Source Code for Module lib.warnings

  1  from __future__ import absolute_import 
  2  ############################################################################### 
  3  #                                                                             # 
  4  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
  5  # Copyright (C) 2014 Troels E. Linnet                                         # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """Module containing all of the RelaxWarning objects.""" 
 26   
 27  # Python module imports. 
 28  import inspect 
 29  import warnings 
 30   
 31  # relax module imports. 
 32  from lib import ansi 
 33  from status import Status; status = Status() 
 34   
 35   
 36  # The warning formatting function. 
 37 -def format(message, category, filename, lineno, line=None): 
 38      """ Replacement for warnings.formatwarning to customise output format.""" 
 39   
 40      # Add the text 'RelaxWarning: ' to the start of the warning message. 
 41      message = "RelaxWarning: %s\n" % message 
 42   
 43      # Print stack-trace in escalate mode. 
 44      if status.escalate: 
 45          tb = "" 
 46          for frame in inspect.stack()[4:]: 
 47              file = frame[1] 
 48              lineNo = frame[2] 
 49              func = frame[3] 
 50              tb_frame = '  File "%s", line %i, in %s\n' % (file, lineNo, func) 
 51              try: 
 52                  context = frame[4][frame[5]] 
 53              except TypeError: 
 54                  pass 
 55              else: 
 56                  tb_frame = '%s    %s\n' % (tb_frame, context.strip()) 
 57              tb = tb_frame + tb 
 58          tb = "Traceback (most recent call last):\n%s" % tb 
 59          message = tb + message 
 60   
 61      # Text colouring 
 62      if ansi.enable_control_chars(stream=2): 
 63          # Strip the last newline, if it exists. 
 64          if message[-1] == '\n': 
 65              message = message[:-1] 
 66   
 67          # Reformat. 
 68          message = "%s%s%s\n" % (ansi.relax_warning, message, ansi.end) 
 69   
 70      # Return the warning message. 
 71      return message 
 72   
 73   
 74 -def setup(): 
 75      """Set up the warning system.""" 
 76   
 77      # Format warning messages. 
 78      warnings.formatwarning = format 
 79   
 80      # Set warning filters. 
 81      if status.escalate: 
 82          warnings.filterwarnings('error', category=BaseWarning) 
 83      else: 
 84          warnings.filterwarnings('always', category=BaseWarning) 
 85   
 86   
 87   
 88  # Base class for all warnings. 
 89  ############################## 
 90   
 91 -class BaseWarning(Warning): 
 92 -    def __str__(self): 
 93          return str(self.text) 
 94   
 95   
 96  # Standard warnings. 
 97  #################### 
 98   
 99 -class RelaxWarning(BaseWarning): 
100 -    def __init__(self, text): 
101          self.text = text 
102   
103   
104  # Sequence errors. 
105  ################## 
106   
107  # Cannot find the spin in the sequence. 
108 -class RelaxNoSpinWarning(BaseWarning): 
109 -    def __init__(self, spin_id): 
110          self.text = "Cannot find the spin %s within the sequence." % spin_id 
111   
112   
113  # PDB warnings. 
114  ############### 
115   
116  # Zero length interactomic vector. 
117 -class RelaxZeroVectorWarning(BaseWarning): 
118 -    def __init__(self, spin_id1, spin_id2): 
119          self.text = "The interatomic vector between the spins '%s' and '%s' is of zero length." % (spin_id1, spin_id2) 
120   
121   
122  # The atom is missing from the PDB file. 
123 -class RelaxNoAtomWarning(BaseWarning): 
124 -    def __init__(self, atom, res): 
125          self.text = "The atom %s could not be found for residue %i" % (atom, res) 
126   
127   
128  # The PDB file is missing. 
129 -class RelaxNoPDBFileWarning(BaseWarning): 
130 -    def __init__(self, file): 
131          self.text = "The PDB file %s cannot be found, no structures will be loaded." % file 
132   
133   
134  # Nuclear warnings. 
135  ################### 
136   
137  # Nucleus not set. 
138 -class RelaxNucleusWarning(BaseWarning): 
139 -    def __init__(self, spin_id=None): 
140          if spin_id != None: 
141              self.text = "The type of nucleus for the spin '%s' has not yet been set." % spin_id 
142          else: 
143              self.text = "The type of nucleus has not yet been set." 
144   
145  # Spin type not set. 
146 -class RelaxSpinTypeWarning(BaseWarning): 
147 -    def __init__(self, spin_id=None): 
148          if spin_id != None: 
149              self.text = "The nuclear isotope type for the spin '%s' has not yet been set.  Please use the spin.isotope user function to set the type." % spin_id 
150          else: 
151              self.text = "The nuclear isotope type has not yet been set.  Please use the spin.isotope user function to set the type." 
152   
153  # File warnings. 
154  ################ 
155   
156  # No data in file. 
157 -class RelaxFileEmptyWarning(BaseWarning): 
158 -    def __init__(self, file): 
159          self.text = "The file '%s' contains no data." % file 
160   
161   
162  # Misc. 
163  ####### 
164   
165  # Deselection warnings 
166 -class RelaxDeselectWarning(BaseWarning): 
167 -    def __init__(self, spin_id, reason): 
168          self.text = "The spin '%s' has been deselected because of %s." % (spin_id, reason) 
169