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.patient_key] 
 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('fk_patient'): 
 68                          return u'fk_patient' 
 69   
 70                  if data.has_key('pk_identity'): 
 71                          return u'pk_identity' 
 72   
 73                  if data.has_key('fk_identity'): 
 74                          return u'fk_identity' 
 75   
 76                  if data.has_key('id_identity'): 
 77                          return u'id_identity' 
 78   
 79                  return gmListWidgets.get_choices_from_list ( 
 80                          parent = self, 
 81                          msg = _( 
 82                                  'The report result list does not contain any columns\n' 
 83                                  'named "%s", "pk_patient", or "pk_identity".\n' 
 84                                  '\n' 
 85                                  'Select the column which contains patient IDs:\n' 
 86                          ) % self.patient_key, 
 87                          caption = _('Choose column from query results ...'), 
 88                          choices = data.keys(), 
 89                          columns = [_('Column name')], 
 90                          single_selection = True 
 91                  ) 
 92          #------------------------------------------------------------ 
 93          # event handling 
 94          #------------------------------------------------------------ 
 95 -        def _on_list_item_activated(self, evt): 
 96                  data = self.get_selected_item_data(only_one = True) 
 97                  pk_pat_col = self.__get_patient_pk_column(data = data) 
 98   
 99                  if pk_pat_col is None: 
100                          gmDispatcher.send(signal = 'statustext', msg = _('List not known to be patient-related.')) 
101                          return 
102   
103                  pat_data = data[pk_pat_col] 
104                  try: 
105                          pat_pk = int(pat_data) 
106                          pat = gmPerson.cIdentity(aPK_obj = pat_pk) 
107                  except (ValueError, TypeError): 
108                          searcher = gmPersonSearch.cPatientSearcher_SQL() 
109                          idents = searcher.get_identities(pat_data) 
110                          if len(idents) == 0: 
111                                  gmDispatcher.send(signal = 'statustext', msg = _('No matching patient found.')) 
112                                  return 
113                          if len(idents) == 1: 
114                                  pat = idents[0] 
115                          else: 
116                                  from Gnumed.wxpython import gmPatSearchWidgets 
117                                  dlg = gmPatSearchWidgets.cSelectPersonFromListDlg(parent=wx.GetTopLevelParent(self), id=-1) 
118                                  dlg.set_persons(persons=idents) 
119                                  result = dlg.ShowModal() 
120                                  if result == wx.ID_CANCEL: 
121                                          dlg.Destroy() 
122                                          return 
123                                  pat = dlg.get_selected_person() 
124                                  dlg.Destroy() 
125   
126                  from Gnumed.wxpython import gmPatSearchWidgets 
127                  gmPatSearchWidgets.set_active_patient(patient = pat) 
128   
129  #================================================================ 
130  from Gnumed.wxGladeWidgets import wxgPatientListingPnl 
131   
132 -class cPatientListingPnl(wxgPatientListingPnl.wxgPatientListingPnl): 
133   
134 -        def __init__(self, *args, **kwargs): 
135   
136                  try: 
137                          button_defs = kwargs['button_defs'][:5] 
138                          del kwargs['button_defs'] 
139                  except KeyError: 
140                          button_defs = [] 
141   
142                  try: 
143                          msg = kwargs['message'] 
144                          del kwargs['message'] 
145                  except KeyError: 
146                          msg = None 
147   
148                  wxgPatientListingPnl.wxgPatientListingPnl.__init__(self, *args, **kwargs) 
149   
150                  if msg is not None: 
151                          self._lbl_msg.SetLabel(msg) 
152   
153                  buttons = [self._BTN_1, self._BTN_2, self._BTN_3, self._BTN_4, self._BTN_5] 
154                  for idx in range(len(button_defs)): 
155                          button_def = button_defs[idx] 
156                          if button_def['label'].strip() == u'': 
157                                  continue 
158                          buttons[idx].SetLabel(button_def['label']) 
159                          buttons[idx].SetToolTipString(button_def['tooltip']) 
160                          buttons[idx].Enable(True) 
161   
162                  self.Fit() 
163          #------------------------------------------------------------ 
164          # event handling 
165          #------------------------------------------------------------ 
166 -        def _on_BTN_1_pressed(self, event): 
167                  event.Skip() 
168          #------------------------------------------------------------ 
169 -        def _on_BTN_2_pressed(self, event): 
170                  event.Skip() 
171          #------------------------------------------------------------ 
172 -        def _on_BTN_3_pressed(self, event): 
173                  event.Skip() 
174          #------------------------------------------------------------ 
175 -        def _on_BTN_4_pressed(self, event): 
176                  event.Skip() 
177          #------------------------------------------------------------ 
178 -        def _on_BTN_5_pressed(self, event): 
