Source Code for Module Gnumed.wxpython.gmDataMiningWidgets

  1  """GNUmed data mining related widgets.""" 
  2   
  3  #================================================================ 
  4  __author__ = 'karsten.hilbert@gmx.net' 
  5  __license__ = 'GPL v2 or later (details at http://www.gnu.org)' 
  6   
  7   
  8  # stdlib 
  9  import sys 
 10  import os 
 11  import fileinput 
 12  import logging 
 13   
 14   
 15  # 3rd party 
 16  import wx 
 17   
 18   
 19  # GNUmed 
 20  if __name__ == '__main__': 
 21          sys.path.insert(0, '../../') 
 22  from Gnumed.pycommon import gmDispatcher 
 23  from Gnumed.pycommon import gmMimeLib 
 24  from Gnumed.pycommon import gmTools 
 25  from Gnumed.pycommon import gmPG2 
 26  from Gnumed.pycommon import gmMatchProvider 
 27  from Gnumed.pycommon import gmI18N 
 28  from Gnumed.pycommon import gmNetworkTools 
 29   
 30  from Gnumed.business import gmPerson 
 31  from Gnumed.business import gmDataMining 
 32  from Gnumed.business import gmPersonSearch 
 33   
 34  from Gnumed.wxpython import gmGuiHelpers 
 35  from Gnumed.wxpython import gmListWidgets 
 36   
 37   
 38  _log = logging.getLogger('gm.ui') 
 39  #================================================================ 
 40 -class cPatientListingCtrl(gmListWidgets.cReportListCtrl): 
 41   
 42 -        def __init__(self, *args, **kwargs): 
 43                  """<patient_key> must index or name a column in self.__data""" 
 44                  try: 
 45                          self.patient_key = kwargs['patient_key'] 
 46                          del kwargs['patient_key'] 
 47                  except KeyError: 
 48                          self.patient_key = None 
 49   
 50                  gmListWidgets.cReportListCtrl.__init__(self, *args, **kwargs) 
 51   
 52                  self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self._on_list_item_activated, self) 
 53          #------------------------------------------------------------ 
 54 -        def __get_patient_pk_column(self, data=None): 
 55                  if self.patient_key is not None: 
 56                          try: 
 57                                  data[self.pk_patient] 
 58                                  return self.patient_key 
 59                          except (KeyError, IndexError, TypeError): 
 60                                  _log.error('misconfigured identifier column <%s>', self.patient_key) 
 61   
 62                  _log.debug('identifier column not configured, trying to detect') 
 63   
 64                  if data.has_key('pk_patient'): 
 65                          return u'pk_patient' 
 66   
 67                  if data.has_key('pk_identity'): 
 68                          return u'pk_identity' 
 69   
 70                  return gmListWidgets.get_choices_from_list ( 
 71                          parent = self, 
 72                          msg = _( 
 73                                  'The report result list does not contain any columns\n' 
 74                                  'named "%s", "pk_patient", or "pk_identity".\n' 
 75                                  '\n' 
 76                                  'Select the column which contains patient IDs:\n' 
 77                          ) % self.patient_key, 
 78                          caption = _('Choose column from query results ...'), 
 79                          choices = data.keys(), 
 80                          columns = [_('Column name')], 
 81                          single_selection = True 
 82                  ) 
 83          #------------------------------------------------------------ 
 84          # event handling 
 85          #------------------------------------------------------------ 
 86 -        def _on_list_item_activated(self, evt): 
 87                  data = self.get_selected_item_data(only_one=True) 
 88                  pk_pat_col = self.__get_patient_pk_column(data = data) 
 89   
 90                  if pk_pat_col is None: 
 91                          gmDispatcher.send(signal = 'statustext', msg = _('List not known to be patient-related.')) 
