# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides an interface to manage URI scheme support in iris.
"""
import collections
from collections import OrderedDict
import glob
import os.path
import pathlib
import re
import iris.exceptions
# Saving routines, indexed by file extension.
class _SaversDict(dict):
"""A dictionary that can only have string keys with no overlap."""
def __setitem__(self, key, value):
if not isinstance(key, str):
raise ValueError("key is not a string")
if key in self:
raise ValueError("A saver already exists for", key)
for k in self.keys():
if k.endswith(key) or key.endswith(k):
raise ValueError(
"key %s conflicts with existing key %s" % (key, k)
)
dict.__setitem__(self, key, value)
_savers = _SaversDict()
[docs]def run_callback(callback, cube, field, filename):
"""
Runs the callback mechanism given the appropriate arguments.
Args:
* callback:
A function to add metadata from the originating field and/or URI which
obeys the following rules:
1. Function signature must be: ``(cube, field, filename)``.
2. Modifies the given cube inplace, unless a new cube is
returned by the function.
3. If the cube is to be rejected the callback must raise
an :class:`iris.exceptions.IgnoreCubeException`.
.. note::
It is possible that this function returns None for certain callbacks,
the caller of this function should handle this case.
"""
from iris.cube import Cube
if callback is None:
return cube
# Call the callback function on the cube, generally the function will
# operate on the cube in place, but it is also possible that the function
# will return a completely new cube instance.
try:
result = callback(cube, field, filename)
except iris.exceptions.IgnoreCubeException:
result = None
else:
if result is None:
result = cube
elif not isinstance(result, Cube):
raise TypeError(
"Callback function returned an " "unhandled data type."
)
return result
[docs]def decode_uri(uri, default="file"):
r"""
Decodes a single URI into scheme and scheme-specific parts.
In addition to well-formed URIs, it also supports bare file paths as strings
or :class:`pathlib.PurePath`. Both Windows and UNIX style paths are
accepted.
.. testsetup::
from iris.io import *
Examples:
>>> from iris.io import decode_uri
>>> print(decode_uri('http://www.thing.com:8080/resource?id=a:b'))
('http', '//www.thing.com:8080/resource?id=a:b')
>>> print(decode_uri('file:///data/local/dataZoo/...'))
('file', '///data/local/dataZoo/...')
>>> print(decode_uri('/data/local/dataZoo/...'))
('file', '/data/local/dataZoo/...')
>>> print(decode_uri('file:///C:\data\local\dataZoo\...'))
('file', '///C:\\data\\local\\dataZoo\\...')
>>> print(decode_uri('C:\data\local\dataZoo\...'))
('file', 'C:\\data\\local\\dataZoo\\...')
>>> print(decode_uri('dataZoo/...'))
('file', 'dataZoo/...')
"""
if isinstance(uri, pathlib.PurePath):
uri = str(uri)
# make sure scheme has at least 2 letters to avoid windows drives
# put - last in the brackets so it refers to the character, not a range
# reference on valid schemes: http://tools.ietf.org/html/std66#section-3.1
match = re.match(r"^([a-zA-Z][a-zA-Z0-9+.-]+):(.+)", uri)
if match:
scheme = match.group(1)
part = match.group(2)
else:
# Catch bare UNIX and Windows paths
scheme = default
part = uri
return scheme, part
[docs]def expand_filespecs(file_specs, files_expected=True):
"""
Find all matching file paths from a list of file-specs.
Parameters
----------
file_specs : iterable of str
File paths which may contain ``~`` elements or wildcards.
files_expected : bool, default=True
Whether file is expected to exist (i.e. for load).
Returns
-------
list of str
if files_expected is ``True``:
A well-ordered list of matching absolute file paths.
If any of the file-specs match no existing files, an
exception is raised.
if files_expected is ``False``:
A list of expanded file paths.
"""
# Remove any hostname component - currently unused
filenames = [
os.path.abspath(
os.path.expanduser(fn[2:] if fn.startswith("//") else fn)
)
for fn in file_specs
]
if files_expected:
# Try to expand all filenames as globs
glob_expanded = OrderedDict(
[[fn, sorted(glob.glob(fn))] for fn in filenames]
)
# If any of the specs expanded to an empty list then raise an error
all_expanded = glob_expanded.values()
if not all(all_expanded):
msg = "One or more of the files specified did not exist:"
for pattern, expanded in glob_expanded.items():
if expanded:
msg += '\n - "{}" matched {} file(s)'.format(
pattern, len(expanded)
)
else:
msg += '\n * "{}" didn\'t match any files'.format(
pattern
)
raise IOError(msg)
result = [fname for fnames in all_expanded for fname in fnames]
else:
result = filenames
return result
[docs]def load_files(filenames, callback, constraints=None):
"""
Takes a list of filenames which may also be globs, and optionally a
constraint set and a callback function, and returns a
generator of Cubes from the given files.
