Source Code for Module test_suite.system_tests.bmrb

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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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_store import Relax_data_store; ds = Relax_data_store() 
 32  import dep_check 
 33  from lib.errors import RelaxError 
 34  from status import Status; status = Status() 
 35  from test_suite.system_tests.base_classes import SystemTestCase 
 36   
 37   
 38 -class Bmrb(SystemTestCase): 
 39      """TestCase class for functional tests of the reading and writing of BMRB STAR formatted files.""" 
 40   
 41 -    def __init__(self, methodName='runTest'): 
 42          """Skip the tests if bmrblib is not installed. 
 43   
 44          @keyword methodName:    The name of the test. 
 45          @type methodName:       str 
 46          """ 
 47   
 48          # Execute the base class method. 
 49          super(Bmrb, self).__init__(methodName) 
 50   
 51          # Missing module. 
 52          if not dep_check.bmrblib_module: 
 53              # Store in the status object.  
 54              status.skipped_tests.append([methodName, 'Bmrblib', self._skip_type]) 
 55   
 56   
 57 -    def setUp(self): 
 58          """Common set up for these system tests.""" 
 59   
 60          # Create a temporary file name. 
 61          ds.tmpfile = mktemp() 
 62   
 63   
 64 -    def data_check(self, old_pipe_name='results', new_pipe_name='new', version=None): 
 65          """Check that all data has been successfully restored from the BMRB files.""" 
 66   
 67          # Print out. 
 68          print("\n\nComparing data pipe contents:") 
 69   
 70          # Blacklists (data that is not restored, and relaxation data which has been reordered and will be checked in data_ri_comp()). 
 71          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'] 
 72          if version == '3.0': 
 73              blacklist_spin = blacklist_spin + ['r', 'local_tm', 'local_tm_err'] 
 74          blacklist_diff = [] 
 75          blacklist_global = ['diff_tensor', 'exp_info', 'hybrid_pipes', 'mol', 'interatomic', 'sim_number', 'sim_state'] + ['ri_ids', 'spectrometer_frq', 'ri_type'] + ['result_files'] 
 76   
 77          # The data pipes. 
 78          old_pipe = ds[old_pipe_name] 
 79          new_pipe = ds[new_pipe_name] 
 80   
 81          # The molecule data structure. 
 82          self.assertEqual(len(old_pipe.mol), len(new_pipe.mol)) 
 83          for i in range(len(old_pipe.mol)): 
 84              # Check the attributes. 
 85              self.assertEqual(old_pipe.mol[i].name, old_pipe.mol[i].name) 
 86              self.assertEqual(old_pipe.mol[i].type, old_pipe.mol[i].type) 
 87   
 88              # The residue data structure. 
 89              self.assertEqual(len(old_pipe.mol[i].res), len(new_pipe.mol[i].res)) 
 90              for j in range(len(old_pipe.mol[i].res)): 
 91                  # Check the attributes. 
 92                  self.assertEqual(old_pipe.mol[i].res[j].name, old_pipe.mol[i].res[j].name) 
 93                  self.assertEqual(old_pipe.mol[i].res[j].num, old_pipe.mol[i].res[j].num) 
 94   
 95                  # The spin data structure. 
 96                  self.assertEqual(len(old_pipe.mol[i].res[j].spin), len(new_pipe.mol[i].res[j].spin)) 
 97                  for k in range(len(old_pipe.mol[i].res[j].spin)): 
 98                      # Skip deselected spins. 
 99                      if not old_pipe.mol[i].res[j].spin[k].select: 
100                          continue 
101   
102                      # Swap the spin indices for the N, H, NE1 and HE1 spins of residue 9. 
103                      k_new = k 
104                      if i == 0 and j == 0: 
105                          if k == 1: 
106                              k_new = 2 
107                          elif k == 2: 
108                              k_new = 1 
109   
110                      # Check the containers. 
111                      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) 
112                      if hasattr(old_pipe.mol[i].res[j].spin[k], 'ri_labels'): 
113                          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]) 
114   
115          # The diffusion tensor. 
116          if version != '3.0': 
117              self.assert_(hasattr(new_pipe, 'diff_tensor')) 
118              self.data_cont_comp(label='Diff tensor', cont_old=old_pipe.diff_tensor, cont_new=new_pipe.diff_tensor, prec=4, blacklist=blacklist_diff) 
119   
120          # The global data structures. 
121          self.data_cont_comp(label='Global', cont_old=old_pipe, cont_new=new_pipe, blacklist=blacklist_global) 
122          if hasattr(old_pipe, 'ri_ids'): 
123              self.data_ri_comp_pipe(cont_old=old_pipe, cont_new=new_pipe) 
124   
125   
126 -    def data_cont_comp(self, label=None, cont_old=None, cont_new=None, prec=7, blacklist=[]): 
127          """Compare the contents of the two data containers.""" 
128   
129          # Print a new line. 
130          print('') 
131   
132          # Check the attributes. 
133          names = dir(cont_old) 
134          for name in names: 
135              # Skip special names. 
136              if search('^__', name): 
137                  continue 
138   
139              # Skip the data store methods. 
140              if name in list(cont_old.__class__.__dict__.keys()): 
141                  continue 
142   
143              # Simulation data. 
144              if search('_sim$', name): 
145                  continue 
146   
147              # Blacklisting. 
148              if name in blacklist: 
149                  continue 
150   
151              # Print out. 