 92                          return 
 93   
 94                  pat_data = data[pk_pat_col] 
 95                  try: 
 96                          pat_pk = int(pat_data) 
 97                          pat = gmPerson.cIdentity(aPK_obj = pat_pk) 
 98                  except (ValueError, TypeError): 
 99                          searcher = gmPersonSearch.cPatientSearcher_SQL() 
100                          idents = searcher.get_identities(pat_data) 
101                          if len(idents) == 0: 
102                                  gmDispatcher.send(signal = 'statustext', msg = _('No matching patient found.')) 
103                                  return 
104                          if len(idents) == 1: 
105                                  pat = idents[0] 
106                          else: 
107                                  from Gnumed.wxpython import gmPatSearchWidgets 
108                                  dlg = gmPatSearchWidgets.cSelectPersonFromListDlg(parent=wx.GetTopLevelParent(self), id=-1) 
109                                  dlg.set_persons(persons=idents) 
110                                  result = dlg.ShowModal() 
111                                  if result == wx.ID_CANCEL: 
112                                          dlg.Destroy() 
113                                          return 
114                                  pat = dlg.get_selected_person() 
115                                  dlg.Destroy() 
116   
117                  from Gnumed.wxpython import gmPatSearchWidgets 
118                  gmPatSearchWidgets.set_active_patient(patient = pat) 
119   
120  #================================================================ 
121  from Gnumed.wxGladeWidgets import wxgPatientListingPnl 
122   
123 -class cPatientListingPnl(wxgPatientListingPnl.wxgPatientListingPnl): 
124   
125 -        def __init__(self, *args, **kwargs): 
126   
127                  try: 
128                          button_defs = kwargs['button_defs'][:5] 
129                          del kwargs['button_defs'] 
130                  except KeyError: 
131                          button_defs = [] 
132   
133                  try: 
134                          msg = kwargs['message'] 
135                          del kwargs['message'] 
136                  except KeyError: 
137                          msg = None 
138   
139                  wxgPatientListingPnl.wxgPatientListingPnl.__init__(self, *args, **kwargs) 
140   
141                  if msg is not None: 
142                          self._lbl_msg.SetLabel(msg) 
143   
144                  buttons = [self._BTN_1, self._BTN_2, self._BTN_3, self._BTN_4, self._BTN_5] 
145                  for idx in range(len(button_defs)): 
146                          button_def = button_defs[idx] 
147                          if button_def['label'].strip() == u'': 
148                                  continue 
149                          buttons[idx].SetLabel(button_def['label']) 
150                          buttons[idx].SetToolTipString(button_def['tooltip']) 
151                          buttons[idx].Enable(True) 
152   
153                  self.Fit() 
154          #------------------------------------------------------------ 
155          # event handling 
156          #------------------------------------------------------------ 
157 -        def _on_BTN_1_pressed(self, event): 
158                  event.Skip() 
159          #------------------------------------------------------------ 
160 -        def _on_BTN_2_pressed(self, event): 
161                  event.Skip() 
162          #------------------------------------------------------------ 
163 -        def _on_BTN_3_pressed(self, event): 
164                  event.Skip() 
165          #------------------------------------------------------------ 
166 -        def _on_BTN_4_pressed(self, event): 
167                  event.Skip() 
168          #------------------------------------------------------------ 
169 -        def _on_BTN_5_pressed(self, event): 
170                  event.Skip() 
171   
172  #================================================================ 
173  from Gnumed.wxGladeWidgets import wxgDataMiningPnl 
174   
175 -class cDataMiningPnl(wxgDataMiningPnl.wxgDataMiningPnl): 
176   
177 -        def __init__(self, *args, **kwargs): 
178                  wxgDataMiningPnl.wxgDataMiningPnl.__init__(self, *args, **kwargs) 
179   
180                  self.__init_ui() 
181   
182                  # make me a file drop target 
183                  dt = gmGuiHelpers.cFileDropTarget(self) 
184                  self.SetDropTarget(dt) 
185          #-------------------------------------------------------- 
186 -        def __init_ui(self): 
187                  mp = gmMatchProvider.cMatchProvider_SQL2 ( 
188                          queries = [u""" 
189                                  SELECT DISTINCT ON (label) 
190                                          cmd, 
191                                          label 
192                                  FROM cfg.report_query 
