795 lines
25 KiB
Python
795 lines
25 KiB
Python
"""A file interface for handling local and remote data files.
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The goal of datasource is to abstract some of the file system operations
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when dealing with data files so the researcher doesn't have to know all the
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low-level details. Through datasource, a researcher can obtain and use a
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file with one function call, regardless of location of the file.
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DataSource is meant to augment standard python libraries, not replace them.
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It should work seamlessly with standard file IO operations and the os
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module.
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DataSource files can originate locally or remotely:
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- local files : '/home/guido/src/local/data.txt'
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- URLs (http, ftp, ...) : 'http://www.scipy.org/not/real/data.txt'
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DataSource files can also be compressed or uncompressed. Currently only
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gzip, bz2 and xz are supported.
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Example::
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>>> # Create a DataSource, use os.curdir (default) for local storage.
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>>> from numpy import DataSource
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>>> ds = DataSource()
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>>>
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>>> # Open a remote file.
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>>> # DataSource downloads the file, stores it locally in:
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>>> # './www.google.com/index.html'
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>>> # opens the file and returns a file object.
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>>> fp = ds.open('http://www.google.com/') # doctest: +SKIP
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>>>
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>>> # Use the file as you normally would
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>>> fp.read() # doctest: +SKIP
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>>> fp.close() # doctest: +SKIP
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"""
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from __future__ import division, absolute_import, print_function
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import os
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import sys
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import warnings
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import shutil
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import io
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from contextlib import closing
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from numpy.core.overrides import set_module
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_open = open
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def _check_mode(mode, encoding, newline):
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"""Check mode and that encoding and newline are compatible.
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Parameters
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----------
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mode : str
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File open mode.
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encoding : str
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File encoding.
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newline : str
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Newline for text files.
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"""
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if "t" in mode:
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if "b" in mode:
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raise ValueError("Invalid mode: %r" % (mode,))
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else:
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if encoding is not None:
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raise ValueError("Argument 'encoding' not supported in binary mode")
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if newline is not None:
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raise ValueError("Argument 'newline' not supported in binary mode")
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def _python2_bz2open(fn, mode, encoding, newline):
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"""Wrapper to open bz2 in text mode.
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Parameters
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----------
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fn : str
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File name
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mode : {'r', 'w'}
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File mode. Note that bz2 Text files are not supported.
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encoding : str
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Ignored, text bz2 files not supported in Python2.
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newline : str
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Ignored, text bz2 files not supported in Python2.
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"""
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import bz2
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_check_mode(mode, encoding, newline)
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if "t" in mode:
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# BZ2File is missing necessary functions for TextIOWrapper
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warnings.warn("Assuming latin1 encoding for bz2 text file in Python2",
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RuntimeWarning, stacklevel=5)
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mode = mode.replace("t", "")
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return bz2.BZ2File(fn, mode)
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def _python2_gzipopen(fn, mode, encoding, newline):
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""" Wrapper to open gzip in text mode.
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Parameters
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----------
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fn : str, bytes, file
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File path or opened file.
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mode : str
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File mode. The actual files are opened as binary, but will decoded
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using the specified `encoding` and `newline`.
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encoding : str
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Encoding to be used when reading/writing as text.
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newline : str
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Newline to be used when reading/writing as text.
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"""
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import gzip
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# gzip is lacking read1 needed for TextIOWrapper
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class GzipWrap(gzip.GzipFile):
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def read1(self, n):
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return self.read(n)
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_check_mode(mode, encoding, newline)
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gz_mode = mode.replace("t", "")
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if isinstance(fn, (str, bytes)):
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binary_file = GzipWrap(fn, gz_mode)
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elif hasattr(fn, "read") or hasattr(fn, "write"):
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binary_file = GzipWrap(None, gz_mode, fileobj=fn)
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else:
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raise TypeError("filename must be a str or bytes object, or a file")
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if "t" in mode:
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return io.TextIOWrapper(binary_file, encoding, newline=newline)
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else:
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return binary_file
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# Using a class instead of a module-level dictionary
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# to reduce the initial 'import numpy' overhead by
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# deferring the import of lzma, bz2 and gzip until needed
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# TODO: .zip support, .tar support?
