Package Gnumed :: Package business :: Module gmClinicalRecord
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Source Code for Module Gnumed.business.gmClinicalRecord

   1  # -*- coding: utf-8 -*- 
   2  """GNUmed clinical patient record.""" 
   3  #============================================================ 
   4  __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>" 
   5  __license__ = "GPL v2 or later" 
   6   
   7  # standard libs 
   8  import sys 
   9  import logging 
  10  import threading 
  11  import datetime as pydt 
  12   
  13  if __name__ == '__main__': 
  14          sys.path.insert(0, '../../') 
  15   
  16  from Gnumed.pycommon import gmI18N 
  17  from Gnumed.pycommon import gmDateTime 
  18   
  19  if __name__ == '__main__': 
  20          from Gnumed.pycommon import gmLog2 
  21          gmI18N.activate_locale() 
  22          gmI18N.install_domain() 
  23          gmDateTime.init() 
  24   
  25  from Gnumed.pycommon import gmExceptions 
  26  from Gnumed.pycommon import gmPG2 
  27  from Gnumed.pycommon import gmDispatcher 
  28  from Gnumed.pycommon import gmCfg 
  29  from Gnumed.pycommon import gmTools 
  30   
  31  from Gnumed.business import gmGenericEMRItem 
  32  from Gnumed.business import gmAllergy 
  33  from Gnumed.business import gmPathLab 
  34  from Gnumed.business import gmLOINC 
  35  from Gnumed.business import gmClinNarrative 
  36  from Gnumed.business import gmSoapDefs 
  37  from Gnumed.business import gmEMRStructItems 
  38  from Gnumed.business import gmMedication 
  39  from Gnumed.business import gmVaccination 
  40  from Gnumed.business import gmFamilyHistory 
  41  from Gnumed.business import gmExternalCare 
  42  from Gnumed.business import gmOrganization 
  43  from Gnumed.business import gmAutoHints 
  44  from Gnumed.business.gmDemographicRecord import get_occupations 
  45   
  46   
  47  _log = logging.getLogger('gm.emr') 
  48   
  49  _here = None 
  50  #============================================================ 
  51  # helper functions 
  52  #------------------------------------------------------------ 
  53  #_func_ask_user = None 
  54  # 
  55  #def set_func_ask_user(a_func = None): 
  56  #       if not callable(a_func): 
  57  #               _log.error('[%] not callable, not setting _func_ask_user', a_func) 
  58  #               return False 
  59  # 
  60  #       _log.debug('setting _func_ask_user to [%s]', a_func) 
  61  # 
  62  #       global _func_ask_user 
  63  #       _func_ask_user = a_func 
  64   
  65  #============================================================ 
  66  from Gnumed.business.gmDocuments import cDocument 
  67  from Gnumed.business.gmProviderInbox import cInboxMessage 
  68   
  69  _map_table2class = { 
  70          'clin.encounter': gmEMRStructItems.cEncounter, 
  71          'clin.episode': gmEMRStructItems.cEpisode, 
  72          'clin.health_issue': gmEMRStructItems.cHealthIssue, 
  73          'clin.external_care': gmExternalCare.cExternalCareItem, 
  74          'clin.vaccination': gmVaccination.cVaccination, 
  75          'clin.clin_narrative': gmClinNarrative.cNarrative, 
  76          'clin.test_result': gmPathLab.cTestResult, 
  77          'clin.substance_intake': gmMedication.cSubstanceIntakeEntry, 
  78          'clin.hospital_stay': gmEMRStructItems.cHospitalStay, 
  79          'clin.procedure': gmEMRStructItems.cPerformedProcedure, 
  80          'clin.allergy': gmAllergy.cAllergy, 
  81          'clin.allergy_state': gmAllergy.cAllergyState, 
  82          'clin.family_history': gmFamilyHistory.cFamilyHistory, 
  83          'clin.suppressed_hint': gmAutoHints.cSuppressedHint, 
  84          'blobs.doc_med': cDocument, 
  85          'dem.message_inbox': cInboxMessage, 
  86          'ref.auto_hint': gmAutoHints.cDynamicHint 
  87  } 
  88   
89 -def instantiate_clin_root_item(table, pk):
90 try: 91 item_class = _map_table2class[table] 92 except KeyError: 93 _log.error('unmapped clin_root_item entry [%s], cannot instantiate', table) 94 return None 95 96 return item_class(aPK_obj = pk)
97 98 #------------------------------------------------------------
99 -def format_clin_root_item(table, pk, patient=None):
100 101 instance = instantiate_clin_root_item(table, pk) 102 if instance is None: 103 return _('cannot instantiate clinical root item <%s(%s)>' % (table, pk)) 104 105 # if patient is not None: 106 # if patient.ID != instance['pk_patient']: 107 # raise ValueError(u'patient passed in: [%s], but instance is: [%s:%s:%s]' % (patient.ID, table, pk, instance['pk_patient'])) 108 109 if hasattr(instance, 'format_maximum_information'): 110 return '\n'.join(instance.format_maximum_information(patient = patient)) 111 112 if hasattr(instance, 'format'): 113 try: 114 formatted = instance.format(patient = patient) 115 except TypeError: 116 formatted = instance.format() 117 if type(formatted) == type([]): 118 return '\n'.join(formatted) 119 return formatted 120 121 d = instance.fields_as_dict ( 122 date_format = '%Y %b %d %H:%M', 123 none_string = gmTools.u_diameter, 124 escape_style = None, 125 bool_strings = [_('True'), _('False')] 126 ) 127 return gmTools.format_dict_like(d, tabular = True, value_delimiters = None)
128 129 #============================================================
130 -def __noop_delayed_execute(*args, **kwargs):
131 pass
132 133 134 _delayed_execute = __noop_delayed_execute 135 136
137 -def set_delayed_executor(executor):
138 if not callable(executor): 139 raise TypeError('executor <%s> is not callable' % executor) 140 global _delayed_execute 141 _delayed_execute = executor 142 _log.debug('setting delayed executor to <%s>', executor)
143 144 #------------------------------------------------------------
145 -class cClinicalRecord(object):
146
147 - def __init__(self, aPKey=None):#, allow_user_interaction=True, encounter=None):
148 """Fails if 149 150 - no connection to database possible 151 - patient referenced by aPKey does not exist 152 """ 153 self.pk_patient = aPKey # == identity.pk == primary key 154 self.gender = None 155 self.dob = None 156 157 from Gnumed.business import gmPraxis 158 global _here 159 if _here is None: 160 _here = gmPraxis.gmCurrentPraxisBranch() 161 162 self.__encounter = None 163 self.__setup_active_encounter() 164 165 # register backend notification interests 166 # (keep this last so we won't hang on threads when 167 # failing this constructor for other reasons ...) 168 if not self._register_interests(): 169 raise gmExceptions.ConstructorError("cannot register signal interests") 170 171 gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) 172 #_delayed_execute(gmAllergy.ensure_has_allergy_state, encounter = self.current_encounter['pk_encounter']) 173 174 self.__calculator = None 175 176 _log.debug('Instantiated clinical record for patient [%s].' % self.pk_patient)
177 178 # #-------------------------------------------------------- 179 # def __old_style_init(self, allow_user_interaction=True): 180 # 181 # _log.error('%s.__old_style_init() used', self.__class__.__name__) 182 # print u'*** GNUmed [%s]: __old_style_init() used ***' % self.__class__.__name__ 183 # 184 # # FIXME: delegate to worker thread 185 # # log access to patient record (HIPAA, for example) 186 # cmd = u'SELECT gm.log_access2emr(%(todo)s)' 187 # args = {'todo': u'patient [%s]' % self.pk_patient} 188 # gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) 189 # 190 # # load current or create new encounter 191 # if _func_ask_user is None: 192 # _log.error('[_func_ask_user] is None') 193 # print "*** GNUmed [%s]: _func_ask_user is not set ***" % self.__class__.__name__ 194 # 195 ## # FIXME: delegate to worker thread ? 196 # self.remove_empty_encounters() 197 # 198 # self.__encounter = None 199 # if not self.__initiate_active_encounter(allow_user_interaction = allow_user_interaction): 200 # raise gmExceptions.ConstructorError("cannot activate an encounter for patient [%s]" % self.pk_patient) 201 # 202 ## # FIXME: delegate to worker thread 203 # gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) 204 205 #--------------------------------------------------------
206 - def cleanup(self):
207 _log.debug('cleaning up after clinical record for patient [%s]' % self.pk_patient) 208 if self.__encounter is not None: 209 self.__encounter.unlock(exclusive = False) 210 return True
211 212 #--------------------------------------------------------
213 - def log_access(self, action=None):
