import enum
import importlib.util
import inspect
import math
import re
import struct
import sys
from functools import lru_cache
import numpy as np
import yaml
from . import constants
# The standard library importlib.metadata returns duplicate entrypoints
# for all python versions up to and including 3.11
# https://github.com/python/importlib_metadata/issues/410#issuecomment-1304258228
# see PR https://github.com/asdf-format/asdf/pull/1260
# see issue https://github.com/asdf-format/asdf/issues/1254
if sys.version_info >= (3, 12):
pass
else:
pass
# We're importing our own copy of urllib.parse because
# we need to patch it to support asdf:// URIs, but it'd
# be irresponsible to do this for all users of a
# standard library.
urllib_parse_spec = importlib.util.find_spec("urllib.parse")
_patched_urllib_parse = importlib.util.module_from_spec(urllib_parse_spec)
urllib_parse_spec.loader.exec_module(_patched_urllib_parse)
del urllib_parse_spec
# urllib.parse needs to know that it should treat asdf://
# URIs like http:// URIs for the purposes of joining
# a relative path to a base URI.
_patched_urllib_parse.uses_relative.append("asdf")
_patched_urllib_parse.uses_netloc.append("asdf")
__all__ = [
"load_yaml",
"get_array_base",
"get_base_uri",
"calculate_padding",
"NotSet",
"uri_match",
"get_class_name",
"get_file_type",
"FileType",
]
[docs]
def load_yaml(init, tagged=False):
"""
Load just the yaml portion of an ASDF file
Parameters
----------
init : filename or file-like
If file-like this must be opened in binary mode.
tagged: bool, optional
Return tree with instances of `asdf.tagged.Tagged` this
can be helpful if the yaml tags are of interest.
If False, the tree will only contain basic python types
(see the pyyaml ``BaseLoader`` documentation).
Returns
-------
tree : dict
Dictionary representing the ASDF tree
"""
from .generic_io import get_file
from .yamlutil import AsdfLoader, _IgnoreCustomTagsLoader
if tagged:
loader = AsdfLoader
else:
loader = _IgnoreCustomTagsLoader
with get_file(init, "r") as gf:
reader = gf.reader_until(
constants.YAML_END_MARKER_REGEX,
7,
"End of YAML marker",
include=True,
)
# The following call to yaml.load is safe because we're
# using only loaders that don't create custom python objects
content = yaml.load(reader, Loader=loader) # noqa: S506
return content
[docs]
def get_array_base(arr):
"""
For a given Numpy array, finds the base array that "owns" the
actual data.
"""
from .tags.core import ndarray
base = arr
while isinstance(base.base, (np.ndarray, ndarray.NDArrayType)):
base = base.base
return base
[docs]
def get_base_uri(uri):
"""
For a given URI, return the part without any fragment.
"""
parts = _patched_urllib_parse.urlparse(uri)
return _patched_urllib_parse.urlunparse([*list(parts[:5]), ""])
def _iter_subclasses(cls):
"""
Returns all subclasses of a class.
"""
for x in cls.__subclasses__():
yield x
yield from _iter_subclasses(x)
[docs]
def calculate_padding(content_size, pad_blocks, block_size):
"""
Calculates the amount of extra space to add to a block given the
user's request for the amount of extra space. Care is given so
that the total of size of the block with padding is evenly
divisible by block size.
Parameters
----------
content_size : int
The size of the actual content
pad_blocks : float or bool
If `False`, 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.
block_size : int
The filesystem block size to use.
Returns
-------
nbytes : int
The number of extra bytes to add for padding.
"""
if not pad_blocks:
return 0
if pad_blocks is True:
pad_blocks = 1.1
new_size = content_size * pad_blocks
new_size = int((math.ceil(float(new_size) / block_size) + 1) * block_size)
return max(new_size - content_size, 0)
class _BinaryStruct:
"""
A wrapper around the Python stdlib struct module to define a
binary struct more like a dictionary than a tuple.
"""
def __init__(self, descr, endian=">"):
"""
Parameters
----------
descr : list of tuple
Each entry is a pair ``(name, format)``, where ``format``
is one of the format types understood by `struct`.
endian : str, optional
The endianness of the struct. Must be ``>`` or ``<``.
"""
self._fmt = [endian]
self._offsets = {}
self._names = []
i = 0
for name, fmt in descr:
self._fmt.append(fmt)
self._offsets[name] = (i, (endian + fmt).encode("ascii"))
self._names.append(name)
i += struct.calcsize(fmt.encode("ascii"))
self._fmt = "".join(self._fmt).encode("ascii")
self._size = struct.calcsize(self._fmt)
@property
def size(self):
"""
Return the size of the struct.
