Source code for asdf.util

import enum
import inspect
import math
import struct
import types
import importlib.util
import re
from functools import lru_cache

from urllib.request import pathname2url

import numpy as np

from . import constants

# 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)
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.

__all__ = ['human_list', 'get_array_base', 'get_base_uri', 'filepath_to_url',
           'iter_subclasses', 'calculate_padding', 'resolve_name', 'NotSet',
           'is_primitive', 'uri_match', 'get_class_name']

[docs]def human_list(l, separator="and"): """ Formats a list for human readability. Parameters ---------- l : sequence A sequence of strings separator : string, optional The word to use between the last two entries. Default: ``"and"``. Returns ------- formatted_list : string Examples -------- >>> human_list(["vanilla", "strawberry", "chocolate"], "or") 'vanilla, strawberry or chocolate' """ if len(l) == 1: return l[0] else: return ', '.join(l[:-1]) + ' ' + separator + ' ' + l[-1]
[docs]def get_array_base(arr): """ For a given Numpy array, finds the base array that "owns" the actual data. """ base = arr while isinstance(base.base, np.ndarray): 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]) + [''])
[docs]def filepath_to_url(path): """ For a given local file path, return a file:// url. """ return patched_urllib_parse.urljoin('file:', pathname2url(path))
[docs]def iter_subclasses(cls): """ Returns all subclasses of a class. """ for x in cls.__subclasses__(): yield x for y in iter_subclasses(x): yield y
[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: raise KeyError("No header field '{0}'".format(key)) 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: raise KeyError("No header field '{0}'".format(key)) updates.append((self._offsets[key], val)) updates.sort() start = fd.tell() for ((offset, datatype), val) in updates: + 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 resolve_name(name): """Resolve a name like ``module.object`` to an object and return it. This ends up working like ``from module import object`` but is easier to deal with than the `__import__` builtin and supports digging into submodules. Parameters ---------- name : `str` A dotted path to a Python object--that is, the name of a function, class, or other object in a module with the full path to that module, including parent modules, separated by dots. Also known as the fully qualified name of the object. Examples -------- >>> resolve_name('asdf.util.resolve_name') <function resolve_name at 0x...> Raises ------ `ImportError` If the module or named object is not found. """ # Note: On python 2 these must be str objects and not unicode parts = [str(part) for part in name.split('.')] if len(parts) == 1: # No dots in the name--just a straight up module import cursor = 1 attr_name = str('') # Must not be unicode on Python 2 else: cursor = len(parts) - 1 attr_name = parts[-1] module_name = parts[:cursor] while cursor > 0: try: ret = __import__(str('.'.join(module_name)), fromlist=[attr_name]) break except ImportError: if cursor == 0: raise cursor -= 1 module_name = parts[:cursor] attr_name = parts[cursor] ret = '' for part in parts[cursor:]: try: ret = getattr(ret, part) except AttributeError: raise ImportError(name) return ret
# Kludge to cover up the fact that BuiltinExtension was moved from # to extension/ Can be removed once BuiltinExtension is dropped # in asdf 3.0. _CLASS_NAME_OVERRIDES = { "asdf.extension._legacy.BuiltinExtension": "asdf.extension.BuiltinExtension", }
[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 class_name = "{}.{}".format(typ.__module__, typ.__qualname__) return _CLASS_NAME_OVERRIDES.get(class_name, class_name)
def minversion(module, version, inclusive=True, version_path='__version__'): """ Returns `True` if the specified Python module satisfies a minimum version requirement, and `False` if not. By default this uses `pkg_resources.parse_version` to do the version comparison if available. Otherwise it falls back on `distutils.version.LooseVersion`. Parameters ---------- module : module or `str` An imported module of which to check the version, or the name of that module (in which case an import of that module is attempted-- if this fails `False` is returned). version : `str` The version as a string that this module must have at a minimum (e.g. ``'0.12'``). inclusive : `bool` The specified version meets the requirement inclusively (i.e. ``>=``) as opposed to strictly greater than (default: `True`). version_path : `str` A dotted attribute path to follow in the module for the version. Defaults to just ``'__version__'``, which should work for most Python modules. """ if isinstance(module, types.ModuleType): module_name = module.__name__ elif isinstance(module, str): module_name = module try: module = resolve_name(module_name) except ImportError: return False else: raise ValueError('module argument must be an actual imported ' 'module, or the import name of the module; ' 'got {0!r}'.format(module)) if '.' not in version_path: have_version = getattr(module, version_path) else: have_version = resolve_name('.'.join([module.__name__, version_path])) try: from pkg_resources import parse_version except ImportError: from distutils.version import LooseVersion as parse_version if inclusive: return parse_version(have_version) >= parse_version(version) else: return parse_version(have_version) > parse_version(version) 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__ u'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(InheritDocstrings, cls).__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 is_primitive(value): """ Determine if a value is an instance of a "primitive" type. Parameters ---------- value : object the value to test Returns ------- bool True if the value is primitive, False otherwise """ return ( value is None or isinstance(value, bool) or isinstance(value, int) or isinstance(value, float) or isinstance(value, complex) or isinstance(value, str) )
[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 else: 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) def get_file_type(fd): """ Determine the file type of an open GenericFile instance. Parameters ---------- fd : GenericFile Returns ------- FileType """ if fd.peek(5) == constants.ASDF_MAGIC: return FileType.ASDF elif fd.peek(6) == constants.FITS_MAGIC: return FileType.FITS else: return FileType.UNKNOWN class FileType(enum.Enum): """ Enum representing file types recognized by asdf. """ ASDF = 1 FITS = 2 UNKNOWN = 3