test_suite.system_tests.state

40 """Class for testing the state saving and loading user functions.""" 41

42 - def __init__(self, methodName='runTest'):

43 """Skip the tests if the C modules are non-functional. 44 45 @keyword methodName: The name of the test. 46 @type methodName: str 47 """ 48 49 # Execute the base class method. 50 super(State, self).__init__(methodName) 51 52 # Missing module. 53 if not dep_check.C_module_exp_fn and methodName in ['test_write_read_pipes']: 54 # Store in the status object. 55 status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type])

56 57

58 - def get_ieee_754(self, lines=None):

59 """Find and convert the IEEE 754 int list from the list of text lines. 60 61 @keyword lines: The lines of XML text to extract the IEEE 754 array from. 62 @type lines: list of str 63 @return: The IEEE 754 array, if it exists. 64 @rtype: list of int 65 """ 66 67 # Loop over the lines, finding the IEEE 754 lines. 68 ieee_754 = "" 69 in_tag = False 70 for line in lines: 71 # The tag start line, so switch the flag. 72 if search("<ieee_754", line): 73 in_tag = True 74 75 # The tag end line, so store the line and switch the flag. 76 if search("</ieee_754", line): 77 ieee_754 += line 78 in_tag = False 79 80 # Store the line. 81 if in_tag: 82 ieee_754 += line 83 84 # Strip the tags and newlines. 85 ieee_754 = ieee_754.replace('<ieee_754_byte_array>', '') 86 ieee_754 = ieee_754.replace('</ieee_754_byte_array>', '') 87 ieee_754 = ieee_754.replace('\n', '') 88 89 # Nothing left. 90 if ieee_754 == '': 91 return None 92 93 # Convert the remaining text to an int list. 94 ieee_754 = eval(ieee_754) 95 96 # Return the array. 97 return ieee_754

98 99 100

101 - def get_xml_tag(self, file=None, name=None):

102 """Extract the text lines for the given XML tag. 103 104 @keyword file: The file name top open. 105 @type file: str 106 @keyword name: The XML tag name to isolate. 107 @type name: str 108 @return: The list of lines corresponding to the XML tag. 109 @rtype: list of str 110 """ 111 112 # Read the contents of the file. 113 file = open(file) 114 lines = file.readlines() 115 file.close() 116 117 # Loop over the lines, finding all corresponding tags. 118 tag_lines = [] 119 in_tag = False 120 for line in lines: 121 # The tag start line, so switch the flag. 122 if search("<%s "%name, line): 123 in_tag = True 124 125 # The tag end line, so store the line and switch the flag. 126 if search("</%s>"%name, line): 127 tag_lines.append(line) 128 in_tag = False 129 130 # Store the line. 131 if in_tag: 132 tag_lines.append(line) 133 134 # Return the lines. 135 return tag_lines

136 137

138 - def setUp(self):

139 """Common set up for these system tests.""" 140 141 # Create a temporary file name. 142 self.tmpfile_handle, self.tmpfile = mkstemp()

143 144

145 - def test_align_tensor_with_mc_sims(self):

146 """Test the loading of a relax state with an alignment tensor with MC simulation structures.""" 147 148 # The file. 149 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states'+sep+'align_tensor_mc.bz2' 150 151 # Load the state. 152 self.interpreter.state.load(path) 153 154 # The data. 155 domains = ['Dy N-dom', 'Dy C-dom'] 156 rdc = { 157 "Dy N-dom" : [-6.41, -21.55], 158 "Dy C-dom" : [-21.55] 159 } 160 rdc_bc = { 161 "Dy N-dom" : [None, -20.87317257368743], 162 "Dy C-dom" : [None] 163 } 164 165 rdc_err = { 166 "Dy N-dom" : [1.0, 1.0], 167 "Dy C-dom" : [1.0] 168 } 169 170 # Check the data. 171 for domain in domains: 172 # Switch to the X-domain data pipe. 173 self.interpreter.pipe.switch(domain) 174 175 # Check the interatomic data. 176 i = 0 177 for interatom in interatomic_loop(): 178 # Check the RDC data. 179 self.assertEqual(interatom.rdc[domain], rdc[domain][i]) 180 if rdc_bc[domain][i]: 181 self.assertEqual(interatom.rdc_bc[domain], rdc_bc[domain][i]) 182 if rdc_err[domain][i]: 183 self.assertEqual(interatom.rdc_err[domain], rdc_err[domain][i]) 184 185 # Increment the index. 186 i += 1

