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"""A file interface for handling local and remote data files.
The goal of datasource is to abstract some of the file system operations
when dealing with data files so the researcher doesn't have to know all the
low-level details. Through datasource, a researcher can obtain and use a
file with one function call, regardless of location of the file.
DataSource is meant to augment standard python libraries, not replace them.
It should work seamlessly with standard file IO operations and the os
module.
DataSource files can originate locally or remotely:
- local files : '/home/guido/src/local/data.txt'
- URLs (http, ftp, ...) : 'http://www.scipy.org/not/real/data.txt'
DataSource files can also be compressed or uncompressed. Currently only
gzip and bz2 are supported.
Example::
>>> # Create a DataSource, use os.curdir (default) for local storage.
>>> ds = datasource.DataSource()
>>>
>>> # Open a remote file.
>>> # DataSource downloads the file, stores it locally in:
>>> # './www.google.com/index.html'
>>> # opens the file and returns a file object.
>>> fp = ds.open('http://www.google.com/index.html')
>>>
>>> # Use the file as you normally would
>>> fp.read()
>>> fp.close()
"""
from __future__ import division, absolute_import, print_function
import os
import sys
import shutil
_open = open
# Using a class instead of a module-level dictionary
# to reduce the initial 'import numpy' overhead by
# deferring the import of bz2 and gzip until needed
# TODO: .zip support, .tar support?
class _FileOpeners(object):
"""
Container for different methods to open (un-)compressed files.
`_FileOpeners` contains a dictionary that holds one method for each
supported file format. Attribute lookup is implemented in such a way
that an instance of `_FileOpeners` itself can be indexed with the keys
of that dictionary. Currently uncompressed files as well as files
compressed with ``gzip`` or ``bz2`` compression are supported.
Notes
-----
`_file_openers`, an instance of `_FileOpeners`, is made available for
use in the `_datasource` module.
Examples
--------
>>> np.lib._datasource._file_openers.keys()
[None, '.bz2', '.gz']
>>> np.lib._datasource._file_openers['.gz'] is gzip.open
True
"""
def __init__(self):
self._loaded = False
self._file_openers = {None: open}
def _load(self):
if self._loaded:
return
try:
import bz2
self._file_openers[".bz2"] = bz2.BZ2File
except ImportError:
pass
try:
import gzip
self._file_openers[".gz"] = gzip.open
except ImportError:
pass
self._loaded = True
def keys(self):
"""
Return the keys of currently supported file openers.
Parameters
----------
None
Returns
-------
keys : list
The keys are None for uncompressed files and the file extension
strings (i.e. ``'.gz'``, ``'.bz2'``) for supported compression
methods.
"""
self._load()
return list(self._file_openers.keys())
def __getitem__(self, key):
self._load()
return self._file_openers[key]
_file_openers = _FileOpeners()
def open(path, mode='r', destpath=os.curdir):
"""
Open `path` with `mode` and return the file object.
If ``path`` is an URL, it will be downloaded, stored in the
`DataSource` `destpath` directory and opened from there.
Parameters
----------
path : str
Local file path or URL to open.
mode : str, optional
Mode to open `path`. Mode 'r' for reading, 'w' for writing, 'a' to
append. Available modes depend on the type of object specified by
path. Default is 'r'.
destpath : str, optional
Path to the directory where the source file gets downloaded to for
use. If `destpath` is None, a temporary directory will be created.
The default path is the current directory.
Returns
-------
out : file object
The opened file.
Notes
-----
This is a convenience function that instantiates a `DataSource` and
returns the file object from ``DataSource.open(path)``.
"""
ds = DataSource(destpath)
return ds.open(path, mode)
class DataSource (object):
"""
DataSource(destpath='.')
A generic data source file (file, http, ftp, ...).
DataSources can be local files or remote files/URLs. The files may
also be compressed or uncompressed. DataSource hides some of the
low-level details of downloading the file, allowing you to simply pass
in a valid file path (or URL) and obtain a file object.
Parameters
----------
destpath : str or None, optional
Path to the directory where the source file gets downloaded to for
use. If `destpath` is None, a temporary directory will be created.