214 if action is None: 215 action = 'EMR access for pk_identity [%s]' % self.pk_patient 216 args = {'action': action} 217 cmd = 'SELECT gm.log_access2emr(%(action)s)' 218 gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
219 220 #--------------------------------------------------------
221 - def _get_calculator(self):
222 if self.__calculator is None: 223 from Gnumed.business.gmClinicalCalculator import cClinicalCalculator 224 self.__calculator = cClinicalCalculator() 225 from Gnumed.business.gmPerson import gmCurrentPatient 226 curr_pat = gmCurrentPatient() 227 if curr_pat.ID == self.pk_patient: 228 self.__calculator.patient = curr_pat 229 else: 230 from Gnumed.business.gmPerson import cPatient 231 self.__calculator.patient = cPatient(self.pk_patient) 232 return self.__calculator
233 234 calculator = property(_get_calculator, lambda x:x) 235 236 #-------------------------------------------------------- 237 # messaging 238 #--------------------------------------------------------
239 - def _register_interests(self):
240 #gmDispatcher.connect(signal = u'clin.encounter_mod_db', receiver = self.db_callback_encounter_mod_db) 241 gmDispatcher.connect(signal = 'gm_table_mod', receiver = self.db_modification_callback) 242 243 return True
244 245 #--------------------------------------------------------
246 - def db_modification_callback(self, **kwds):
247 248 if kwds['table'] != 'clin.encounter': 249 return True 250 if self.current_encounter is None: 251 _log.debug('no local current-encounter, ignoring encounter modification signal') 252 return True 253 if int(kwds['pk_of_row']) != self.current_encounter['pk_encounter']: 254 _log.debug('modified encounter [%s] != local encounter [%s], ignoring signal', kwds['pk_of_row'], self.current_encounter['pk_encounter']) 255 return True 256 257 _log.debug('modification of our encounter (%s) signalled (%s)', self.current_encounter['pk_encounter'], kwds['pk_of_row']) 258 259 # get the current encounter as an extra instance 260 # from the database to check for changes 261 curr_enc_in_db = gmEMRStructItems.cEncounter(aPK_obj = self.current_encounter['pk_encounter']) 262 263 # the encounter just retrieved and the active encounter 264 # have got the same transaction ID so there's no change 265 # in the database, there could be a local change in 266 # the active encounter but that doesn't matter because 267 # no one else can have written to the DB so far 268 if curr_enc_in_db['xmin_encounter'] == self.current_encounter['xmin_encounter']: 269 _log.debug('same XMIN, no difference between DB and in-client instance of current encounter expected') 270 if self.current_encounter.is_modified(): 271 _log.error('encounter modification signal from DB with same XMIN as in local in-client instance of encounter BUT local instance ALSO has .is_modified()=True') 272 _log.error('this hints at an error in .is_modified handling') 273 gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') 274 return True 275 276 # there must have been a change to the active encounter 277 # committed to the database from elsewhere, 278 # we must fail propagating the change, however, if 279 # there are local changes pending 280 if self.current_encounter.is_modified(): 281 gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB') 282 raise ValueError('unsaved changes in locally active encounter [%s], cannot switch to DB state of encounter [%s]' % ( 283 self.current_encounter['pk_encounter'], 284 curr_enc_in_db['pk_encounter'] 285 )) 286 287 # don't do this: same_payload() does not compare _all_ fields 288 # so we can get into a reality disconnect if we don't 289 # announce the mod 290 # if self.current_encounter.same_payload(another_object = curr_enc_in_db): 291 # _log.debug('clin.encounter_mod_db received but no change to active encounter payload') 292 # return True 293 294 # there was a change in the database from elsewhere, 295 # locally, however, we don't have any pending changes, 296 # therefore we can propagate the remote change locally 297 # without losing anything 298 # this really should be the standard case 299 gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') 300 _log.debug('active encounter modified remotely, no locally pending changes, reloading from DB and locally announcing the remote modification') 301 self.current_encounter.refetch_payload() 302 gmDispatcher.send('current_encounter_modified') 303 304 return True
305 306 #--------------------------------------------------------
307 - def db_callback_encounter_mod_db(self, **kwds):
308 309 # get the current encounter as an extra instance 310 # from the database to check for changes 311 curr_enc_in_db = gmEMRStructItems.cEncounter(aPK_obj = self.current_encounter['pk_encounter']) 312 313 # the encounter just retrieved and the active encounter 314 # have got the same transaction ID so there's no change 315 # in the database, there could be a local change in 316 # the active encounter but that doesn't matter because 317 # no one else can have written to the DB so far 318 # THIS DOES NOT WORK 319 # if curr_enc_in_db['xmin_encounter'] == self.current_encounter['xmin_encounter']: 320 # return True 321 322 # there must have been a change to the active encounter 323 # committed to the database from elsewhere, 324 # we must fail propagating the change, however, if 325 # there are local changes 326 if self.current_encounter.is_modified(): 327 gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') 328 _log.error('current in client: %s', self.current_encounter) 329 raise ValueError('unsaved changes in active encounter [%s], cannot switch [%s]' % ( 330 self.current_encounter['pk_encounter'], 331 curr_enc_in_db['pk_encounter'] 332 )) 333 334 if self.current_encounter.same_payload(another_object = curr_enc_in_db): 335 _log.debug('clin.encounter_mod_db received but no change to active encounter payload') 336 return True 337 338 # there was a change in the database from elsewhere, 339 # locally, however, we don't have any changes, therefore 340 # we can propagate the remote change locally without 341 # losing anything 342 gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') 343 _log.debug('active encounter modified remotely, reloading from DB and locally announcing the modification') 344 self.current_encounter.refetch_payload() 345 gmDispatcher.send('current_encounter_modified') 346 347 return True
348 349 #-------------------------------------------------------- 350 # API: family history 351 #--------------------------------------------------------
352 - def get_family_history(self, episodes=None, issues=None, encounters=None):
353 fhx = gmFamilyHistory.get_family_history ( 354 order_by = 'l10n_relation, condition', 355 patient = self.pk_patient 356 ) 357 358 if episodes is not None: 359 fhx = [ f for f in fhx if f['pk_episode'] in episodes ] 360 361 if issues is not None: 362 fhx = [ f for f in fhx if f['pk_health_issue'] in issues ] 363 364 if encounters is not None: 365 fhx = [ f for f in fhx if f['pk_encounter'] in encounters ] 366 367 return fhx
368 369 #--------------------------------------------------------
370 - def add_family_history(self, episode=None, condition=None, relation=None):
371 return gmFamilyHistory.create_family_history ( 372 encounter = self.current_encounter['pk_encounter'], 373 episode = episode, 374 condition = condition, 375 relation = relation 376 )
377 378 #-------------------------------------------------------- 379 # API: pregnancy 380 #--------------------------------------------------------
381 - def _get_gender(self):
382 if self.__gender is not None: 383 return self.__gender 384 cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' 385 args = {'pat': self.pk_patient} 386 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 387 self.__gender = rows[0]['gender'] 388 self.__dob = rows[0]['dob']
389
390 - def _set_gender(self, gender):
391 self.__gender = gender
392 393 gender = property(_get_gender, _set_gender) 394 395 #--------------------------------------------------------
396 - def _get_dob(self):
397 if self.__dob is not None: 398 return self.__dob 399 cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' 400 args = {'pat': self.pk_patient} 401 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 402 self.__gender = rows[0]['gender'] 403 self.__dob = rows[0]['dob']
404
405 - def _set_dob(self, dob):
406 self.__dob = dob
407 408 dob = property(_get_dob, _set_dob) 409 410 #--------------------------------------------------------