187 188

189 - def test_bug_21716_no_cdp_state_save(self):

190 """Catch U{bug #21716<https://web.archive.org/web/https://gna.org/bugs/?21716>}, the failure to save the relax state when no current data pipe is set.""" 191 192 # Create two data pipes. 193 self.interpreter.pipe.create('a', 'mf') 194 self.interpreter.pipe.create('b', 'mf') 195 196 # Delete the current data pipe. 197 self.interpreter.pipe.delete('b') 198 199 # Save the state. 200 self.interpreter.state.save(self.tmpfile, force=True)

201 202

203 - def test_bug_23017_ieee_754_multidim_numpy_arrays(self):

204 """Test catching U{bug #23017<https://web.archive.org/web/https://gna.org/bugs/?23017>}, the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files.""" 205 206 # Create a data pipe. 207 self.interpreter.pipe.create('test', 'mf') 208 209 # The numpy structure. 210 cdp.test = array([[1, 2, 3], [4, 5, 6]], float64) 211 212 # Save the state. 213 self.interpreter.state.save(self.tmpfile, compress_type=0, force=True) 214 215 # Get the tag lines. 216 lines = self.get_xml_tag(file=self.tmpfile, name='test') 217 218 # Extract the IEEE 754 array as an int list. 219 ieee_754 = self.get_ieee_754(lines=lines) 220 221 # Check. 222 self.assertEqual(ieee_754, [[[0, 0, 0, 0, 0, 0, 240, 63], [0, 0, 0, 0, 0, 0, 0, 64], [0, 0, 0, 0, 0, 0, 8, 64]], [[0, 0, 0, 0, 0, 0, 16, 64], [0, 0, 0, 0, 0, 0, 20, 64], [0, 0, 0, 0, 0, 0, 24, 64]]])

223 224

225 - def test_state_xml(self):

226 """Test the saving, loading, and second saving and loading of the program state in XML format.""" 227 228 # Create a data pipe. 229 self.interpreter.pipe.create('test', 'mf') 230 231 # Save the state. 232 self.interpreter.state.save(self.tmpfile, compress_type=0, force=True) 233 234 # Load the state. 235 self.interpreter.state.load(self.tmpfile, force=True) 236 237 # Save the state. 238 self.interpreter.state.save(self.tmpfile, compress_type=0, force=True) 239 240 # Load the state. 241 self.interpreter.state.load(self.tmpfile, force=True)

242 243

244 - def test_write_read_pipes(self):

245 """Test the writing out, and re-reading of data pipes from the state file.""" 246 247 # Create a data pipe. 248 self.interpreter.pipe.create('test', 'mf') 249 250 # Reset relax. 251 reset() 252 253 # The data pipe list. 254 pipe_types = deepcopy(VALID_TYPES) 255 pipe_types.pop(pipe_types.index("frame order")) 256 257 # Create a few data pipes. 258 for i in range(len(pipe_types)): 259 self.interpreter.pipe.create('test' + repr(i), pipe_types[i]) 260 261 # Write the results. 262 self.interpreter.state.save(self.tmpfile, compress_type=0, force=True) 263 264 # Reset relax. 265 reset() 266 267 # Re-read the results. 268 self.interpreter.state.load(self.tmpfile) 269 270 # Test the pipes. 271 for i in range(len(pipe_types)): 272 # Name. 273 name = 'test' + repr(i) 274 self.assertTrue(name in ds) 275 276 # Type. 277 pipe = get_pipe(name) 278 self.assertEqual(pipe.pipe_type, pipe_types[i])

Source Code for Module test_suite.system_tests.state