152              print("%s object: '%s'" % (label, name)) 
153   
154              # Get the objects. 
155              obj_old = getattr(cont_old, name) 
156              obj_new = getattr(cont_new, name) 
157   
158              # Functions and methods. 
159              if inspect.isfunction(obj_old) or inspect.ismethod(obj_old): 
160                  continue 
161   
162              # Does it exist? 
163              self.assert_(hasattr(cont_new, name)) 
164   
165              # Compare lists. 
166              if (isinstance(obj_old, list) or isinstance(obj_old, ndarray)): 
167                  self.assertEqual(len(obj_old), len(obj_new)) 
168   
169                  # List of lists (or rank-2 array). 
170                  if (isinstance(obj_old[0], list) or isinstance(obj_old[0], ndarray)): 
171                      for i in range(len(obj_old)): 
172                          for j in range(len(obj_old[i])): 
173                              if isinstance(obj_old[i][j], float): 
174                                  self.assertAlmostEqual(obj_old[i][j], obj_new[i][j], prec) 
175                              else: 
176                                  self.assertEqual(obj_old[i][j], obj_new[i][j]) 
177   
178                  # Standard list. 
179                  else: 
180                      for i in range(len(obj_old)): 
181                          if isinstance(obj_old[i], float): 
182                              self.assertAlmostEqual(obj_old[i], obj_new[i], prec) 
183                          else: 
184                              self.assertEqual(obj_old[i], obj_new[i]) 
185   
186              # Compare floats. 
187              elif isinstance(obj_old, float): 
188                  self.assertAlmostEqual(obj_old, obj_new, prec) 
189   
190              # Compare ints and strings. 
191              else: 
192                  self.assertEqual(obj_old, obj_new) 
193   
194   
195 -    def data_ri_comp_pipe(self, cont_old=None, cont_new=None): 
196          """Compare the contents of the two pipe data containers.""" 
197   
198          # Check that the new container has relaxation data. 
199          for name in ['spectrometer_frq', 'ri_ids', 'ri_type']: 
200              self.assert_(hasattr(cont_new, name)) 
201   
202          # Check the IDs. 
203          old_ids = deepcopy(cont_old.ri_ids) 
204          new_ids = deepcopy(cont_new.ri_ids) 
205          old_ids.sort() 
206          new_ids.sort() 
207          self.assertEqual(old_ids, new_ids) 
208   
209          # Check the frequencies and types. 
210          for ri_id in old_ids: 
211              self.assertEqual(cont_old.spectrometer_frq[ri_id], cont_new.spectrometer_frq[ri_id]) 
212              self.assertEqual(cont_old.ri_type[ri_id], cont_new.ri_type[ri_id]) 
213   
214   
215 -    def data_ri_comp_spin(self, cont_old=None, cont_new=None): 
216          """Compare the contents of the two spin data containers.""" 
217   
218          # Check that the new container has relaxation data. 
219          for name in ['ri_data', 'ri_data_err']: 
220              self.assert_(hasattr(cont_new, name)) 
221   
222          # Check the IDs. 
223          old_ids = cont_old.ri_data.keys() 
224          new_ids = cont_new.ri_data.keys() 
225          old_ids.sort() 
226          new_ids.sort() 
227          self.assertEqual(old_ids, new_ids) 
228   
229          # Check the data and errors. 
230          for ri_id in old_ids: 
231              self.assertEqual(cont_old.ri_data[ri_id], cont_new.ri_data[ri_id]) 
232              self.assertEqual(cont_old.ri_data_err[ri_id], cont_new.ri_data_err[ri_id]) 
233   
234   
235 -    def test_bug_20471_structure_present(self): 
236          """Catch U{bug #20471<https://web.archive.org/web/https://gna.org/bugs/?20471>}, with structural data present prior to a bmrb.read call.""" 
237   
238          # Create the data pipe. 
239          self.interpreter.pipe.create('test', 'mf') 
240   
241          # Load the PDB file. 
242          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 
243          self.interpreter.structure.read_pdb(file='1RTE_H_trunc.pdb', dir=path, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, alt_loc='A') 
244   
245          # Set up the 15N and 1H spins. 
246          self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True) 
247          self.interpreter.structure.load_spins(spin_id='@H', ave_pos=True) 
248          self.interpreter.spin.isotope(isotope='15N', spin_id='@N', force=False) 
249          self.interpreter.spin.isotope(isotope='1H', spin_id='@H', force=False) 
250   
251          # Load the relaxation data. 
252          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'bmrb' 
253          self.assertRaises(RelaxError, self.interpreter.bmrb.read, file='17226.txt', dir=path, version=None, sample_conditions=None) 
254   
255   
256 -    def test_rw_bmrb_3_0_model_free(self): 
257          """Write and then read a BRMB STAR formatted file containing model-free results.""" 
258   
259          # Set the NMR-STAR version. 
260          ds.version = '3.0' 
261   
262          # Execute the script. 
263          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 
264   
265          # Test the data. 
266          self.data_check(version='3.0') 
267   
268   
269 -    def test_rw_bmrb_3_1_model_free(self): 
270          """Write and then read a BRMB STAR formatted file containing model-free results.""" 
271   
272          # Set the NMR-STAR version. 
273          ds.version = '3.1' 
274   
275          # Execute the script. 
276          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 
277   
278          # Test the data. 
279          self.data_check(version='3.1') 
280