Source Code for Module gui.export_bmrb

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2012-2013 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 graphics import IMAGE_PATH, fetch_icon 
 30  from gui.components.citations import Citations 
 31  from gui.components.molecule import Molecule 
 32  from gui.components.relax_data_meta import Relax_data_meta_list 
 33  from gui.components.scripts import Scripts 
 34  from gui.components.software import Software 
 35  from gui.message import Missing_data 
 36  from gui.fonts import font 
 37  from gui.icons import relax_icons 
 38  from gui.misc import add_border, bitmap_setup 
 39  from gui.string_conv import gui_to_str, str_to_gui 
 40  from gui.uf_objects import Uf_storage; uf_store = Uf_storage() 
 41  from pipe_control.mol_res_spin import molecule_loop 
 42  from pipe_control.pipes import cdp_name, pipe_names, switch 
 43  from status import Status; status = Status() 
 44   
 45   
 46 -class Export_bmrb_window(wx.Frame): 
 47      """The BMRB export window.""" 
 48   
 49 -    def __init__(self, gui): 
 50          """Set up the export window. 
 51   
 52          @param gui:     The GUI object. 
 53          @type gui:      wx.Frame instance 
 54          """ 
 55   
 56          # The window style. 
 57          style = wx.DEFAULT_FRAME_STYLE 
 58          if not status.debug and status.wx_info["os"] != 'darwin': 
 59              style = style | wx.MAXIMIZE 
 60   
 61          # Initialise the base class, setting the main GUI window as the parent. 
 62          super(Export_bmrb_window, self).__init__(gui, -1, style=style) 
 63   
 64          # Some default values. 
 65          self.size = (1200, 900) 
 66          self.size_min = (900, 700) 
 67          self.border = 5 
 68          self.spacer = 10 
 69          self.button_size = (200, 40) 
 70          self.button_spacing = 10 
 71          self.main_spacing = 20 
 72   
 73          # Set up the frame. 
 74          sizer = self.setup_frame() 
 75   
 76          # Add the header. 
 77          self.add_header(sizer) 
 78   
 79          # Top spacing. 
 80          sizer.AddSpacer(10) 
 81   
 82          # Add the data pipe selection element. 
 83          self.add_pipe(sizer) 
 84   
 85          # Spacing. 
 86          sizer.AddSpacer(self.main_spacing) 
 87   
 88          # Add the relaxation data metadata list GUI element. 
 89          self.relax_data = Relax_data_meta_list(parent=self.main_panel, box=sizer, id='BMRB export', proportion=2) 
 90   
 91          # Spacing. 
 92          sizer.AddSpacer(self.main_spacing) 
 93   
 94          # Add the molecule GUI element. 
 95          self.molecule = Molecule(parent=self.main_panel, box=sizer, id='BMRB export', proportion=1) 
 96   
 97          # Spacing. 
 98          sizer.AddSpacer(self.main_spacing) 
 99   
100          # Create a horizontal layout for the software, script and citations GUI elements. 
101          sub_sizer = wx.BoxSizer(wx.HORIZONTAL) 
102   
103          # Add the software GUI element. 
104          self.software = Software(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
105   
106          # Vertical spacing. 
107          sub_sizer.AddSpacer(self.main_spacing) 
108   
109          # Add the scripts GUI element. 
110          self.scripts = Scripts(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
111   
112          # Vertical spacing. 
113          sub_sizer.AddSpacer(self.main_spacing) 
114   
115          # Add the citation GUI element. 
116          self.citation = Citations(parent=self.main_panel, box=sub_sizer, id='BMRB export', proportion=1) 
117   
118          # Add the sizer. 
119          sizer.Add(sub_sizer, 2, wx.ALL|wx.EXPAND, 0) 
120   
121          # Bottom spacing. 
122          sizer.AddSpacer(10) 
123   
124          # Add the buttons. 
125          self.add_buttons(sizer) 
126   
127          # Open the window. 
128          if status.show_gui: 
129              self.Show() 
130   
131   
132 -    def action_cancel(self, event=None): 
133          """Cancel the export. 
134   
135          @keyword event: The wx event. 
136          @type event:    wx event 
137          """ 
138   
139          # Close the window. 