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class _FileOpeners(object):
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"""
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Container for different methods to open (un-)compressed files.
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`_FileOpeners` contains a dictionary that holds one method for each
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supported file format. Attribute lookup is implemented in such a way
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that an instance of `_FileOpeners` itself can be indexed with the keys
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of that dictionary. Currently uncompressed files as well as files
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compressed with ``gzip``, ``bz2`` or ``xz`` compression are supported.
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Notes
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-----
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`_file_openers`, an instance of `_FileOpeners`, is made available for
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use in the `_datasource` module.
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Examples
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--------
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>>> import gzip
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>>> np.lib._datasource._file_openers.keys()
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[None, '.bz2', '.gz', '.xz', '.lzma']
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>>> np.lib._datasource._file_openers['.gz'] is gzip.open
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True
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"""
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def __init__(self):
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self._loaded = False
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self._file_openers = {None: io.open}
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def _load(self):
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if self._loaded:
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return
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try:
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import bz2
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if sys.version_info[0] >= 3:
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self._file_openers[".bz2"] = bz2.open
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else:
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self._file_openers[".bz2"] = _python2_bz2open
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except ImportError:
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pass
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try:
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import gzip
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if sys.version_info[0] >= 3:
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self._file_openers[".gz"] = gzip.open
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else:
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self._file_openers[".gz"] = _python2_gzipopen
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except ImportError:
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pass
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try:
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import lzma
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self._file_openers[".xz"] = lzma.open
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self._file_openers[".lzma"] = lzma.open
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except (ImportError, AttributeError):
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# There are incompatible backports of lzma that do not have the
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# lzma.open attribute, so catch that as well as ImportError.
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pass
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self._loaded = True
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def keys(self):
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"""
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Return the keys of currently supported file openers.
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Parameters
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----------
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None
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Returns
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-------
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keys : list
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The keys are None for uncompressed files and the file extension
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strings (i.e. ``'.gz'``, ``'.xz'``) for supported compression
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methods.
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"""
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self._load()
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return list(self._file_openers.keys())
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def __getitem__(self, key):
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self._load()
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return self._file_openers[key]
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_file_openers = _FileOpeners()
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def open(path, mode='r', destpath=os.curdir, encoding=None, newline=None):
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"""
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Open `path` with `mode` and return the file object.
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If ``path`` is an URL, it will be downloaded, stored in the
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`DataSource` `destpath` directory and opened from there.
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Parameters
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----------
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path : str
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Local file path or URL to open.
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mode : str, optional
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Mode to open `path`. Mode 'r' for reading, 'w' for writing, 'a' to
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append. Available modes depend on the type of object specified by
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path. Default is 'r'.
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destpath : str, optional
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Path to the directory where the source file gets downloaded to for
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use. If `destpath` is None, a temporary directory will be created.
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The default path is the current directory.
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encoding : {None, str}, optional
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Open text file with given encoding. The default encoding will be
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what `io.open` uses.
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newline : {None, str}, optional
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Newline to use when reading text file.
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Returns
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-------
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out : file object
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The opened file.
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Notes
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-----
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This is a convenience function that instantiates a `DataSource` and
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returns the file object from ``DataSource.open(path)``.
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"""
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ds = DataSource(destpath)
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return ds.open(path, mode, encoding=encoding, newline=newline)
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@set_module('numpy')
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class DataSource(object):
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"""
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DataSource(destpath='.')
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A generic data source file (file, http, ftp, ...).
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DataSources can be local files or remote files/URLs. The files may
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also be compressed or uncompressed. DataSource hides some of the
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low-level details of downloading the file, allowing you to simply pass
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in a valid file path (or URL) and obtain a file object.
