import copy
import datetime
import io
import os
import pathlib
import time
import warnings
from packaging.version import Version
from . import _compression as mcompression
from . import _display as display
from . import _node_info as node_info
from . import _version as version
from . import constants, generic_io, reference, schema, treeutil, util, versioning, yamlutil
from ._block.manager import Manager as BlockManager
from ._helpers import validate_version
from .config import config_context, get_config
from .exceptions import (
AsdfConversionWarning,
AsdfDeprecationWarning,
AsdfWarning,
DelimiterNotFoundError,
ValidationError,
)
from .extension import Extension, ExtensionProxy, _serialization_context, get_cached_extension_manager
from .search import AsdfSearchResult
from .tags.core import AsdfObject, ExtensionMetadata, HistoryEntry, Software
from .util import NotSet
def __getattr__(name):
if name == "SerializationContext":
warnings.warn(
"importing SerializationContext from asdf.asdf is deprecated. "
"Please import SerializationContext from asdf.extension",
AsdfDeprecationWarning,
)
from .extension._serialization_context import SerializationContext
return SerializationContext
msg = f"module {__name__!r} has no attribute {name!r}"
raise AttributeError(msg)
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/asdf-format/asdf",
"author": "The ASDF Developers",
},
)
[docs]
class AsdfFile:
"""
The main class that represents an ASDF file object.
"""
def __init__(
self,
tree=None,
uri=None,
extensions=None,
version=None,
ignore_version_mismatch=True,
ignore_unrecognized_tag=False,
ignore_implicit_conversion=False,
copy_arrays=False,
memmap=NotSet,
lazy_load=True,
custom_schema=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 `asdf.open`.
extensions : object, optional
Additional extensions to use when reading and writing the file.
May be an `asdf.extension.Extension` or a `list` of extensions.
version : str, optional
The ASDF Standard version. If not provided, defaults to the
configured default version. See `asdf.config.AsdfConfig.default_version`.
ignore_version_mismatch : bool, optional
When `True`, do not raise warnings for mismatched schema versions.
Set to `True` by default.
ignore_unrecognized_tag : bool, optional
When `True`, do not raise warnings for unrecognized tags. Set to
`False` by default.
ignore_implicit_conversion : bool
When `True`, do not raise warnings when types in the tree are
implicitly converted into a serializable object. The motivating
case for this is currently ``namedtuple``, which cannot be serialized
as-is.
copy_arrays : bool, optional
When `False`, when reading files, attempt to memmap underlying data
arrays when possible.
memmap : bool, optional
When `True`, when reading files, attempt to memmap underlying data
arrays when possible. When set, this argument will override
``copy_arrays``. When not set, the ``copy_arrays`` will determine
if arrays are memory mapped or copied. ``copy_arrays`` will be
deprecated and the default will change in an upcoming asdf version
which by default will not memory map arrays.
lazy_load : bool, optional
When `True` and the underlying file handle is seekable, data
arrays will only be loaded lazily: i.e. when they are accessed
for the first time. In this case the underlying file must stay
open during the lifetime of the tree. Setting to False causes
all data arrays to be loaded up front, which means that they
can be accessed even after the underlying file is closed.
Note: even if ``lazy_load`` is `False`, ``copy_arrays`` is still taken
into account.
custom_schema : str, optional
Path to a custom schema file that will be used for a secondary
validation pass. This can be used to ensure that particular ASDF
files follow custom conventions beyond those enforced by the
standard.
"""
self._fname = ""
# make a new AsdfVersion instance here so files don't share the same instance
self._file_format_version = versioning.AsdfVersion(versioning._FILE_FORMAT_VERSION)
# Don't use the version setter here; it tries to access
# the extensions, which haven't been assigned yet.
if version is None:
self._version = versioning.AsdfVersion(get_config().default_version)
else:
self._version = versioning.AsdfVersion(validate_version(version))
self._user_extensions = self._process_user_extensions(extensions)
self._plugin_extensions = self._process_plugin_extensions()
self._extension_manager = None
if custom_schema is not None:
self._custom_schema = schema._load_schema_cached(custom_schema, None, True)
else:
self._custom_schema = None
self._ignore_version_mismatch = ignore_version_mismatch
self._ignore_unrecognized_tag = ignore_unrecognized_tag
self._ignore_implicit_conversion = ignore_implicit_conversion
# Set of (string, string) tuples representing tag version mismatches
# that we've already warned about for this file.
self._warned_tag_pairs = set()
# Context of a call to treeutil.walk_and_modify, needed in the AsdfFile
# in case walk_and_modify is re-entered by extension code (via
# custom_tree_to_tagged_tree or tagged_tree_to_custom_tree).
self._tree_modification_context = treeutil._TreeModificationContext()
self._fd = None
self._closed = False
self._external_asdf_by_uri = {}
# if memmap is set, it overrides copy_arrays
if memmap is not NotSet:
copy_arrays = not memmap
self._blocks = BlockManager(uri=uri, lazy_load=lazy_load, memmap=not copy_arrays)
# this message is passed into find_references to only warn if
# a reference was found
find_ref_warning_msg = (
"find_references during AsdfFile.__init__ is deprecated. "
"call AsdfFile.find_references after AsdfFile.__init__"
)
if tree is None:
# Bypassing the tree property here, to avoid validating
# an empty tree.
self._tree = AsdfObject()
elif isinstance(tree, AsdfFile):
if self.extensions != tree.extensions:
# TODO(eslavich): Why not? What if that's the goal
# of copying the file?
msg = "Can not copy AsdfFile and change active extensions"
raise ValueError(msg)
self._blocks._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.find_references(_warning_msg=find_ref_warning_msg)
else:
self._tree = AsdfObject(tree)
try:
self.validate()
except ValidationError:
warnings.warn(
"Validation during AsdfFile.__init__ is deprecated. "
"Please use AsdfFile.validate to validate the tree",
AsdfDeprecationWarning,
)
raise
self.find_references(_warning_msg=find_ref_warning_msg)
self._comments = []
@property
def version(self):
"""
Get this AsdfFile's ASDF Standard version.
Returns
-------
asdf.versioning.AsdfVersion
"""
return self._version
@version.setter
def version(self, value):
"""
Set this AsdfFile's ASDF Standard version.
Parameters
----------
value : str or asdf.versioning.AsdfVersion
"""
self._version = versioning.AsdfVersion(validate_version(value))
# The new version may not be compatible with the previous
# set of extensions, so we need to check them again:
self._user_extensions = self._process_user_extensions(self._user_extensions)
self._plugin_extensions = self._process_plugin_extensions()
self._extension_manager = None
@property
def version_string(self):
"""
Get this AsdfFile's ASDF Standard version as a string.
Returns
-------
str
"""
return str(self._version)
@property
def version_map(self):
warnings.warn(
"AsdfFile.version_map is deprecated. Please use the extension_manager",
AsdfDeprecationWarning,
)
return versioning._get_version_map(self.version_string)
@property
def extensions(self):
"""
Get the list of user extensions that are enabled for
use with this AsdfFile.
Returns
-------
list of asdf.extension.ExtensionProxy
"""
return self._user_extensions
@extensions.setter
def extensions(self, value):
"""
Set the list of user extensions that are enabled for
use with this AsdfFile.
Parameters
----------
value : list of asdf.extension.Extension
"""
self._user_extensions = self._process_user_extensions(value)
self._extension_manager = None
@property
def extension_manager(self):
"""
Get the ExtensionManager for this AsdfFile.
Returns
-------
asdf.extension.ExtensionManager
"""
if self._extension_manager is None:
self._extension_manager = get_cached_extension_manager(self._user_extensions + self._plugin_extensions)
return self._extension_manager
def __enter__(self):
return self
def __exit__(self, type_, value, traceback):
self.close()
def _check_extensions(self, tree, strict=False):
"""
Compare the user's installed extensions to metadata in the tree
and warn when a) an extension is missing or b) an extension is
present but the file was written with a later version of the
extension's package.
Parameters
----------
tree : AsdfObject
Fully converted tree of custom types.
strict : bool, optional
Set to `True` to convert warnings to exceptions.
"""
if "history" not in tree or not isinstance(tree["history"], dict) or "extensions" not in tree["history"]:
return
for extension in tree["history"]["extensions"]:
installed = None
for ext in self._user_extensions + self._plugin_extensions:
if (
extension.extension_uri is not None
and extension.extension_uri == ext.extension_uri
or extension.extension_uri is None
and extension.extension_class in ext.legacy_class_names
):
installed = ext
break
filename = f"'{self._fname}' " if self._fname else ""
if extension.extension_uri is not None:
extension_description = f"URI '{extension.extension_uri}'"
else:
extension_description = f"class '{extension.extension_class}'"
if extension.software is not None:
extension_description += (
f" (from package {extension.software['name']}=={extension.software['version']})"
)
if installed is None:
msg = (
f"File {filename}was created with extension "
f"{extension_description}, which is not currently installed"
)
if strict:
raise RuntimeError(msg)
warnings.warn(msg, AsdfWarning)
elif extension.software:
# Local extensions may not have a real version. If the package name changed,
# then the version sequence may have been reset.
if installed.package_version is None or installed.package_name != extension.software["name"]:
continue
# Compare version in file metadata with installed version
if Version(installed.package_version) < Version(extension.software["version"]):
msg = (
f"File {filename}was created with extension {extension_description}, "
f"but older package ({installed.package_name}=={installed.package_version}) is installed."