140          self.Close() 
141   
142   
143 -    def action_export(self, event=None): 
144          """Write out the NMR-STAR formatted data. 
145   
146          @keyword event: The wx event. 
147          @type event:    wx event 
148          """ 
149   
150          # Checks. 
151          missing = self.is_complete() 
152   
153          # Missing data. 
154          if len(missing): 
155              Missing_data(missing, parent=self) 
156              return 
157   
158          # Execute the user function. 
159          uf_store['bmrb.write'](wx_parent=self, wx_wizard_sync=True, wx_wizard_modal=True) 
160   
161          # Close the window. 
162          self.Close() 
163   
164   
165 -    def action_preview(self, event=None): 
166          """Preview the NMR-STAR formatted data. 
167   
168          @keyword event: The wx event. 
169          @type event:    wx event 
170          """ 
171   
172          # Execute the user function. 
173          uf_store['bmrb.display'](wx_parent=self) 
174   
175   
176 -    def add_buttons(self, sizer): 
177          """Build and add the bottom buttons. 
178   
179          @param sizer:   The sizer element to pack the buttons into. 
180          @type sizer:    wx.Sizer instance 
181          """ 
182   
183          # Button sizer. 
184          button_sizer = wx.BoxSizer(wx.HORIZONTAL) 
185          sizer.Add(button_sizer, 0, wx.ALIGN_RIGHT, 0) 
186   
187          # Preview button. 
188          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Preview") 
189          button.SetBitmapLabel(wx.Bitmap(fetch_icon('oxygen.actions.document-preview', "32x32"), wx.BITMAP_TYPE_ANY)) 
190          button.SetFont(font.normal) 
191          button.SetMinSize(self.button_size) 
192          button_sizer.Add(button, 0, 0, 0) 
193          self.Bind(wx.EVT_BUTTON, self.action_preview, button) 
194          button.SetToolTipString("Preview the NMR-STAR formatted data.") 
195   
196          # Spacing. 
197          button_sizer.AddSpacer(self.button_spacing) 
198   
199          # Export button. 
200          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Export") 
201          button.SetBitmapLabel(wx.Bitmap(fetch_icon('relax.bmrb', "32x32"), wx.BITMAP_TYPE_ANY)) 
202          button.SetFont(font.normal) 
203          button.SetMinSize(self.button_size) 
204          button_sizer.Add(button, 0, 0, 0) 
205          self.Bind(wx.EVT_BUTTON, self.action_export, button) 
206          button.SetToolTipString("Create the NMR-STAR formatted file for BMRB deposition.") 
207   
208          # Spacing. 
209          button_sizer.AddSpacer(self.button_spacing) 
210   
211          # Cancel button. 
212          button = wx.lib.buttons.ThemedGenBitmapTextButton(self.main_panel, -1, None, " Cancel") 
213          button.SetBitmapLabel(wx.Bitmap(fetch_icon('oxygen.actions.dialog-cancel', "32x32"), wx.BITMAP_TYPE_ANY)) 
214          button.SetFont(font.normal) 
215          button.SetMinSize(self.button_size) 
216          button_sizer.Add(button, 0, 0, 0) 
217          self.Bind(wx.EVT_BUTTON, self.action_cancel, button) 
218          button.SetToolTipString("Cancel the BMRB export.") 
219   
220   
221 -    def add_header(self, sizer): 
222          """Build and add the header to the sizer. 
223   
224          @param sizer:   The sizer element to pack the header into. 
225          @type sizer:    wx.Sizer instance 
226          """ 
227   
228          # Create a horizontal layout. 
229          sub_sizer = wx.BoxSizer(wx.HORIZONTAL) 
230   
231          # Left spacing. 
232          sub_sizer.AddStretchSpacer(3) 
233   
234          # Add the BMRB logo (left side). 
235          logo = wx.StaticBitmap(self.main_panel, -1, bitmap_setup(IMAGE_PATH+"bmrb_100x100.png")) 
236          sub_sizer.Add(logo, 0, wx.TOP|wx.ALIGN_CENTER_HORIZONTAL, 0) 
237   
238          # Spacing. 
239          sub_sizer.AddStretchSpacer() 
240   
241          # The text sizer. 