179                  event.Skip() 
180   
181  #================================================================ 
182  from Gnumed.wxGladeWidgets import wxgDataMiningPnl 
183   
184 -class cDataMiningPnl(wxgDataMiningPnl.wxgDataMiningPnl): 
185   
186 -        def __init__(self, *args, **kwargs): 
187                  wxgDataMiningPnl.wxgDataMiningPnl.__init__(self, *args, **kwargs) 
188   
189                  self.__init_ui() 
190   
191                  # make me a file drop target 
192                  dt = gmGuiHelpers.cFileDropTarget(self) 
193                  self.SetDropTarget(dt) 
194          #-------------------------------------------------------- 
195 -        def __init_ui(self): 
196                  mp = gmMatchProvider.cMatchProvider_SQL2 ( 
197                          queries = [u""" 
198                                  SELECT DISTINCT ON (label) 
199                                          cmd, 
200                                          label 
201                                  FROM cfg.report_query 
202                                  WHERE 
203                                          label %(fragment_condition)s 
204                                                  OR 
205                                          cmd %(fragment_condition)s 
206                          """] 
207                  ) 
208                  mp.setThresholds(2,3,5) 
209                  self._PRW_report_name.matcher = mp 
210                  self._PRW_report_name.add_callback_on_selection(callback = self._on_report_selected) 
211                  self._PRW_report_name.add_callback_on_lose_focus(callback = self._auto_load_report) 
212          #-------------------------------------------------------- 
213 -        def _auto_load_report(self, *args, **kwargs): 
214                  if self._TCTRL_query.GetValue() == u'': 
215                          if self._PRW_report_name.GetData() is not None: 
216                                  self._TCTRL_query.SetValue(self._PRW_report_name.GetData()) 
217                                  self._BTN_run.SetFocus() 
218          #-------------------------------------------------------- 
219 -        def _on_report_selected(self, *args, **kwargs): 
220                  self._TCTRL_query.SetValue(self._PRW_report_name.GetData()) 
221                  self._BTN_run.SetFocus() 
222          #-------------------------------------------------------- 
223          # file drop target API 
224          #-------------------------------------------------------- 
225 -        def add_filenames(self, filenames): 
226                  # act on first file only 
227                  fname = filenames[0] 
228                  _log.debug('importing SQL from <%s>', fname) 
229                  # act on text files only 
230                  mime_type = gmMimeLib.guess_mimetype(fname) 
231                  _log.debug('mime type: %s', mime_type) 
232                  if not mime_type.startswith('text/'): 
233                          _log.debug('not a text file') 
234                          gmDispatcher.send(signal='statustext', msg = _('Cannot read SQL from [%s]. Not a text file.') % fname, beep = True) 
235                          return False 
236  #               # act on "small" files only 
237  #               stat_val = os.stat(fname) 
238  #               if stat_val.st_size > 5000: 
239  #                       gmDispatcher.send(signal='statustext', msg = _('Cannot read SQL from [%s]. File too big (> 2000 bytes).') % fname, beep = True) 
240  #                       return False 
241                  # all checks passed 
242                  for line in fileinput.input(fname): 
243                          self._TCTRL_query.AppendText(line) 
244          #-------------------------------------------------------- 
245          # notebook plugin API 
246          #-------------------------------------------------------- 
247 -        def repopulate_ui(self): 
248                  pass 
249          #-------------------------------------------------------- 
250          # event handlers 
251          #-------------------------------------------------------- 
252 -        def _on_contribute_button_pressed(self, evt): 
253                  report = self._PRW_report_name.GetValue().strip() 
254                  if report == u'': 
255                          gmDispatcher.send(signal = 'statustext', msg = _('Report must have a name for contribution.'), beep = False) 
256                          return 
257   
258                  query = self._TCTRL_query.GetValue().strip() 
259                  if query == u'': 
260                          gmDispatcher.send(signal = 'statustext', msg = _('Report must have a query for contribution.'), beep = False) 
261                          return 
262   
263                  do_it = gmGuiHelpers.gm_show_question ( 
264                          _(      'Be careful that your contribution (the query itself) does\n' 
265                                  'not contain any person-identifiable search parameters.\n' 
266                                  '\n' 
267                                  'Note, however, that no query result data whatsoever\n' 
268                                  'is included in the contribution that will be sent.\n' 
269                                  '\n' 
270                                  'Are you sure you wish to send this query to\n' 
271                                  'the gnumed community mailing list?\n' 
272                          ), 
273                          _('Contributing custom report') 
274                  ) 
275                  if not do_it: 
276                          return 
277   
278                  auth = {'user': gmNetworkTools.default_mail_sender, 'password': u'gnumed-at-gmx-net'} 
279                  msg = u"""--- This is a report definition contributed by a GNUmed user. 
