/usr/lib/python2.7/dist-packages/asdf/asdf.py is in python-asdf 1.2.1-2.
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# -*- 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
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