Source Code for Module gui.export_bmrb

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2012 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """The BMRB export wizard.""" 
 24   
 25  # Python module imports. 
 26  import wx 
 27   
 28  # relax module imports. 
 29  from generic_fns.mol_res_spin import molecule_loop 
 30  from generic_fns.pipes import cdp_name, pipe_names, switch 
 31  from graphics import IMAGE_PATH, fetch_icon 
 32  from status import Status; status = Status() 
 33   
 34  # relax GUI module imports. 
 35  from gui.components.citations import Citations 
 36  from gui.components.molecule import Molecule 
 37  from gui.components.relax_data_meta import Relax_data_meta_list 
 38  from gui.components.scripts import Scripts 
 39  from gui.components.software import Software 
 40  from gui.message import Missing_data 
 41  from gui.fonts import font 
 42  from gui.icons import relax_icons 
 43  from gui.input_elements.value import Value 
 44  from gui.misc import add_border, bitmap_setup 
 45  from gui.string_conv import gui_to_str, str_to_gui 
 46  from gui.uf_objects import Uf_storage; uf_store = Uf_storage() 
 47   
 48   
 49 -class Export_bmrb_window(wx.Frame): 
 50      """The BMRB export window.""" 
 51   
 52 -    def __init__(self, gui): 
 53          """Set up the export window. 
 54   
 55          @param gui:     The GUI object. 
 56          @type gui:      wx.Frame instance 
 57          """ 
 58   
 59          # The window style. 
 60          style = wx.DEFAULT_FRAME_STYLE 
 61          if not status.debug and status.wx_info["os"] != 'darwin': 
 62              style = style | wx.MAXIMIZE 
 63   
 64          # Initialise the base class, setting the main GUI window as the parent. 
 65          super(Export_bmrb_window, self).__init__(gui, -1, style=style) 
 66   
 67          # Some default values. 
 68          self.size = (1200, 900) 
 69          self.size_min = (900, 700) 
 70          self.border = 5 
 71          self.spacer = 10 
 72          self.button_size = (200, 40) 
 73          self.button_spacing = 10 
 74          self.main_spacing = 20 
 75   
 76          # Set up the frame. 
 77          sizer = self.setup_frame() 
 78   
 79          # Add the header. 
 80          self.add_header(sizer) 
 81   
 82          # Top spacing. 
 83          sizer.AddSpacer(10) 
 84   
 85          # Add the data pipe selection element. 
 86          self.add_pipe(sizer) 
 87   
 88          # Spacing. 
 89          sizer.AddSpacer(self.main_spacing) 
 90   
 91          # Add the relaxation data metadata list GUI element. 
 92          self.relax_data = Relax_data_meta_list(parent=self.main_panel, box=sizer, id='BMRB export', proportion=2) 
 93   
 94          # Spacing. 
 95          sizer.AddSpacer(self.main_spacing) 
 96   
 97          # Add the molecule GUI element. 
 98          self.molecule = Molecule(parent=self.main_panel, box=sizer, id='BMRB export', proportion=1) 
 99   
100          # Spacing. 
101          sizer.AddSpacer(self.main_spacing) 
102   
103          # Create a horizontal layout for the software, script and citations GUI elements. 
104          sub_sizer = wx.BoxSizer(wx.HORIZONTAL) 
105   
106          # Add the software GUI element. 
107          self.software = Software(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
108   
109          # Vertical spacing. 
110          sub_sizer.AddSpacer(self.main_spacing) 
111   
112          # Add the scripts GUI element. 
113          self.scripts = Scripts(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
114   
115          # Vertical spacing. 
116          sub_sizer.AddSpacer(self.main_spacing) 
117   
118          # Add the citation GUI element. 
119          self.citation = Citations(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
120   
121          # Add the sizer. 
122          sizer.Add(sub_sizer, 2, wx.ALL|wx.EXPAND, 0) 
123   
124          # Bottom spacing. 
125          sizer.AddSpacer(10) 
126   
127          # Add the buttons. 
128          self.add_buttons(sizer) 
129   
130          # Open the window. 
131          if status.show_gui: 
132              self.Show() 
133   
134   
135 -    def action_cancel(self, event=None): 
136          """Cancel the export. 
137   
138          @keyword event: The wx event. 
139          @type event:    wx event 
140          """ 
141   
142          # Close the window. 
