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 copy
import datetime
import warnings
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 . import _display as display
from .exceptions import AsdfDeprecationWarning, AsdfWarning, AsdfConversionWarning
from .extension import AsdfExtensionList, default_extensions
from .util import NotSet
from .search import AsdfSearchResult

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'
    })


[docs]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. """ self._extensions = [] self._extension_metadata = {} self._process_extensions(extensions) if custom_schema is not None: self._custom_schema = schema._load_schema_cached(custom_schema, self.resolver, True, False) else: self._custom_schema = None self._ignore_version_mismatch = ignore_version_mismatch self._ignore_unrecognized_tag = ignore_unrecognized_tag self._ignore_implicit_conversion = ignore_implicit_conversion # Set of (string, string) tuples representing tag version mismatches # that we've already warned about for this file. self._warned_tag_pairs = set() self._file_format_version = None # Context of a call to treeutil.walk_and_modify, needed in the AsdfFile # in case walk_and_modify is re-entered by extension code (via # custom_tree_to_tagged_tree or tagged_tree_to_custom_tree). self._tree_modification_context = treeutil._TreeModificationContext() self._fd = None self._closed = False self._external_asdf_by_uri = {} self._blocks = block.BlockManager( self, copy_arrays=copy_arrays, lazy_load=lazy_load, readonly=_readonly) self._uri = None 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: 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, AsdfWarning) 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, AsdfWarning) 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 self.version < versioning.NEW_HISTORY_FORMAT_MIN_VERSION: return 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'].", AsdfWarning) 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'] = Software(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
[docs] 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()
[docs] 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
[docs] def resolve_uri(self, uri): """ Resolve a (possibly relative) URI against the URI of this ASDF file. May be overridden by base classes to change how URIs are resolved. This does not apply any `uri_mapping` that was passed to the constructor. Parameters ---------- uri : str An absolute or relative URI to resolve against the URI of this ASDF file. Returns ------- uri : str The resolved URI. """ return generic_io.resolve_uri(self.uri, uri)
[docs] def open_external(self, uri, 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
[docs] def keys(self): return self.tree.keys()
def __getitem__(self, key): return self.tree[key] def __setitem__(self, key, value): self.tree[key] = value def __contains__(self, item): return item in self.tree @property def comments(self): """ Get the comments after the header, before the tree. """ return self._comments def _validate(self, tree, custom=True, reading=False): if reading: # If we're validating on read then the tree # is already guaranteed to be in tagged form. tagged_tree = tree else: 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)
[docs] def validate(self): """ Validate the current state of the tree against the ASDF schema. """ self._validate(self._tree)
[docs] def make_reference(self, path=[]): """ 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
[docs] def set_array_storage(self, arr, array_storage): """ Set the block type to use for the given array data. Parameters ---------- arr : numpy.ndarray The array to set. If multiple views of the array are in the tree, only the most recent block type setting will be used, since all views share a single block. array_storage : str Must be one of: - ``internal``: The default. The array data will be stored in a binary block in the same ASDF file. - ``external``: Store the data in a binary block in a separate ASDF file. - ``inline``: Store the data as YAML inline in the tree. """ block = self.blocks[arr] self.blocks.set_array_storage(block, array_storage)
[docs] def get_array_storage(self, arr): """ Get the block type for the given array data. Parameters ---------- arr : numpy.ndarray """ return self.blocks[arr].array_storage
[docs] 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
[docs] def get_array_compression(self, arr): """ Get the compression type for the given array data. Parameters ---------- arr : numpy.ndarray Returns ------- compression : str or None """ return self.blocks[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, validate_on_read=True): """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) has_blocks = False 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) 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 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 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) if validate_on_read: try: self._validate(tree, reading=True) except ValidationError: self.close() raise tree = yamlutil.tagged_tree_to_custom_tree(tree, self, _force_raw_types) if not (ignore_missing_extensions or _force_raw_types): self._check_extensions(tree, strict=strict_extension_check) self._tree = tree 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, validate_on_read=True): """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, validate_on_read=validate_on_read) 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, validate_on_read=validate_on_read)
[docs] @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
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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, ignore_implicit_conversion=self._ignore_implicit_conversion) if validate: self._validate(tree) self._tree = tree return self._tree