.. note::
Typically, this function should not be called directly; instead, the
intended interface for loading is :func:`iris.load`.
"""
from iris.fileformats import FORMAT_AGENT
all_file_paths = expand_filespecs(filenames)
# Create default dict mapping iris format handler to its associated filenames
handler_map = collections.defaultdict(list)
for fn in all_file_paths:
with open(fn, "rb") as fh:
handling_format_spec = FORMAT_AGENT.get_spec(
os.path.basename(fn), fh
)
handler_map[handling_format_spec].append(fn)
# Call each iris format handler with the approriate filenames
for handling_format_spec in sorted(handler_map):
fnames = handler_map[handling_format_spec]
if handling_format_spec.constraint_aware_handler:
for cube in handling_format_spec.handler(
fnames, callback, constraints
):
yield cube
else:
for cube in handling_format_spec.handler(fnames, callback):
yield cube
[docs]def load_http(urls, callback):
"""
Takes a list of OPeNDAP URLs and a callback function, and returns a generator
of Cubes from the given URLs.
.. note::
Typically, this function should not be called directly; instead, the
intended interface for loading is :func:`iris.load`.
"""
# Create default dict mapping iris format handler to its associated filenames
from iris.fileformats import FORMAT_AGENT
handler_map = collections.defaultdict(list)
for url in urls:
handling_format_spec = FORMAT_AGENT.get_spec(url, None)
handler_map[handling_format_spec].append(url)
# Call each iris format handler with the appropriate filenames
for handling_format_spec in sorted(handler_map):
fnames = handler_map[handling_format_spec]
for cube in handling_format_spec.handler(fnames, callback):
yield cube
def _dot_save(cube, target):
# A simple wrapper for `iris.fileformats.dot.save` which allows the
# saver to be registered without triggering the import of
# `iris.fileformats.dot`.
from iris.fileformats.dot import save
return save(cube, target)
def _dot_save_png(cube, target, **kwargs):
# A simple wrapper for `iris.fileformats.dot.save_png` which allows the
# saver to be registered without triggering the import of
# `iris.fileformats.dot`.
from iris.fileformats.dot import save_png
return save_png(cube, target, **kwargs)
def _grib_save(cube, target, append=False, **kwargs):
# A simple wrapper for the grib save routine, which allows the saver to be
# registered without having the grib implementation installed.
try:
from iris_grib import save_grib2
except ImportError:
raise RuntimeError(
"Unable to save GRIB file - "
'"iris_grib" package is not installed.'
)
save_grib2(cube, target, append, **kwargs)
def _check_init_savers():
from iris.fileformats import netcdf, pp
if "pp" not in _savers:
_savers.update(
{
"pp": pp.save,
"nc": netcdf.save,
"dot": _dot_save,
"dotpng": _dot_save_png,
"grib2": _grib_save,
}
)
[docs]def add_saver(file_extension, new_saver):
"""
Add a custom saver to the Iris session.
Args:
* file_extension: A string such as "pp" or "my_format".
* new_saver: A function of the form ``my_saver(cube, target)``.
See also :func:`iris.io.save`
"""
# Make sure it's a func with 2+ args
if (
not hasattr(new_saver, "__call__")
or new_saver.__code__.co_argcount < 2
):
raise ValueError("Saver routines must be callable with 2+ arguments.")
# Try to add this saver. Invalid keys will be rejected.
_savers[file_extension] = new_saver
[docs]def find_saver(filespec):
"""
Find the saver function appropriate to the given filename or extension.
Args:
* filespec
A string such as "my_file.pp" or "PP".
Returns:
A save function or None.
Save functions can be passed to :func:`iris.io.save`.