193                                  WHERE 
194                                          label %(fragment_condition)s 
195                                                  OR 
196                                          cmd %(fragment_condition)s 
197                          """] 
198                  ) 
199                  mp.setThresholds(2,3,5) 
200                  self._PRW_report_name.matcher = mp 
201                  self._PRW_report_name.add_callback_on_selection(callback = self._on_report_selected) 
202                  self._PRW_report_name.add_callback_on_lose_focus(callback = self._auto_load_report) 
203          #-------------------------------------------------------- 
204 -        def _auto_load_report(self, *args, **kwargs): 
205                  if self._TCTRL_query.GetValue() == u'': 
206                          if self._PRW_report_name.GetData() is not None: 
207                                  self._TCTRL_query.SetValue(self._PRW_report_name.GetData()) 
208                                  self._BTN_run.SetFocus() 
209          #-------------------------------------------------------- 
210 -        def _on_report_selected(self, *args, **kwargs): 
211                  self._TCTRL_query.SetValue(self._PRW_report_name.GetData()) 
212                  self._BTN_run.SetFocus() 
213          #-------------------------------------------------------- 
214          # file drop target API 
215          #-------------------------------------------------------- 
216 -        def add_filenames(self, filenames): 
217                  # act on first file only 
218                  fname = filenames[0] 
219                  _log.debug('importing SQL from <%s>', fname) 
220                  # act on text files only 
221                  mime_type = gmMimeLib.guess_mimetype(fname) 
222                  _log.debug('mime type: %s', mime_type) 
223                  if not mime_type.startswith('text/'): 
224                          _log.debug('not a text file') 
225                          gmDispatcher.send(signal='statustext', msg = _('Cannot read SQL from [%s]. Not a text file.') % fname, beep = True) 
226                          return False 
227  #               # act on "small" files only 
228  #               stat_val = os.stat(fname) 
229  #               if stat_val.st_size > 5000: 
230  #                       gmDispatcher.send(signal='statustext', msg = _('Cannot read SQL from [%s]. File too big (> 2000 bytes).') % fname, beep = True) 
231  #                       return False 
232                  # all checks passed 
233                  for line in fileinput.input(fname): 
234                          self._TCTRL_query.AppendText(line) 
235          #-------------------------------------------------------- 
236          # notebook plugin API 
237          #-------------------------------------------------------- 
238 -        def repopulate_ui(self): 
239                  pass 
240          #-------------------------------------------------------- 
241          # event handlers 
242          #-------------------------------------------------------- 
243 -        def _on_contribute_button_pressed(self, evt): 
244                  report = self._PRW_report_name.GetValue().strip() 
245                  if report == u'': 
246                          gmDispatcher.send(signal = 'statustext', msg = _('Report must have a name for contribution.'), beep = False) 
247                          return 
248   
249                  query = self._TCTRL_query.GetValue().strip() 
250                  if query == u'': 
251                          gmDispatcher.send(signal = 'statustext', msg = _('Report must have a query for contribution.'), beep = False) 
252                          return 
253   
254                  do_it = gmGuiHelpers.gm_show_question ( 
255                          _(      'Be careful that your contribution (the query itself) does\n' 
256                                  'not contain any person-identifiable search parameters.\n' 
257                                  '\n' 
258                                  'Note, however, that no query result data whatsoever\n' 
259                                  'is included in the contribution that will be sent.\n' 
260                                  '\n' 
261                                  'Are you sure you wish to send this query to\n' 
262                                  'the gnumed community mailing list?\n' 
263                          ), 
264                          _('Contributing custom report') 
265                  ) 
266                  if not do_it: 
267                          return 
268   
269                  auth = {'user': gmNetworkTools.default_mail_sender, 'password': u'gnumed-at-gmx-net'} 
270                  msg = u"""--- This is a report definition contributed by a GNUmed user. 
271   
272  --- Save it as a text file and drop it onto the Report Generator 
273  --- inside GNUmed in order to take advantage of the contribution. 
