test_suite.system

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 # Create a temporary directory for dumping files. 64 self.tmpdir = mkdtemp()

65 66

67 - def data_check(self, old_pipe_name='results', new_pipe_name='new', version=None):

68 """Check that all data has been successfully restored from the BMRB files.""" 69 70 # Print out. 71 print("\n\nComparing data pipe contents:") 72 73 # Blacklists (data that is not restored, and relaxation data which has been reordered and will be checked in data_ri_comp()). 74 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'] 75 if version == '3.0': 76 blacklist_spin = blacklist_spin + ['r', 'local_tm', 'local_tm_err'] 77 blacklist_diff = [] 78 blacklist_global = ['diff_tensor', 'exp_info', 'hybrid_pipes', 'mol', 'interatomic', 'sim_number', 'sim_state'] + ['ri_ids', 'spectrometer_frq', 'ri_type'] + ['result_files'] 79 80 # The data pipes. 81 old_pipe = ds[old_pipe_name] 82 new_pipe = ds[new_pipe_name] 83 84 # The molecule data structure. 85 self.assertEqual(len(old_pipe.mol), len(new_pipe.mol)) 86 for i in range(len(old_pipe.mol)): 87 # Check the attributes. 88 self.assertEqual(old_pipe.mol[i].name, old_pipe.mol[i].name) 89 self.assertEqual(old_pipe.mol[i].type, old_pipe.mol[i].type) 90 91 # The residue data structure. 92 self.assertEqual(len(old_pipe.mol[i].res), len(new_pipe.mol[i].res)) 93 for j in range(len(old_pipe.mol[i].res)): 94 # Check the attributes. 95 self.assertEqual(old_pipe.mol[i].res[j].name, old_pipe.mol[i].res[j].name) 96 self.assertEqual(old_pipe.mol[i].res[j].num, old_pipe.mol[i].res[j].num) 97 98 # The spin data structure. 99 self.assertEqual(len(old_pipe.mol[i].res[j].spin), len(new_pipe.mol[i].res[j].spin)) 100 for k in range(len(old_pipe.mol[i].res[j].spin)): 101 # Skip deselected spins. 102 if not old_pipe.mol[i].res[j].spin[k].select: 103 continue 104 105 # Swap the spin indices for the N, H, NE1 and HE1 spins of residue 9. 106 k_new = k 107 if i == 0 and j == 0: 108 if k == 1: 109 k_new = 2 110 elif k == 2: 111 k_new = 1 112 113 # Check the containers. 114 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) 115 if hasattr(old_pipe.mol[i].res[j].spin[k], 'ri_labels'): 116 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]) 117 118 # The diffusion tensor. 119 if version != '3.0': 120 self.assert_(hasattr(new_pipe, 'diff_tensor')) 121 self.data_cont_comp(label='Diff tensor', cont_old=old_pipe.diff_tensor, cont_new=new_pipe.diff_tensor, prec=4, blacklist=blacklist_diff) 122 123 # The global data structures. 124 self.data_cont_comp(label='Global', cont_old=old_pipe, cont_new=new_pipe, blacklist=blacklist_global) 125 if hasattr(old_pipe, 'ri_ids'): 126 self.data_ri_comp_pipe(cont_old=old_pipe, cont_new=new_pipe)

127 128

129 - def data_cont_comp(self, label=None, cont_old=None, cont_new=None, prec=7, blacklist=[]):

130 """Compare the contents of the two data containers.""" 131 132 # Print a new line. 133 print('') 134 135 # Check the attributes. 136 names = dir(cont_old) 137 for name in names: 138 # Skip special names. 139 if search('^__', name): 140 continue 141 142 # Skip the data store methods. 143 if name in cont_old.__class__.__dict__: 144 continue 145 146 # Simulation data. 147 if search('_sim$', name): 148 continue 149 150 # Blacklisting. 151 if name in blacklist: 152 continue 153 154 # Print out. 155 print("%s object: '%s'" % (label, name)) 156 157 # Get the objects. 158 obj_old = getattr(cont_old, name) 159 obj_new = getattr(cont_new, name) 160 161 # Functions and methods. 162 if inspect.isfunction(obj_old) or inspect.ismethod(obj_old): 163 continue 164 165 # Does it exist? 166 self.assert_(hasattr(cont_new, name)) 167 168 # Compare lists. 169 if (isinstance(obj_old, list) or isinstance(obj_old, ndarray)): 170 self.assertEqual(len(obj_old), len(obj_new)) 171 172 # List of lists (or rank-2 array). 173 if (isinstance(obj_old[0], list) or isinstance(obj_old[0], ndarray)): 174 for i in range(len(obj_old)): 175 for j in range(len(obj_old[i])): 176 if isinstance(obj_old[i][j], float): 177 self.assertAlmostEqual(obj_old[i][j], obj_new[i][j], prec) 178 else: 179 self.assertEqual(obj_old[i][j], obj_new[i][j]) 180 181 # Standard list. 182 else: 183 for i in range(len(obj_old)): 184 if isinstance(obj_old[i], float): 185 self.assertAlmostEqual(obj_old[i], obj_new[i], prec) 186 else: 187 self.assertEqual(obj_old[i], obj_new[i]) 188 189 # Compare floats. 190 elif isinstance(obj_old, float): 191 self.assertAlmostEqual(obj_old, obj_new, prec) 192 193 # Compare ints and strings. 194 else: 195 self.assertEqual(obj_old, obj_new)

196 197

198 - def data_ri_comp_pipe(self, cont_old=None, cont_new=None):

