Source Code for Module test_suite.system_tests.bmrb

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 15  # GNU General Public License for more details.                                # 
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 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from copy import deepcopy 
 24  import inspect 
 25  from numpy import ndarray 
 26  from os import sep 
 27  from re import search 
 28  from tempfile import mktemp 
 29   
 30  # relax module imports. 
 31  from data import Relax_data_store; ds = Relax_data_store() 
 32  import dep_check 
 33  from status import Status; status = Status() 
 34  from test_suite.system_tests.base_classes import SystemTestCase 
 35   
 36   
 37 -class Bmrb(SystemTestCase): 
 38      """TestCase class for functional tests of the reading and writing of BMRB STAR formatted files.""" 
 39   
 40 -    def __init__(self, methodName='runTest'): 
 41          """Skip the tests if bmrblib is not installed. 
 42   
 43          @keyword methodName:    The name of the test. 
 44          @type methodName:       str 
 45          """ 
 46   
 47          # Execute the base class method. 
 48          super(Bmrb, self).__init__(methodName) 
 49   
 50          # Missing module. 
 51          if not dep_check.bmrblib_module: 
 52              # Store in the status object.  
 53              status.skipped_tests.append([methodName, 'Bmrblib', self._skip_type]) 
 54   
 55   
 56 -    def setUp(self): 
 57          """Common set up for these system tests.""" 
 58   
 59          # Create a temporary file name. 
 60          ds.tmpfile = mktemp() 
 61   
 62   
 63 -    def data_check(self, old_pipe_name='results', new_pipe_name='new', version=None): 
 64          """Check that all data has been successfully restored from the BMRB files.""" 
 65   
 66          # Print out. 
 67          print("\n\nComparing data pipe contents:") 
 68   
 69          # Blacklists (data that is not restored, and relaxation data which has been reordered and will be checked in data_ri_comp()). 
 70          blacklist_spin = ['attached_proton', 'fixed', 'nucleus', 'proton_type', 'relax_sim_data', 'select', 'xh_vect'] + ['r_err', 'csa_err'] + ['chi2_sim', 'f_count', 'g_count', 'h_count', 'iter', 'warning'] + ['frq', 'frq_labels', 'noe_r1_table', 'remap_table', 'ri_labels', 'relax_data', 'relax_error'] + ['_spin_index'] 
 71          if version == '3.0': 
 72              blacklist_spin = blacklist_spin + ['r', 'local_tm', 'local_tm_err'] 
 73          blacklist_diff = [] 
 74          blacklist_global = ['diff_tensor', 'exp_info', 'hybrid_pipes', 'mol', 'interatomic', 'sim_number', 'sim_state'] + ['ri_ids', 'frq', 'ri_type'] + ['result_files'] 
 75   
 76          # The data pipes. 
 77          old_pipe = ds[old_pipe_name] 
 78          new_pipe = ds[new_pipe_name] 
 79   
 80          # The molecule data structure. 
 81          self.assertEqual(len(old_pipe.mol), len(new_pipe.mol)) 
 82          for i in range(len(old_pipe.mol)): 
 83              # Check the attributes. 
 84              self.assertEqual(old_pipe.mol[i].name, old_pipe.mol[i].name) 
 85              self.assertEqual(old_pipe.mol[i].type, old_pipe.mol[i].type) 
 86   
 87              # The residue data structure. 
 88              self.assertEqual(len(old_pipe.mol[i].res), len(new_pipe.mol[i].res)) 
 89              for j in range(len(old_pipe.mol[i].res)): 
 90                  # Check the attributes. 
 91                  self.assertEqual(old_pipe.mol[i].res[j].name, old_pipe.mol[i].res[j].name) 
 92                  self.assertEqual(old_pipe.mol[i].res[j].num, old_pipe.mol[i].res[j].num) 
 93   
 94                  # The spin data structure. 
 95                  self.assertEqual(len(old_pipe.mol[i].res[j].spin), len(new_pipe.mol[i].res[j].spin)) 
 96                  for k in range(len(old_pipe.mol[i].res[j].spin)): 
 97                      # Skip deselected spins. 
 98                      if not old_pipe.mol[i].res[j].spin[k].select: 
 99                          continue 
100   
101                      # Swap the spin indices for the N, H, NE1 and HE1 spins of residue 9. 
102                      k_new = k 
103                      if i == 0 and j == 0: 
104                          if k == 1: 
105                              k_new = 2 
106                          elif k == 2: 
107                              k_new = 1 
108   
109                      # Check the containers. 
110                      self.data_cont_comp(label='Spin', cont_old=old_pipe.mol[i].res[j].spin[k], cont_new=new_pipe.mol[i].res[j].spin[k_new], blacklist=blacklist_spin) 
111                      if hasattr(old_pipe.mol[i].res[j].spin[k], 'ri_labels'): 
112                          self.data_ri_comp_spin(cont_old=old_pipe.mol[i].res[j].spin[k], cont_new=new_pipe.mol[i].res[j].spin[k_new]) 
113   
114          # The diffusion tensor. 
115          if version != '3.0': 
116              self.assert_(hasattr(new_pipe, 'diff_tensor')) 
117              self.data_cont_comp(label='Diff tensor', cont_old=old_pipe.diff_tensor, cont_new=new_pipe.diff_tensor, prec=4, blacklist=blacklist_diff) 
118   
119          # The global data structures. 
