import copy import datetime import io import os import pathlib import time import warnings import weakref 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, lazy_nodes, 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 ( AsdfManifestURIMismatchWarning, AsdfPackageVersionWarning, 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 _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", }, ) class AsdfFile: """ The main class that represents an ASDF file object. """ def __init__( self, tree=None, uri=None, extensions=None, version=None, ignore_unrecognized_tag=False, memmap=False, 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_unrecognized_tag : bool, optional When `True`, do not raise warnings for unrecognized tags. Set to `False` by default. memmap : bool, optional When `True`, when reading files, attempt to memmap underlying data arrays when possible. Defaults to ``False``. 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. 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_unrecognized_tag = ignore_unrecognized_tag # 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() # A cache of tagged objects and their converted custom objects used when # a file is read with "lazy_tree=True". Used by lazy_nodes. self._tagged_object_cache = lazy_nodes._TaggedObjectCache() self._fd = None self._closed = False self._external_asdf_by_uri = {} self._blocks = BlockManager(uri=uri, lazy_load=lazy_load, memmap=memmap) 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. # Call "walk_and_modify" here to use it's logic for # creating a "copy" of the other tree. This mimics what was previously # a call to find_references (which we longer do in AsdfFile.__init__) self._tree = treeutil.walk_and_modify(tree.tree, lambda o: o) else: self._tree = AsdfObject(tree) 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 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, AsdfPackageVersionWarning) 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, AsdfPackageVersionWarning) # check version of manifest providing package (if one was recorded) if "manifest_software" in extension: package_name = extension["manifest_software"]["name"] package_version = Version(extension["manifest_software"]["version"]) package_description = f"{package_name}=={package_version}" installed_version = None for mapping in get_config().resource_manager._resource_mappings: if mapping.package_name == package_name: installed_version = Version(mapping.package_version) break msg = None if installed_version is None: msg = ( f"File {filename}was created with package {package_description}, " "which is currently not installed" ) elif installed_version < package_version: msg = ( f"File {filename}was created with package {package_description}, " f"but older package({package_name}=={installed_version}) is installed." ) if msg: if strict: raise RuntimeError(msg) warnings.warn(msg, AsdfPackageVersionWarning) 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] manifest = getattr(extension._delegate, "_manifest", None) if manifest is not None: # check if this extension was built from a manifest is a different package resource_mapping = get_config().resource_manager._mappings_by_uri.get(manifest["id"]) # if an extension was registered with a manifest uri that does not match the id the # resource_mapping lookup will fail (resource_mapping will be None) if resource_mapping is None: warnings.warn( f"Extension ({extension.extension_uri}) uses a manifest with a uri that " "does not match it's id. Please open an issue with the extension maintainer", AsdfManifestURIMismatchWarning, ) elif resource_mapping.package_name != extension.package_name: ext_meta["manifest_software"] = Software( name=resource_mapping.package_name, version=resource_mapping.package_version, ) 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 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() self._tagged_object_cache.clear() 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._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 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, **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): self._tree = AsdfObject(tree) 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, 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) def validate(self): """ Validate the current state of the tree against the ASDF schema. """ self._validate(self._tree) 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) 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) 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) 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) 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) def get_array_compression_kwargs(self, arr): """ """ return self._blocks._get_array_compression_kwargs(arr) def set_array_save_base(self, arr, save_base): """ Set the ``save_base`` option for ``arr``. When ``arr`` is written to a file, if ``save_base`` is ``True`` the base array for ``arr`` will be saved. Note that similar to other array options this setting is linked to the base array if ``arr`` is a view. Parameters ---------- arr : numpy.ndarray save_base : bool or None if ``None`` the ``default_array_save_base`` value from asdf config will be used """ self._blocks._set_array_save_base(arr, save_base) def get_array_save_base(self, arr): """ Returns the ``save_base`` option for ``arr``. When ``arr`` is written to a file, if ``save_base`` is ``True`` the base array for ``arr`` will be saved. Parameters ---------- arr : numpy.ndarray Returns ------- save_base : bool or None """ return self._blocks._get_array_save_base(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, lazy_tree=NotSet, _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() as cfg: # 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) 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 if lazy_tree is NotSet: lazy_tree = cfg.lazy_tree if lazy_tree and not _force_raw_types: obj = AsdfObject() obj.data = lazy_nodes.AsdfDictNode(tree, weakref.ref(self)) tree = obj else: 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, lazy_tree=NotSet, _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, lazy_tree=lazy_tree, _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) 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) 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 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): """ 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. """ self._tree = reference.resolve_references(self._tree, self) 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) 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 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 [] def schema_info(self, key="description", path=None, preserve_list=True, refresh_extension_manager=NotSet): """ Get a nested dictionary of the schema information for a given key, relative to the path. This method will only return unambiguous info. If a property is subject to multiple subschemas or contains ambiguous entries (multiple titles) no result will be returned for that property. 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 refresh_extension_manager is not NotSet: warnings.warn("refresh_extension_manager is deprecated", DeprecationWarning) 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, extension_manager=self.extension_manager, ) def info( self, max_rows=display.DEFAULT_MAX_ROWS, max_cols=display.DEFAULT_MAX_COLS, show_values=display.DEFAULT_SHOW_VALUES, refresh_extension_manager=NotSet, ): """ 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. """ if refresh_extension_manager is not NotSet: warnings.warn("refresh_extension_manager is deprecated", DeprecationWarning) 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, extension_manager=self.extension_manager, ) print("\n".join(lines)) 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 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_unrecognized_tag=False, _force_raw_types=False, memmap=False, lazy_tree=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_unrecognized_tag : bool, optional When `True`, do not raise warnings for unrecognized tags. Set to `False` by default. memmap : bool, optional When `True`, when reading files, attempt to memmap underlying data arrays when possible. Defaults to ``False``. 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. lazy_tree : bool, optional When `True` the ASDF tree will not be converted to custom objects when the file is loaded. Instead, objects will be "lazily" converted only when they are accessed. Note that the tree will not contain dict and list instances for containers and instead return instances of classes defined in `asdf.lazy_nodes`. Since objects are converted when they are accessed, traversing the tree (like is done during `AsdfFile.info` and `AsdfFile.search`) will result in nodes being converted. 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_unrecognized_tag=ignore_unrecognized_tag, 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, lazy_tree=lazy_tree, _get_yaml_content=_get_yaml_content, _force_raw_types=_force_raw_types, strict_extension_check=strict_extension_check, ignore_missing_extensions=ignore_missing_extensions, )