)
if strict:
raise RuntimeError(msg)
warnings.warn(msg, AsdfWarning)
def _process_plugin_extensions(self):
"""
Select installed extensions that are compatible with this
file's ASDF Standard version.
Returns
-------
list of asdf.extension.ExtensionProxy
"""
return [e for e in get_config().extensions if self.version_string in e.asdf_standard_requirement]
def _process_user_extensions(self, extensions):
"""
Validate a list of extensions requested by the user
add missing extensions registered with the current `AsdfConfig`.
Parameters
----------
extensions : object
May be an `asdf.extension.Extension` or a `list` of extensions.
Returns
-------
list of asdf.extension.ExtensionProxy
"""
if extensions is None:
extensions = []
elif isinstance(extensions, (Extension, ExtensionProxy)):
extensions = [extensions]
if not isinstance(extensions, list):
msg = "The extensions parameter must be an extension or list of extensions"
raise TypeError(msg)
extensions = [ExtensionProxy.maybe_wrap(e) for e in extensions]
result = []
for extension in extensions:
if self.version_string not in extension.asdf_standard_requirement:
warnings.warn(
f"Extension {extension} does not support ASDF Standard {self.version_string}. "
"It has been disabled.",
AsdfWarning,
)
else:
result.append(extension)
return result
def _update_extension_history(self, tree, serialization_context):
"""
Update the extension metadata on this file's tree to reflect
extensions used during serialization.
Parameters
----------
serialization_context : asdf.extension.SerializationContext
The context that was used to serialize the tree.
"""
if serialization_context.version < versioning.NEW_HISTORY_FORMAT_MIN_VERSION:
return
if "history" not in tree:
tree["history"] = {"extensions": []}
# Support clients who are still using the old history format
elif isinstance(tree["history"], list):
histlist = tree["history"]
tree["history"] = {"entries": histlist, "extensions": []}
warnings.warn(
"The ASDF history format has changed in order to "
"support metadata about extensions. History entries "
"should now be stored under tree['history']['entries'].",
AsdfWarning,
)
elif "extensions" not in tree["history"]:
tree["history"]["extensions"] = []
for extension in serialization_context._extensions_used:
ext_name = extension.class_name
ext_meta = ExtensionMetadata(extension_class=ext_name)
if extension.package_name is not None:
ext_meta["software"] = Software(name=extension.package_name, version=extension.package_version)
if extension.extension_uri is not None:
ext_meta["extension_uri"] = extension.extension_uri
if extension.compressors:
ext_meta["supported_compression"] = [comp.label.decode("ascii") for comp in extension.compressors]
for i, entry in enumerate(tree["history"]["extensions"]):
# Update metadata about this extension if it already exists
if (
entry.extension_uri is not None
and entry.extension_uri == extension.extension_uri
or entry.extension_class in extension.legacy_class_names
):
tree["history"]["extensions"][i] = ext_meta
break
else:
tree["history"]["extensions"].append(ext_meta)
@property
def file_format_version(self):
return self._file_format_version
[docs]
def close(self):
"""
Close the file handles associated with the `asdf.AsdfFile`.
"""
if self._fd and not self._closed:
# This is ok to always do because GenericFile knows
# whether it "owns" the file and should close it.
self._fd.close()
self._fd = None
self._closed = True
# as we're closing the file, also empty out the
# tree so that references to array data can be released
self._tree = AsdfObject()
for external in self._external_asdf_by_uri.values():
external.close()
self._external_asdf_by_uri.clear()
self._blocks.close()
[docs]
def copy(self):
return self.__class__(
copy.deepcopy(self._tree),
self._blocks._uri,
self._user_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.
"""
return self._blocks._uri
[docs]
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)
[docs]
def open_external(self, uri, **kwargs):
"""
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.
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 = open_asdf(resolved_uri, mode="r", **kwargs)
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.
