# Source code for asdf.asdf

    # Licensed under a 3-clause BSD style license - see LICENSE.rst
    # -*- coding: utf-8 -*-

    import io
    import os
    import time
    import re
    import copy
    import datetime
    import warnings
    import importlib
    from pkg_resources import parse_version

    import numpy as np
    from jsonschema import ValidationError

    from . import block
    from . import constants
    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 .exceptions import AsdfDeprecationWarning
    from .extension import AsdfExtensionList, default_extensions

    from .tags.core import AsdfObject, Software, HistoryEntry, ExtensionMetadata

    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 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,
                     lazy_load=True, custom_schema=None, _readonly=False):
            """
            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 use when reading and writing ASDF files.
                See `~asdf.types.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.

            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.

            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.

            """

            if custom_schema is not None:
                self._custom_schema = schema.load_custom_schema(custom_schema)
                schema.check_schema(self._custom_schema)
            else:
                self._custom_schema = None

            self._extensions = []
            self._extension_metadata = {}

            self._process_extensions(extensions)
            self._ignore_version_mismatch = ignore_version_mismatch
            self._ignore_unrecognized_tag = ignore_unrecognized_tag
            self._ignore_implicit_conversion = ignore_implicit_conversion

            self._file_format_version = None

            self._fd = None
            self._closed = False
            self._external_asdf_by_uri = {}
            self._blocks = block.BlockManager(
                self, copy_arrays=copy_arrays, lazy_load=lazy_load,
                readonly=_readonly)
            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):
            self.close()

        def _check_extensions(self, tree, strict=False):
            if 'history' not in tree or not isinstance(tree['history'], dict) or \
                    'extensions' not in tree['history']:
                return

            for extension in tree['history']['extensions']:
                filename = "'{}' ".format(self._fname) if self._fname else ''
                if extension.extension_class not in self._extension_metadata:
                    msg = "File {}was created with extension '{}', which is " \
                        "not currently installed"
                    if extension.software:
                        msg += " (from package {}-{})".format(
                            extension.software['name'],
                            extension.software['version'])
                    fmt_msg = msg.format(filename, extension.extension_class)
                    if strict:
                        raise RuntimeError(fmt_msg)
                    else:
                        warnings.warn(fmt_msg)

                elif extension.software:
                    installed = self._extension_metadata[extension.extension_class]
                    # Local extensions may not have a real version
                    if not installed[1]:
                        continue
                    # Compare version in file metadata with installed version
                    if parse_version(installed[1]) < parse_version(extension.software['version']):
                        msg = "File {}was created with extension '{}' from " \
                        "package {}-{}, but older version {}-{} is installed"
                        fmt_msg = msg.format(
                            filename, extension.extension_class,
                            extension.software['name'],
                            extension.software['version'],
                            installed[0], installed[1])
                        if strict:
                            raise RuntimeError(fmt_msg)
                        else:
                            warnings.warn(fmt_msg)

        def _process_extensions(self, extensions):
            if extensions is None or extensions == []:
                self._extensions = default_extensions.extension_list
                self._extension_metadata = default_extensions.package_metadata
                return

            if isinstance(extensions, AsdfExtensionList):
                self._extensions = extensions
                return

            if not isinstance(extensions, list):
                extensions = [extensions]

            # Process metadata about custom extensions
            for extension in extensions:
                ext_name = util.get_class_name(extension)
                self._extension_metadata[ext_name] = ('', '')

            extensions = default_extensions.extensions + extensions
            self._extensions = AsdfExtensionList(extensions)
            self._extension_metadata.update(default_extensions.package_metadata)

        def _update_extension_history(self):

            if 'history' not in self.tree:
                self.tree['history'] = dict(extensions=[])
            # Support clients who are still using the old history format
            elif isinstance(self.tree['history'], list):
                histlist = self.tree['history']
                self.tree['history'] = dict(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'].")
            elif 'extensions' not in self.tree['history']:
                self.tree['history']['extensions'] = []

            for extension in self.type_index.get_extensions_used():
                ext_name = util.get_class_name(extension)
                ext_meta = ExtensionMetadata(extension_class=ext_name)
                metadata = self._extension_metadata.get(ext_name)
                if metadata is not None:
                    ext_meta.software = dict(name=metadata[0], version=metadata[1])

                for i, entry in enumerate(self.tree['history']['extensions']):
                    # Update metadata about this extension if it already exists
                    if entry.extension_class == ext_meta.extension_class:
                        self.tree['history']['extensions'][i] = ext_meta
                        break
                else:
                    self.tree['history']['extensions'].append(ext_meta)

        @property
        def file_format_version(self):
            if self._file_format_version is None:
                return versioning.AsdfVersion(self.version_map['FILE_FORMAT'])
            else:
                return self._file_format_version

        def close(self):
            """
            Close the file handles associated with the `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
            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):
            warnings.warn(
                "The 'tag_to_schema_resolver' property is deprecated. Use "
                "'tag_mapping' instead.",
                AsdfDeprecationWarning)
            return self._extensions.tag_mapping