[docs] def resolve_and_inline(self): """ Resolves all external references and inlines all data. This produces something that, when saved, is a 100% valid YAML file. """ self.blocks.finish_reading_internal_blocks() self.resolve_references() for b in list(self.blocks.blocks): self.blocks.set_array_storage(b, 'inline')
[docs] def fill_defaults(self): """ Fill in any values that are missing in the tree using default values from the schema. """ tree = yamlutil.custom_tree_to_tagged_tree(self._tree, self) schema.fill_defaults(tree, self) self._tree = yamlutil.tagged_tree_to_custom_tree(tree, self)
[docs] def remove_defaults(self): """ Remove any values in the tree that are the same as the default values in the schema """ tree = yamlutil.custom_tree_to_tagged_tree(self._tree, self) schema.remove_defaults(tree, self) self._tree = yamlutil.tagged_tree_to_custom_tree(tree, self)
[docs] def add_history_entry(self, description, software=None): """ Add an entry to the history list. Parameters ---------- description : str A description of the change. software : dict or list of dict A description of the software used. It should not include asdf itself, as that is automatically notated in the `asdf_library` entry. Each dict must have the following keys: - ``name``: The name of the software - ``author``: The author or institution that produced the software - ``homepage``: A URI to the homepage of the software - ``version``: The version of the software """ if isinstance(software, list): software = [Software(x) for x in software] elif software is not None: software = Software(software) time_ = datetime.datetime.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 self.version >= versioning.NEW_HISTORY_FORMAT_MIN_VERSION: if 'history' not in self.tree: self.tree['history'] = dict(entries=[]) elif 'entries' not in self.tree['history']: self.tree['history']['entries'] = [] self.tree['history']['entries'].append(entry) try: self.validate() except Exception: self.tree['history']['entries'].pop() raise else: if 'history' not in self.tree: self.tree['history'] = [] self.tree['history'].append(entry) try: self.validate() except Exception: self.tree['history'].pop() raise
[docs] def get_history_entries(self): """ Get a list of history entries from the file object. Returns ------- entries : list A list of history entries. """ if 'history' not in self.tree: return [] if isinstance(self.tree['history'], list): return self.tree['history'] if 'entries' in self.tree['history']: return self.tree['history']['entries'] return []
[docs] def info(self, max_rows=display.DEFAULT_MAX_ROWS, max_cols=display.DEFAULT_MAX_COLS, show_values=display.DEFAULT_SHOW_VALUES): """ Print a rendering of this file's tree to stdout. Parameters ---------- max_rows : int, tuple, or None, optional Maximum number of lines to print. Nodes that cannot be displayed will be elided with a message. If int, constrain total number of displayed lines. If tuple, constrain lines per node at the depth corresponding \ to the tuple index. If None, display all lines. max_cols : int or None, optional Maximum length of line to print. Nodes that cannot be fully displayed will be truncated with a message. If int, constrain length of displayed lines. If None, line length is unconstrained. show_values : bool, optional Set to False to disable display of primitive values in the rendered tree. """ lines = display.render_tree(self.tree, max_rows=max_rows, max_cols=max_cols, show_values=show_values, identifier="root.tree") print("\n".join(lines))
[docs] def search(self, key=NotSet, type=NotSet, value=NotSet, filter=None): """ Search this file's tree. Parameters ---------- key : NotSet, str, or any other object Search query that selects nodes by dict key or list index. If NotSet, the node key is unconstrained. If str, the input is searched among keys/indexes as a regular expression pattern. If any other object, node's key or index must equal the queried key. type : NotSet, str, or builtins.type Search query that selects nodes by type. If NotSet, the node type is unconstrained. If str, the input is searched among (fully qualified) node type names as a regular expression pattern. If builtins.type, the node must be an instance of the input. value : NotSet, str, or any other object Search query that selects nodes by value. If NotSet, the node value is unconstrained. If str, the input is searched among values as a regular expression pattern. If any other object, node's value must equal the queried value. filter : callable Callable that filters nodes by arbitrary criteria. The callable accepts one or two arguments: - the node - the node's list index or dict key (optional) and returns True to retain the node, or False to remove it from the search results. Returns ------- asdf.search.AsdfSearchResult the result of the search """ result = AsdfSearchResult(["root.tree"], self.tree) return result.search(key=key, type=type, value=value, filter=filter)
# This function is called from within TypeIndex when deserializing # the tree for this file. It is kept here so that we can keep # state on the AsdfFile and prevent a flood of warnings for the # same tag. def _warn_tag_mismatch(self, tag, best_tag): if not self._ignore_version_mismatch and (tag, best_tag) not in self._warned_tag_pairs: message = ( "No explicit ExtensionType support provided for tag '{}'. " "The ExtensionType subclass for tag '{}' will be used instead. " "This fallback behavior will be removed in asdf 3.0." ).format(tag, best_tag) warnings.warn(message, AsdfConversionWarning) self._warned_tag_pairs.add((tag, best_tag))
# 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, validate_on_read=True, _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`. validate_on_read : bool, optional When `True`, validate the newly opened file against tag and custom schemas. Recommended unless the file is already known to be valid. 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, validate_on_read=validate_on_read) 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