"""
if self._closed:
msg = "Cannot access data from closed ASDF file"
raise OSError(msg)
return self._tree
@tree.setter
def tree(self, tree):
asdf_object = AsdfObject(tree)
# Only perform custom validation if the tree is not empty
try:
self._validate(asdf_object, custom=bool(tree))
except ValidationError:
warnings.warn(
"Validation on tree assignment is deprecated. Please use AsdfFile.validate", AsdfDeprecationWarning
)
raise
self._tree = asdf_object
[docs]
def keys(self):
return self.tree.keys()
def __getitem__(self, key):
return self.tree[key]
def __setitem__(self, key, value):
self.tree[key] = value
def __contains__(self, item):
return item in self.tree
@property
def comments(self):
"""
Get the comments after the header, before the tree.
"""
return self._comments
def _validate(self, tree, custom=True, reading=False):
with self._blocks.options_context():
# If we're validating on read then the tree
# is already guaranteed to be in tagged form.
tagged_tree = tree if reading else yamlutil.custom_tree_to_tagged_tree(tree, self)
schema.validate(tagged_tree, self, reading=reading)
# Perform secondary validation pass if requested
if custom and self._custom_schema:
schema.validate(tagged_tree, self, self._custom_schema, reading=reading)
[docs]
def validate(self):
"""
Validate the current state of the tree against the ASDF schema.
"""
self._validate(self._tree)
[docs]
def make_reference(self, path=None):
"""
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 :
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, [] if path is None else path)
[docs]
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.
"""
self._blocks._set_array_storage(arr, array_storage)
[docs]
def get_array_storage(self, arr):
"""
Get the block type for the given array data.
Parameters
----------
arr : numpy.ndarray
"""
return self._blocks._get_array_storage(arr)
[docs]
def set_array_compression(self, arr, compression, **compression_kwargs):
"""
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.
compression : str or None
Must be one of:
- ``''`` or `None`: no compression
- ``zlib``: Use zlib compression
- ``bzp2``: Use bzip2 compression
- ``lz4``: Use lz4 compression
- ``input``: Use the same compression as in the file read.
If there is no prior file, acts as None.
"""
self._blocks._set_array_compression(arr, compression, **compression_kwargs)
[docs]
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._get_array_compression(arr)
[docs]
def get_array_compression_kwargs(self, arr):
""" """
return self._blocks._get_array_compression_kwargs(arr)
@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:
msg = "Does not appear to be a ASDF file."
raise ValueError(msg)
try:
version = versioning.AsdfVersion(parts[1].decode("ascii"))
except ValueError as err:
msg = f"Unparsable version in ASDF file: {parts[1]}"
raise ValueError(msg) from err
if version != versioning._FILE_FORMAT_VERSION:
msg = f"Unsupported ASDF file format version {version}"
raise ValueError(msg)
return version
@classmethod
def _read_comment_section(cls, fd):
"""
Reads the comment section, between the header line and the
Tree or first block.
"""
content = fd.read_until(
b"(%YAML)|(" + constants.BLOCK_MAGIC + b")",
5,
"start of content",
include=False,
exception=False,
)
comments = []
lines = content.splitlines()
for line in lines:
if not line.startswith(b"#"):
msg = "Invalid content between header and tree"
raise ValueError(msg)
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 = versioning.AsdfVersion(parts[1].decode("ascii"))
except ValueError:
pass
else:
return version
return None
@classmethod
def _open_asdf(
cls,
self,
fd,
validate_checksums=False,
extensions=None,
_get_yaml_content=False,
_force_raw_types=False,
strict_extension_check=False,
ignore_missing_extensions=False,
):
"""Attempt to populate AsdfFile data from file-like object"""
if strict_extension_check and ignore_missing_extensions:
msg = "'strict_extension_check' and 'ignore_missing_extensions' are incompatible options"
raise ValueError(msg)
with config_context():
# validate_checksums (unlike memmap and lazy_load) is provided
# here instead of in __init__
self._blocks._validate_checksums = validate_checksums
self._mode = fd.mode
self._fd = fd
if self._fd._uri:
self._blocks._uri = self._fd._uri
# The filename is currently only used for tracing warning information
self._fname = self._fd._uri if self._fd._uri else ""
try:
header_line = fd.read_until(b"\r?\n", 2, "newline", include=True)
except DelimiterNotFoundError as e:
msg = "Does not appear to be a ASDF file."