143          self.Close() 
144   
145   
146 -    def action_export(self, event=None): 
147          """Write out the NMR-STAR formatted data. 
148   
149          @keyword event: The wx event. 
150          @type event:    wx event 
151          """ 
152   
153          # Checks. 
154          missing = self.is_complete() 
155   
156          # Missing data. 
157          if len(missing): 
158              Missing_data(missing, parent=self) 
159              return 
160   
161          # Execute the user function. 
162          uf_store['bmrb.write'](wx_parent=self, wx_wizard_sync=True, wx_wizard_modal=True) 
163   
164          # Close the window. 
165          self.Close() 
166   
167   
168 -    def action_preview(self, event=None): 
169          """Preview the NMR-STAR formatted data. 
170   
171          @keyword event: The wx event. 
172          @type event:    wx event 
173          """ 
174   
175          # Execute the user function. 
176          uf_store['bmrb.display'](wx_parent=self) 
177   
178   
179 -    def add_buttons(self, sizer): 
180          """Build and add the bottom buttons. 
181   
182          @param sizer:   The sizer element to pack the buttons into. 
183          @type sizer:    wx.Sizer instance 
184          """ 
185   
186          # Button sizer. 
187          button_sizer = wx.BoxSizer(wx.HORIZONTAL) 
188          sizer.Add(button_sizer, 0, wx.ALIGN_RIGHT, 0) 
189   
190          # Preview button. 
191          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Preview") 
192          button.SetBitmapLabel(wx.Bitmap(fetch_icon('oxygen.actions.document-preview', "32x32"), wx.BITMAP_TYPE_ANY)) 
193          button.SetFont(font.normal) 
194          button.SetMinSize(self.button_size) 
195          button_sizer.Add(button, 0, 0, 0) 
196          self.Bind(wx.EVT_BUTTON, self.action_preview, button) 
197          button.SetToolTipString("Preview the NMR-STAR formatted data.") 
198   
199          # Spacing. 
200          button_sizer.AddSpacer(self.button_spacing) 
201   
202          # Export button. 
203          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Export") 
204          button.SetBitmapLabel(wx.Bitmap(fetch_icon('relax.bmrb', "32x32"), wx.BITMAP_TYPE_ANY)) 
205          button.SetFont(font.normal) 
206          button.SetMinSize(self.button_size) 
207          button_sizer.Add(button, 0, 0, 0) 
208          self.Bind(wx.EVT_BUTTON, self.action_export, button) 
209          button.SetToolTipString("Create the NMR-STAR formatted file for BMRB deposition.") 
210   
211          # Spacing. 
212          button_sizer.AddSpacer(self.button_spacing) 
213   
214          # Cancel button. 
215          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Cancel") 
216          button.SetBitmapLabel(wx.Bitmap(fetch_icon('oxygen.actions.dialog-cancel', "32x32"), wx.BITMAP_TYPE_ANY)) 
217          button.SetFont(font.normal) 
218          button.SetMinSize(self.button_size) 
219          button_sizer.Add(button, 0, 0, 0) 
220          self.Bind(wx.EVT_BUTTON, self.action_cancel, button) 
221          button.SetToolTipString("Cancel the BMRB export.") 
222   
223   
224 -    def add_header(self, sizer): 
225          """Build and add the header to the sizer. 
226   
227          @param sizer:   The sizer element to pack the header into. 
228          @type sizer:    wx.Sizer instance 
229          """ 
230   
231          # Create a horizontal layout. 
232          sub_sizer = wx.BoxSizer(wx.HORIZONTAL) 
233   
234          # Left spacing. 
235          sub_sizer.AddStretchSpacer(3) 
236   
237          # Add the BMRB logo (left side). 
238          logo = wx.StaticBitmap(self.main_panel, -1, bitmap_setup(IMAGE_PATH+"bmrb_100x100.png")) 
239          sub_sizer.Add(logo, 0, wx.TOP|wx.ALIGN_CENTER_HORIZONTAL, 0) 
240   
241          # Spacing. 
242          sub_sizer.AddStretchSpacer() 
243   
244          # The text sizer. 
245          text_sizer = wx.BoxSizer(wx.VERTICAL) 
246   
247          # The title. 