"""
_check_init_savers()
matches = [
ext
for ext in _savers
if filespec.lower().endswith("." + ext) or filespec.lower() == ext
]
# Multiple matches could occur if one of the savers included a '.':
# e.g. _savers = {'.dot.png': dot_png_saver, '.png': png_saver}
if len(matches) > 1:
fmt = "Multiple savers found for %r: %s"
matches = ", ".join(map(repr, matches))
raise ValueError(fmt % (filespec, matches))
return _savers[matches[0]] if matches else None
[docs]def save(source, target, saver=None, **kwargs):
"""
Save one or more Cubes to file (or other writeable).
Iris currently supports three file formats for saving, which it can
recognise by filename extension:
* netCDF - the Unidata network Common Data Format:
* see :func:`iris.fileformats.netcdf.save`
* GRIB2 - the WMO GRIdded Binary data format:
* see :func:`iris_grib.save_grib2`.
* PP - the Met Office UM Post Processing Format:
* see :func:`iris.fileformats.pp.save`
A custom saver can be provided to the function to write to a different
file format.
Parameters
----------
source : :class:`iris.cube.Cube` or :class:`iris.cube.CubeList`
target : str or pathlib.PurePath or io.TextIOWrapper
When given a filename or file, Iris can determine the
file format.
saver : str or function, optional
Specifies the file format to save.
If omitted, Iris will attempt to determine the format.
If a string, this is the recognised filename extension
(where the actual filename may not have it).
Otherwise the value is a saver function, of the form:
``my_saver(cube, target)`` plus any custom keywords. It
is assumed that a saver will accept an ``append`` keyword
if its file format can handle multiple cubes. See also
:func:`iris.io.add_saver`.
**kwargs : dict, optional
All other keywords are passed through to the saver function; see the
relevant saver documentation for more information on keyword arguments.
Warnings
--------
Saving a cube whose data has been loaded lazily
(if `cube.has_lazy_data()` returns `True`) to the same file it expects
to load data from will cause both the data in-memory and the data on
disk to be lost.
.. code-block:: python
cube = iris.load_cube("somefile.nc")
# The next line causes data loss in 'somefile.nc' and the cube.
iris.save(cube, "somefile.nc")
In general, overwriting a file which is the source for any lazily loaded
data can result in corruption. Users should proceed with caution when
attempting to overwrite an existing file.
Examples
--------
>>> # Setting up
>>> import iris
>>> my_cube = iris.load_cube(iris.sample_data_path('air_temp.pp'))
>>> my_cube_list = iris.load(iris.sample_data_path('space_weather.nc'))
>>> # Save a cube to PP
>>> iris.save(my_cube, "myfile.pp")
>>> # Save a cube list to a PP file, appending to the contents of the file
>>> # if it already exists
>>> iris.save(my_cube_list, "myfile.pp", append=True)
>>> # Save a cube to netCDF, defaults to NETCDF4 file format
>>> iris.save(my_cube, "myfile.nc")
>>> # Save a cube list to netCDF, using the NETCDF3_CLASSIC storage option
>>> iris.save(my_cube_list, "myfile.nc", netcdf_format="NETCDF3_CLASSIC")
"""
from iris.cube import Cube, CubeList
# Determine format from filename
if isinstance(target, pathlib.PurePath):
target = str(target)
if isinstance(target, str) and saver is None:
# Converts tilde or wildcards to absolute path
(target,) = expand_filespecs([str(target)], False)
saver = find_saver(target)
elif hasattr(target, "name") and saver is None:
saver = find_saver(target.name)
elif isinstance(saver, str):
saver = find_saver(saver)
if saver is None:
raise ValueError("Cannot save; no saver")
# Single cube?
if isinstance(source, Cube):
saver(source, target, **kwargs)
# CubeList or sequence of cubes?
elif isinstance(source, CubeList) or (
isinstance(source, (list, tuple))
and all([isinstance(i, Cube) for i in source])
):
# Only allow cubelist saving for those fileformats that are capable.
if "iris.fileformats.netcdf" not in saver.__module__:
# Make sure the saver accepts an append keyword
if "append" not in saver.__code__.co_varnames:
raise ValueError(
"Cannot append cubes using saver function "
"'%s' in '%s'"
% (saver.__code__.co_name, saver.__code__.co_filename)
)
# Force append=True for the tail cubes. Don't modify the incoming
# kwargs.
kwargs = kwargs.copy()
for i, cube in enumerate(source):
if i != 0:
kwargs["append"] = True
saver(cube, target, **kwargs)
# Netcdf saver.
else:
saver(source, target, **kwargs)
else:
raise ValueError("Cannot save; non Cube found in source")