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Parameters
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----------
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destpath : str or None, optional
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Path to the directory where the source file gets downloaded to for
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use. If `destpath` is None, a temporary directory will be created.
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The default path is the current directory.
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Notes
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-----
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URLs require a scheme string (``http://``) to be used, without it they
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will fail::
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>>> repos = np.DataSource()
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>>> repos.exists('www.google.com/index.html')
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False
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>>> repos.exists('http://www.google.com/index.html')
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True
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Temporary directories are deleted when the DataSource is deleted.
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Examples
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--------
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::
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>>> ds = np.DataSource('/home/guido')
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>>> urlname = 'http://www.google.com/'
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>>> gfile = ds.open('http://www.google.com/')
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>>> ds.abspath(urlname)
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'/home/guido/www.google.com/index.html'
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>>> ds = np.DataSource(None) # use with temporary file
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>>> ds.open('/home/guido/foobar.txt')
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<open file '/home/guido.foobar.txt', mode 'r' at 0x91d4430>
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>>> ds.abspath('/home/guido/foobar.txt')
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'/tmp/.../home/guido/foobar.txt'
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"""
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def __init__(self, destpath=os.curdir):
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"""Create a DataSource with a local path at destpath."""
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if destpath:
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self._destpath = os.path.abspath(destpath)
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self._istmpdest = False
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else:
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import tempfile # deferring import to improve startup time
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self._destpath = tempfile.mkdtemp()
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self._istmpdest = True
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def __del__(self):
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# Remove temp directories
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if hasattr(self, '_istmpdest') and self._istmpdest:
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shutil.rmtree(self._destpath)
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def _iszip(self, filename):
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"""Test if the filename is a zip file by looking at the file extension.
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"""
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fname, ext = os.path.splitext(filename)
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return ext in _file_openers.keys()
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def _iswritemode(self, mode):
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"""Test if the given mode will open a file for writing."""
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# Currently only used to test the bz2 files.
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_writemodes = ("w", "+")
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for c in mode:
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if c in _writemodes:
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return True
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return False
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def _splitzipext(self, filename):
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"""Split zip extension from filename and return filename.
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*Returns*:
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base, zip_ext : {tuple}
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"""
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if self._iszip(filename):
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return os.path.splitext(filename)
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else:
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return filename, None
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def _possible_names(self, filename):
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"""Return a tuple containing compressed filename variations."""
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names = [filename]
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if not self._iszip(filename):
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for zipext in _file_openers.keys():
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if zipext:
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names.append(filename+zipext)
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return names
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def _isurl(self, path):
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"""Test if path is a net location. Tests the scheme and netloc."""
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# We do this here to reduce the 'import numpy' initial import time.
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if sys.version_info[0] >= 3:
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from urllib.parse import urlparse
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else:
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from urlparse import urlparse
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# BUG : URLs require a scheme string ('http://') to be used.
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# www.google.com will fail.
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# Should we prepend the scheme for those that don't have it and
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# test that also? Similar to the way we append .gz and test for
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# for compressed versions of files.
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scheme, netloc, upath, uparams, uquery, ufrag = urlparse(path)
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return bool(scheme and netloc)
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def _cache(self, path):
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"""Cache the file specified by path.
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Creates a copy of the file in the datasource cache.
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"""
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# We import these here because importing urllib2 is slow and
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# a significant fraction of numpy's total import time.
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if sys.version_info[0] >= 3:
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from urllib.request import urlopen
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from urllib.error import URLError
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else:
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from urllib2 import urlopen
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from urllib2 import URLError
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upath = self.abspath(path)
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# ensure directory exists
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if not os.path.exists(os.path.dirname(upath)):
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os.makedirs(os.path.dirname(upath))
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# TODO: Doesn't handle compressed files!