The default path is the current directory.
Notes
-----
URLs require a scheme string (``http://``) to be used, without it they
will fail::
>>> repos = DataSource()
>>> repos.exists('www.google.com/index.html')
False
>>> repos.exists('http://www.google.com/index.html')
True
Temporary directories are deleted when the DataSource is deleted.
Examples
--------
::
>>> ds = DataSource('/home/guido')
>>> urlname = 'http://www.google.com/index.html'
>>> gfile = ds.open('http://www.google.com/index.html') # remote file
>>> ds.abspath(urlname)
'/home/guido/www.google.com/site/index.html'
>>> ds = DataSource(None) # use with temporary file
>>> ds.open('/home/guido/foobar.txt')
<open file '/home/guido.foobar.txt', mode 'r' at 0x91d4430>
>>> ds.abspath('/home/guido/foobar.txt')
'/tmp/tmpy4pgsP/home/guido/foobar.txt'
"""
def __init__(self, destpath=os.curdir):
"""Create a DataSource with a local path at destpath."""
if destpath:
self._destpath = os.path.abspath(destpath)
self._istmpdest = False
else:
import tempfile # deferring import to improve startup time
self._destpath = tempfile.mkdtemp()
self._istmpdest = True
def __del__(self):
# Remove temp directories
if self._istmpdest:
shutil.rmtree(self._destpath)
def _iszip(self, filename):
"""Test if the filename is a zip file by looking at the file extension.
"""
fname, ext = os.path.splitext(filename)
return ext in _file_openers.keys()
def _iswritemode(self, mode):
"""Test if the given mode will open a file for writing."""
# Currently only used to test the bz2 files.
_writemodes = ("w", "+")
for c in mode:
if c in _writemodes:
return True
return False
def _splitzipext(self, filename):
"""Split zip extension from filename and return filename.
*Returns*:
base, zip_ext : {tuple}
"""
if self._iszip(filename):
return os.path.splitext(filename)
else:
return filename, None
def _possible_names(self, filename):
"""Return a tuple containing compressed filename variations."""
names = [filename]
if not self._iszip(filename):
for zipext in _file_openers.keys():
if zipext:
names.append(filename+zipext)
return names
def _isurl(self, path):
"""Test if path is a net location. Tests the scheme and netloc."""
# We do this here to reduce the 'import numpy' initial import time.
if sys.version_info[0] >= 3:
from urllib.parse import urlparse
else:
from urlparse import urlparse
# BUG : URLs require a scheme string ('http://') to be used.
# www.google.com will fail.
# Should we prepend the scheme for those that don't have it and
# test that also? Similar to the way we append .gz and test for
# for compressed versions of files.
scheme, netloc, upath, uparams, uquery, ufrag = urlparse(path)
return bool(scheme and netloc)
def _cache(self, path):
"""Cache the file specified by path.
Creates a copy of the file in the datasource cache.
"""
# We import these here because importing urllib2 is slow and
# a significant fraction of numpy's total import time.
if sys.version_info[0] >= 3:
from urllib.request import urlopen
from urllib.error import URLError
else:
from urllib2 import urlopen
from urllib2 import URLError
upath = self.abspath(path)
# ensure directory exists
if not os.path.exists(os.path.dirname(upath)):
os.makedirs(os.path.dirname(upath))
# TODO: Doesn't handle compressed files!
if self._isurl(path):
try:
openedurl = urlopen(path)
f = _open(upath, 'wb')
try:
shutil.copyfileobj(openedurl, f)
finally:
f.close()
openedurl.close()
except URLError:
raise URLError("URL not found: %s" % path)
else:
shutil.copyfile(path, upath)
return upath
def _findfile(self, path):
"""Searches for ``path`` and returns full path if found.
If path is an URL, _findfile will cache a local copy and return the
path to the cached file. If path is a local file, _findfile will
return a path to that local file.
The search will include possible compressed versions of the file
and return the first occurrence found.