raise ValueError(msg) from e
self._file_format_version = cls._parse_header_line(header_line)
self._comments = cls._read_comment_section(fd)
version = cls._find_asdf_version_in_comments(self._comments)
if version is not None:
self.version = version
else:
# If no ASDF_STANDARD comment is found...
self.version = versioning.AsdfVersion("1.0.0")
# Now that version is set for good, we can add any additional
# extensions, which may have narrow ASDF Standard version
# requirements.
if extensions:
self.extensions = extensions
yaml_token = fd.read(4)
tree = None
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,
)
# For testing: just return the raw YAML content
if _get_yaml_content:
yaml_content = reader.read()
fd.close()
return yaml_content
# 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._blocks.read(fd)
elif yaml_token == constants.BLOCK_MAGIC:
# this file has only blocks and we're already read the first block magic
self._blocks.read(fd, after_magic=True)
elif yaml_token != b"":
msg = "ASDF file appears to contain garbage after header."
raise OSError(msg)
if tree is None:
# At this point the tree should be tagged, but we want it to be
# tagged with the core/asdf version appropriate to this file's
# ASDF Standard version. We're using custom_tree_to_tagged_tree
# to select the correct tag for us.
tree = yamlutil.custom_tree_to_tagged_tree(AsdfObject(), self)
find_ref_warning_msg = "find_references during open is deprecated. call AsdfFile.find_references after open"
tree = reference.find_references(tree, self, _warning_msg=find_ref_warning_msg)
if self.version <= versioning.FILL_DEFAULTS_MAX_VERSION and get_config().legacy_fill_schema_defaults:
schema.fill_defaults(tree, self, reading=True)
if get_config().validate_on_read:
try:
self._validate(tree, reading=True)
except ValidationError:
self.close()
raise
tree = yamlutil.tagged_tree_to_custom_tree(tree, self, _force_raw_types)
if not (ignore_missing_extensions or _force_raw_types):
self._check_extensions(tree, strict=strict_extension_check)
self._tree = tree
return self
@classmethod
def _open_impl(
cls,
self,
fd,
uri=None,
mode="r",
validate_checksums=False,
extensions=None,
_get_yaml_content=False,
_force_raw_types=False,
strict_extension_check=False,
ignore_missing_extensions=False,
):
"""Attempt to open file-like object as an AsdfFile"""
close_on_fail = isinstance(fd, (str, pathlib.Path))
generic_file = generic_io.get_file(fd, mode=mode, uri=uri)
try:
return cls._open_asdf(
self,
generic_file,
validate_checksums=validate_checksums,
extensions=extensions,
_get_yaml_content=_get_yaml_content,
_force_raw_types=_force_raw_types,
strict_extension_check=strict_extension_check,
ignore_missing_extensions=ignore_missing_extensions,
)
except Exception:
if close_on_fail:
generic_file.close()
raise
def _write_tree(self, tree, fd, pad_blocks):
fd.write(constants.ASDF_MAGIC)
fd.write(b" ")
fd.write(f"{self.file_format_version}".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):
serialization_context = self._create_serialization_context(_serialization_context.BlockAccess.WRITE)
for compression in self._blocks.get_output_compressions():
# lookup extension
compressor = mcompression._get_compressor_from_extensions(compression, return_extension=True)
if compressor is not None:
# mark it as used
serialization_context._mark_extension_used(compressor[1])
def _tree_finalizer(tagged_tree):
"""
The list of extensions used is not known until after
serialization, so we're using a hook provided by
yamlutil.dump_tree to update extension metadata
after the tree has been converted to tagged objects.
"""
self._update_extension_history(tree, serialization_context)
if "history" in tree:
tagged_tree["history"] = yamlutil.custom_tree_to_tagged_tree(
tree["history"],
self,
_serialization_context=serialization_context,
)
else:
tagged_tree.pop("history", None)
yamlutil.dump_tree(
tree,
fd,
self,
tree_finalizer=_tree_finalizer,
_serialization_context=serialization_context,
)
if pad_blocks:
padding = util.calculate_padding(fd.tell(), pad_blocks, fd.block_size)
fd.fast_forward(padding)
def _pre_write(self, fd):
pass
def _post_write(self, fd):
pass
def _serial_write(self, fd, pad_blocks, include_block_index):
with self._blocks.write_context(fd):
self._pre_write(fd)
try:
# prep a tree for a writing
tree = copy.copy(self._tree)
tree["asdf_library"] = _get_asdf_library_info()
if "history" in self._tree:
tree["history"] = copy.deepcopy(self._tree["history"])
self._write_tree(tree, fd, pad_blocks)
self._blocks.write(pad_blocks, include_block_index)
finally:
self._post_write(fd)
[docs]
def update(
self,
all_array_storage=NotSet,
all_array_compression=NotSet,
compression_kwargs=NotSet,
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:
- ``''`` or `None`: No compression.
