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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, bz2 and xz 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()
"""
"""Check mode and that encoding and newline are compatible.
Parameters ---------- mode : str File open mode. encoding : str File encoding. newline : str Newline for text files.
""" if "t" in mode: if "b" in mode: raise ValueError("Invalid mode: %r" % (mode,)) else: if encoding is not None: raise ValueError("Argument 'encoding' not supported in binary mode") if newline is not None: raise ValueError("Argument 'newline' not supported in binary mode")
"""Wrapper to open bz2 in text mode.
Parameters ---------- fn : str File name mode : {'r', 'w'} File mode. Note that bz2 Text files are not supported. encoding : str Ignored, text bz2 files not supported in Python2. newline : str Ignored, text bz2 files not supported in Python2. """ import bz2
_check_mode(mode, encoding, newline)
if "t" in mode: # BZ2File is missing necessary functions for TextIOWrapper warnings.warn("Assuming latin1 encoding for bz2 text file in Python2", RuntimeWarning, stacklevel=5) mode = mode.replace("t", "") return bz2.BZ2File(fn, mode)
""" Wrapper to open gzip in text mode.
Parameters ---------- fn : str, bytes, file File path or opened file. mode : str File mode. The actual files are opened as binary, but will decoded using the specified `encoding` and `newline`. encoding : str Encoding to be used when reading/writing as text. newline : str Newline to be used when reading/writing as text.
""" import gzip # gzip is lacking read1 needed for TextIOWrapper class GzipWrap(gzip.GzipFile): def read1(self, n): return self.read(n)
_check_mode(mode, encoding, newline)
gz_mode = mode.replace("t", "")
if isinstance(fn, (str, bytes)): binary_file = GzipWrap(fn, gz_mode) elif hasattr(fn, "read") or hasattr(fn, "write"): binary_file = GzipWrap(None, gz_mode, fileobj=fn) else: raise TypeError("filename must be a str or bytes object, or a file")
if "t" in mode: return io.TextIOWrapper(binary_file, encoding, newline=newline) else: return binary_file
# Using a class instead of a module-level dictionary # to reduce the initial 'import numpy' overhead by # deferring the import of lzma, bz2 and gzip until needed
# TODO: .zip support, .tar support? """ 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``, ``bz2`` or ``xz`` 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', '.xz', '.lzma'] >>> np.lib._datasource._file_openers['.gz'] is gzip.open True
"""
if self._loaded: return
try: import bz2 if sys.version_info[0] >= 3: self._file_openers[".bz2"] = bz2.open else: self._file_openers[".bz2"] = _python2_bz2open except ImportError: pass
try: import gzip if sys.version_info[0] >= 3: self._file_openers[".gz"] = gzip.open else: self._file_openers[".gz"] = _python2_gzipopen except ImportError: pass
try: import lzma self._file_openers[".xz"] = lzma.open self._file_openers[".lzma"] = lzma.open except (ImportError, AttributeError): # There are incompatible backports of lzma that do not have the # lzma.open attribute, so catch that as well as ImportError. pass
self._loaded = True
""" 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'``, ``'.xz'``) for supported compression methods.
""" self._load() return list(self._file_openers.keys())
self._load() return self._file_openers[key]
""" 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. encoding : {None, str}, optional Open text file with given encoding. The default encoding will be what `io.open` uses. newline : {None, str}, optional Newline to use when reading text file.
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, encoding=encoding, newline=newline)
""" 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'
"""
"""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
# Remove temp directories if hasattr(self, '_istmpdest') and self._istmpdest: shutil.rmtree(self._destpath)
"""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()
"""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
"""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
"""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
"""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)
"""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
"""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
""" 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)
"""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
""" 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.
"""
# First test for local path if os.path.exists(path): return True
# 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 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
""" 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'. encoding : {None, str}, optional Open text file with given encoding. The default encoding will be what `io.open` uses. newline : {None, str}, optional Newline to use when reading text file.
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, encoding=encoding, newline=newline) else: raise IOError("%s not found." % path)
""" 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')
"""
"""Create a Repository with a shared url or directory of baseurl.""" DataSource.__init__(self, destpath=destpath) self._baseurl = baseurl
DataSource.__del__(self)
"""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
"""Extend DataSource method to prepend baseurl to ``path``.""" return DataSource._findfile(self, self._fullpath(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))
""" 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))
""" 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'. encoding : {None, str}, optional Open text file with given encoding. The default encoding will be what `io.open` uses. newline : {None, str}, optional Newline to use when reading text file.
Returns ------- out : file object File object.
""" return DataSource.open(self, self._fullpath(path), mode, encoding=encoding, newline=newline)
""" 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) |