199 """Compare the contents of the two pipe data containers.""" 200 201 # Check that the new container has relaxation data. 202 for name in ['spectrometer_frq', 'ri_ids', 'ri_type']: 203 self.assert_(hasattr(cont_new, name)) 204 205 # Check the IDs. 206 old_ids = deepcopy(cont_old.ri_ids) 207 new_ids = deepcopy(cont_new.ri_ids) 208 old_ids.sort() 209 new_ids.sort() 210 self.assertEqual(old_ids, new_ids) 211 212 # Check the frequencies and types. 213 for ri_id in old_ids: 214 self.assertEqual(cont_old.spectrometer_frq[ri_id], cont_new.spectrometer_frq[ri_id]) 215 self.assertEqual(cont_old.ri_type[ri_id], cont_new.ri_type[ri_id])

216 217

218 - def data_ri_comp_spin(self, cont_old=None, cont_new=None):

219 """Compare the contents of the two spin data containers.""" 220 221 # Check that the new container has relaxation data. 222 for name in ['ri_data', 'ri_data_err']: 223 self.assert_(hasattr(cont_new, name)) 224 225 # Check the IDs. 226 old_ids = sorted(cont_old.ri_data.keys()) 227 new_ids = sorted(cont_new.ri_data.keys()) 228 old_ids.sort() 229 new_ids.sort() 230 self.assertEqual(old_ids, new_ids) 231 232 # Check the data and errors. 233 for ri_id in old_ids: 234 self.assertEqual(cont_old.ri_data[ri_id], cont_new.ri_data[ri_id]) 235 self.assertEqual(cont_old.ri_data_err[ri_id], cont_new.ri_data_err[ri_id])

236 237

238 - def test_bug_20471_structure_present(self):

239 """Catch U{bug #20471<https://web.archive.org/web/https://gna.org/bugs/?20471>}, with structural data present prior to a bmrb.read call.""" 240 241 # Create the data pipe. 242 self.interpreter.pipe.create('test', 'mf') 243 244 # Load the PDB file. 245 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 246 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') 247 248 # Set up the 15N and 1H spins. 249 self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True) 250 self.interpreter.structure.load_spins(spin_id='@H', ave_pos=True) 251 self.interpreter.spin.isotope(isotope='15N', spin_id='@N', force=False) 252 self.interpreter.spin.isotope(isotope='1H', spin_id='@H', force=False) 253 254 # Load the relaxation data. 255 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'bmrb' 256 self.assertRaises(RelaxError, self.interpreter.bmrb.read, file='17226.txt', dir=path, version=None, sample_conditions=None)

257 258

259 - def test_bug_22703_display_empty(self):

260 """Catch U{bug #22703<https://web.archive.org/web/https://gna.org/bugs/?22703>}, the failure of the bmrb.display user function with an AttributeError when no data is present.""" 261 262 # Create the data pipe. 263 self.interpreter.pipe.create('test', 'mf') 264 265 # Display. 266 self.assertRaises(RelaxNoFrqError, self.interpreter.bmrb.display, version='3.1') 267 268 # Reset and create a new data pipe. 269 self.interpreter.reset() 270 self.interpreter.pipe.create('test2', 'mf') 271 272 # Display again to show a GUI breakage. 273 self.assertRaises(RelaxNoFrqError, self.interpreter.bmrb.display, version='3.1')

274 275

276 - def test_bug_22704_corrupted_state_file(self):

277 """Catch U{bug #22704<https://web.archive.org/web/https://gna.org/bugs/?22704>}, the corrupted relax state files.""" 278 279 # Create the data pipe. 280 self.interpreter.pipe.create('test', 'mf') 281 282 # Set the relax references. 283 self.interpreter.bmrb.software('relax') 284 285 # Save the relax state, reset, and try loading it again. 286 self.interpreter.state.save('corrupted_state', dir=self.tmpdir) 287 self.interpreter.reset() 288 self.interpreter.state.load('corrupted_state', dir=self.tmpdir) 289 290 # Checks. 291 self.assert_(hasattr(cdp, 'exp_info')) 292 self.assert_(hasattr(cdp.exp_info, 'software')) 293 self.assertEqual(len(cdp.exp_info.software), 1) 294 self.assertEqual(cdp.exp_info.software[0].name, 'software') 295 self.assertEqual(cdp.exp_info.software[0].desc, 'Software program used in the analysis') 296 self.assertEqual(cdp.exp_info.software[0].software_name, 'relax') 297 self.assertEqual(cdp.exp_info.software[0].version, None) 298 self.assertEqual(cdp.exp_info.software[0].url, None) 299 self.assertEqual(cdp.exp_info.software[0].vendor_name, None) 300 self.assertEqual(cdp.exp_info.software[0].cite_ids, None) 301 self.assertEqual(cdp.exp_info.software[0].tasks, None)

302 303

304 - def test_rw_bmrb_3_0_model_free(self):

305 """Write and then read a BRMB STAR formatted file containing model-free results.""" 306 307 # Set the NMR-STAR version. 308 ds.version = '3.0' 309 310 # Execute the script. 311 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 312 313 # Test the data. 314 self.data_check(version='3.0')

315 316

317 - def test_rw_bmrb_3_1_model_free(self):

318 """Write and then read a BRMB STAR formatted file containing model-free results.""" 319 320 # Set the NMR-STAR version. 321 ds.version = '3.1' 322 323 # Execute the script. 324 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bmrb_rw.py') 325 326 # Test the data. 327 self.data_check(version='3.1')

Source Code for Module test_suite.system_tests.bmrb