- ``zlib``: Use zlib compression.
- ``bzp2``: Use bzip2 compression.
- ``lz4``: Use lz4 compression.
- ``input``: Use the same compression as in the file read.
If there is no prior file, acts as None
compression_kwargs : dict, optional
If provided, set this as the compression keyword arguments
for all binary blocks in the file.
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
Update the ASDF Standard version of this AsdfFile before
writing.
"""
with config_context() as config:
if all_array_storage is not NotSet:
config.all_array_storage = all_array_storage
if all_array_compression is not NotSet:
config.all_array_compression = all_array_compression
if compression_kwargs is not NotSet:
config.all_array_compression_kwargs = compression_kwargs
fd = self._fd
if fd is None:
msg = "Can not update, since there is no associated file"
raise ValueError(msg)
if not fd.writable():
msg = (
"Can not update, since associated file is read-only. Make "
"sure that the AsdfFile was opened with mode='rw' and the "
"underlying file handle is writable."
)
raise OSError(msg)
if not fd.seekable():
msg = "Can not update, since associated file is not seekable"
raise OSError(msg)
if version is not None:
self.version = version
# flush all pending memmap writes
if fd.can_memmap():
fd.flush_memmap()
def rewrite():
self._fd.seek(0)
self._serial_write(self._fd, pad_blocks, include_block_index)
self._fd.truncate()
if self._fd.can_memmap():
self._fd.close_memmap()
# if we have no read blocks, we can just call write_to as no internal blocks are reused
if len(self._blocks.blocks) == 0:
rewrite()
return
# if we have all external blocks, we can just call write_to as no internal blocks are reused
if config.all_array_storage == "external":
rewrite()
return
self._pre_write(fd)
try:
self._tree["asdf_library"] = _get_asdf_library_info()
# prepare block manager for writing
with self._blocks.write_context(self._fd, copy_options=False):
# write out tree to temporary buffer
tree_fd = generic_io.get_file(io.BytesIO(), mode="rw")
self._write_tree(self._tree, tree_fd, False)
new_tree_size = tree_fd.tell()
# update blocks
self._blocks.update(new_tree_size, pad_blocks, include_block_index)
end_of_file = self._fd.tell()
# now write the tree
self._fd.seek(0)
tree_fd.seek(0)
self._fd.write(tree_fd.read())
self._fd.flush()
# close memmap to trigger arrays to reload themselves
self._fd.seek(end_of_file)
self._fd.truncate()
if self._fd.can_memmap():
self._fd.close_memmap()
finally:
self._post_write(fd)
[docs]
def write_to(
self,
fd,
all_array_storage=NotSet,
all_array_compression=NotSet,
compression_kwargs=NotSet,
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 `asdf.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, it is the
caller's responsibility to close the object.
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:
- ``''`` or `None`: No compression.
- ``zlib``: Use zlib compression.
- ``bzp2``: Use bzip2 compression.
- ``lz4``: Use lz4 compression.
- ``input``: Use the same compression as in the file read.
If there is no prior file, acts as None.
compression_kwargs : dict, optional
If provided, set this as the compression keyword arguments
for all binary blocks in the file.
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
Update the ASDF Standard version of this AsdfFile before
writing.
"""
with config_context() as config:
if all_array_storage is not NotSet:
config.all_array_storage = all_array_storage
if all_array_compression is not NotSet:
config.all_array_compression = all_array_compression
if compression_kwargs is not NotSet:
config.all_array_compression_kwargs = compression_kwargs
if version is not None:
previous_version = self.version
self.version = version
try:
with generic_io.get_file(fd, mode="w") as fd:
self._serial_write(fd, pad_blocks, include_block_index)
finally:
if version is not None:
self.version = previous_version
[docs]
def find_references(self, _warning_msg=False):
"""
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, _warning_msg=_warning_msg)
[docs]
def resolve_references(self, **kwargs):
"""
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.
"""
if len(kwargs):
warnings.warn("Passing kwargs to resolve_references is deprecated and does nothing", AsdfDeprecationWarning)
self._tree = reference.resolve_references(self._tree, self)
try:
self.validate()
except ValidationError:
warnings.warn(
"Validation during resolve_references is deprecated. "
"Please use AsdfFile.validate after resolve_references to validate the resolved tree",
AsdfDeprecationWarning,
)
raise
[docs]
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.