274   
275  ---------------------------------------- 
276   
277  --- %s 
278   
279  %s 
280   
281  ---------------------------------------- 
282   
283  --- The GNUmed client. 
284  """ % (report, query) 
285   
286                  if not gmNetworkTools.send_mail ( 
287                          sender = u'GNUmed Report Generator <gnumed@gmx.net>', 
288                          receiver = [u'gnumed-devel@gnu.org'], 
289                          subject = u'user contributed report', 
290                          message = msg, 
291                          encoding = gmI18N.get_encoding(), 
292                          server = gmNetworkTools.default_mail_server, 
293                          auth = auth 
294                  ): 
295                          gmDispatcher.send(signal = 'statustext', msg = _('Unable to send mail. Cannot contribute report [%s] to GNUmed community.') % report, beep = True) 
296                          return False 
297   
298                  gmDispatcher.send(signal = 'statustext', msg = _('Thank you for your contribution to the GNUmed community!'), beep = False) 
299                  return True 
300          #-------------------------------------------------------- 
301 -        def _on_schema_button_pressed(self, evt): 
302                  # will block when called in text mode (that is, from a terminal, too !) 
303                  gmNetworkTools.open_url_in_browser(url = u'http://wiki.gnumed.de/bin/view/Gnumed/DatabaseSchema') 
304          #-------------------------------------------------------- 
305 -        def _on_delete_button_pressed(self, evt): 
306                  report = self._PRW_report_name.GetValue().strip() 
307                  if report == u'': 
308                          return True 
309                  if gmDataMining.delete_report_definition(name=report): 
310                          self._PRW_report_name.SetText() 
311                          self._TCTRL_query.SetValue(u'') 
312                          gmDispatcher.send(signal='statustext', msg = _('Deleted report definition [%s].') % report, beep=False) 
313                          return True 
314                  gmDispatcher.send(signal='statustext', msg = _('Error deleting report definition [%s].') % report, beep=True) 
315                  return False 
316          #-------------------------------------------------------- 
317 -        def _on_clear_button_pressed(self, evt): 
318                  self._PRW_report_name.SetText() 
319                  self._TCTRL_query.SetValue(u'') 
320                  self._LCTRL_result.set_columns() 
321          #-------------------------------------------------------- 
322 -        def _on_save_button_pressed(self, evt): 
323                  report = self._PRW_report_name.GetValue().strip() 
324                  if report == u'': 
325                          gmDispatcher.send(signal='statustext', msg = _('Cannot save report definition without name.'), beep=True) 
326                          return False 
327                  query = self._TCTRL_query.GetValue().strip() 
328                  if query == u'': 
329                          gmDispatcher.send(signal='statustext', msg = _('Cannot save report definition without query.'), beep=True) 
330                          return False 
331                  # FIXME: check for exists and ask for permission 
332                  if gmDataMining.save_report_definition(name=report, query=query, overwrite=True): 
333                          gmDispatcher.send(signal='statustext', msg = _('Saved report definition [%s].') % report, beep=False) 
334                          return True 
335                  gmDispatcher.send(signal='statustext', msg = _('Error saving report definition [%s].') % report, beep=True) 
336                  return False 
337          #-------------------------------------------------------- 
338 -        def _on_visualize_button_pressed(self, evt): 
339   
340                  try: 
341                          # better fail early 
342                          import Gnuplot 
343                  except ImportError: 
344                          gmGuiHelpers.gm_show_info ( 
345                                  aMessage = _('Cannot import "Gnuplot" python module.'), 
346                                  aTitle = _('Query result visualizer') 
347                          ) 
348                          return 
349   
350                  x_col = gmListWidgets.get_choices_from_list ( 
351                          parent = self, 
352                          msg = _('Choose a column to be used as the X-Axis:'), 
353                          caption = _('Choose column from query results ...'), 
354                          choices = self.query_results[0].keys(), 
355                          columns = [_('Column name')], 
356                          single_selection = True 
357                  ) 
358                  if x_col is None: 
359                          return 
360   
361                  y_col = gmListWidgets.get_choices_from_list ( 
362                          parent = self, 
363                          msg = _('Choose a column to be used as the Y-Axis:'), 
364                          caption = _('Choose column from query results ...'), 