"""
# Build list of possible local file paths
if not self._isurl(path):
# Valid local paths
filelist = self._possible_names(path)
# Paths in self._destpath
filelist += self._possible_names(self.abspath(path))
else:
# Cached URLs in self._destpath
filelist = self._possible_names(self.abspath(path))
# Remote URLs
filelist = filelist + self._possible_names(path)
for name in filelist:
if self.exists(name):
if self._isurl(name):
name = self._cache(name)
return name
return None
def abspath(self, path):
"""
Return absolute path of file in the DataSource directory.
If `path` is an URL, then `abspath` will return either the location
the file exists locally or the location it would exist when opened
using the `open` method.
Parameters
----------
path : str
Can be a local file or a remote URL.
Returns
-------
out : str
Complete path, including the `DataSource` destination directory.
Notes
-----
The functionality is based on `os.path.abspath`.
"""
# We do this here to reduce the 'import numpy' initial import time.
if sys.version_info[0] >= 3:
from urllib.parse import urlparse
else:
from urlparse import urlparse
# TODO: This should be more robust. Handles case where path includes
# the destpath, but not other sub-paths. Failing case:
# path = /home/guido/datafile.txt
# destpath = /home/alex/
# upath = self.abspath(path)
# upath == '/home/alex/home/guido/datafile.txt'
# handle case where path includes self._destpath
splitpath = path.split(self._destpath, 2)
if len(splitpath) > 1:
path = splitpath[1]
scheme, netloc, upath, uparams, uquery, ufrag = urlparse(path)
netloc = self._sanitize_relative_path(netloc)
upath = self._sanitize_relative_path(upath)
return os.path.join(self._destpath, netloc, upath)
def _sanitize_relative_path(self, path):
"""Return a sanitised relative path for which
os.path.abspath(os.path.join(base, path)).startswith(base)
"""
last = None
path = os.path.normpath(path)
while path != last:
last = path
# Note: os.path.join treats '/' as os.sep on Windows
path = path.lstrip(os.sep).lstrip('/')
path = path.lstrip(os.pardir).lstrip('..')
drive, path = os.path.splitdrive(path) # for Windows
return path
def exists(self, path):
"""
Test if path exists.
Test if `path` exists as (and in this order):
- a local file.
- a remote URL that has been downloaded and stored locally in the
`DataSource` directory.
- a remote URL that has not been downloaded, but is valid and
accessible.
Parameters
----------
path : str
Can be a local file or a remote URL.
Returns
-------
out : bool
True if `path` exists.
Notes
-----
When `path` is an URL, `exists` will return True if it's either
stored locally in the `DataSource` directory, or is a valid remote
URL. `DataSource` does not discriminate between the two, the file
is accessible if it exists in either location.
"""
# We import this here because importing urllib2 is slow and
# a significant fraction of numpy's total import time.
if sys.version_info[0] >= 3:
from urllib.request import urlopen
from urllib.error import URLError
else:
from urllib2 import urlopen
from urllib2 import URLError
# Test local path
if os.path.exists(path):
return True
# Test cached url
upath = self.abspath(path)
if os.path.exists(upath):
return True
# Test remote url
if self._isurl(path):
try:
netfile = urlopen(path)
netfile.close()
del(netfile)
return True
except URLError:
return False
return False
def open(self, path, mode='r'):
"""
Open and return file-like object.
If `path` is an URL, it will be downloaded, stored in the
`DataSource` directory and opened from there.
Parameters
----------
path : str
Local file path or URL to open.
mode : {'r', 'w', 'a'}, optional
Mode to open `path`. Mode 'r' for reading, 'w' for writing,
'a' to append. Available modes depend on the type of object
specified by `path`. Default is 'r'.
Returns
-------
out : file object
File object.
"""
# TODO: There is no support for opening a file for writing which
# doesn't exist yet (creating a file). Should there be?
# TODO: Add a ``subdir`` parameter for specifying the subdirectory
# used to store URLs in self._destpath.
if self._isurl(path) and self._iswritemode(mode):
raise ValueError("URLs are not writeable")
# NOTE: _findfile will fail on a new file opened for writing.
found = self._findfile(path)
if found:
_fname, ext = self._splitzipext(found)
if ext == 'bz2':
mode.replace("+", "")
return _file_openers[ext](found, mode=mode)
else:
raise IOError("%s not found." % path)
class Repository (DataSource):
"""
Repository(baseurl, destpath='.')