"""
warnings.warn(
"resolve_and_inline is deprecated. "
"Use AsdfFile.resolve_references and all_array_storage=inline "
"during AsdfFile.write_to",
AsdfDeprecationWarning,
)
self.resolve_references()
for b in self._blocks.blocks:
self.set_array_storage(b.data, "inline")
[docs]
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)
[docs]
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)
[docs]
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)
time_ = datetime.datetime.fromtimestamp(
int(os.environ.get("SOURCE_DATE_EPOCH", time.time())), datetime.timezone.utc
)
entry = HistoryEntry(
{
"description": description,
"time": time_,
},
)
if software is not None:
entry["software"] = software
if self.version >= versioning.NEW_HISTORY_FORMAT_MIN_VERSION:
if "history" not in self.tree:
self.tree["history"] = {"entries": []}
elif "entries" not in self.tree["history"]:
self.tree["history"]["entries"] = []
self.tree["history"]["entries"].append(entry)
try:
self.validate()
except Exception:
self.tree["history"]["entries"].pop()
raise
else:
if "history" not in self.tree:
self.tree["history"] = []
self.tree["history"].append(entry)
try:
self.validate()
except Exception:
self.tree["history"].pop()
raise
[docs]
def get_history_entries(self):
"""
Get a list of history entries from the file object.
Returns
-------
entries : list
A list of history entries.
"""
if "history" not in self.tree:
return []
if isinstance(self.tree["history"], list):
return self.tree["history"]
if "entries" in self.tree["history"]:
return self.tree["history"]["entries"]
return []
[docs]
def schema_info(self, key="description", path=None, preserve_list=True, refresh_extension_manager=False):
"""
Get a nested dictionary of the schema information for a given key, relative to the path.
Parameters
----------
key : str
The key to look up.
Default: "description"
path : str or asdf.search.AsdfSearchResult
A dot-separated path to the parameter to find the key information on or
an `asdf.search.AsdfSearchResult` object.
Default = None (full dictionary).
preserve_list : bool
If True, then lists are preserved. Otherwise, they are turned into dicts.
refresh_extension_manager : bool
If `True`, refresh the extension manager before looking up the
key. This is useful if you want to make sure that the schema
data for a given key is up to date.
"""
if isinstance(path, AsdfSearchResult):
return path.schema_info(
key,
preserve_list=preserve_list,
refresh_extension_manager=refresh_extension_manager,
)
return node_info.collect_schema_info(
key,
path,
self.tree,
preserve_list=preserve_list,
refresh_extension_manager=refresh_extension_manager,
)
[docs]
def info(
self,
max_rows=display.DEFAULT_MAX_ROWS,
max_cols=display.DEFAULT_MAX_COLS,
show_values=display.DEFAULT_SHOW_VALUES,
refresh_extension_manager=False,
):
"""
Print a rendering of this file's tree to stdout.
Parameters
----------
max_rows : int, tuple, or None, optional
Maximum number of lines to print. Nodes that cannot be
displayed will be elided with a message.
If int, constrain total number of displayed lines.
If tuple, constrain lines per node at the depth corresponding \
to the tuple index.
If None, display all lines.
max_cols : int or None, optional
Maximum length of line to print. Nodes that cannot
be fully displayed will be truncated with a message.
If int, constrain length of displayed lines.
If None, line length is unconstrained.
show_values : bool, optional
Set to False to disable display of primitive values in
the rendered tree.
"""
lines = display.render_tree(
self.tree,
max_rows=max_rows,
max_cols=max_cols,
show_values=show_values,
identifier="root",
refresh_extension_manager=refresh_extension_manager,
)
print("\n".join(lines))
[docs]
def search(self, key=NotSet, type_=NotSet, value=NotSet, filter_=None):
"""
Search this file's tree.
Parameters
----------
key : NotSet, str, or any other object
Search query that selects nodes by dict key or list index.
If NotSet, the node key is unconstrained.
If str, the input is searched among keys/indexes as a regular
expression pattern.
If any other object, node's key or index must equal the queried key.
type_ : NotSet, str, or builtins.type
Search query that selects nodes by type.
If NotSet, the node type is unconstrained.
If str, the input is searched among (fully qualified) node type
names as a regular expression pattern.
If builtins.type, the node must be an instance of the input.
value : NotSet, str, or any other object
Search query that selects nodes by value.
If NotSet, the node value is unconstrained.
If str, the input is searched among values as a regular
expression pattern.
If any other object, node's value must equal the queried value.
filter_ : callable
Callable that filters nodes by arbitrary criteria.