365                          choices = self.query_results[0].keys(), 
366                          columns = [_('Column name')], 
367                          single_selection = True 
368                  ) 
369                  if y_col is None: 
370                          return 
371   
372                  # FIXME: support debugging (debug=1) depending on --debug 
373                  gp = Gnuplot.Gnuplot(persist=1) 
374                  if self._PRW_report_name.GetValue().strip() != u'': 
375                          gp.title(_('GNUmed report: %s') % self._PRW_report_name.GetValue().strip()[:40]) 
376                  else: 
377                          gp.title(_('GNUmed report results')) 
378                  gp.xlabel(x_col) 
379                  gp.ylabel(y_col) 
380                  try: 
381                          gp.plot([ [r[x_col], r[y_col]] for r in self.query_results ]) 
382                  except StandardError: 
383                          _log.exception('unable to plot results from [%s:%s]' % (x_col, y_col)) 
384                          gmDispatcher.send(signal = 'statustext', msg = _('Error plotting data.'), beep = True) 
385   
386                  return 
387          #-------------------------------------------------------- 
388 -        def _on_run_button_pressed(self, evt): 
389   
390                  self._BTN_visualize.Enable(False) 
391   
392                  user_query = self._TCTRL_query.GetValue().strip().strip(';') 
393                  if user_query == u'': 
394                          return True 
395   
396                  # FIXME: make LIMIT configurable 
397                  limit = u'1001' 
398   
399                  wrapper_query = u""" 
400                          SELECT * 
401                          FROM ( 
402                                  %%s 
403                          ) AS user_query 
404                          LIMIT %s 
405                  """ % limit 
406   
407                  # does user want to insert current patient ID ? 
408                  patient_id_token = u'$<ID_active_patient>$' 
409                  if user_query.find(patient_id_token) != -1: 
410                          # she does, but is it possible ? 
411                          curr_pat = gmPerson.gmCurrentPatient() 
412                          if not curr_pat.connected: 
413                                  gmGuiHelpers.gm_show_error ( 
414                                          aMessage = _( 
415                                                  'This query requires a patient to be\n' 
416                                                  'active in the client.\n' 
417                                                  '\n' 
418                                                  'Please activate the patient you are interested\n' 
419                                                  'in and re-run the query.\n' 
420                                          ), 
421                                          aTitle = _('Active patient query') 
422                                  ) 
423                                  return False 
424                          wrapper_query = u""" 
425                                  SELECT 
426                                          %s AS pk_patient, 
427                                          * 
428                                  FROM ( 
429                                          %%s 
430                                  ) AS user_query 
431                                  LIMIT %s 
432                          """ % (str(curr_pat.ID), limit) 
433                          user_query = user_query.replace(patient_id_token, str(curr_pat.ID)) 
434   
435                  self._LCTRL_result.set_columns() 
436   
437                  query = wrapper_query % user_query 
438                  try: 
439                          # read-only for safety reasons 
440                          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': query}], get_col_idx = True) 
441                  except StandardError: 
442                          _log.exception('report query failed') 
443                          self._LCTRL_result.set_columns([_('Error')]) 
444                          t, v = sys.exc_info()[:2] 
445                          rows = [ 
446                                  [_('The query failed.')], 
447                                  [u''], 
448                                  [unicode(t)] 
449                          ] 
450                          for line in str(v).decode(gmI18N.get_encoding()).split('\n'): 
451                                  rows.append([line]) 
452                          rows.append([u'']) 
453                          for line in user_query.split('\n'): 
454                                  rows.append([line]) 
455                          self._LCTRL_result.set_string_items(rows) 
456                          self._LCTRL_result.set_column_widths() 
457                          gmDispatcher.send('statustext', msg = _('The query failed.'), beep = True) 
458                          return False 
459   
460                  if len(rows) == 0: 
461                          self._LCTRL_result.set_columns([_('Results')]) 
462                          self._LCTRL_result.set_string_items([[_('Report returned no data.')]]) 
