Author: bugman
Date: Tue Nov 20 17:55:36 2007
New Revision: 3702
URL: http://svn.gna.org/viewcvs/relax?rev=3702&view=rev
Log:
Renamed the relax io module to relax_io as it clashes with the Python io
module.
Added:
1.3/relax_io.py
- copied unchanged from r3692, 1.3/io.py
Removed:
1.3/io.py
Removed: 1.3/io.py
URL: http://svn.gna.org/viewcvs/relax/1.3/io.py?rev=3701&view=auto
==============================================================================
--- 1.3/io.py (original)
+++ 1.3/io.py (removed)
@@ -1,429 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2006 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# BZ2 compression module.
-try:
- from bz2 import BZ2File
- bz2_module = 1
-except ImportError, message:
- bz2_module = 0
- bz2_module_message = message.args[0]
-
-# Gzip compression module.
-from gzip import GzipFile
-
-# Devnull.
-try:
- from os import devnull
- devnull_import = 1
-except ImportError, message:
- devnull_import = 0
- devnull_import_message = message.args[0]
-
-from os import F_OK, X_OK, access, altsep, getenv, makedirs, pathsep,
remove, sep, stat
-from os.path import expanduser, basename, splitext
-from re import match, search
-from string import split
-import sys
-from sys import stdin, stdout, stderr
-
-from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxMissingBinaryError, RelaxNoInPathError,
RelaxNonExecError
-
-
-class IO:
- def __init__(self, relax):
- """Class containing the file operations.
-
- IO streams
- ~~~~~~~~~~
-
- Standard python IO streams:
-
- sys.stdin = self.python_stdin
- sys.stdout = self.python_stdout
- sys.stderr = self.python_stderr
-
- Logging IO streams:
-
- sys.stdin = self.log_stdin = self.python_stdin
- sys.stdout = self.log_stdout = self.log_file
- sys.stderr = self.log_stdout = (self.python_stderr, self.log_file)
-
- Tee IO streams:
-
- sys.stdin = self.tee_stdin = self.python_stdin
- sys.stdout = self.tee_stdout = (self.python_stdout, self.tee_file)
- sys.stderr = self.tee_stdout = (self.python_stderr, self.tee_file)
- """
-
- self.relax = relax
-
- # Standard python IO streams.
- self.python_stdin = stdin
- self.python_stdout = stdout
- self.python_stderr = stderr
-
- # Logging IO streams.
- self.log_stdin = stdin
- self.log_stdout = None
- self.log_stderr = SplitIO()
-
- # Tee IO streams.
- self.tee_stdin = stdin
- self.tee_stdout = SplitIO()
- self.tee_stderr = SplitIO()
-
-
- def delete(self, file_name=None, dir=None):
- """Function for deleting the given file."""
-
- # File path.
- file_path = self.file_path(file_name, dir)
-
- # Test if the file exists and determine the compression type.
- if access(file_path, F_OK):
- pass
- elif access(file_path + '.bz2', F_OK):
- file_path = file_path + '.bz2'
- elif access(file_path + '.gz', F_OK):
- file_path = file_path + '.gz'
- else:
- raise RelaxFileError, file_path
-
- # Remove the file.
- remove(file_path)
-
-
- def extract_data(self, file_name=None, dir=None, file_data=None,
sep=None, compress_type=0):
- """Open the file 'file' and return all the data."""
-
- # Data not already extracted from the file.
- if not file_data:
- # Open the file.
- file = self.open_read_file(file_name=file_name, dir=dir,
compress_type=compress_type)
-
- # Read lines.
- file_data = file.readlines()
-
- # Create a data structure from the contents of the file split by
either whitespace or the separator, sep.
- data = []
- for i in xrange(len(file_data)):
- if sep:
- row = split(file_data[i], sep)
- else:
- row = split(file_data[i])
- data.append(row)
- return data
-
- # Close the file.
- if not file_data:
- file.close()
-
-
- def file_path(self, file_name=None, dir=None):
- """Generate and expand the full file path."""
-
- # File name.
- file_path = file_name
-
- # Add the directory.
- if dir:
- file_path = dir + '/' + file_path
-
- # Expand any ~ characters.