411 - def _get_EDC(self):
412 cmd = 'SELECT edc FROM clin.patient WHERE fk_identity = %(pat)s' 413 args = {'pat': self.pk_patient} 414 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 415 if len(rows) == 0: 416 return None 417 return rows[0]['edc']
418
419 - def _set_EDC(self, edc):
420 cmd = """ 421 INSERT INTO clin.patient (fk_identity, edc) SELECT 422 %(pat)s, 423 %(edc)s 424 WHERE NOT EXISTS ( 425 SELECT 1 FROM clin.patient WHERE fk_identity = %(pat)s 426 ) 427 RETURNING pk""" 428 args = {'pat': self.pk_patient, 'edc': edc} 429 rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False, return_data = True) 430 if len(rows) == 0: 431 cmd = 'UPDATE clin.patient SET edc = %(edc)s WHERE fk_identity = %(pat)s' 432 gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
433 434 EDC = property(_get_EDC, _set_EDC) 435 436 #--------------------------------------------------------
437 - def _EDC_is_fishy(self):
438 edc = self.EDC 439 if edc is None: 440 return False 441 if self.gender != 'f': 442 return True 443 now = gmDateTime.pydt_now_here() 444 # mother too young 445 if (self.dob + pydt.timedelta(weeks = 5 * 52)) > now: 446 return True 447 # mother too old 448 if (self.dob + pydt.timedelta(weeks = 55 * 52)) < now: 449 return True 450 # Beulah Hunter, 375 days (http://www.reference.com/motif/health/longest-human-pregnancy-on-record) 451 # EDC too far in the future 452 if (edc - pydt.timedelta(days = 380)) > now: 453 return True 454 # even if the pregnancy would have *started* when it 455 # was documented to *end* it would be over by now by 456 # all accounts 457 # EDC too far in the past 458 if edc < (now - pydt.timedelta(days = 380)): 459 return True
460 461 EDC_is_fishy = property(_EDC_is_fishy, lambda x:x) 462 463 #--------------------------------------------------------
464 - def __normalize_smoking_details(self, details):
465 try: 466 details['quit_when'] 467 except KeyError: 468 details['quit_when'] = None 469 470 try: 471 details['last_confirmed'] 472 if details['last_confirmed'] is None: 473 details['last_confirmed'] = gmDateTime.pydt_now_here() 474 except KeyError: 475 details['last_confirmed'] = gmDateTime.pydt_now_here() 476 477 try: 478 details['comment'] 479 if details['comment'].strip() == '': 480 details['comment'] = None 481 except KeyError: 482 details['comment'] = None 483 484 return details
485 486 #--------------------------------------------------------
487 - def _get_smoking_status(self):
488 use = self.harmful_substance_use 489 if use is None: 490 return None 491 return use['tobacco']
492
493 - def _set_smoking_status(self, status):
494 # valid ? 495 status_flag, details = status 496 self.__harmful_substance_use = None 497 args = { 498 'pat': self.pk_patient, 499 'status': status_flag 500 } 501 if status_flag is None: 502 cmd = 'UPDATE clin.patient SET smoking_status = %(status)s, smoking_details = NULL WHERE fk_identity = %(pat)s' 503 elif status_flag == 0: 504 details['quit_when'] = None 505 args['details'] = gmTools.dict2json(self.__normalize_smoking_details(details)) 506 cmd = 'UPDATE clin.patient SET smoking_status = %(status)s, smoking_details = %(details)s WHERE fk_identity = %(pat)s' 507 else: 508 args['details'] = gmTools.dict2json(self.__normalize_smoking_details(details)) 509 cmd = 'UPDATE clin.patient SET smoking_status = %(status)s, smoking_details = %(details)s WHERE fk_identity = %(pat)s' 510 rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
511 512 smoking_status = property(_get_smoking_status, _set_smoking_status) 513 514 #--------------------------------------------------------
515 - def _get_alcohol_status(self):
516 use = self.harmful_substance_use 517 if use is None: 518 return None 519 return use['alcohol']
520
521 - def _set_alcohol_status(self, status):
522 # valid ? 523 harmful, details = status 524 self.__harmful_substance_use = None 525 args = {'pat': self.pk_patient} 526 if harmful is None: 527 cmd = 'UPDATE clin.patient SET c2_currently_harmful_use = NULL, c2_details = NULL WHERE fk_identity = %(pat)s' 528 elif harmful is False: 529 cmd = 'UPDATE clin.patient SET c2_currently_harmful_use = FALSE, c2_details = gm.nullify_empty_string(%(details)s) WHERE fk_identity = %(pat)s' 530 else: 531 cmd = 'UPDATE clin.patient SET c2_currently_harmful_use = TRUE, c2_details = gm.nullify_empty_string(%(details)s) WHERE fk_identity = %(pat)s' 532 rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
533 534 alcohol_status = property(_get_alcohol_status, _set_alcohol_status) 535 536 #--------------------------------------------------------
537 - def _get_drugs_status(self):
538 use = self.harmful_substance_use 539 if use is None: 540 return None 541 return use['drugs']
542
543 - def _set_drugs_status(self, status):
544 # valid ? 545 harmful, details = status 546 self.__harmful_substance_use = None 547 args = {'pat': self.pk_patient} 548 if harmful is None: 549 cmd = 'UPDATE clin.patient SET drugs_currently_harmful_use = NULL, drugs_details = NULL WHERE fk_identity = %(pat)s' 550 elif harmful is False: 551 cmd = 'UPDATE clin.patient SET drugs_currently_harmful_use = FALSE, drugs_details = gm.nullify_empty_string(%(details)s) WHERE fk_identity = %(pat)s' 552 else: 553 cmd = 'UPDATE clin.patient SET drugs_currently_harmful_use = TRUE, drugs_details = gm.nullify_empty_string(%(details)s) WHERE fk_identity = %(pat)s' 554 rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
555 556 drugs_status = property(_get_drugs_status, _set_drugs_status) 557 558 #--------------------------------------------------------
559 - def _get_harmful_substance_use(self):
560 # caching does not take into account status changes from elsewhere 561 try: 562 self.__harmful_substance_use 563 except AttributeError: 564 self.__harmful_substance_use = None 565 566 if self.__harmful_substance_use is not None: 567 return self.__harmful_substance_use 568 569 args = {'pat': self.pk_patient} 570 cmd = """ 571 SELECT 572 -- tobacco use 573 smoking_status, 574 smoking_details, 575 (smoking_details->>'last_confirmed')::timestamp with time zone 576 AS ts_last, 577 (smoking_details->>'quit_when')::timestamp with time zone 578 AS ts_quit, 579 -- c2 use 580 c2_currently_harmful_use, 581 c2_details, 582 -- other drugs use 583 drugs_currently_harmful_use, 584 drugs_details 585 FROM clin.patient 586 WHERE fk_identity = %(pat)s 587 """ 588 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 589 if len(rows) == 0: 590 return None 591 # disentangle smoking 592 status = rows[0]['smoking_status'] 593 details = rows[0]['smoking_details'] 594 if status is not None: 595 details['last_confirmed'] = rows[0]['ts_last'] 596 details['quit_when'] = rows[0]['ts_quit'] 597 # set fields 598 self.__harmful_substance_use = { 599 'tobacco': (status, details), 600 'alcohol': (rows[0]['c2_currently_harmful_use'], rows[0]['c2_details']), 601 'drugs': (rows[0]['drugs_currently_harmful_use'], rows[0]['drugs_details']) 602 } 603 604 return self.__harmful_substance_use
605 606
607 - def _get_harmful_substance_use2(self):
608 cmd = 'SELECT * FROM clin.v_substance_intakes WHERE harmful_use_type = %s'
609 610 harmful_substance_use = property(_get_harmful_substance_use, lambda x:x) 611 612 #--------------------------------------------------------
613 - def format_harmful_substance_use(self, include_tobacco=True, include_alcohol=True, include_drugs=True, include_nonuse=True, include_unknown=True):