463                          self._LCTRL_result.set_column_widths() 
464                          gmDispatcher.send('statustext', msg = _('No data returned for this report.'), beep = True) 
465                          return True 
466   
467                  gmDispatcher.send(signal = 'statustext', msg = _('Found %s results.') % len(rows)) 
468   
469                  if len(rows) == 1001: 
470                          gmGuiHelpers.gm_show_info ( 
471                                  aMessage = _( 
472                                          'This query returned at least 1001 results.\n' 
473                                          '\n' 
474                                          'GNUmed will only show the first 1000 rows.\n' 
475                                          '\n' 
476                                          'You may want to narrow down the WHERE conditions\n' 
477                                          'or use LIMIT and OFFSET to batchwise go through\n' 
478                                          'all the matching rows.' 
479                                  ), 
480                                  aTitle = _('Report Generator') 
481                          ) 
482                          rows = rows[:-1]                # make it true :-) 
483   
484                  # swap (col_name, col_idx) to (col_idx, col_name) as needed by 
485                  # set_columns() and sort them according to position-in-query 
486                  cols = [ (value, key) for key, value in idx.items() ] 
487                  cols.sort() 
488                  cols = [ pair[1] for pair in cols ] 
489                  self._LCTRL_result.set_columns(cols) 
490                  for row in rows: 
491                          try: 
492                                  label = unicode(gmTools.coalesce(row[0], u'')).replace('\n', '<LF>').replace('\r', '<CR>') 
493                          except UnicodeDecodeError: 
494                                  label = _('not unicode()able') 
495                          if len(label) > 150: 
496                                  label = label[:150] + gmTools.u_ellipsis 
497                          row_num = self._LCTRL_result.InsertStringItem(sys.maxint, label = label) 
498                          for col_idx in range(1, len(row)): 
499                                  try: 
500                                          label = unicode(gmTools.coalesce(row[col_idx], u'')).replace('\n', '<LF>').replace('\r', '<CR>')[:250] 
501                                  except UnicodeDecodeError: 
502                                          label = _('not unicode()able') 
503                                  if len(label) > 150: 
504                                          label = label[:150] + gmTools.u_ellipsis 
505                                  self._LCTRL_result.SetStringItem ( 
506                                          index = row_num, 
507                                          col = col_idx, 
508                                          label = label 
509                                  ) 
510                  # must be called explicitely, because string items are set above without calling set_string_items 
511                  self._invalidate_item2data_idx_map() 
512                  self._LCTRL_result.set_column_widths() 
513                  self._LCTRL_result.set_data(data = rows) 
514   
515                  self.query_results = rows 
516                  self._BTN_visualize.Enable(True) 
517   
518                  return True 
519  #================================================================ 
520  # main 
521  #---------------------------------------------------------------- 
522  if __name__ == '__main__': 
523          from Gnumed.pycommon import gmI18N, gmDateTime 
524   
525          gmI18N.activate_locale() 
526          gmI18N.install_domain() 
527          gmDateTime.init() 
528   
529          #------------------------------------------------------------ 
530 -        def test_pat_list_ctrl(): 
531                  app = wx.PyWidgetTester(size = (400, 500)) 
532                  lst = cPatientListingCtrl(app.frame, patient_key = 0) 
533                  lst.set_columns(['name', 'comment']) 
534                  lst.set_string_items([ 
535                          ['Kirk', 'Kirk by name'], 
536                          ['#12', 'Kirk by ID'], 
537                          ['unknown', 'unknown patient'] 
538                  ]) 
539  #               app.SetWidget(cPatientListingCtrl, patient_key = 0) 
540                  app.frame.Show() 
541                  app.MainLoop() 
542          #------------------------------------------------------------ 
543   
544          test_pat_list_ctrl() 
545