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if self._isurl(path):
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try:
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with closing(urlopen(path)) as openedurl:
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with _open(upath, 'wb') as f:
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shutil.copyfileobj(openedurl, f)
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except URLError:
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raise URLError("URL not found: %s" % path)
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else:
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shutil.copyfile(path, upath)
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return upath
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def _findfile(self, path):
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"""Searches for ``path`` and returns full path if found.
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If path is an URL, _findfile will cache a local copy and return the
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path to the cached file. If path is a local file, _findfile will
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return a path to that local file.
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The search will include possible compressed versions of the file
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and return the first occurrence found.
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"""
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# Build list of possible local file paths
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if not self._isurl(path):
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# Valid local paths
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filelist = self._possible_names(path)
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# Paths in self._destpath
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filelist += self._possible_names(self.abspath(path))
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else:
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# Cached URLs in self._destpath
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filelist = self._possible_names(self.abspath(path))
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# Remote URLs
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filelist = filelist + self._possible_names(path)
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for name in filelist:
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if self.exists(name):
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if self._isurl(name):
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name = self._cache(name)
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return name
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return None
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def abspath(self, path):
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"""
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Return absolute path of file in the DataSource directory.
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If `path` is an URL, then `abspath` will return either the location
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the file exists locally or the location it would exist when opened
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using the `open` method.
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Parameters
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----------
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path : str
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Can be a local file or a remote URL.
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Returns
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-------
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out : str
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Complete path, including the `DataSource` destination directory.
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Notes
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-----
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The functionality is based on `os.path.abspath`.
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"""
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# We do this here to reduce the 'import numpy' initial import time.
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if sys.version_info[0] >= 3:
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from urllib.parse import urlparse
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else:
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from urlparse import urlparse
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# TODO: This should be more robust. Handles case where path includes
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# the destpath, but not other sub-paths. Failing case:
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# path = /home/guido/datafile.txt
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# destpath = /home/alex/
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# upath = self.abspath(path)
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# upath == '/home/alex/home/guido/datafile.txt'
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# handle case where path includes self._destpath
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splitpath = path.split(self._destpath, 2)
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if len(splitpath) > 1:
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path = splitpath[1]
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scheme, netloc, upath, uparams, uquery, ufrag = urlparse(path)
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netloc = self._sanitize_relative_path(netloc)
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upath = self._sanitize_relative_path(upath)
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return os.path.join(self._destpath, netloc, upath)
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def _sanitize_relative_path(self, path):
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"""Return a sanitised relative path for which
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os.path.abspath(os.path.join(base, path)).startswith(base)
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"""
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last = None
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path = os.path.normpath(path)
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while path != last:
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last = path
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# Note: os.path.join treats '/' as os.sep on Windows
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path = path.lstrip(os.sep).lstrip('/')
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path = path.lstrip(os.pardir).lstrip('..')
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drive, path = os.path.splitdrive(path) # for Windows
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return path
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def exists(self, path):
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"""
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Test if path exists.
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Test if `path` exists as (and in this order):
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- a local file.
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- a remote URL that has been downloaded and stored locally in the
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`DataSource` directory.
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- a remote URL that has not been downloaded, but is valid and
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accessible.
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Parameters
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----------
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path : str
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Can be a local file or a remote URL.
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Returns
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-------
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out : bool
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True if `path` exists.
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Notes
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-----
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When `path` is an URL, `exists` will return True if it's either
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stored locally in the `DataSource` directory, or is a valid remote
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URL. `DataSource` does not discriminate between the two, the file
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is accessible if it exists in either location.
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"""
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# First test for local path
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if os.path.exists(path):
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return True
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|
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# We import this here because importing urllib2 is slow and
|
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# a significant fraction of numpy's total import time.
|
|
if sys.version_info[0] >= 3:
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from urllib.request import urlopen
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from urllib.error import URLError
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else:
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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
|
|
|
|
def open(self, path, mode='r', encoding=None, newline=None):
|
|
"""
|
|
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)
|
|
|
|
|
|
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', encoding=None, newline=None):
|
|
"""
|
|
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)
|
|
|
|
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)
|