614 use = self.harmful_substance_use 615 if use is None: 616 return [] 617 618 lines = [] 619 620 if include_tobacco: 621 status, details = use['tobacco'] 622 add_details = False 623 if status is None: 624 if include_unknown: 625 lines.append(_('unknown smoking status')) 626 elif status == 0: 627 if include_nonuse: 628 lines.append('%s (%s)' % (_('non-smoker'), gmDateTime.pydt_strftime(details['last_confirmed'], '%Y %b %d'))) 629 add_details = True 630 elif status == 1: # now or previous 631 if details['quit_when'] is None: 632 lines.append('%s (%s)' % (_('current smoker'), gmDateTime.pydt_strftime(details['last_confirmed'], '%Y %b %d'))) 633 add_details = True 634 elif details['quit_when'] < gmDateTime.pydt_now_here(): 635 if include_nonuse: 636 lines.append('%s (%s)' % (_('ex-smoker'), gmDateTime.pydt_strftime(details['last_confirmed'], '%Y %b %d'))) 637 add_details = True 638 else: 639 lines.append('%s (%s)' % (_('current smoker'), gmDateTime.pydt_strftime(details['last_confirmed'], '%Y %b %d'))) 640 add_details = True 641 elif status == 2: # addicted 642 lines.append('%s (%s)' % (_('tobacco addiction'), gmDateTime.pydt_strftime(details['last_confirmed'], '%Y %b %d'))) 643 add_details = True 644 if add_details: 645 if details['quit_when'] is not None: 646 lines.append(' %s: %s' % (_('Quit date'), gmDateTime.pydt_strftime(details['quit_when'], '%Y %b %d'))) 647 if details['comment'] is not None: 648 lines.append(' %s' % details['comment']) 649 650 if include_alcohol: 651 status, details = use['alcohol'] 652 if status is False: 653 if include_nonuse: 654 if len(lines) > 0: 655 lines.append('') 656 lines.append(_('no or non-harmful alcohol use')) 657 lines.append(' %s' % details) 658 elif status is True: 659 if len(lines) > 0: 660 lines.append('') 661 lines.append(_('harmful alcohol use')) 662 lines.append(' %s' % details) 663 else: 664 if include_unknown: 665 if len(lines) > 0: 666 lines.append('') 667 lines.append(_('unknown alcohol use')) 668 lines.append(' %s' % details) 669 670 if include_drugs: 671 status, details = use['drugs'] 672 if status is False: 673 if include_nonuse: 674 if len(lines) > 0: 675 lines.append('') 676 lines.append(_('no or non-harmful drug use')) 677 lines.append(' %s' % details) 678 elif status is True: 679 if len(lines) > 0: 680 lines.append('') 681 lines.append(_('harmful drug use')) 682 lines.append(' %s' % details) 683 else: 684 if include_unknown: 685 if len(lines) > 0: 686 lines.append('') 687 lines.append(_('unknown drug use')) 688 lines.append(' %s' % details) 689 690 return lines
691 692 #--------------------------------------------------------
693 - def _get_currently_abuses_substances(self):
694 # returns True / False / None (= unknown) 695 696 use = self.harmful_substance_use 697 # we know that at least one group is used: 698 if use['alcohol'][0] is True: 699 return True 700 if use['drugs'][0] is True: 701 return True 702 if use['tobacco'][0] > 0: 703 # is True: 704 if use['tobacco'][1]['quit_when'] is None: 705 return True 706 # at this point no group is currently used for sure 707 # we don't know about some of the groups so we can NOT say: no abuse at all: 708 if use['alcohol'][0] is None: 709 return None 710 if use['drugs'][0] is None: 711 return None 712 if use['tobacco'][0] is None: 713 return None 714 # at this point all groups must be FALSE, except for 715 # tobacco which can also be TRUE _but_, if so, a quit 716 # date has been set, which is considered non-abuse 717 return False
718 719 currently_abuses_substances = property(_get_currently_abuses_substances, lambda x:x) 720 721 #-------------------------------------------------------- 722 # API: performed procedures 723 #--------------------------------------------------------
724 - def get_performed_procedures(self, episodes=None, issues=None):
725 726 procs = gmEMRStructItems.get_performed_procedures(patient = self.pk_patient) 727 728 if episodes is not None: 729 procs = [ p for p in procs if p['pk_episode'] in episodes ] 730 731 if issues is not None: 732 procs = [ p for p in procs if p['pk_health_issue'] in issues ] 733 734 return procs
735 736 performed_procedures = property(get_performed_procedures, lambda x:x) 737 #--------------------------------------------------------
738 - def get_latest_performed_procedure(self):
739 return gmEMRStructItems.get_latest_performed_procedure(patient = self.pk_patient)
740 #--------------------------------------------------------
741 - def add_performed_procedure(self, episode=None, location=None, hospital_stay=None, procedure=None):
742 return gmEMRStructItems.create_performed_procedure ( 743 encounter = self.current_encounter['pk_encounter'], 744 episode = episode, 745 location = location, 746 hospital_stay = hospital_stay, 747 procedure = procedure 748 )
749 #--------------------------------------------------------
750 - def get_procedure_locations_as_org_units(self):
751 where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_procedures_not_at_hospital WHERE pk_patient = %(pat)s)' 752 args = {'pat': self.pk_patient} 753 cmd = gmOrganization._SQL_get_org_unit % where 754 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 755 return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
756 757 #-------------------------------------------------------- 758 # API: hospitalizations 759 #--------------------------------------------------------
760 - def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False):
761 stays = gmEMRStructItems.get_patient_hospital_stays(patient = self.pk_patient, ongoing_only = ongoing_only) 762 if episodes is not None: 763 stays = [ s for s in stays if s['pk_episode'] in episodes ] 764 if issues is not None: 765 stays = [ s for s in stays if s['pk_health_issue'] in issues ] 766 return stays
767 768 hospital_stays = property(get_hospital_stays, lambda x:x) 769 #--------------------------------------------------------
770 - def get_latest_hospital_stay(self):
771 return gmEMRStructItems.get_latest_patient_hospital_stay(patient = self.pk_patient)
772 #--------------------------------------------------------
773 - def add_hospital_stay(self, episode=None, fk_org_unit=None):
774 return gmEMRStructItems.create_hospital_stay ( 775 encounter = self.current_encounter['pk_encounter'], 776 episode = episode, 777 fk_org_unit = fk_org_unit 778 )
779 #--------------------------------------------------------
780 - def get_hospital_stay_stats_by_hospital(self, cover_period=None):
781 args = {'pat': self.pk_patient, 'range': cover_period} 782 where_parts = ['pk_patient = %(pat)s'] 783 if cover_period is not None: 784 where_parts.append('discharge > (now() - %(range)s)') 785 786 cmd = """ 787 SELECT hospital, count(1) AS frequency 788 FROM clin.v_hospital_stays 789 WHERE 790 %s 791 GROUP BY hospital 792 ORDER BY frequency DESC 793 """ % ' AND '.join(where_parts) 794 795 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 796 return rows
797 #--------------------------------------------------------
798 - def get_attended_hospitals_as_org_units(self):
799 where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s)' 800 args = {'pat': self.pk_patient} 801 cmd = gmOrganization._SQL_get_org_unit % where 802 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 803 return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
804 805 #-------------------------------------------------------- 806 # API: narrative 807 #--------------------------------------------------------
808 - def add_notes(self, notes=None, episode=None, encounter=None):
809 enc = gmTools.coalesce ( 810 encounter, 811 self.current_encounter['pk_encounter'] 812 ) 813 for note in notes: 814 gmClinNarrative.create_narrative_item ( 815 narrative = note[1], 816 soap_cat = note[0], 817 episode_id = episode, 818 encounter_id = enc 819 ) 820 return True
821 822 #--------------------------------------------------------
823 - def add_clin_narrative(self, note='', soap_cat='s', episode=None, link_obj=None):
824 if note.strip() == '': 825 _log.info('will not create empty clinical note') 826 return None 827 if isinstance(episode, gmEMRStructItems.cEpisode): 828 episode = episode['pk_episode'] 829 instance = gmClinNarrative.create_narrative_item ( 830 link_obj = link_obj, 831 narrative = note, 832 soap_cat = soap_cat, 833 episode_id = episode, 834 encounter_id = self.current_encounter['pk_encounter'] 835 ) 836 return instance
837 838 #--------------------------------------------------------
839 - def get_clin_narrative(self, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None):
