDF to support when reading
and writing ASDF files. See `asdftypes.AsdfExtension` for
more information.
do_not_fill_defaults : bool, optional
When `True`, do not fill in missing default values.
Returns
-------
asdffile : AsdfFile
The new AsdfFile object.
"""
self = cls(extensions=extensions)
return cls._open_impl(
self, fd, uri=uri, mode=mode,
validate_checksums=validate_checksums,
do_not_fill_defaults=do_not_fill_defaults)
def _write_tree(self, tree, fd, pad_blocks):
fd.write(constants.ASDF_MAGIC)
fd.write(b' ')
fd.write(self.version_map['FILE_FORMAT'].encode('ascii'))
fd.write(b'\n')
fd.write(b'#')
fd.write(constants.ASDF_STANDARD_COMMENT)
fd.write(b' ')
fd.write(self.version_string.encode('ascii'))
fd.write(b'\n')
if len(tree):
yamlutil.dump_tree(tree, fd, self)
if pad_blocks:
padding = util.calculate_padding(
fd.tell(), pad_blocks, fd.block_size)
fd.fast_forward(padding)
def _pre_write(self, fd, all_array_storage, all_array_compression,
auto_inline):
if all_array_storage not in (None, 'internal', 'external', 'inline'):
raise ValueError(
"Invalid value for all_array_storage: '{0}'".format(
all_array_storage))
self._all_array_storage = all_array_storage
self._all_array_compression = all_array_compression
if auto_inline in (True, False):
raise ValueError(
"Invalid value for auto_inline: '{0}'".format(auto_inline))
if auto_inline is not None:
try:
self._auto_inline = int(auto_inline)
except ValueError:
raise ValueError(
"Invalid value for auto_inline: '{0}'".format(auto_inline))
else:
self._auto_inline = None
if len(self._tree):
self.run_hook('pre_write')
# This is where we'd do some more sophisticated block
# reorganization, if necessary
self._blocks.finalize(self)
self._tree['asdf_library'] = get_asdf_library_info()
def _serial_write(self, fd, pad_blocks, include_block_index):
self._write_tree(self._tree, fd, pad_blocks)
self.blocks.write_internal_blocks_serial(fd, pad_blocks)
self.blocks.write_external_blocks(fd.uri, pad_blocks)
if include_block_index:
self.blocks.write_block_index(fd, self)
def _random_write(self, fd, pad_blocks, include_block_index):
self._write_tree(self._tree, fd, False)
self.blocks.write_internal_blocks_random_access(fd)
self.blocks.write_external_blocks(fd.uri, pad_blocks)
if include_block_index:
self.blocks.write_block_index(fd, self)
fd.truncate()
def _post_write(self, fd):
if len(self._tree):
self.run_hook('post_write')
if hasattr(self, '_all_array_storage'):
del self._all_array_storage
if hasattr(self, '_all_array_compression'):
del self._all_array_compression
if hasattr(self, '_auto_inline'):
del self._auto_inline
def update(self, all_array_storage=None, all_array_compression=None,
auto_inline=None, pad_blocks=False, include_block_index=True,
version=None):
"""
Update the file on disk in place.
Parameters
----------
all_array_storage : string, optional
If provided, override the array storage type of all blocks
in the file immediately before writing. Must be one of:
- ``internal``: The default. The array data will be
stored in a binary block in the same ASDF file.
- ``external``: Store the data in a binary block in a
separate ASDF file.
- ``inline``: Store the data as YAML inline in the tree.
all_array_compression : string, optional
If provided, set the compression type on all binary blocks
in the file. Must be one of:
- ``''``: No compression.
- ``zlib``: Use zlib compression.
- ``bzp2``: Use bzip2 compression.
auto_inline : int, optional
When the number of elements in an array is less than this
threshold, store the array as inline YAML, rather than a
binary block. This only works on arrays that do not share
data with other arrays. Default is 0.
pad_blocks : float or bool, optional
Add extra space between blocks to allow for updating of
the file. If `False` (default), add no padding (always
return 0). If `True`, add a default amount of padding of
10% If a float, it is a factor to multiple content_size by
to get the new total size.
include_block_index : bool, optional
If `False`, don't include a block index at the end of the
file. (Default: `True`) A block index is never written
if the file has a streamed block.
version : str, optional
The ASDF version to write out. If not provided, it will
write out in the latest version supported by asdf.
