Source Code for Module test_suite.system_tests.state

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2014 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  from numpy import array, float64 
 25  from os import sep 
 26  from re import search 
 27  from tempfile import mktemp 
 28   
 29  # relax module imports. 
 30  from data_store import Relax_data_store; ds = Relax_data_store() 
 31  import dep_check 
 32  from pipe_control.interatomic import interatomic_loop 
 33  from pipe_control.pipes import VALID_TYPES, get_pipe 
 34  from pipe_control.reset import reset 
 35  from status import Status; status = Status() 
 36  from test_suite.system_tests.base_classes import SystemTestCase 
 37   
 38   
 39 -class State(SystemTestCase): 
 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 = mktemp() 
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, 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, 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) 
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.assert_(name in ds) 
275   
276              # Type. 
277              pipe = get_pipe(name) 
278              self.assertEqual(pipe.pipe_type, pipe_types[i]) 
279