280   
281  --- Save it as a text file and drop it onto the Report Generator 
282  --- inside GNUmed in order to take advantage of the contribution. 
283   
284  ---------------------------------------- 
285   
286  --- %s 
287   
288  %s 
289   
290  ---------------------------------------- 
291   
292  --- The GNUmed client. 
293  """ % (report, query) 
294   
295                  if not gmNetworkTools.send_mail ( 
296                          sender = u'GNUmed Report Generator <gnumed@gmx.net>', 
297                          receiver = [u'gnumed-devel@gnu.org'], 
298                          subject = u'user contributed report', 
299                          message = msg, 
300                          encoding = gmI18N.get_encoding(), 
301                          server = gmNetworkTools.default_mail_server, 
302                          auth = auth 
303                  ): 
304                          gmDispatcher.send(signal = 'statustext', msg = _('Unable to send mail. Cannot contribute report [%s] to GNUmed community.') % report, beep = True) 
305                          return False 
306   
307                  gmDispatcher.send(signal = 'statustext', msg = _('Thank you for your contribution to the GNUmed community!'), beep = False) 
308                  return True 
309          #-------------------------------------------------------- 
310 -        def _on_schema_button_pressed(self, evt): 
311                  # will block when called in text mode (that is, from a terminal, too !) 
312                  gmNetworkTools.open_url_in_browser(url = u'http://wiki.gnumed.de/bin/view/Gnumed/DatabaseSchema') 
313          #-------------------------------------------------------- 
314 -        def _on_delete_button_pressed(self, evt): 
315                  report = self._PRW_report_name.GetValue().strip() 
316                  if report == u'': 
317                          return True 
318                  if gmDataMining.delete_report_definition(name=report): 
319                          self._PRW_report_name.SetText() 
320                          self._TCTRL_query.SetValue(u'') 
321                          gmDispatcher.send(signal='statustext', msg = _('Deleted report definition [%s].') % report, beep=False) 
322                          return True 
323                  gmDispatcher.send(signal='statustext', msg = _('Error deleting report definition [%s].') % report, beep=True) 
324                  return False 
325          #-------------------------------------------------------- 
326 -        def _on_clear_button_pressed(self, evt): 
327                  self._PRW_report_name.SetText() 
328                  self._TCTRL_query.SetValue(u'') 
329                  self._LCTRL_result.set_columns() 
330          #-------------------------------------------------------- 
331 -        def _on_save_button_pressed(self, evt): 
332                  report = self._PRW_report_name.GetValue().strip() 
333                  if report == u'': 
334                          gmDispatcher.send(signal='statustext', msg = _('Cannot save report definition without name.'), beep=True) 
335                          return False 
336                  query = self._TCTRL_query.GetValue().strip() 
337                  if query == u'': 
338                          gmDispatcher.send(signal='statustext', msg = _('Cannot save report definition without query.'), beep=True) 
339                          return False 
340                  # FIXME: check for exists and ask for permission 
341                  if gmDataMining.save_report_definition(name=report, query=query, overwrite=True): 
342                          gmDispatcher.send(signal='statustext', msg = _('Saved report definition [%s].') % report, beep=False) 
343                          return True 
344                  gmDispatcher.send(signal='statustext', msg = _('Error saving report definition [%s].') % report, beep=True) 
345                  return False 
346          #-------------------------------------------------------- 
347 -        def _on_visualize_button_pressed(self, evt): 
348   
349                  try: 
350                          # better fail early 
351                          import Gnuplot 
352                  except ImportError: 
353                          gmGuiHelpers.gm_show_info ( 
354                                  aMessage = _('Cannot import "Gnuplot" python module.'), 
355                                  aTitle = _('Query result visualizer') 
356                          ) 
357                          return 
358   
359                  x_col = gmListWidgets.get_choices_from_list ( 
360                          parent = self, 
361                          msg = _('Choose a column to be used as the X-Axis:'), 
362                          caption = _('Choose column from query results ...'), 
363                          choices = self.query_results[0].keys(), 
364                          columns = [_('Column name')], 
365                          single_selection = True 
366                  ) 
367                  if x_col is None: 
368                          return 
369   
370                  y_col = gmListWidgets.get_choices_from_list ( 
371                          parent = self, 
372                          msg = _('Choose a column to be used as the Y-Axis:'), 
