Source Code for Module pipe_control.results

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
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  8  # it under the terms of the GNU General Public License as published by        # 
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 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  #                                                                             # 
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 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.model_free.back_compat import read_columnar_results 
 36   
 37   
 38 -def determine_format(file): 
 39      """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   
 64   
 65 -def display(): 
 66      """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   
 74   
 75 -def read(file='results', dir=None): 
 76      """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 (for backwards compatibility with ancient relax results model-free files). 
 99      elif format == 'columnar': 
100          # Extract the data from the file. 
101          file_data = extract_data(file=file) 
102   
103          # Strip data. 
104          file_data = strip(file_data) 
105   
106          # Do nothing if the file does not exist. 
107          if not file_data: 
108              raise RelaxFileEmptyError 
109   
110          # Read the results. 
111          read_columnar_results(file_data) 
112   
113      # Unknown results file. 
114      else: 
115          raise RelaxError("The format of the results file " + repr(file_path) + " cannot be determined.") 
116   
117   
118 -def write(file="results", dir=None, force=False, compress_type=1, verbosity=1): 
119      """Create the results file.""" 
120   
121      # Test if the current data pipe exists. 
122      pipes.test() 
123   
124      # The special data pipe name directory. 
125      if dir == 'pipe_name': 
126          dir = pipes.cdp_name() 
127   
128      # Open the file for writing. 
129      results_file = open_write_file(file_name=file, dir=dir, force=force, compress_type=compress_type, verbosity=verbosity) 
130   
131      # Write the results. 
132      ds.to_xml(results_file, pipes=pipes.cdp_name()) 
133   
134      # Close the results file. 
135      results_file.close() 
136