"""
fd = self._fd
if fd is None:
raise ValueError(
"Can not update, since there is no associated file")
if not fd.writable():
raise IOError(
"Can not update, since associated file is read-only")
if version is not None:
self.version = version
if all_array_storage == 'external':
# If the file is fully exploded, there's no benefit to
# update, so just use write_to()
self.write_to(fd, all_array_storage=all_array_storage)
fd.truncate()
return
if not fd.seekable():
raise IOError(
"Can not update, since associated file is not seekable")
self.blocks.finish_reading_internal_blocks()
self._pre_write(fd, all_array_storage, all_array_compression,
auto_inline)
try:
fd.seek(0)
if not self.blocks.has_blocks_with_offset():
# If we don't have any blocks that are being reused, just
# write out in a serial fashion.
self._serial_write(fd, pad_blocks, include_block_index)
fd.truncate()
return
# Estimate how big the tree will be on disk by writing the
# YAML out in memory. Since the block indices aren't yet
# known, we have to count the number of block references and
# add enough space to accommodate the largest block number
# possible there.
tree_serialized = io.BytesIO()
self._write_tree(self._tree, tree_serialized, pad_blocks=False)
array_ref_count = [0]
from .tags.core.ndarray import NDArrayType
for node in treeutil.iter_tree(self._tree):
if (isinstance(node, (np.ndarray, NDArrayType)) and
self.blocks[node].array_storage == 'internal'):
array_ref_count[0] += 1
serialized_tree_size = (
tree_serialized.tell() +
constants.MAX_BLOCKS_DIGITS * array_ref_count[0])
if not block.calculate_updated_layout(
self.blocks, serialized_tree_size,
pad_blocks, fd.block_size):
# If we don't have any blocks that are being reused, just
# write out in a serial fashion.
self._serial_write(fd, pad_blocks, include_block_index)
fd.truncate()
return
fd.seek(0)
self._random_write(fd, pad_blocks, include_block_index)
fd.flush()
finally:
self._post_write(fd)
def write_to(self, fd, all_array_storage=None, all_array_compression=None,
auto_inline=None, pad_blocks=False, include_block_index=True,
version=None):
"""
Write the ASDF file to the given file-like object.
`write_to` does not change the underlying file descriptor in
the `AsdfFile` object, but merely copies the content to a new
file.
Parameters
----------
fd : string or file-like object
May be a string path to a file, or a Python file-like
object. If a string path, the file is automatically
closed after writing. If not a string path,
all_array_storage : string, optional
If provided, override the array storage type of all blocks
in the file immediately before writing. Must be one of:
- ``internal``: The default. The array data will be
stored in a binary block in the same ASDF file.
- ``external``: Store the data in a binary block in a
separate ASDF file.
- ``inline``: Store the data as YAML inline in the tree.
all_array_compression : string, optional
If provided, set the compression type on all binary blocks
in the file. Must be one of:
- ``''``: No compression.
- ``zlib``: Use zlib compression.
- ``bzp2``: Use bzip2 compression.
auto_inline : int, optional
When the number of elements in an array is less than this
threshold, store the array as inline YAML, rather than a
binary block. This only works on arrays that do not share
data with other arrays. Default is 0.
pad_blocks : float or bool, optional
Add extra space between blocks to allow for updating of
the file. If `False` (default), add no padding (always
return 0). If `True`, add a default amount of padding of
10% If a float, it is a factor to multiple content_size by
to get the new total size.
include_block_index : bool, optional
If `False`, don't include a block index at the end of the
file. (Default: `True`) A block index is never written
if the file has a streamed block.
version : str, optional
The ASDF version to write out. If not provided, it will
write out in the latest version supported by asdf.