840 """Get SOAP notes pertinent to this encounter. 841 842 encounters 843 - list of encounters the narrative of which are to be retrieved 844 episodes 845 - list of episodes the narrative of which are to be retrieved 846 issues 847 - list of health issues the narrative of which are to be retrieved 848 soap_cats 849 - list of SOAP categories of the narrative to be retrieved 850 """ 851 where_parts = ['pk_patient = %(pat)s'] 852 args = {'pat': self.pk_patient} 853 854 if issues is not None: 855 where_parts.append('pk_health_issue IN %(issues)s') 856 if len(issues) == 0: 857 args['issues'] = tuple() 858 else: 859 if isinstance(issues[0], gmEMRStructItems.cHealthIssue): 860 args['issues'] = tuple([ i['pk_health_issue'] for i in issues ]) 861 elif isinstance(issues[0], int): 862 args['issues'] = tuple(issues) 863 else: 864 raise ValueError('<issues> must be list of type int (=pk) or cHealthIssue, but 1st issue is: %s' % issues[0]) 865 866 if episodes is not None: 867 where_parts.append('pk_episode IN %(epis)s') 868 if len(episodes) == 0: 869 args['epis'] = tuple() 870 else: 871 if isinstance(episodes[0], gmEMRStructItems.cEpisode): 872 args['epis'] = tuple([ e['pk_episode'] for e in episodes ]) 873 elif isinstance(episodes[0], int): 874 args['epis'] = tuple(episodes) 875 else: 876 raise ValueError('<episodes> must be list of type int (=pk) or cEpisode, but 1st episode is: %s' % episodes[0]) 877 878 if encounters is not None: 879 where_parts.append('pk_encounter IN %(encs)s') 880 if len(encounters) == 0: 881 args['encs'] = tuple() 882 else: 883 if isinstance(encounters[0], gmEMRStructItems.cEncounter): 884 args['encs'] = tuple([ e['pk_encounter'] for e in encounters ]) 885 elif isinstance(encounters[0], int): 886 args['encs'] = tuple(encounters) 887 else: 888 raise ValueError('<encounters> must be list of type int (=pk) or cEncounter, but 1st encounter is: %s' % encounters[0]) 889 890 if soap_cats is not None: 891 where_parts.append('c_vn.soap_cat IN %(cats)s') 892 args['cats'] = tuple(gmSoapDefs.soap_cats2list(soap_cats)) 893 894 if providers is not None: 895 where_parts.append('c_vn.modified_by IN %(docs)s') 896 args['docs'] = tuple(providers) 897 898 cmd = """ 899 SELECT 900 c_vn.*, 901 c_scr.rank AS soap_rank 902 FROM 903 clin.v_narrative c_vn 904 LEFT JOIN clin.soap_cat_ranks c_scr on c_vn.soap_cat = c_scr.soap_cat 905 WHERE %s 906 ORDER BY date, soap_rank 907 """ % ' AND '.join(where_parts) 908 909 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 910 return [ gmClinNarrative.cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ]
911 912 #--------------------------------------------------------
913 - def search_narrative_simple(self, search_term=''):
914 915 search_term = search_term.strip() 916 if search_term == '': 917 return [] 918 919 cmd = """ 920 SELECT 921 *, 922 coalesce((SELECT description FROM clin.episode WHERE pk = vn4s.pk_episode), vn4s.src_table) 923 as episode, 924 coalesce((SELECT description FROM clin.health_issue WHERE pk = vn4s.pk_health_issue), vn4s.src_table) 925 as health_issue, 926 (SELECT started FROM clin.encounter WHERE pk = vn4s.pk_encounter) 927 as encounter_started, 928 (SELECT last_affirmed FROM clin.encounter WHERE pk = vn4s.pk_encounter) 929 as encounter_ended, 930 (SELECT _(description) FROM clin.encounter_type WHERE pk = (SELECT fk_type FROM clin.encounter WHERE pk = vn4s.pk_encounter)) 931 as encounter_type 932 from clin.v_narrative4search vn4s 933 WHERE 934 pk_patient = %(pat)s and 935 vn4s.narrative ~ %(term)s 936 order by 937 encounter_started 938 """ # case sensitive 939 rows, idx = gmPG2.run_ro_queries(queries = [ 940 {'cmd': cmd, 'args': {'pat': self.pk_patient, 'term': search_term}} 941 ]) 942 return rows
943 #--------------------------------------------------------
944 - def get_text_dump(self, since=None, until=None, encounters=None, episodes=None, issues=None):
945 fields = [ 946 'age', 947 "to_char(modified_when, 'YYYY-MM-DD @ HH24:MI') as modified_when", 948 'modified_by', 949 'clin_when', 950 "case is_modified when false then '%s' else '%s' end as modified_string" % (_('original entry'), _('modified entry')), 951 'pk_item', 952 'pk_encounter', 953 'pk_episode', 954 'pk_health_issue', 955 'src_table' 956 ] 957 select_from = "SELECT %s FROM clin.v_pat_items" % ', '.join(fields) 958 # handle constraint conditions 959 where_snippets = [] 960 params = {} 961 where_snippets.append('pk_patient=%(pat_id)s') 962 params['pat_id'] = self.pk_patient 963 if not since is None: 964 where_snippets.append('clin_when >= %(since)s') 965 params['since'] = since 966 if not until is None: 967 where_snippets.append('clin_when <= %(until)s') 968 params['until'] = until 969 # FIXME: these are interrelated, eg if we constrain encounter 970 # we automatically constrain issue/episode, so handle that, 971 # encounters 972 if not encounters is None and len(encounters) > 0: 973 params['enc'] = encounters 974 if len(encounters) > 1: 975 where_snippets.append('fk_encounter in %(enc)s') 976 else: 977 where_snippets.append('fk_encounter=%(enc)s') 978 # episodes 979 if not episodes is None and len(episodes) > 0: 980 params['epi'] = episodes 981 if len(episodes) > 1: 982 where_snippets.append('fk_episode in %(epi)s') 983 else: 984 where_snippets.append('fk_episode=%(epi)s') 985 # health issues 986 if not issues is None and len(issues) > 0: 987 params['issue'] = issues 988 if len(issues) > 1: 989 where_snippets.append('fk_health_issue in %(issue)s') 990 else: 991 where_snippets.append('fk_health_issue=%(issue)s') 992 993 where_clause = ' and '.join(where_snippets) 994 order_by = 'order by src_table, age' 995 cmd = "%s WHERE %s %s" % (select_from, where_clause, order_by) 996 997 rows, view_col_idx = gmPG.run_ro_query('historica', cmd, 1, params) 998 if rows is None: 999 _log.error('cannot load item links for patient [%s]' % self.pk_patient) 1000 return None 1001 1002 # -- sort the data -- 1003 # FIXME: by issue/encounter/episode, eg formatting 1004 # aggregate by src_table for item retrieval 1005 items_by_table = {} 1006 for item in rows: 1007 src_table = item[view_col_idx['src_table']] 1008 pk_item = item[view_col_idx['pk_item']] 1009 if src_table not in items_by_table: 1010 items_by_table[src_table] = {} 1011 items_by_table[src_table][pk_item] = item 1012 1013 # get mapping for issue/episode IDs 1014 issues = self.get_health_issues() 1015 issue_map = {} 1016 for issue in issues: 1017 issue_map[issue['pk_health_issue']] = issue['description'] 1018 episodes = self.get_episodes() 1019 episode_map = {} 1020 for episode in episodes: 1021 episode_map[episode['pk_episode']] = episode['description'] 1022 emr_data = {} 1023 # get item data from all source tables 1024 ro_conn = self._conn_pool.GetConnection('historica') 1025 curs = ro_conn.cursor() 1026 for src_table in items_by_table.keys(): 1027 item_ids = items_by_table[src_table].keys() 1028 # we don't know anything about the columns of 1029 # the source tables but, hey, this is a dump 1030 if len(item_ids) == 0: 1031 _log.info('no items in table [%s] ?!?' % src_table) 1032 continue 1033 elif len(item_ids) == 1: 1034 cmd = "SELECT * FROM %s WHERE pk_item=%%s order by modified_when" % src_table 1035 if not gmPG.run_query(curs, None, cmd, item_ids[0]): 1036 _log.error('cannot load items from table [%s]' % src_table) 1037 # skip this table 1038 continue 1039 elif len(item_ids) > 1: 1040 cmd = "SELECT * FROM %s WHERE pk_item in %%s order by modified_when" % src_table 1041 if not gmPG.run_query(curs, None, cmd, (tuple(item_ids),)): 1042 _log.error('cannot load items from table [%s]' % src_table) 1043 # skip this table 1044 continue 1045 rows = curs.fetchall() 1046 table_col_idx = gmPG.get_col_indices(curs) 1047 # format per-table items 1048 for row in rows: 1049 # FIXME: make this get_pkey_name() 1050 pk_item = row[table_col_idx['pk_item']] 1051 view_row = items_by_table[src_table][pk_item] 1052 age = view_row[view_col_idx['age']] 1053 # format metadata 1054 try: 1055 episode_name = episode_map[view_row[view_col_idx['pk_episode']]] 1056 except: 1057 episode_name = view_row[view_col_idx['pk_episode']] 1058 try: 1059 issue_name = issue_map[view_row[view_col_idx['pk_health_issue']]] 1060 except: 1061 issue_name = view_row[view_col_idx['pk_health_issue']] 1062 1063 if age not in emr_data: 1064 emr_data[age] = [] 1065 1066 emr_data[age].append( 1067 _('%s: encounter (%s)') % ( 1068 view_row[view_col_idx['clin_when']], 1069 view_row[view_col_idx['pk_encounter']] 1070 ) 1071 ) 1072 emr_data[age].append(_('health issue: %s') % issue_name) 1073 emr_data[age].append(_('episode : %s') % episode_name) 1074 # format table specific data columns 1075 # - ignore those, they are metadata, some 1076 # are in clin.v_pat_items data already 1077 cols2ignore = [ 1078 'pk_audit', 'row_version', 'modified_when', 'modified_by', 1079 'pk_item', 'id', 'fk_encounter', 'fk_episode', 'pk' 1080 ] 1081 col_data = [] 1082 for col_name in table_col_idx.keys(): 1083 if col_name in cols2ignore: 1084 continue 1085 emr_data[age].append("=> %s: %s" % (col_name, row[table_col_idx[col_name]])) 1086 emr_data[age].append("----------------------------------------------------") 1087 emr_data[age].append("-- %s from table %s" % ( 1088 view_row[view_col_idx['modified_string']], 1089 src_table 1090 )) 1091 emr_data[age].append("-- written %s by %s" % ( 1092 view_row[view_col_idx['modified_when']], 1093 view_row[view_col_idx['modified_by']] 1094 )) 1095 emr_data[age].append("----------------------------------------------------") 1096 curs.close() 1097 return emr_data
