Trees | Indices | Help |
|
---|
|
1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2013 Edward d'Auvergne # 4 # # 5 # This file is part of the program relax (http://www.nmr-relax.com). # 6 # # 7 # This program is free software: you can redistribute it and/or modify # 8 # it under the terms of the GNU General Public License as published by # 9 # the Free Software Foundation, either version 3 of the License, or # 10 # (at your option) any later version. # 11 # # 12 # This program is distributed in the hope that it will be useful, # 13 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 15 # GNU General Public License for more details. # 16 # # 17 # You should have received a copy of the GNU General Public License # 18 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 19 # # 20 ############################################################################### 21 22 # Module docstring. 23 """Module for reading/writing/displaying the results in a data pipe.""" 24 25 # Python module imports. 26 from os.path import dirname 27 from re import search 28 import sys 29 30 # relax module imports. 31 from data_store import Relax_data_store; ds = Relax_data_store() 32 from lib.errors import RelaxError, RelaxFileEmptyError 33 from lib.io import extract_data, get_file_path, open_read_file, open_write_file, strip 34 from pipe_control import pipes 35 from specific_analyses.setup import get_specific_fn 36 3739 """Determine the format of the results file. 40 41 @keyword file: The file object representing the results file. 42 @type file: file object 43 @return: The results file format. This can be 'xml' or 'columnar'. 44 @rtype: str or None 45 """ 46 47 # Header line. 48 header = file.readline() 49 header = header[:-1] # Strip the trailing newline. 50 if hasattr(header, 'decode'): # Python 3 byte type conversion. 51 header = header.decode() 52 53 # Be nice and go back to the start of the file. 54 file.seek(0) 55 56 # XML. 57 if search(r"<\?xml", header): 58 return 'xml' 59 60 # Columnar. 61 if header.split()[0:3] == ['Num', 'Name', 'Selected']: 62 return 'columnar'63 6466 """Displaying the results/contents of the current data pipe.""" 67 68 # Test if the current data pipe exists. 69 pipes.test() 70 71 # Write the results. 72 ds.to_xml(sys.stdout)73 7476 """Function for reading the data out of a file.""" 77 78 # Test if the current data pipe exists. 79 pipes.test() 80 81 # Make sure that the data pipe is empty. 82 if not cdp.is_empty(): 83 raise RelaxError("The current data pipe is not empty.") 84 85 # Get the full file path, for later use. 86 file_path = get_file_path(file_name=file, dir=dir) 87 88 # Open the file. 89 file = open_read_file(file_name=file_path) 90 91 # Determine the format of the file. 92 format = determine_format(file) 93 94 # XML results. 95 if format == 'xml': 96 ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name()) 97 98 # Columnar results. 99 elif format == 'columnar': 100 read_function = get_specific_fn('read_columnar_results', pipes.get_type(), raise_error=False) 101 102 # Extract the data from the file. 103 file_data = extract_data(file=file) 104 105 # Strip data. 106 file_data = strip(file_data) 107 108 # Do nothing if the file does not exist. 109 if not file_data: 110 raise RelaxFileEmptyError 111 112 # Read the results. 113 read_function(file_data) 114 115 # Unknown results file. 116 else: 117 raise RelaxError("The format of the results file " + repr(file_path) + " cannot be determined.")118 119121 """Create the results file.""" 122 123 # Test if the current data pipe exists. 124 pipes.test() 125 126 # The special data pipe name directory. 127 if dir == 'pipe_name': 128 dir = pipes.cdp_name() 129 130 # Open the file for writing. 131 results_file = open_write_file(file_name=file, dir=dir, force=force, compress_type=compress_type, verbosity=verbosity) 132 133 # Write the results. 134 ds.to_xml(results_file, pipes=pipes.cdp_name()) 135 136 # Close the results file. 137 results_file.close()138
Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Mon Mar 17 15:12:22 2014 | http://epydoc.sourceforge.net |