Source Code for Module pipe_control.results

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2002-2004,2007-2008 Edward d'Auvergne                         # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 15  # GNU General Public License for more details.                                # 
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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 interatomic, mol_res_spin, pipes 
 35  from pipe_control.pipes import check_pipe 
 36  from specific_analyses.model_free.back_compat import read_columnar_results 
 37   
 38   
 39 -def determine_format(file): 
 40      """Determine the format of the results file. 
 41   
 42      @keyword file:  The file object representing the results file. 
 43      @type file:     file object 
 44      @return:        The results file format.  This can be 'xml' or 'columnar'. 
 45      @rtype:         str or None 
 46      """ 
 47   
 48      # Header line. 
 49      header = file.readline() 
 50      header = header[:-1]    # Strip the trailing newline. 
 51      if hasattr(header, 'decode'):     # Python 3 byte type conversion. 
 52          header = header.decode() 
 53   
 54      # Be nice and go back to the start of the file. 
 55      file.seek(0) 
 56   
 57      # XML. 
 58      if search(r"<\?xml", header): 
 59          return 'xml' 
 60   
 61      # Columnar. 
 62      if header.split()[0:3] == ['Num', 'Name', 'Selected']: 
 63          return 'columnar' 
 64   
 65   
 66 -def display(): 
 67      """Displaying the results/contents of the current data pipe.""" 
 68   
 69      # Test if the current data pipe exists. 
 70      check_pipe() 
 71   
 72      # Write the results. 
 73      ds.to_xml(sys.stdout) 
 74   
 75   
 76 -def read(file='results', dir=None): 
 77      """Function for reading the data out of a file.""" 
 78   
 79      # Test if the current data pipe exists. 
 80      check_pipe() 
 81   
 82      # Make sure that the data pipe is empty. 
 83      if not cdp.is_empty(): 
 84          raise RelaxError("The current data pipe is not empty.") 
 85   
 86      # Get the full file path, for later use. 
 87      file_path = get_file_path(file_name=file, dir=dir) 
 88   
 89      # Open the file. 
 90      file = open_read_file(file_name=file_path) 
 91   
 92      # Determine the format of the file. 
 93      format = determine_format(file) 
 94   
 95      # XML results. 
 96      if format == 'xml': 
 97          ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name()) 
 98   
 99      # Columnar results (for backwards compatibility with ancient relax results model-free files). 
100      elif format == 'columnar': 
101          # Extract the data from the file. 
102          file_data = extract_data(file=file) 
103   
104          # Strip data. 
105          file_data = strip(file_data) 
106   
107          # Do nothing if the file does not exist. 
108          if not file_data: 
109              raise RelaxFileEmptyError 
110   
111          # Read the results. 
112          read_columnar_results(file_data) 
113   
114      # Unknown results file. 
115      else: 
116          raise RelaxError("The format of the results file " + repr(file_path) + " cannot be determined.") 
117   
118      # Update all of the required metadata structures. 
119      mol_res_spin.metadata_update() 
120      interatomic.metadata_update() 
121   
122   
123 -def write(file="results", dir=None, force=False, compress_type=1, verbosity=1): 
124      """Create the results file.""" 
125   
126      # Test if the current data pipe exists. 
127      check_pipe() 
128   
129      # The special data pipe name directory. 
130      if dir == 'pipe_name': 
131          dir = pipes.cdp_name() 
132   
133      # Open the file for writing. 
134      results_file = open_write_file(file_name=file, dir=dir, force=force, compress_type=compress_type, verbosity=verbosity) 
135   
136      # Write the results. 
137      ds.to_xml(results_file, pipes=pipes.cdp_name()) 
138   
139      # Close the results file. 
140      results_file.close() 
141