1098 #--------------------------------------------------------
1099 - def get_patient_ID(self):
1100 return self.pk_patient
1101 #--------------------------------------------------------
1102 - def get_statistics(self):
1103 union_query = '\n union all\n'.join ([ 1104 """ 1105 SELECT (( 1106 -- all relevant health issues + active episodes WITH health issue 1107 SELECT COUNT(1) 1108 FROM clin.v_problem_list 1109 WHERE 1110 pk_patient = %(pat)s 1111 AND 1112 pk_health_issue is not null 1113 ) + ( 1114 -- active episodes WITHOUT health issue 1115 SELECT COUNT(1) 1116 FROM clin.v_problem_list 1117 WHERE 1118 pk_patient = %(pat)s 1119 AND 1120 pk_health_issue is null 1121 ))""", 1122 'SELECT count(1) FROM clin.encounter WHERE fk_patient = %(pat)s', 1123 'SELECT count(1) FROM clin.v_pat_items WHERE pk_patient = %(pat)s', 1124 'SELECT count(1) FROM blobs.v_doc_med WHERE pk_patient = %(pat)s', 1125 'SELECT count(1) FROM clin.v_test_results WHERE pk_patient = %(pat)s', 1126 'SELECT count(1) FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s', 1127 'SELECT count(1) FROM clin.v_procedures WHERE pk_patient = %(pat)s', 1128 # active and approved substances == medication 1129 """ 1130 SELECT count(1) 1131 FROM clin.v_substance_intakes 1132 WHERE 1133 pk_patient = %(pat)s 1134 AND 1135 is_currently_active IN (null, true) 1136 AND 1137 intake_is_approved_of IN (null, true)""", 1138 'SELECT count(1) FROM clin.v_vaccinations WHERE pk_patient = %(pat)s' 1139 ]) 1140 1141 rows, idx = gmPG2.run_ro_queries ( 1142 queries = [{'cmd': union_query, 'args': {'pat': self.pk_patient}}], 1143 get_col_idx = False 1144 ) 1145 1146 stats = dict ( 1147 problems = rows[0][0], 1148 encounters = rows[1][0], 1149 items = rows[2][0], 1150 documents = rows[3][0], 1151 results = rows[4][0], 1152 stays = rows[5][0], 1153 procedures = rows[6][0], 1154 active_drugs = rows[7][0], 1155 vaccinations = rows[8][0] 1156 ) 1157 1158 return stats
1159 #--------------------------------------------------------
1160 - def format_statistics(self):
1161 return _( 1162 'Medical problems: %(problems)s\n' 1163 'Total encounters: %(encounters)s\n' 1164 'Total EMR entries: %(items)s\n' 1165 'Active medications: %(active_drugs)s\n' 1166 'Documents: %(documents)s\n' 1167 'Test results: %(results)s\n' 1168 'Hospitalizations: %(stays)s\n' 1169 'Procedures: %(procedures)s\n' 1170 'Vaccinations: %(vaccinations)s' 1171 ) % self.get_statistics()
1172 #--------------------------------------------------------
1173 - def format_summary(self):
1174 1175 cmd = "SELECT dob FROM dem.v_all_persons WHERE pk_identity = %(pk)s" 1176 args = {'pk': self.pk_patient} 1177 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 1178 dob = rows[0]['dob'] 1179 1180 stats = self.get_statistics() 1181 first = self.get_first_encounter() 1182 last = self.get_last_encounter() 1183 probs = self.get_problems() 1184 1185 txt = '' 1186 if len(probs) > 0: 1187 txt += _(' %s known problems, clinically relevant thereof:\n') % stats['problems'] 1188 else: 1189 txt += _(' %s known problems\n') % stats['problems'] 1190 for prob in probs: 1191 if not prob['clinically_relevant']: 1192 continue 1193 txt += ' \u00BB%s\u00AB (%s)\n' % ( 1194 prob['problem'], 1195 gmTools.bool2subst(prob['problem_active'], _('active'), _('inactive')) 1196 ) 1197 txt += '\n' 1198 txt += _(' %s encounters from %s to %s\n') % ( 1199 stats['encounters'], 1200 gmDateTime.pydt_strftime(first['started'], '%Y %b %d'), 1201 gmDateTime.pydt_strftime(last['started'], '%Y %b %d') 1202 ) 1203 txt += _(' %s active medications\n') % stats['active_drugs'] 1204 txt += _(' %s documents\n') % stats['documents'] 1205 txt += _(' %s test results\n') % stats['results'] 1206 txt += _(' %s hospitalizations') % stats['stays'] 1207 if stats['stays'] == 0: 1208 txt += '\n' 1209 else: 1210 txt += _(', most recently:\n%s\n') % self.get_latest_hospital_stay().format(left_margin = 3) 1211 # FIXME: perhaps only count "ongoing ones" 1212 txt += _(' %s performed procedures') % stats['procedures'] 1213 if stats['procedures'] == 0: 1214 txt += '\n' 1215 else: 1216 txt += _(', most recently:\n%s\n') % self.get_latest_performed_procedure().format(left_margin = 3) 1217 1218 txt += '\n' 1219 txt += _('Allergies and Intolerances\n') 1220 1221 allg_state = self.allergy_state 1222 txt += (' ' + allg_state.state_string) 1223 if allg_state['last_confirmed'] is not None: 1224 txt += _(' (last confirmed %s)') % gmDateTime.pydt_strftime(allg_state['last_confirmed'], '%Y %b %d') 1225 txt += '\n' 1226 txt += gmTools.coalesce(allg_state['comment'], '', ' %s\n') 1227 for allg in self.get_allergies(): 1228 txt += ' %s: %s\n' % ( 1229 allg['descriptor'], 1230 gmTools.coalesce(allg['reaction'], _('unknown reaction')) 1231 ) 1232 1233 meds = self.get_current_medications(order_by = 'intake_is_approved_of DESC, substance') 1234 if len(meds) > 0: 1235 txt += '\n' 1236 txt += _('Medications and Substances') 1237 txt += '\n' 1238 for m in meds: 1239 txt += '%s\n' % m.format_as_single_line(left_margin = 1) 1240 1241 fhx = self.get_family_history() 1242 if len(fhx) > 0: 1243 txt += '\n' 1244 txt += _('Family History') 1245 txt += '\n' 1246 for f in fhx: 1247 txt += '%s\n' % f.format(left_margin = 1) 1248 1249 jobs = get_occupations(pk_identity = self.pk_patient) 1250 if len(jobs) > 0: 1251 txt += '\n' 1252 txt += _('Occupations') 1253 txt += '\n' 1254 for job in jobs: 1255 txt += ' %s%s\n' % ( 1256 job['l10n_occupation'], 1257 gmTools.coalesce(job['activities'], '', ': %s') 1258 ) 1259 1260 vaccs = self.get_latest_vaccinations() 1261 if len(vaccs) > 0: 1262 txt += '\n' 1263 txt += _('Vaccinations') 1264 txt += '\n' 1265 inds = sorted(vaccs.keys()) 1266 for ind in inds: 1267 ind_count, vacc = vaccs[ind] 1268 if dob is None: 1269 age_given = '' 1270 else: 1271 age_given = ' @ %s' % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age ( 1272 start = dob, 1273 end = vacc['date_given'] 1274 )) 1275 since = _('%s ago') % gmDateTime.format_interval_medically(vacc['interval_since_given']) 1276 txt += ' %s (%s%s): %s%s (%s %s%s%s)\n' % ( 1277 ind, 1278 gmTools.u_sum, 1279 ind_count, 1280 #gmDateTime.pydt_strftime(vacc['date_given'], '%b %Y'), 1281 since, 1282 age_given, 1283 vacc['vaccine'], 1284 gmTools.u_left_double_angle_quote, 1285 vacc['batch_no'], 1286 gmTools.u_right_double_angle_quote 1287 ) 1288 1289 care = self.get_external_care_items(order_by = 'issue, organization, unit, provider', exclude_inactive = True) 1290 if len(care) > 0: 1291 txt += '\n' 1292 txt += _('External care') 1293 txt += '\n' 1294 for item in care: 1295 txt += ' %s: %s\n' % ( 1296 item['issue'], 1297 gmTools.coalesce ( 1298 item['provider'], 1299 '%s@%s' % (item['unit'], item['organization']), 1300 '%%s (%s@%s)' % (item['unit'], item['organization']) 1301 ) 1302 ) 1303 1304 return txt
1305 1306 #--------------------------------------------------------
1307 - def format_as_journal(self, left_margin=0, patient=None):
1308 txt = '' 1309 for enc in self.get_encounters(skip_empty = True): 1310 txt += gmTools.u_box_horiz_4dashes * 70 + '\n' 1311 txt += enc.format ( 1312 episodes = None, # means: each touched upon 1313 left_margin = left_margin, 1314 patient = patient, 1315 fancy_header = False, 1316 with_soap = True, 1317 with_docs = True, 1318 with_tests = True, 1319 with_vaccinations = True, 1320 with_co_encountlet_hints = False, # irrelevant 1321 with_rfe_aoe = True, 1322 with_family_history = True, 1323 by_episode = True 1324 ) 1325 1326 return txt
1327 1328 #--------------------------------------------------------
1329 - def get_as_journal(self, since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None):
1330 return gmClinNarrative.get_as_journal ( 1331 patient = self.pk_patient, 1332 since = since, 1333 until = until, 1334 encounters = encounters, 1335 episodes = episodes, 1336 issues = issues, 1337 soap_cats = soap_cats, 1338 providers = providers, 1339 order_by = order_by, 1340 time_range = time_range, 1341 active_encounter = self.active_encounter 1342 )
1343 1344 #------------------------------------------------------------------
1345 - def get_generic_emr_items(self, pk_encounters=None, pk_episodes=None, pk_health_issues=None, use_active_encounter=False, order_by=None):