        @property
        def tag_mapping(self):
            return self._extensions.tag_mapping

        @property
        def url_mapping(self):
            return self._extensions.url_mapping

        @property
        def resolver(self):
            return self._extensions.resolver

        @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 = open_asdf(
                    resolved_uri,
                    mode='r', 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.
            """
            if self._closed:
                raise OSError("Cannot access data from closed ASDF file")
            return self._tree

        @tree.setter
        def tree(self, tree):
            asdf_object = AsdfObject(tree)
            # Only perform custom validation if the tree is not empty
            self._validate(asdf_object, custom=bool(tree))
            self._tree = asdf_object

        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):
            tagged_tree = 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)

        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.

            compression : str or None
                Must be one of:

                - ``''`` or `None`: no compression

                - ``zlib``: Use zlib compression

                - ``bzp2``: Use bzip2 compression

                - ``lz4``: Use lz4 compression

                - ``''`` or `None`: no compression

                - ``input``: Use the same compression as in the file read.
                  If there is no prior file, acts as None.

            """
            self.blocks[arr].output_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].output_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 = versioning.AsdfVersion(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 = versioning.AsdfVersion(parts[1].decode('ascii'))
                    except ValueError:
                        pass
                    else:
                        return version

            return None

        @classmethod
        def _open_asdf(cls, self, fd, uri=None, mode='r',
                       validate_checksums=False,
                       do_not_fill_defaults=False,
                       _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:
                raise ValueError(
                    "'strict_extension_check' and 'ignore_missing_extensions' are "
                    "incompatible options")

            self._mode = mode

            fd = generic_io.get_file(fd, mode=self._mode, uri=uri)
            self._fd = fd
            # The filename is currently only used for tracing warning information
            self._fname = self._fd._uri if self._fd._uri else ''
            header_line = fd.read_until(b'\r?\n', 2, "newline", include=True)
            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)
            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)

                # 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, self._ignore_version_mismatch)
                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.")

            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, reading=True)

            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
            self.run_hook('post_read')

            return self

        @classmethod
        def _open_impl(cls, self, fd, uri=None, mode='r',
                       validate_checksums=False,
                       do_not_fill_defaults=False,
                       _get_yaml_content=False,
                       _force_raw_types=False,
                       strict_extension_check=False,
                       ignore_missing_extensions=False):
            """Attempt to open file-like object as either AsdfFile or AsdfInFits"""
            if not is_asdf_file(fd):
                try:
                    # TODO: this feels a bit circular, try to clean up. Also
                    # this introduces another dependency on astropy which may
                    # not be desireable.
                    from . import fits_embed
                    return fits_embed.AsdfInFits._open_impl(fd, uri=uri,
                                validate_checksums=validate_checksums,
                                ignore_version_mismatch=self._ignore_version_mismatch,
                                extensions=self._extensions,
                                strict_extension_check=strict_extension_check,
                                ignore_missing_extensions=ignore_missing_extensions,
                                ignore_unrecognized_tag=self._ignore_unrecognized_tag,
                                _extension_metadata=self._extension_metadata)
                except ValueError:
                    raise ValueError(
                        "Input object does not appear to be an ASDF file or a FITS with " +
                        "ASDF extension") from None
                except ImportError:
                    raise ValueError(
                        "Input object does not appear to be an ASDF file. Cannot check " +
                        "if it is a FITS with ASDF extension because 'astropy' is not " +
                        "installed") from None
            return cls._open_asdf(self, fd, uri=uri, mode=mode,
                    validate_checksums=validate_checksums,
                    do_not_fill_defaults=do_not_fill_defaults,
                    _get_yaml_content=_get_yaml_content,
                    _force_raw_types=_force_raw_types,
                    strict_extension_check=strict_extension_check,
                    ignore_missing_extensions=ignore_missing_extensions)

        @classmethod
        def open(cls, fd, uri=None, mode='r',
                 validate_checksums=False,
                 extensions=None,
                 do_not_fill_defaults=False,
                 ignore_version_mismatch=True,
                 ignore_unrecognized_tag=False,
                 _force_raw_types=False,
                 copy_arrays=False,
                 lazy_load=True,
                 custom_schema=None,
                 strict_extension_check=False,
                 ignore_missing_extensions=False):
            """
            Open an existing ASDF file.

            .. deprecated:: 2.2
                Use `asdf.open` instead.
            """

            warnings.warn(
                "The method AsdfFile.open has been deprecated and will be removed "
                "in asdf-3.0. Use the top-level asdf.open function instead.",
                AsdfDeprecationWarning)

            return open_asdf(
                fd, uri=uri, mode=mode,
                validate_checksums=validate_checksums,
                extensions=extensions,
                do_not_fill_defaults=do_not_fill_defaults,
                ignore_version_mismatch=ignore_version_mismatch,
                ignore_unrecognized_tag=ignore_unrecognized_tag,
                _force_raw_types=_force_raw_types,
                copy_arrays=copy_arrays, lazy_load=lazy_load,
                custom_schema=custom_schema,
                strict_extension_check=strict_extension_check,
                ignore_missing_extensions=ignore_missing_extensions,
                _compat=True)

        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()
            self._update_extension_history()

        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')

            # TODO: there has got to be a better way to do this...
            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='input',
                   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:

                - ``''`` 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

            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. Make "
                    "sure that the AsdfFile was opened with mode='rw' and the "
                    "underlying file handle is writable.")