- file_path = expanduser(file_path)
-
- # Return the file path.
- return file_path
-
-
- def file_root(self, file_path):
- """Return the root file name, striped of path and extension
details"""
-
- root,ext = splitext(file_path)
- return basename(root)
-
-
- def log(self, file_name=None, dir=None, compress_type=0, print_flag=1):
- """Function for turning logging on."""
-
- # Log file.
- self.log_file, file_path = self.open_write_file(file_name=file_name,
dir=dir, force=1, compress_type=compress_type, print_flag=print_flag,
return_path=1)
-
- # Print out.
- if print_flag:
- print "Redirecting the sys.stdin IO stream to the python stdin
IO stream."
- print "Redirecting the sys.stdout IO stream to the log file
'%s'." % file_path
- print "Redirecting the sys.stderr IO stream to both the python
stderr IO stream and the log file '%s'." % file_path
-
- # Set the logging IO streams.
- self.log_stdout = self.log_file
- self.log_stderr.split(self.python_stderr, self.log_file)
-
- # IO stream redirection.
- sys.stdin = self.log_stdin
- sys.stdout = self.log_stdout
- sys.stderr = self.log_stderr
-
-
- def logging_off(self, file_name=None, dir=None, print_flag=1):
- """Function for turning logging and teeing off."""
-
- # Print out.
- if print_flag:
- print "Redirecting the sys.stdin IO stream to the python stdin
IO stream."
- print "Redirecting the sys.stdout IO stream to the python stdout
IO stream."
- print "Redirecting the sys.stderr IO stream to the python stderr
IO stream."
-
- # IO stream redirection.
- sys.stdin = self.python_stdin
- sys.stdout = self.python_stdout
- sys.stderr = self.python_stderr
-
-
- def mkdir(self, dir=None, print_flag=1):
- """Create the given directory, or exit if the directory exists."""
-
- # No directory given.
- if dir == None:
- return
-
- # Make the directory.
- try:
- makedirs(dir)
- except OSError:
- if print_flag:
- print "Directory ./" + dir + " already exists.\n"
-
-
- def open_read_file(self, file_name=None, dir=None, compress_type=0,
print_flag=1):
- """Open the file 'file' and return all the data."""
-
- # File path.
- file_path = self.file_path(file_name, dir)
-
- # Test if the file exists and determine the compression type.
- if access(file_path, F_OK):
- compress_type = 0
- if search('.bz2$', file_path):
- compress_type = 1
- elif search('.gz$', file_path):
- compress_type = 2
- elif access(file_path + '.bz2', F_OK):
- file_path = file_path + '.bz2'
- compress_type = 1
- elif access(file_path + '.gz', F_OK):
- file_path = file_path + '.gz'
- compress_type = 2
- else:
- raise RelaxFileError, file_path
-
- # Open the file for reading.
- try:
- if print_flag:
- print "Opening the file " + `file_path` + " for reading."
- if compress_type == 0:
- file = open(file_path, 'r')
- elif compress_type == 1:
- if bz2_module:
- file = BZ2File(file_path, 'r')
- else:
- raise RelaxError, "Cannot open the file " + `file_path`
+ ", try uncompressing first. " + bz2_module_message + "."
- elif compress_type == 2:
- file = GzipFile(file_path, 'r')
- except IOError, message:
- raise RelaxError, "Cannot open the file " + `file_path` + ". "
+ message.args[1] + "."
-
- # Return the opened file.
- return file
-
-
- def open_write_file(self, file_name=None, dir=None, force=0,
compress_type=0, print_flag=1, return_path=0):
- """Function for opening a file for writing and creating directories
if necessary."""
-
- # The null device.
- if search('devnull', file_name):
- # Devnull could not be imported!
- if not devnull_import:
- raise RelaxError, devnull_import_message + ". To use
devnull, please upgrade to Python >= 2.4."
-
- # Print out.
- if print_flag:
- print "Opening the null device file for writing."
-
- # Open the null device.
- file = open(devnull, 'w')
-
- # Return the file.
- if return_path:
- return file, None
- else:
- return file
-
- # Create the directories.
- self.mkdir(dir, print_flag=0)
-
- # File path.
- file_path = self.file_path(file_name, dir)
-
- # Bzip2 compression.