1346 if use_active_encounter: 1347 active_encounter = self.active_encounter 1348 else: 1349 active_encounter = None 1350 return gmGenericEMRItem.get_generic_emr_items ( 1351 patient = self.pk_patient, 1352 encounters = pk_encounters, 1353 episodes = pk_episodes, 1354 issues = pk_health_issues, 1355 active_encounter = active_encounter, 1356 order_by = order_by 1357 )
1358 1359 #-------------------------------------------------------- 1360 # API: allergy 1361 #--------------------------------------------------------
1362 - def get_allergies(self, remove_sensitivities=False, since=None, until=None, encounters=None, episodes=None, issues=None, ID_list=None):
1363 """Retrieves patient allergy items. 1364 1365 remove_sensitivities 1366 - retrieve real allergies only, without sensitivities 1367 since 1368 - initial date for allergy items 1369 until 1370 - final date for allergy items 1371 encounters 1372 - list of encounters whose allergies are to be retrieved 1373 episodes 1374 - list of episodes whose allergies are to be retrieved 1375 issues 1376 - list of health issues whose allergies are to be retrieved 1377 """ 1378 cmd = "SELECT * FROM clin.v_pat_allergies WHERE pk_patient=%s order by descriptor" 1379 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}], get_col_idx = True) 1380 filtered_allergies = [] 1381 for r in rows: 1382 filtered_allergies.append(gmAllergy.cAllergy(row = {'data': r, 'idx': idx, 'pk_field': 'pk_allergy'})) 1383 1384 # ok, let's constrain our list 1385 if ID_list is not None: 1386 filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_allergy'] in ID_list ] 1387 if len(filtered_allergies) == 0: 1388 _log.error('no allergies of list [%s] found for patient [%s]' % (str(ID_list), self.pk_patient)) 1389 # better fail here contrary to what we do elsewhere 1390 return None 1391 else: 1392 return filtered_allergies 1393 1394 if remove_sensitivities: 1395 filtered_allergies = [ allg for allg in filtered_allergies if allg['type'] == 'allergy' ] 1396 if since is not None: 1397 filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] >= since ] 1398 if until is not None: 1399 filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] < until ] 1400 if issues is not None: 1401 filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_health_issue'] in issues ] 1402 if episodes is not None: 1403 filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_episode'] in episodes ] 1404 if encounters is not None: 1405 filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_encounter'] in encounters ] 1406 1407 return filtered_allergies
1408 #--------------------------------------------------------
1409 - def add_allergy(self, allergene=None, allg_type=None, encounter_id=None, episode_id=None):
1410 if encounter_id is None: 1411 encounter_id = self.current_encounter['pk_encounter'] 1412 1413 if episode_id is None: 1414 issue = self.add_health_issue(issue_name = _('Allergies/Intolerances')) 1415 epi = self.add_episode(episode_name = _('Allergy detail: %s') % allergene, pk_health_issue = issue['pk_health_issue']) 1416 episode_id = epi['pk_episode'] 1417 1418 new_allergy = gmAllergy.create_allergy ( 1419 allergene = allergene, 1420 allg_type = allg_type, 1421 encounter_id = encounter_id, 1422 episode_id = episode_id 1423 ) 1424 1425 return new_allergy
1426 #--------------------------------------------------------
1427 - def delete_allergy(self, pk_allergy=None):
1428 cmd = 'delete FROM clin.allergy WHERE pk=%(pk_allg)s' 1429 args = {'pk_allg': pk_allergy} 1430 gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
1431 1432 #--------------------------------------------------------
1433 - def is_allergic_to(self, atcs=None, inns=None, product_name=None):
1434 """Cave: only use with one potential allergic agent 1435 otherwise you won't know which of the agents the allergy is to.""" 1436 1437 # we don't know the state 1438 if self.allergy_state is None: 1439 return None 1440 1441 # we know there's no allergies 1442 if self.allergy_state == 0: 1443 return False 1444 1445 args = { 1446 'atcs': atcs, 1447 'inns': inns, 1448 'prod_name': product_name, 1449 'pat': self.pk_patient 1450 } 1451 allergenes = [] 1452 where_parts = [] 1453 1454 if len(atcs) == 0: 1455 atcs = None 1456 if atcs is not None: 1457 where_parts.append('atc_code in %(atcs)s') 1458 if len(inns) == 0: 1459 inns = None 1460 if inns is not None: 1461 where_parts.append('generics in %(inns)s') 1462 allergenes.extend(inns) 1463 if product_name is not None: 1464 where_parts.append('substance = %(prod_name)s') 1465 allergenes.append(product_name) 1466 1467 if len(allergenes) != 0: 1468 where_parts.append('allergene in %(allgs)s') 1469 args['allgs'] = tuple(allergenes) 1470 1471 cmd = """ 1472 SELECT * FROM clin.v_pat_allergies 1473 WHERE 1474 pk_patient = %%(pat)s 1475 AND ( %s )""" % ' OR '.join(where_parts) 1476 1477 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 1478 1479 if len(rows) == 0: 1480 return False 1481 1482 return gmAllergy.cAllergy(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_allergy'})
1483 #--------------------------------------------------------
1484 - def _set_allergy_state(self, state):
1485 1486 if state not in gmAllergy.allergy_states: 1487 raise ValueError('[%s].__set_allergy_state(): <state> must be one of %s' % (self.__class__.__name__, gmAllergy.allergy_states)) 1488 1489 allg_state = gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) 1490 allg_state['has_allergy'] = state 1491 allg_state.save_payload() 1492 return True
1493
1494 - def _get_allergy_state(self):
1495 return gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter'])
1496 1497 allergy_state = property(_get_allergy_state, _set_allergy_state) 1498 #-------------------------------------------------------- 1499 # API: external care 1500 #--------------------------------------------------------
1501 - def get_external_care_items(self, order_by=None, exclude_inactive=False):
1502 return gmExternalCare.get_external_care_items ( 1503 pk_identity = self.pk_patient, 1504 order_by = order_by, 1505 exclude_inactive = exclude_inactive 1506 )
1507 1508 external_care_items = property(get_external_care_items, lambda x:x) 1509 1510 #-------------------------------------------------------- 1511 # API: episodes 1512 #--------------------------------------------------------
1513 - def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False):
1514 """Fetches from backend patient episodes. 1515 1516 id_list - Episodes' PKs list 1517 issues - Health issues' PKs list to filter episodes by 1518 open_status - return all (None) episodes, only open (True) or closed (False) one(s) 1519 """ 1520 if (unlinked_only is True) and (issues is not None): 1521 raise ValueError('<unlinked_only> cannot be TRUE if <issues> is not None') 1522 1523 if order_by is None: 1524 order_by = '' 1525 else: 1526 order_by = 'ORDER BY %s' % order_by 1527 1528 args = { 1529 'pat': self.pk_patient, 1530 'open': open_status 1531 } 1532 where_parts = ['pk_patient = %(pat)s'] 1533 1534 if open_status is not None: 1535 where_parts.append('episode_open IS %(open)s') 1536 1537 if unlinked_only: 1538 where_parts.append('pk_health_issue is NULL') 1539 1540 if issues is not None: 1541 where_parts.append('pk_health_issue IN %(issues)s') 1542 args['issues'] = tuple(issues) 1543 1544 if id_list is not None: 1545 where_parts.append('pk_episode IN %(epis)s') 1546 args['epis'] = tuple(id_list) 1547 1548 cmd = "SELECT * FROM clin.v_pat_episodes WHERE %s %s" % ( 1549 ' AND '.join(where_parts), 1550 order_by 1551 ) 1552 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 1553 1554 return [ gmEMRStructItems.cEpisode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_episode'}) for r in rows ]
1555 1556 episodes = property(get_episodes, lambda x:x) 1557 #------------------------------------------------------------------
1558 - def get_unlinked_episodes(self, open_status=None, order_by=None):
1559 return self.get_episodes(open_status = open_status, order_by = order_by, unlinked_only = True)
1560 1561 unlinked_episodes = property(get_unlinked_episodes, lambda x:x) 1562 #------------------------------------------------------------------
1563 - def get_episodes_by_encounter(self, pk_encounter=None):
1564 cmd = """SELECT distinct pk_episode 1565 from clin.v_pat_items 1566 WHERE pk_encounter=%(enc)s and pk_patient=%(pat)s""" 1567 args = { 1568 'enc': gmTools.coalesce(pk_encounter, self.current_encounter['pk_encounter']), 1569 'pat': self.pk_patient 1570 } 1571 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) 1572 if len(rows) == 0: 1573 return [] 1574 epis = [] 1575 for row in rows: 1576 epis.append(row[0]) 1577 return self.get_episodes(id_list=epis)
