Source Code for Module test_suite.gui_tests.noe

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  2  #                                                                             # 
  3  # Copyright (C) 2006-2008,2011-2014 Edward d'Auvergne                         # 
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  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 21   
 22  # Python module imports. 
 23  from os import F_OK, access, sep 
 24  import wx 
 25   
 26  # relax module imports. 
 27  from data_store import Relax_data_store; ds = Relax_data_store() 
 28  from gui.interpreter import Interpreter; interpreter = Interpreter() 
 29  from gui.string_conv import str_to_gui 
 30  from pipe_control.mol_res_spin import spin_loop 
 31  from pipe_control.pipes import cdp_name 
 32  from status import Status; status = Status() 
 33  from test_suite.gui_tests.base_classes import GuiTestCase 
 34   
 35   
 36 -class Noe(GuiTestCase): 
 37      """Class for testing various aspects specific to the NOE analysis.""" 
 38   
 39 -    def __init__(self, methodName=None): 
 40          """Set up the test case class for the system tests.""" 
 41   
 42          # Execute the base __init__ methods. 
 43          super(Noe, self).__init__(methodName) 
 44   
 45          # Tests to skip. 
 46          blacklist = [ 
 47              'test_noe_analysis_memory_leaks' 
 48          ] 
 49   
 50          # Skip the blacklisted tests. 
 51          if methodName in blacklist: 
 52              status.skipped_tests.append([methodName, None, self._skip_type]) 
 53   
 54   
 55 -    def test_noe_analysis(self): 
 56          """Test the NOE analysis.""" 
 57   
 58          # Initialise all the special windows (to sometimes catch rare race conditions). 
 59          self.app.gui.show_prompt(None) 
 60          self.app.gui.show_tree(None) 
 61          self.app.gui.show_pipe_editor(None) 
 62   
 63          # Simulate the new analysis wizard. 
 64          analysis = self.new_analysis_wizard(analysis_type='noe') 
 65   
 66          # The frequency label. 
 67          analysis.field_nmr_frq.SetValue(str_to_gui('500')) 
 68   
 69          # Change the results directory. 
 70          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
 71   
 72          # Load the sequence. 
 73          file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'Ap4Aase.seq' 
 74          self._execute_uf(uf_name='sequence.read', file=file, mol_name_col=None, res_name_col=2, res_num_col=1, spin_name_col=None, spin_num_col=None) 
 75   
 76          # Unresolved spins. 
 77          self._execute_uf(uf_name='deselect.spin', spin_id=":3") 
 78   
 79          # Name the spins. 
 80          self._execute_uf(uf_name='spin.name', name="N") 
 81   
 82          # Create a Trp indole N spin. 
 83          self._execute_uf(uf_name='spin.create', res_num=40, spin_name="NE1") 
 84   
 85          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
 86          interpreter.flush() 
 87   
 88          # The intensity data. 
 89          ids = ['ref', 'sat'] 
 90          files = [ 
 91              status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'peak_lists' + sep + 'ref_ave.list', 
 92              status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'peak_lists' + sep + 'sat_ave.list' 
 93          ] 
 94          errors = [3600, 3000] 
 95          errors_5 = [122000, 8500] 
 96          types = ['ref', 'sat'] 
 97   
 98          # Loop over the 2 spectra. 
 99          for i in range(2): 
100              # Set up the peak intensity wizard. 
101              analysis.peak_wizard_launch(None) 
102              wizard = analysis.peak_wizard 
103   
104              # The spectrum. 
105              wizard.setup_page(page='read', file=files[i], spectrum_id=ids[i]) 
106              wizard._go_next(None) 
107   
108              # Move down one pages. 
109              wizard._go_next(None) 
110   
111              # Set the errors. 
112              wizard.setup_page(page='rmsd', error=errors[i]) 
113              wizard._apply(None) 
114              wizard.setup_page(page='rmsd', error=errors_5[i], spin_id=':5') 
115              wizard._go_next(None) 
116   
117              # Set the type and finish. 
118              wizard.setup_page(page='spectrum_type', spectrum_type=types[i]) 
119              wizard._go_next(None) 
120   
121          # Execute relax. 
122          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
123   
124          # Wait for execution to complete. 
125          analysis.thread.join() 
126   
127          # Flush all wx events. 
128          wx.Yield() 
129   
130          # Exceptions in the thread. 
131          self.check_exceptions() 
132   
133          # Check the relax controller. 
134          # FIXME: skipping the checks for certain wxPython bugs. 
135          if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)': 
136              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
137   
138          # The real data. 
139          res_nums = [4, 5, 6, 40, 40, 55] 
140          sat = [5050.0, 51643.0, 53663.0, -65111.0, -181131.0, -105322.0] 
141          ref = [148614.0, 166842.0, 128690.0, 99566.0, 270047.0, 130959.0] 
142          noe = [0.033980647852826784, 0.30953237194471417, 0.4169943274535706, -0.6539481349054899, -0.6707387973204665, -0.8042364404126482] 
143          noe_err = [0.02020329903276632, 0.2320024671657343, 0.026067523940084526, 0.038300618865378507, 0.014260663438353431, 0.03183614777183591] 
144   
145          # Check the data pipe. 
146          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
147   
148          # Check the data. 
149          i = 0 
150          for spin_cont, mol_name, res_num, res_name in spin_loop(full_info=True): 
151              # Skip deselected spins. 
152              if not spin_cont.select: 
153                  continue 
154   
155              # Spin info. 
156              self.assertEqual(res_nums[i], res_num) 
157   
158              # Check the intensity data. 
159              self.assertEqual(sat[i], spin_cont.peak_intensity['sat']) 
160              self.assertEqual(ref[i], spin_cont.peak_intensity['ref']) 
161   
162              # Check the NOE data. 
163              self.assertEqual(noe[i], spin_cont.noe) 
164              self.assertAlmostEqual(noe_err[i], spin_cont.noe_err) 
165   
166              # Increment the spin index. 
167              i += 1 
168   
169          # Check the created files. 
170          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'noe.agr', F_OK)) 
171   
172   
173 -    def test_noe_analysis_memory_leaks(self): 
174          """Test for memory leaks in the NOE analysis. 
175   
176          This can be monitored using the MS Windows task manager, once the 'USER Objects' column is shown. 
177          """ 
178   
179          # A large loop (to try to reach the USER Object limit in MS Windows). 
180          for i in range(1000): 
181              # Printout for debugging. 
182              print("\n\n\nCreating the analysis number %i." % (i+1)) 
183   
184              # Simulate the new analysis wizard. 
185              analysis = self.new_analysis_wizard(analysis_type='noe') 
186   
187              # Close the analysis. 
188              self.app.gui.analysis.delete_analysis(0) 
189   
190              # Printout for debugging. 
191              print("\n\nClosing the analysis number %i.\n\n\n" % (i+1)) 
192