- if compress_type == 1 and not search('.bz2$', file_path):
- # Bz2 module exists.
- if bz2_module:
- file_path = file_path + '.bz2'
-
- # Switch to gzip compression.
- else:
- print "Cannot use bz2 compression, using gzip compression
instead. " + bz2_module_message + "."
- compress_type = 2
-
- # Gzip compression.
- if compress_type == 2 and not search('.gz$', file_path):
- file_path = file_path + '.gz'
-
- # Fail if the file already exists and the force flag is set to 0.
- if access(file_path, F_OK) and not force:
- raise RelaxFileOverwriteError, (file_path, 'force flag')
-
- # Open the file for writing.
- try:
- if print_flag:
- print "Opening the file " + `file_path` + " for writing."
- if compress_type == 0:
- file = open(file_path, 'w')
- elif compress_type == 1:
- file = BZ2File(file_path, 'w')
- elif compress_type == 2:
- file = GzipFile(file_path, 'w')
- except IOError, message:
- raise RelaxError, "Cannot open the file " + `file_path` + ". "
+ message.args[1] + "."
-
- # Return the opened file.
- if return_path:
- return file, file_path
- else:
- return file
-
-
- def strip(self, data):
- """Function to remove all comment and empty lines from the file data
structure."""
-
- # Initialise the new data array.
- new = []
-
- # Loop over the data.
- for i in xrange(len(data)):
- # Empty lines.
- if len(data[i]) == 0:
- continue
-
- # Comment lines.
- elif match("#", data[i][0]):
- continue
-
- # Data lines.
- else:
- new.append(data[i])
-
- # Return the new data structure.
- return new
-
-
- def tee(self, file_name=None, dir=None, compress_type=0, print_flag=1):
- """Function for turning logging on."""
-
- # Tee file.
- self.tee_file, file_path = self.open_write_file(file_name=file_name,
dir=dir, force=1, compress_type=compress_type, print_flag=print_flag,
return_path=1)
-
- # Print out.
- if print_flag:
- print "Redirecting the sys.stdin IO stream to the python stdin
IO stream."
- print "Redirecting the sys.stdout IO stream to both the python
stdout IO stream and the log file '%s'." % file_path
- print "Redirecting the sys.stderr IO stream to both the python
stderr IO stream and the log file '%s'." % file_path
-
- # Set the tee IO streams.
- self.tee_stdout.split(self.python_stdout, self.tee_file)
- self.tee_stderr.split(self.python_stderr, self.tee_file)
-
- # IO stream redirection.
- sys.stdin = self.tee_stdin
- sys.stdout = self.tee_stdout
- sys.stderr = self.tee_stderr
-
-
- def test_binary(self, binary):
- """Function for testing that the binary string corresponds to a
valid executable file."""
-
- # Path separator RE string.
- if altsep:
- path_sep = '[' + sep + altsep + ']'
- else:
- path_sep = sep
-
- # The full path of the program has been given (if a directory
separatory has been supplied).
- if search(path_sep, binary):
- # Test that the binary exists.
- if not access(binary, F_OK):
- raise RelaxMissingBinaryError, binary
-
- # Test that if the binary is executable.
- if not access(binary, X_OK):
- raise RelaxNonExecError, binary
-
- # The path to the binary has not been given.
- else:
- # Get the PATH environmental variable.
- path = getenv('PATH')
-
- # Split PATH by the path separator.
- path_list = split(path, pathsep)
-
- # Test that the binary exists within the system path (and exit
this function instantly once it has been found).
- for path in path_list:
- if access(path + sep + binary, F_OK):
- return
-
- # The binary is not located in the system path!
- raise RelaxNoInPathError, binary
-
-
-class SplitIO:
- def __init__(self):
- """Class for splitting an IO stream to two outputs."""
-
-
- def split(self, stream1, stream2):
- """Function for setting the streams."""
-
- # Arguments.
- self.stream1 = stream1
- self.stream2 = stream2
-
-
- def write(self, text):
- """Replacement write function."""
-
- # Write to stream1.
- self.stream1.write(text)
-
- # Write to stream2.
- self.stream2.write(text)
r3702 - in /1.3: io.py relax_io.py