373                          caption = _('Choose column from query results ...'), 
374                          choices = self.query_results[0].keys(), 
375                          columns = [_('Column name')], 
376                          single_selection = True 
377                  ) 
378                  if y_col is None: 
379                          return 
380   
381                  # FIXME: support debugging (debug=1) depending on --debug 
382                  gp = Gnuplot.Gnuplot(persist=1) 
383                  if self._PRW_report_name.GetValue().strip() != u'': 
384                          gp.title(_('GNUmed report: %s') % self._PRW_report_name.GetValue().strip()[:40]) 
385                  else: 
386                          gp.title(_('GNUmed report results')) 
387                  gp.xlabel(x_col) 
388                  gp.ylabel(y_col) 
389                  try: 
390                          gp.plot([ [r[x_col], r[y_col]] for r in self.query_results ]) 
391                  except StandardError: 
392                          _log.exception('unable to plot results from [%s:%s]' % (x_col, y_col)) 
393                          gmDispatcher.send(signal = 'statustext', msg = _('Error plotting data.'), beep = True) 
394   
395                  return 
396          #-------------------------------------------------------- 
397 -        def _on_run_button_pressed(self, evt): 
398   
399                  self._BTN_visualize.Enable(False) 
400   
401                  user_query = self._TCTRL_query.GetValue().strip().strip(';') 
402                  if user_query == u'': 
403                          return True 
404   
405                  # FIXME: make LIMIT configurable 
406                  limit = u'1001' 
407   
408                  wrapper_query = u""" 
409                          SELECT * 
410                          FROM ( 
411                                  %%s 
412                          ) AS user_query 
413                          LIMIT %s 
414                  """ % limit 
415   
416                  # does user want to insert current patient ID ? 
417                  patient_id_token = u'$<ID_active_patient>$' 
418                  if user_query.find(patient_id_token) != -1: 
419                          # she does, but is it possible ? 
420                          curr_pat = gmPerson.gmCurrentPatient() 
421                          if not curr_pat.connected: 
422                                  gmGuiHelpers.gm_show_error ( 
423                                          aMessage = _( 
424                                                  'This query requires a patient to be\n' 
425                                                  'active in the client.\n' 
426                                                  '\n' 
427                                                  'Please activate the patient you are interested\n' 
428                                                  'in and re-run the query.\n' 
429                                          ), 
430                                          aTitle = _('Active patient query') 
431                                  ) 
432                                  return False 
433                          wrapper_query = u""" 
434                                  SELECT 
435                                          %s AS pk_patient, 
436                                          * 
437                                  FROM ( 
438                                          %%s 
439                                  ) AS user_query 
440                                  LIMIT %s 
441                          """ % (str(curr_pat.ID), limit) 
442                          user_query = user_query.replace(patient_id_token, str(curr_pat.ID)) 
443   
444                  self._LCTRL_result.set_columns() 
445   
446                  query = wrapper_query % user_query 
447                  try: 
448                          # read-only for safety reasons 
449                          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': query}], get_col_idx = True) 
450                  except StandardError: 
451                          _log.exception('report query failed') 
452                          self._LCTRL_result.set_columns([_('Error')]) 
453                          t, v = sys.exc_info()[:2] 
454                          rows = [ 
455                                  [_('The query failed.')], 
456                                  [u''], 
457                                  [unicode(t)] 
458                          ] 
459                          for line in str(v).decode(gmI18N.get_encoding()).split('\n'): 
460                                  rows.append([line]) 
461                          rows.append([u'']) 
462                          for line in user_query.split('\n'): 
463                                  rows.append([line]) 
464                          self._LCTRL_result.set_string_items(rows) 
465                          self._LCTRL_result.set_column_widths() 
466                          gmDispatcher.send('statustext', msg = _('The query failed.'), beep = True) 
467                          return False 
468   
469                  if len(rows) == 0: 
470                          self._LCTRL_result.set_columns([_('Results')]) 
471                          self._LCTRL_result.set_string_items([[_('Report returned no data.')]]) 