A data repository where multiple DataSource's share a base
URL/directory.
`Repository` extends `DataSource` by prepending a base URL (or
directory) to all the files it handles. Use `Repository` when you will
be working with multiple files from one base URL. Initialize
`Repository` with the base URL, then refer to each file by its filename
only.
Parameters
----------
baseurl : str
Path to the local directory or remote location that contains the
data files.
destpath : str or None, optional
Path to the directory where the source file gets downloaded to for
use. If `destpath` is None, a temporary directory will be created.
The default path is the current directory.
Examples
--------
To analyze all files in the repository, do something like this
(note: this is not self-contained code)::
>>> repos = np.lib._datasource.Repository('/home/user/data/dir/')
>>> for filename in filelist:
... fp = repos.open(filename)
... fp.analyze()
... fp.close()
Similarly you could use a URL for a repository::
>>> repos = np.lib._datasource.Repository('http://www.xyz.edu/data')
"""
def __init__(self, baseurl, destpath=os.curdir):
"""Create a Repository with a shared url or directory of baseurl."""
DataSource.__init__(self, destpath=destpath)
self._baseurl = baseurl
def __del__(self):
DataSource.__del__(self)
def _fullpath(self, path):
"""Return complete path for path. Prepends baseurl if necessary."""
splitpath = path.split(self._baseurl, 2)
if len(splitpath) == 1:
result = os.path.join(self._baseurl, path)
else:
result = path # path contains baseurl already
return result
def _findfile(self, path):
"""Extend DataSource method to prepend baseurl to ``path``."""
return DataSource._findfile(self, self._fullpath(path))
def abspath(self, path):
"""
Return absolute path of file in the Repository directory.
If `path` is an URL, then `abspath` will return either the location
the file exists locally or the location it would exist when opened
using the `open` method.
Parameters
----------
path : str
Can be a local file or a remote URL. This may, but does not
have to, include the `baseurl` with which the `Repository` was
initialized.
Returns
-------
out : str
Complete path, including the `DataSource` destination directory.
"""
return DataSource.abspath(self, self._fullpath(path))
def exists(self, path):
"""
Test if path exists prepending Repository base URL to path.
Test if `path` exists as (and in this order):
- a local file.
- a remote URL that has been downloaded and stored locally in the
`DataSource` directory.
- a remote URL that has not been downloaded, but is valid and
accessible.
Parameters
----------
path : str
Can be a local file or a remote URL. This may, but does not
have to, include the `baseurl` with which the `Repository` was
initialized.
Returns
-------
out : bool
True if `path` exists.
Notes
-----
When `path` is an URL, `exists` will return True if it's either
stored locally in the `DataSource` directory, or is a valid remote
URL. `DataSource` does not discriminate between the two, the file
is accessible if it exists in either location.
"""
return DataSource.exists(self, self._fullpath(path))
def open(self, path, mode='r'):
"""
Open and return file-like object prepending Repository base URL.
If `path` is an URL, it will be downloaded, stored in the
DataSource directory and opened from there.
Parameters
----------
path : str
Local file path or URL to open. This may, but does not have to,
include the `baseurl` with which the `Repository` was
initialized.
mode : {'r', 'w', 'a'}, optional
Mode to open `path`. Mode 'r' for reading, 'w' for writing,
'a' to append. Available modes depend on the type of object
specified by `path`. Default is 'r'.
Returns
-------
out : file object
File object.
"""
return DataSource.open(self, self._fullpath(path), mode)
def listdir(self):
"""
List files in the source Repository.
Returns
-------
files : list of str
List of file names (not containing a directory part).
Notes
-----
Does not currently work for remote repositories.
"""
if self._isurl(self._baseurl):
raise NotImplementedError(
"Directory listing of URLs, not supported yet.")
else:
return os.listdir(self._baseurl)
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