248          text = wx.StaticText(self.main_panel, -1, 'Data export for BMRB deposition', style=wx.ALIGN_LEFT) 
249          text.SetFont(font.title) 
250          text_sizer.Add(text, 0, wx.ALIGN_CENTER_HORIZONTAL, 0) 
251   
252          # Spacing. 
253          text_sizer.AddSpacer(15) 
254   
255          # The text. 
256          main_text = 'This wizard will help in executing all of the relevant user functions required to convert the contents of the selected data pipe to the NMR-STAR format for deposition within the BioMagResBank.  Note that this is currently only for the deposition of model-free analysis results or simple NMR relaxation data.' 
257          text = wx.StaticText(self.main_panel, -1, main_text, style=wx.ALIGN_LEFT) 
258          text.Wrap(600) 
259          text.SetFont(font.normal) 
260          text_sizer.Add(text, 0, 0, 0) 
261   
262          # Add the text sizer. 
263          sub_sizer.Add(text_sizer, 0, 0, 0) 
264   
265          # Spacing. 
266          sub_sizer.AddStretchSpacer() 
267   
268          # Add the BMRB logo (right side). 
269          logo = wx.StaticBitmap(self.main_panel, -1, bitmap_setup(IMAGE_PATH+"bmrb_100x100.png")) 
270          sub_sizer.Add(logo, 0, wx.TOP|wx.ALIGN_CENTER_HORIZONTAL, 0) 
271   
272          # Right spacing. 
273          sub_sizer.AddStretchSpacer(3) 
274   
275          # Add the sizer. 
276          sizer.Add(sub_sizer, 0, wx.ALL|wx.EXPAND, 0) 
277   
278          # A line with spacing. 
279          sizer.AddSpacer(10) 
280          sizer.Add(wx.StaticLine(self.main_panel, -1), 0, wx.EXPAND|wx.ALL, 0) 
281          sizer.AddSpacer(10) 
282   
283   
284 -    def add_pipe(self, sizer): 
285          """Build and add the data pipe selection element. 
286   
287          @param sizer:   The sizer element to pack the buttons into. 
288          @type sizer:    wx.Sizer instance 
289          """ 
290   
291          # A sizer for the element. 
292          pipe_sizer = wx.BoxSizer(wx.HORIZONTAL) 
293          sizer.Add(pipe_sizer, 0, wx.ALIGN_LEFT, 0) 
294   
295          # The pipe text. 
296          text = wx.StaticText(self.main_panel, -1, ' The data pipe to export:  ', style=wx.ALIGN_LEFT) 
297          tooltip = "The name of the data pipe to export to NMR-STAR format for BMRB export." 
298          text.SetFont(font.normal) 
299          text.SetToolTipString(tooltip) 
300          pipe_sizer.Add(text, 0, wx.ALIGN_CENTER_VERTICAL, 0) 
301   
302          # Spacing. 
303          pipe_sizer.AddSpacer(20) 
304   
305          # The pipe selection. 
306          self.pipe_name = wx.ComboBox(self.main_panel, -1, "", style=wx.CB_DROPDOWN|wx.CB_READONLY, choices=[]) 
307          self.pipe_name.SetToolTipString(tooltip) 
308          self.Bind(wx.EVT_COMBOBOX, self.update_pipes, self.pipe_name) 
309          pipe_sizer.Add(self.pipe_name, 0, wx.ALIGN_CENTER_VERTICAL, 0) 
310   
311          # Update the pipe selection. 
312          self.update_pipes() 
313   
314   
315 -    def handler_close(self, event): 
316          """Event handler for the close window action. 
317   
318          @param event:   The wx event. 
319          @type event:    wx event 
320          """ 
321   
322          # Unregister the observers. 
323          self.observer_register(remove=True) 
324   
325          # Close the window. 
326          event.Skip() 
327   
328   
329 -    def is_complete(self): 
330          """Determine if the data input is complete. 
331   
332          @return:    A list of all the missing components. 
333          @rtype:     list of str 
334          """ 
335   
336          # Initialise. 
337          missing = [] 
338   
339          # Relaxation data metadata. 
340          if hasattr(cdp, 'ri_ids'): 
341              # Loop over the data. 
342              for i in range(len(cdp.ri_ids)): 
343                  # Check the peak intensity types. 
344                  if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'peak_intensity_type') or not cdp.ri_ids[i] in cdp.exp_info.peak_intensity_type.keys(): 
345                      missing.append("The peak intensity type for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
346   
347                  # Check the temperature calibration methods. 