            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='input',
                     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:

                - ``''`` 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.

            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.
            """

            if version is not None:
                self.version = version

            with generic_io.get_file(fd, mode='w') as fd:
                # TODO: This is not ideal: we really should pass the URI through
                # explicitly to wherever it is required instead of making it an
                # attribute of the AsdfFile.
                if self._uri is None:
                    self._uri = fd.uri
                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)

        def find_references(self):
            """
            Finds all external "JSON References" in the tree and converts
            them to `reference.Reference` objects.
            """
            # Since this is the first place that the tree is processed when
            # creating a new ASDF object, this is where we pass the option to
            # ignore warnings about implicit type conversions.
            # Set directly to self._tree, since it doesn't need to be re-validated.
            self._tree = reference.find_references(self._tree, self,
                    ignore_implicit_conversion=self._ignore_implicit_conversion)

        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)

            time_ = datetime.datetime.utcfromtimestamp(
                int(os.environ.get('SOURCE_DATE_EPOCH', time.time())),
            )

            entry = HistoryEntry({
                'description': description,
                'time': time_,
            })

            if software is not None:
                entry['software'] = software

            if 'history' not in self.tree:
                self.tree['history'] = dict(entries=[])

            self.tree['history']['entries'].append(entry)

            try:
                self.validate()
            except Exception:
                self.tree['history']['entries'].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 []

    # Inherit docstring from dictionary
    AsdfFile.keys.__doc__ = dict.keys.__doc__

    def _check_and_set_mode(fileobj, asdf_mode):

        if asdf_mode is not None and asdf_mode not in ['r', 'rw']:
            msg = "Unrecognized asdf mode '{}'. Must be either 'r' or 'rw'"
            raise ValueError(msg.format(asdf_mode))

        if asdf_mode is None:
            if isinstance(fileobj, io.IOBase):
                return 'rw' if fileobj.writable() else 'r'

            if isinstance(fileobj, generic_io.GenericFile):
                return fileobj.mode

            # This is the safest assumption for the default fallback
            return 'r'

        return asdf_mode

    def open_asdf(fd, uri=None, mode=None, validate_checksums=False,
                  extensions=None, do_not_fill_defaults=False,
                  ignore_version_mismatch=True, ignore_unrecognized_tag=False,
                  _force_raw_types=False, copy_arrays=False, lazy_load=True,
                  custom_schema=None, strict_extension_check=False,
                  ignore_missing_extensions=False, _compat=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 use when reading and writing ASDF files.
            See `~asdf.types.AsdfExtension` for more information.

        do_not_fill_defaults : bool, optional
            When `True`, do not fill in missing default values.

        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.

        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.

        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.
        """

        readonly = False

        # For now retain backwards compatibility with the old API behavior,
        # specifically when being called from AsdfFile.open
        if not _compat:
            mode = _check_and_set_mode(fd, mode)
            readonly = (mode == 'r' and not copy_arrays)

        instance = AsdfFile(extensions=extensions,
                       ignore_version_mismatch=ignore_version_mismatch,
                       ignore_unrecognized_tag=ignore_unrecognized_tag,
                       copy_arrays=copy_arrays, lazy_load=lazy_load,
                       custom_schema=custom_schema, _readonly=readonly)

        return AsdfFile._open_impl(instance,
            fd, uri=uri, mode=mode,
            validate_checksums=validate_checksums,
            do_not_fill_defaults=do_not_fill_defaults,
            _force_raw_types=_force_raw_types,
            strict_extension_check=strict_extension_check,
            ignore_missing_extensions=ignore_missing_extensions)

    def is_asdf_file(fd):
        """
        Determine if fd is an ASDF file.

        Reads the first five bytes and looks for the ``#ASDF`` string.

        Parameters
        ----------
        fd : str, `~asdf.generic_io.GenericFile`

        """
        if isinstance(fd, generic_io.InputStream):
            # If it's an InputStream let ASDF deal with it.
            return True

        to_close = False
        if isinstance(fd, AsdfFile):
            return True
        elif isinstance(fd, generic_io.GenericFile):
            pass
        else:
            try:
                fd = generic_io.get_file(fd, mode='r', uri=None)
                if not isinstance(fd, io.IOBase):
                    to_close = True
            except ValueError:
                return False
        asdf_magic = fd.read(5)
        if fd.seekable():
            fd.seek(0)
        if to_close:
            fd.close()
        if asdf_magic == constants.ASDF_MAGIC:
            return True
        return False