"""
return self._size
def pack(self, **kwargs):
"""
Pack the given arguments, which are given as kwargs, and
return the binary struct.
"""
fields = [0] * len(self._names)
for key, val in kwargs.items():
if key not in self._offsets:
msg = f"No header field '{key}'"
raise KeyError(msg)
i = self._names.index(key)
fields[i] = val
return struct.pack(self._fmt, *fields)
def unpack(self, buff):
"""
Unpack the given binary buffer into the fields. The result
is a dictionary mapping field names to values.
"""
args = struct.unpack_from(self._fmt, buff[: self._size])
return dict(zip(self._names, args))
def update(self, fd, **kwargs):
"""
Update part of the struct in-place.
Parameters
----------
fd : generic_io.GenericIO instance
A writable, seekable file descriptor, currently seeked
to the beginning of the struct.
**kwargs : values
The values to update on the struct.
"""
updates = []
for key, val in kwargs.items():
if key not in self._offsets:
msg = f"No header field '{key}'"
raise KeyError(msg)
updates.append((self._offsets[key], val))
updates.sort()
start = fd.tell()
for (offset, datatype), val in updates:
fd.seek(start + offset)
fd.write(struct.pack(datatype, val))
class HashableDict(dict):
"""
A simple wrapper around dict to make it hashable.
This is sure to be slow, but for small dictionaries it shouldn't
matter.
"""
def __hash__(self):
return hash(frozenset(self.items()))
[docs]
def get_class_name(obj, instance=True):
"""
Given a class or instance of a class, returns a string representing the
fully specified path of the class.
Parameters
----------
obj : object
An instance of any object
instance: bool
Indicates whether given object is an instance of the class to be named
"""
typ = type(obj) if instance else obj
return f"{typ.__module__}.{typ.__qualname__}"
class _InheritDocstrings(type):
"""
This metaclass makes methods of a class automatically have their
docstrings filled in from the methods they override in the base
class.
If the class uses multiple inheritance, the docstring will be
chosen from the first class in the bases list, in the same way as
methods are normally resolved in Python. If this results in
selecting the wrong docstring, the docstring will need to be
explicitly included on the method.
For example::
>>> from asdf.util import _InheritDocstrings
>>> class A(metaclass=_InheritDocstrings):
... def wiggle(self):
... "Wiggle the thingamajig"
... pass
>>> class B(A):
... def wiggle(self):
... pass
>>> B.wiggle.__doc__
'Wiggle the thingamajig'
"""
def __init__(cls, name, bases, dct):
def is_public_member(key):
return (key.startswith("__") and key.endswith("__") and len(key) > 4) or not key.startswith("_")
for key, val in dct.items():
if inspect.isfunction(val) and is_public_member(key) and val.__doc__ is None:
for base in cls.__mro__[1:]:
super_method = getattr(base, key, None)
if super_method is not None:
val.__doc__ = super_method.__doc__
break
super().__init__(name, bases, dct)
class _NotSetType:
def __repr__(self):
return "NotSet"
"""
Special value indicating that a parameter is not set. Distinct
from None, which may for example be a value of interest in a search.
"""
NotSet = _NotSetType()
[docs]
def uri_match(pattern, uri):
"""
Determine if a URI matches a URI pattern with possible
wildcards. The two recognized wildcards:
"*": match any character except /
"**": match any character
Parameters
----------
pattern : str
URI pattern.
uri : str
URI to check against the pattern.
Returns
-------
bool
`True` if URI matches the pattern.
"""
if not isinstance(uri, str):
return False
if "*" in pattern:
return _compile_uri_match_pattern(pattern).fullmatch(uri) is not None
return pattern == uri
@lru_cache(1024)
def _compile_uri_match_pattern(pattern):
# Escape the pattern in case it contains regex special characters
# ('.' in particular is common in URIs) and then replace the
# escaped asterisks with the appropriate regex matchers.
pattern = re.escape(pattern)
pattern = pattern.replace(r"\*\*", r".*")
pattern = pattern.replace(r"\*", r"[^/]*")
return re.compile(pattern)
[docs]
def get_file_type(fd):
"""
Determine the file type of an open GenericFile instance.
Parameters
----------
fd : ``asdf.generic_io.GenericFile``
Returns
-------
`asdf.util.FileType`
"""
if fd.peek(5) == constants.ASDF_MAGIC:
return FileType.ASDF
if fd.peek(6) == constants.FITS_MAGIC:
return FileType.FITS
return FileType.UNKNOWN
[docs]
class FileType(enum.Enum):
"""
Enum representing if a file is ASDF, FITS or UNKNOWN.
"""
ASDF = 1
FITS = 2
UNKNOWN = 3