120          self.data_cont_comp(label='Global', cont_old=old_pipe, cont_new=new_pipe, blacklist=blacklist_global) 
121          if hasattr(old_pipe, 'ri_ids'): 
122              self.data_ri_comp_pipe(cont_old=old_pipe, cont_new=new_pipe) 
123   
124   
125 -    def data_cont_comp(self, label=None, cont_old=None, cont_new=None, prec=7, blacklist=[]): 
126          """Compare the contents of the two data containers.""" 
127   
128          # Print a new line. 
129          print('') 
130   
131          # Check the attributes. 
132          names = dir(cont_old) 
133          for name in names: 
134              # Skip special names. 
135              if search('^__', name): 
136                  continue 
137   
138              # Skip the data store methods. 
139              if name in list(cont_old.__class__.__dict__.keys()): 
140                  continue 
141   
142              # Simulation data. 
143              if search('_sim$', name): 
144                  continue 
145   
146              # Blacklisting. 
147              if name in blacklist: 
148                  continue 
149   
150              # Print out. 
151              print("%s object: '%s'" % (label, name)) 
152   
153              # Get the objects. 
154              obj_old = getattr(cont_old, name) 
155              obj_new = getattr(cont_new, name) 
156   
157              # Functions and methods. 
158              if inspect.isfunction(obj_old) or inspect.ismethod(obj_old): 
159                  continue 
160   
161              # Does it exist? 
162              self.assert_(hasattr(cont_new, name)) 
163   
164              # Compare lists. 
165              if (isinstance(obj_old, list) or isinstance(obj_old, ndarray)): 
166                  self.assertEqual(len(obj_old), len(obj_new)) 
167   
168                  # List of lists (or rank-2 array). 
169                  if (isinstance(obj_old[0], list) or isinstance(obj_old[0], ndarray)): 
170                      for i in range(len(obj_old)): 
171                          for j in range(len(obj_old[i])): 
172                              if isinstance(obj_old[i][j], float): 
173                                  self.assertAlmostEqual(obj_old[i][j], obj_new[i][j], prec) 
174                              else: 
175                                  self.assertEqual(obj_old[i][j], obj_new[i][j]) 
176   
177                  # Standard list. 
178                  else: 
179                      for i in range(len(obj_old)): 
180                          if isinstance(obj_old[i], float): 
181                              self.assertAlmostEqual(obj_old[i], obj_new[i], prec) 
182                          else: 
183                              self.assertEqual(obj_old[i], obj_new[i]) 
184   
185              # Compare floats. 
186              elif isinstance(obj_old, float): 
187                  self.assertAlmostEqual(obj_old, obj_new, prec) 
188   
189              # Compare ints and strings. 
190              else: 
191                  self.assertEqual(obj_old, obj_new) 
192   
193   
194 -    def data_ri_comp_pipe(self, cont_old=None, cont_new=None): 
195          """Compare the contents of the two pipe data containers.""" 
196   
197          # Check that the new container has relaxation data. 
198          for name in ['frq', 'ri_ids', 'ri_type']: 
199              self.assert_(hasattr(cont_new, name)) 
200   
201          # Check the IDs. 
202          old_ids = deepcopy(cont_old.ri_ids) 
203          new_ids = deepcopy(cont_new.ri_ids) 
204          old_ids.sort() 
205          new_ids.sort() 
206          self.assertEqual(old_ids, new_ids) 
207   
208          # Check the frequencies and types. 
209          for ri_id in old_ids: 
210              self.assertEqual(cont_old.frq[ri_id], cont_new.frq[ri_id]) 
211              self.assertEqual(cont_old.ri_type[ri_id], cont_new.ri_type[ri_id]) 
212   
213   
214 -    def data_ri_comp_spin(self, cont_old=None, cont_new=None): 
215          """Compare the contents of the two spin data containers.""" 
216   
217          # Check that the new container has relaxation data. 
218          for name in ['ri_data', 'ri_data_err']: 
219              self.assert_(hasattr(cont_new, name)) 
220   
221          # Check the IDs. 
222          old_ids = cont_old.ri_data.keys() 
223          new_ids = cont_new.ri_data.keys() 
224          old_ids.sort() 
225          new_ids.sort() 
226          self.assertEqual(old_ids, new_ids) 
227   
228          # Check the data and errors. 
229          for ri_id in old_ids: 
230              self.assertEqual(cont_old.ri_data[ri_id], cont_new.ri_data[ri_id]) 
231              self.assertEqual(cont_old.ri_data_err[ri_id], cont_new.ri_data_err[ri_id]) 
232   
233   
234 -    def test_rw_bmrb_3_0_model_free(self): 
235          """Write and then read a BRMB STAR formatted file containing model-free results.""" 
236   
237          # Set the NMR-STAR version. 
238          ds.version = '3.0' 
239   
240          # Execute the script. 
241          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 
242   
243          # Test the data. 
244          self.data_check(version='3.0') 
245   
246   
247 -    def test_rw_bmrb_3_1_model_free(self): 
248          """Write and then read a BRMB STAR formatted file containing model-free results.""" 
249   
250          # Set the NMR-STAR version. 
251          ds.version = '3.1' 
252   
253          # Execute the script. 
254          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 
255   
256          # Test the data. 
257          self.data_check(version='3.1') 
258