242          text_sizer = wx.BoxSizer(wx.VERTICAL) 
243   
244          # The title. 
245          text = wx.StaticText(self.main_panel, -1, 'Data export for BMRB deposition', style=wx.ALIGN_LEFT) 
246          text.SetFont(font.title) 
247          text_sizer.Add(text, 0, wx.ALIGN_CENTER_HORIZONTAL, 0) 
248   
249          # Spacing. 
250          text_sizer.AddSpacer(15) 
251   
252          # The text. 
253          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.' 
254          text = wx.StaticText(self.main_panel, -1, main_text, style=wx.ALIGN_LEFT) 
255          text.Wrap(600) 
256          text.SetFont(font.normal) 
257          text_sizer.Add(text, 0, 0, 0) 
258   
259          # Add the text sizer. 
260          sub_sizer.Add(text_sizer, 0, 0, 0) 
261   
262          # Spacing. 
263          sub_sizer.AddStretchSpacer() 
264   
265          # Add the BMRB logo (right side). 
266          logo = wx.StaticBitmap(self.main_panel, -1, bitmap_setup(IMAGE_PATH+"bmrb_100x100.png")) 
267          sub_sizer.Add(logo, 0, wx.TOP|wx.ALIGN_CENTER_HORIZONTAL, 0) 
268   
269          # Right spacing. 
270          sub_sizer.AddStretchSpacer(3) 
271   
272          # Add the sizer. 
273          sizer.Add(sub_sizer, 0, wx.ALL|wx.EXPAND, 0) 
274   
275          # A line with spacing. 
276          sizer.AddSpacer(10) 
277          sizer.Add(wx.StaticLine(self.main_panel, -1), 0, wx.EXPAND|wx.ALL, 0) 
278          sizer.AddSpacer(10) 
279   
280   
281 -    def add_pipe(self, sizer): 
282          """Build and add the data pipe selection element. 
283   
284          @param sizer:   The sizer element to pack the buttons into. 
285          @type sizer:    wx.Sizer instance 
286          """ 
287   
288          # A sizer for the element. 
289          pipe_sizer = wx.BoxSizer(wx.HORIZONTAL) 
290          sizer.Add(pipe_sizer, 0, wx.ALIGN_LEFT, 0) 
291   
292          # The pipe text. 
293          text = wx.StaticText(self.main_panel, -1, ' The data pipe to export:  ', style=wx.ALIGN_LEFT) 
294          tooltip = "The name of the data pipe to export to NMR-STAR format for BMRB export." 
295          text.SetFont(font.normal) 
296          text.SetToolTipString(tooltip) 
297          pipe_sizer.Add(text, 0, wx.ALIGN_CENTER_VERTICAL, 0) 
298   
299          # Spacing. 
300          pipe_sizer.AddSpacer(20) 
301   
302          # The pipe selection. 
303          self.pipe_name = wx.ComboBox(self.main_panel, -1, "", style=wx.CB_DROPDOWN|wx.CB_READONLY, choices=[]) 
304          self.pipe_name.SetToolTipString(tooltip) 
305          self.Bind(wx.EVT_COMBOBOX, self.update_pipes, self.pipe_name) 
306          pipe_sizer.Add(self.pipe_name, 0, wx.ALIGN_CENTER_VERTICAL, 0) 
307   
308          # Update the pipe selection. 
309          self.update_pipes() 
310   
311   
312 -    def handler_close(self, event): 
313          """Event handler for the close window action. 
314   
315          @param event:   The wx event. 
316          @type event:    wx event 
317          """ 
318   
319          # Unregister the observers. 
320          self.observer_register(remove=True) 
321   
322          # Close the window. 
323          event.Skip() 
324   
325   
326 -    def is_complete(self): 
327          """Determine if the data input is complete. 
328   
329          @return:    A list of all the missing components. 
330          @rtype:     list of str 
331          """ 
332   
333          # Initialise. 
334          missing = [] 
335   
336          # Relaxation data metadata. 
337          if hasattr(cdp, 'ri_ids'): 
338              # Loop over the data. 
339              for i in range(len(cdp.ri_ids)): 
340                  # Check the peak intensity types. 
341                  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(): 
342                      missing.append("The peak intensity type for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
343   
344                  # Check the temperature calibration methods. 