The callable accepts one or two arguments:
- the node
- the node's list index or dict key (optional)
and returns True to retain the node, or False to remove it from
the search results.
Returns
-------
asdf.search.AsdfSearchResult
the result of the search
"""
result = AsdfSearchResult(["root"], self.tree)
return result.search(key=key, type_=type_, value=value, filter_=filter_)
# This function is called from within TypeIndex when deserializing
# the tree for this file. It is kept here so that we can keep
# state on the AsdfFile and prevent a flood of warnings for the
# same tag.
def _warn_tag_mismatch(self, tag, best_tag):
if not self._ignore_version_mismatch and (tag, best_tag) not in self._warned_tag_pairs:
message = (
f"No explicit ExtensionType support provided for tag '{tag}'. "
f"The ExtensionType subclass for tag '{best_tag}' will be used instead. "
"This fallback behavior will be removed in asdf 3.0."
)
warnings.warn(message, AsdfConversionWarning)
self._warned_tag_pairs.add((tag, best_tag))
# This function is called from within yamlutil methods to create
# a context when one isn't explicitly passed in.
def _create_serialization_context(self, operation=_serialization_context.BlockAccess.NONE):
return _serialization_context.create(self, operation)
def open_asdf(
fd,
uri=None,
mode=None,
validate_checksums=False,
extensions=None,
ignore_version_mismatch=True,
ignore_unrecognized_tag=False,
_force_raw_types=False,
copy_arrays=False,
memmap=NotSet,
lazy_load=True,
custom_schema=None,
strict_extension_check=False,
ignore_missing_extensions=False,
_get_yaml_content=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 : object, optional
Additional extensions to use when reading and writing the file.
May be an `asdf.extension.Extension` or a `list` of extensions.
ignore_version_mismatch : bool, optional
When `True`, do not raise warnings for mismatched schema versions.
Set to `True` by default.
ignore_unrecognized_tag : bool, optional
When `True`, do not raise warnings for unrecognized tags. Set to
`False` by default.
copy_arrays : bool, optional
When `False`, when reading files, attempt to memmap underlying data
arrays when possible.
memmap : bool, optional
When `True`, when reading files, attempt to memmap underlying data
arrays when possible. When set, this argument will override
``copy_arrays``. When not set, the ``copy_arrays`` will determine
if arrays are memory mapped or copied. ``copy_arrays`` will be
deprecated and the default will change in an upcoming asdf version
which by default will not memory map arrays.
lazy_load : bool, optional
When `True` and the underlying file handle is seekable, data
arrays will only be loaded lazily: i.e. when they are accessed
for the first time. In this case the underlying file must stay
open during the lifetime of the tree. Setting to False causes
all data arrays to be loaded up front, which means that they
can be accessed even after the underlying file is closed.
Note: even if ``lazy_load`` is `False`, ``memmap`` is still taken
into account.
custom_schema : str, optional
Path to a custom schema file that will be used for a secondary
validation pass. This can be used to ensure that particular ASDF
files follow custom conventions beyond those enforced by the
standard.
strict_extension_check : bool, optional
When `True`, if the given ASDF file contains metadata about the
extensions used to create it, and if those extensions are not
installed, opening the file will fail. When `False`, opening a file
under such conditions will cause only a warning. Defaults to
`False`.
ignore_missing_extensions : bool, optional
When `True`, do not raise warnings when a file is read that
contains metadata about extensions that are not available. Defaults
to `False`.
Returns
-------
asdffile : AsdfFile
The new AsdfFile object.
"""
if mode is not None and mode not in ["r", "rw"]:
msg = f"Unrecognized asdf mode '{mode}'. Must be either 'r' or 'rw'"
raise ValueError(msg)
if mode is None:
if isinstance(fd, io.IOBase):
mode = "rw" if fd.writable() else "r"
elif isinstance(fd, generic_io.GenericFile):
mode = fd.mode
else:
# This is the safest assumption for the default fallback
mode = "r"
instance = AsdfFile(
ignore_version_mismatch=ignore_version_mismatch,
ignore_unrecognized_tag=ignore_unrecognized_tag,
copy_arrays=copy_arrays,
memmap=memmap,
lazy_load=lazy_load,
custom_schema=custom_schema,
)
return AsdfFile._open_impl(
instance,
fd,
uri=uri,
mode=mode,
validate_checksums=validate_checksums,
extensions=extensions,
_get_yaml_content=_get_yaml_content,
_force_raw_types=_force_raw_types,
strict_extension_check=strict_extension_check,
ignore_missing_extensions=ignore_missing_extensions,
)