472                          self._LCTRL_result.set_column_widths() 
473                          gmDispatcher.send('statustext', msg = _('No data returned for this report.'), beep = True) 
474                          return True 
475   
476                  gmDispatcher.send(signal = 'statustext', msg = _('Found %s results.') % len(rows)) 
477   
478                  if len(rows) == 1001: 
479                          gmGuiHelpers.gm_show_info ( 
480                                  aMessage = _( 
481                                          'This query returned at least 1001 results.\n' 
482                                          '\n' 
483                                          'GNUmed will only show the first 1000 rows.\n' 
484                                          '\n' 
485                                          'You may want to narrow down the WHERE conditions\n' 
486                                          'or use LIMIT and OFFSET to batchwise go through\n' 
487                                          'all the matching rows.' 
488                                  ), 
489                                  aTitle = _('Report Generator') 
490                          ) 
491                          rows = rows[:-1]                # make it true :-) 
492   
493                  # swap (col_name, col_idx) to (col_idx, col_name) as needed by 
494                  # set_columns() and sort them according to position-in-query 
495                  cols = [ (value, key) for key, value in idx.items() ] 
496                  cols.sort() 
497                  cols = [ pair[1] for pair in cols ] 
498                  self._LCTRL_result.set_columns(cols) 
499                  for row in rows: 
500                          try: 
501                                  label = unicode(gmTools.coalesce(row[0], u'')).replace('\n', '<LF>').replace('\r', '<CR>') 
502                          except UnicodeDecodeError: 
503                                  label = _('not unicode()able') 
504                          if len(label) > 150: 
505                                  label = label[:150] + gmTools.u_ellipsis 
506                          row_num = self._LCTRL_result.InsertStringItem(sys.maxint, label = label) 
507                          for col_idx in range(1, len(row)): 
508                                  try: 
509                                          label = unicode(gmTools.coalesce(row[col_idx], u'')).replace('\n', '<LF>').replace('\r', '<CR>')[:250] 
510                                  except UnicodeDecodeError: 
511                                          label = _('not unicode()able') 
512                                  if len(label) > 150: 
513                                          label = label[:150] + gmTools.u_ellipsis 
514                                  self._LCTRL_result.SetStringItem ( 
515                                          index = row_num, 
516                                          col = col_idx, 
517                                          label = label 
518                                  ) 
519                  # must be called explicitely, because string items are set above without calling set_string_items 
520                  self._LCTRL_result._invalidate_sorting_metadata() 
521                  self._LCTRL_result.set_column_widths() 
522                  self._LCTRL_result.set_data(data = rows) 
523   
524                  self.query_results = rows 
525                  self._BTN_visualize.Enable(True) 
526   
527                  return True 
528  #================================================================ 
529  # main 
530  #---------------------------------------------------------------- 
531  if __name__ == '__main__': 
532          from Gnumed.pycommon import gmI18N, gmDateTime 
533   
534          gmI18N.activate_locale() 
535          gmI18N.install_domain() 
536          gmDateTime.init() 
537   
538          #------------------------------------------------------------ 
539 -        def test_pat_list_ctrl(): 
540                  app = wx.PyWidgetTester(size = (400, 500)) 
541                  lst = cPatientListingCtrl(app.frame, patient_key = 0) 
542                  lst.set_columns(['name', 'comment']) 
543                  lst.set_string_items([ 
544                          ['Kirk', 'Kirk by name'], 
545                          ['#12', 'Kirk by ID'], 
546                          ['unknown', 'unknown patient'] 
547                  ]) 
548  #               app.SetWidget(cPatientListingCtrl, patient_key = 0) 
549                  app.frame.Show() 
550                  app.MainLoop() 
551          #------------------------------------------------------------ 
552   
553          test_pat_list_ctrl() 
554