345                  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(): 
346                      missing.append("The temperature calibration method for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
347   
348                  # Check the temperature control methods. 
349                  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(): 
350                      missing.append("The temperature control method for the relaxation data ID '%s'." % cdp.ri_ids[i]) 
351   
352   
353          # Loop over the molecules. 
354          for mol, mol_id in molecule_loop(return_id=True): 
355              # No name. 
356              if mol.name == None: 
357                  missing.append("The name of the molecule for %s." % mol_id) 
358                  continue 
359   
360              # No molecule type. 
361              if not hasattr(mol, 'type') or mol.type == None: 
362                  missing.append("The type of the molecule %s." % mol_id) 
363   
364              # No thiol state. 
365              if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'): 
366                  missing.append("The thiol state of the molecule %s." % mol_id) 
367   
368          # Return the list of missing data. 
369          return missing 
370   
371   
372 -    def observer_register(self, remove=False): 
373          """Register and unregister methods with the observer objects. 
374   
375          @keyword remove:    If set to True, then the methods will be unregistered. 
376          @type remove:       False 
377          """ 
378   
379          # Register. 
380          if not remove: 
381              status.observers.pipe_alteration.register('BMRB export', self.update_pipes, method_name='update_pipes') 
382   
383          # Unregister. 
384          else: 
385              # The class methods. 
386              status.observers.pipe_alteration.unregister('BMRB export') 
387   
388              # The embedded objects methods. 
389              self.relax_data.observer_register(remove=True) 
390              self.molecule.observer_register(remove=True) 
391              self.software.observer_register(remove=True) 
392              self.scripts.observer_register(remove=True) 
393              self.citation.observer_register(remove=True) 
394   
395   
396 -    def setup_frame(self): 
397          """Set up the relax controller frame. 
398          @return:    The sizer object. 
399          @rtype:     wx.Sizer instance 
400          """ 
401   
402          # Set the frame title. 
403          self.SetTitle("BMRB export window") 
404   
405          # Set up the window icon. 
406          self.SetIcons(relax_icons) 
407   
408          # Place all elements within a panel (to remove the dark grey in MS Windows). 
409          self.main_panel = wx.Panel(self, -1) 
410   
411          # Use a grid sizer for packing the main elements. 
412          main_sizer = wx.BoxSizer(wx.VERTICAL) 
413          self.main_panel.SetSizer(main_sizer) 
414   
415          # Build the central sizer, with borders. 
416          sizer = add_border(main_sizer, border=self.border, packing=wx.VERTICAL) 
417   
418          # Close the window cleanly (unregistering observers). 
419          self.Bind(wx.EVT_CLOSE, self.handler_close) 
420   
421          # Set the default size of the controller. 
422          self.SetSize(self.size) 
423          self.SetMinSize(self.size_min) 
424   
425          # Centre the frame. 
426          self.Centre() 
427   
428          # Return the central sizer. 
429          return sizer 
430   
431   
432 -    def update_pipes(self, event=None): 
433          """Update the spin view data pipe selector. 
434   
435          @keyword event: The wx event. 
436          @type event:    wx event 
437          """ 
438   
439          # Change the cursor to busy. 
440          wx.BeginBusyCursor() 
441   
442          # Init. 
443          pipe_switch = False 
444   
445          # The selected pipe. 
446          if event: 
447              # The name of the selected pipe. 
448              pipe = gui_to_str(self.pipe_name.GetString(event.GetSelection())) 
449   
450              # A pipe change. 
451              if pipe != cdp_name(): 
452                  pipe_switch = True 
453          else: 
454              pipe = cdp_name() 
455          if not pipe: 
456              pipe = '' 
457   
458          # Clear the previous data. 
459          self.pipe_name.Clear() 
460   
461          # The list of pipe names. 
462          for name in pipe_names(): 
463              self.pipe_name.Append(str_to_gui(name)) 
464   
465          # Switch data pipes. 
466          if pipe_switch: 
467              switch(pipe) 
468   
469          # Set the pipe name to the cdp. 
470          self.pipe_name.SetValue(str_to_gui(pipe)) 
471   
472          # Reset the cursor. 
473          if wx.IsBusy(): 
474              wx.EndBusyCursor() 
475