348                  if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_calibration') or not cdp.ri_ids[i] in cdp.exp_info.temp_calibration.keys(): 
349                      missing.append("The temperature calibration method for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
350   
351                  # Check the temperature control methods. 
352                  if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_control') or not cdp.ri_ids[i] in cdp.exp_info.temp_control.keys(): 
353                      missing.append("The temperature control method for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
354   
355   
356          # Loop over the molecules. 
357          for mol, mol_id in molecule_loop(return_id=True): 
358              # No name. 
359              if mol.name == None: 
360                  missing.append("The name of the molecule for %s." % mol_id) 
361                  continue 
362   
363              # No molecule type. 
364              if not hasattr(mol, 'type') or mol.type == None: 
365                  missing.append("The type of the molecule %s." % mol_id) 
366   
367              # No thiol state. 
368              if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'): 
369                  missing.append("The thiol state of the molecule %s." % mol_id) 
370   
371          # Return the list of missing data. 
372          return missing 
373   
374   
375 -    def observer_register(self, remove=False): 
376          """Register and unregister methods with the observer objects. 
377   
378          @keyword remove:    If set to True, then the methods will be unregistered. 
379          @type remove:       False 
380          """ 
381   
382          # Register. 
383          if not remove: 
384              status.observers.pipe_alteration.register('BMRB export', self.update_pipes, method_name='update_pipes') 
385   
386          # Unregister. 
387          else: 
388              # The class methods. 
389              status.observers.pipe_alteration.unregister('BMRB export') 
390   
391              # The embedded objects methods. 
392              self.relax_data.observer_register(remove=True) 
393              self.molecule.observer_register(remove=True) 
394              self.software.observer_register(remove=True) 
395              self.scripts.observer_register(remove=True) 
396              self.citation.observer_register(remove=True) 
397   
398   
399 -    def setup_frame(self): 
400          """Set up the relax controller frame. 
401          @return:    The sizer object. 
402          @rtype:     wx.Sizer instance 
403          """ 
404   
405          # Set the frame title. 
406          self.SetTitle("BMRB export window") 
407   
408          # Set up the window icon. 
409          self.SetIcons(relax_icons) 
410   
411          # Place all elements within a panel (to remove the dark grey in MS Windows). 
412          self.main_panel = wx.Panel(self, -1) 
413   
414          # Use a grid sizer for packing the main elements. 
415          main_sizer = wx.BoxSizer(wx.VERTICAL) 
416          self.main_panel.SetSizer(main_sizer) 
417   
418          # Build the central sizer, with borders. 
419          sizer = add_border(main_sizer, border=self.border, packing=wx.VERTICAL) 
420   
421          # Close the window cleanly (unregistering observers). 
422          self.Bind(wx.EVT_CLOSE, self.handler_close) 
423   
424          # Set the default size of the controller. 
425          self.SetSize(self.size) 
426          self.SetMinSize(self.size_min) 
427   
428          # Centre the frame. 
429          self.Centre() 
430   
431          # Return the central sizer. 
432          return sizer 
433   
434   
435 -    def update_pipes(self, event=None): 
436          """Update the spin view data pipe selector. 
437   
438          @keyword event: The wx event. 
439          @type event:    wx event 
440          """ 
441   
442          # Change the cursor to busy. 
443          wx.BeginBusyCursor() 
444   
445          # Init. 
446          pipe_switch = False 
447   
448          # The selected pipe. 
449          if event: 
450              # The name of the selected pipe. 
451              pipe = gui_to_str(self.pipe_name.GetString(event.GetSelection())) 
452   
453              # A pipe change. 
454              if pipe != cdp_name(): 
455                  pipe_switch = True 
456          else: 
457              pipe = cdp_name() 
458          if not pipe: 
459              pipe = '' 
460   
461          # Clear the previous data. 
462          self.pipe_name.Clear() 
463   
464          # The list of pipe names. 
465          for name in pipe_names(): 
466              self.pipe_name.Append(str_to_gui(name)) 
467   
468          # Switch data pipes. 
469          if pipe_switch: 
470              switch(pipe) 
471   
472          # Set the pipe name to the cdp. 
473          self.pipe_name.SetValue(str_to_gui(pipe)) 
474   
475          # Reset the cursor. 
476          if wx.IsBusy(): 
477              wx.EndBusyCursor() 
478