"""
original_fd = self._fd
if version is not None:
self.version = version
try:
with generic_io.get_file(fd, mode='w') as fd:
self._fd = fd
self._pre_write(fd, all_array_storage, all_array_compression,
auto_inline)
try:
self._serial_write(fd, pad_blocks, include_block_index)
fd.flush()
finally:
self._post_write(fd)
finally:
self._fd = original_fd
def find_references(self):
"""
Finds all external "JSON References" in the tree and converts
them to `reference.Reference` objects.
"""
# Set directly to self._tree, since it doesn't need to be
# re-validated.
self._tree = reference.find_references(self._tree, self)
def resolve_references(self, do_not_fill_defaults=False):
"""
Finds all external "JSON References" in the tree, loads the
external content, and places it directly in the tree. Saving
a ASDF file after this operation means it will have no
external references, and will be completely self-contained.
"""
# Set to the property self.tree so the resulting "complete"
# tree will be validated.
self.tree = reference.resolve_references(self._tree, self)
def run_hook(self, hookname):
"""
Run a "hook" for each custom type found in the tree.
Parameters
----------
hookname : str
The name of the hook. If a `AsdfType` is found with a method
with this name, it will be called for every instance of the
corresponding custom type in the tree.
"""
type_index = self.type_index
if not type_index.has_hook(hookname):
return
for node in treeutil.iter_tree(self._tree):
hook = type_index.get_hook_for_type(hookname, type(node),
self.version_string)
if hook is not None:
hook(node, self)
def run_modifying_hook(self, hookname, validate=True):
"""
Run a "hook" for each custom type found in the tree. The hook
is free to return a different object in order to modify the
tree.
Parameters
----------
hookname : str
The name of the hook. If a `AsdfType` is found with a method
with this name, it will be called for every instance of the
corresponding custom type in the tree.
validate : bool
When `True` (default) validate the resulting tree.
"""
type_index = self.type_index
if not type_index.has_hook(hookname):
return
def walker(node):
hook = type_index.get_hook_for_type(hookname, type(node),
self.version_string)
if hook is not None:
return hook(node, self)
return node
tree = treeutil.walk_and_modify(self.tree, walker)
if validate:
self._validate(tree)
self._tree = tree
return self._tree
def resolve_and_inline(self):
"""
Resolves all external references and inlines all data. This
produces something that, when saved, is a 100% valid YAML
file.
"""
self.blocks.finish_reading_internal_blocks()
self.resolve_references()
for b in list(self.blocks.blocks):
self.blocks.set_array_storage(b, 'inline')
def fill_defaults(self):
"""
Fill in any values that are missing in the tree using default
values from the schema.
"""
tree = yamlutil.custom_tree_to_tagged_tree(self._tree, self)
schema.fill_defaults(tree, self)
self._tree = yamlutil.tagged_tree_to_custom_tree(tree, self)
def remove_defaults(self):
"""
Remove any values in the tree that are the same as the default
values in the schema
"""
tree = yamlutil.custom_tree_to_tagged_tree(self._tree, self)
schema.remove_defaults(tree, self)
self._tree = yamlutil.tagged_tree_to_custom_tree(tree, self)
def add_history_entry(self, description, software=None):
"""
Add an entry to the history list.
Parameters
----------
description : str
A description of the change.
software : dict or list of dict
A description of the software used. It should not include
asdf itself, as that is automatically notated in the
`asdf_library` entry.
Each dict must have the following keys:
- ``name``: The name of the software
- ``author``: The author or institution that produced the software
- ``homepage``: A URI to the homepage of the software
- ``version``: The version of the software
"""
if isinstance(software, list):
software = [Software(x) for x in software]
elif software is not None:
software = Software(software)
entry = HistoryEntry({
'description': description,
'time': datetime.datetime.utcnow()
})
if software is not None:
entry['software'] = software
if 'history' not in self.tree:
self.tree['history'] = []
self.tree['history'].append(entry)
try:
self.validate()
except:
self.tree['history'].pop()
raise
|