1578 #------------------------------------------------------------------
1579 - def add_episode(self, episode_name=None, pk_health_issue=None, is_open=False, allow_dupes=False, link_obj=None):
1580 """Add episode 'episode_name' for a patient's health issue. 1581 1582 - silently returns if episode already exists 1583 """ 1584 episode = gmEMRStructItems.create_episode ( 1585 link_obj = link_obj, 1586 pk_health_issue = pk_health_issue, 1587 episode_name = episode_name, 1588 is_open = is_open, 1589 encounter = self.current_encounter['pk_encounter'], 1590 allow_dupes = allow_dupes 1591 ) 1592 return episode
1593 #--------------------------------------------------------
1594 - def get_most_recent_episode(self, issue=None):
1595 # try to find the episode with the most recently modified clinical item 1596 1597 issue_where = gmTools.coalesce(issue, '', 'and pk_health_issue = %(issue)s') 1598 1599 cmd = """ 1600 SELECT pk 1601 from clin.episode 1602 WHERE pk = ( 1603 SELECT distinct on(pk_episode) pk_episode 1604 from clin.v_pat_items 1605 WHERE 1606 pk_patient = %%(pat)s 1607 and 1608 modified_when = ( 1609 SELECT max(vpi.modified_when) 1610 from clin.v_pat_items vpi 1611 WHERE vpi.pk_patient = %%(pat)s 1612 ) 1613 %s 1614 -- guard against several episodes created at the same moment of time 1615 limit 1 1616 )""" % issue_where 1617 rows, idx = gmPG2.run_ro_queries(queries = [ 1618 {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} 1619 ]) 1620 if len(rows) != 0: 1621 return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) 1622 1623 # no clinical items recorded, so try to find 1624 # the youngest episode for this patient 1625 cmd = """ 1626 SELECT vpe0.pk_episode 1627 from 1628 clin.v_pat_episodes vpe0 1629 WHERE 1630 vpe0.pk_patient = %%(pat)s 1631 and 1632 vpe0.episode_modified_when = ( 1633 SELECT max(vpe1.episode_modified_when) 1634 from clin.v_pat_episodes vpe1 1635 WHERE vpe1.pk_episode = vpe0.pk_episode 1636 ) 1637 %s""" % issue_where 1638 rows, idx = gmPG2.run_ro_queries(queries = [ 1639 {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} 1640 ]) 1641 if len(rows) != 0: 1642 return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) 1643 1644 return None
1645 #--------------------------------------------------------
1646 - def episode2problem(self, episode=None):
1647 return gmEMRStructItems.episode2problem(episode=episode)
1648 #-------------------------------------------------------- 1649 # API: problems 1650 #--------------------------------------------------------
1651 - def get_problems(self, episodes=None, issues=None, include_closed_episodes=False, include_irrelevant_issues=False):
1652 """Retrieve a patient's problems. 1653 1654 "Problems" are the UNION of: 1655 1656 - issues which are .clinically_relevant 1657 - episodes which are .is_open 1658 1659 Therefore, both an issue and the open episode 1660 thereof can each be listed as a problem. 1661 1662 include_closed_episodes/include_irrelevant_issues will 1663 include those -- which departs from the definition of 1664 the problem list being "active" items only ... 1665 1666 episodes - episodes' PKs to filter problems by 1667 issues - health issues' PKs to filter problems by 1668 """ 1669 # FIXME: this could use a good measure of streamlining, probably 1670 1671 args = {'pat': self.pk_patient} 1672 1673 cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_problem_list WHERE pk_patient = %(pat)s ORDER BY problem""" 1674 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 1675 1676 # Instantiate problem items 1677 problems = [] 1678 for row in rows: 1679 pk_args = { 1680 'pk_patient': self.pk_patient, 1681 'pk_health_issue': row['pk_health_issue'], 1682 'pk_episode': row['pk_episode'] 1683 } 1684 problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = False)) 1685 1686 # include non-problems ? 1687 other_rows = [] 1688 if include_closed_episodes: 1689 cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'episode'""" 1690 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 1691 other_rows.extend(rows) 1692 1693 if include_irrelevant_issues: 1694 cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'health issue'""" 1695 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 1696 other_rows.extend(rows) 1697 1698 if len(other_rows) > 0: 1699 for row in other_rows: 1700 pk_args = { 1701 'pk_patient': self.pk_patient, 1702 'pk_health_issue': row['pk_health_issue'], 1703 'pk_episode': row['pk_episode'] 1704 } 1705 problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = True)) 1706 1707 # filter 1708 if issues is not None: 1709 problems = [ p for p in problems if p['pk_health_issue'] in issues ] 1710 if episodes is not None: 1711 problems = [ p for p in problems if p['pk_episode'] in episodes ] 1712 1713 return problems
1714 1715 #--------------------------------------------------------
1716 - def problem2episode(self, problem=None):
1717 return gmEMRStructItems.problem2episode(problem = problem)
1718 1719 #--------------------------------------------------------
1720 - def problem2issue(self, problem=None):
1721 return gmEMRStructItems.problem2issue(problem = problem)
1722 1723 #--------------------------------------------------------
1724 - def reclass_problem(self, problem):
1725 return gmEMRStructItems.reclass_problem(problem = problem)
1726 1727 #--------------------------------------------------------
1728 - def get_candidate_diagnoses(self):
1729 cmd = "SELECT * FROM clin.v_candidate_diagnoses WHERE pk_patient = %(pat)s" 1730 rows, idx = gmPG2.run_ro_queries ( 1731 queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], 1732 get_col_idx = False 1733 ) 1734 return rows
1735 1736 candidate_diagnoses = property(get_candidate_diagnoses) 1737 1738 #-------------------------------------------------------- 1739 # API: health issues 1740 #--------------------------------------------------------
1741 - def get_health_issues(self, id_list = None):
1742 1743 cmd = "SELECT *, xmin_health_issue FROM clin.v_health_issues WHERE pk_patient = %(pat)s ORDER BY description" 1744 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = True) 1745 issues = [ gmEMRStructItems.cHealthIssue(row = {'idx': idx, 'data': r, 'pk_field': 'pk_health_issue'}) for r in rows ] 1746 1747 if id_list is None: 1748 return issues 1749 1750 if len(id_list) == 0: 1751 raise ValueError('id_list to filter by is empty, most likely a programming error') 1752 1753 filtered_issues = [] 1754 for issue in issues: 1755 if issue['pk_health_issue'] in id_list: 1756 filtered_issues.append(issue) 1757 1758 return filtered_issues
1759 1760 health_issues = property(get_health_issues, lambda x:x) 1761 1762 #------------------------------------------------------------------
1763 - def add_health_issue(self, issue_name=None):
1764 """Adds patient health issue.""" 1765 return gmEMRStructItems.create_health_issue ( 1766 description = issue_name, 1767 encounter = self.current_encounter['pk_encounter'], 1768 patient = self.pk_patient 1769 )
1770 #--------------------------------------------------------
1771 - def health_issue2problem(self, issue=None):
1772 return gmEMRStructItems.health_issue2problem(issue = issue)
1773 #-------------------------------------------------------- 1774 # API: substance intake 1775 #--------------------------------------------------------
1776 - def get_current_medications(self, include_inactive=True, include_unapproved=False, order_by=None, episodes=None, issues=None):
1777 return self._get_current_substance_intakes ( 1778 include_inactive = include_inactive, 1779 include_unapproved = include_unapproved, 1780 order_by = order_by, 1781 episodes = episodes, 1782 issues = issues, 1783 exclude_medications = False, 1784 exclude_potential_abuses = True 1785 )
1786 1787 #--------------------------------------------------------
1788 - def _get_abused_substances(self, order_by=None):
1789 return self._get_current_substance_intakes ( 1790 include_inactive = True, 1791 include_unapproved = True, 1792 order_by = order_by, 1793 episodes = None, 1794 issues = None, 1795 exclude_medications = True, 1796 exclude_potential_abuses = False 1797 )
1798 1799 abused_substances = property(_get_abused_substances, lambda x:x) 1800 1801 #--------------------------------------------------------
1802 - def _get_current_substance_intakes(self, include_inactive=True, include_unapproved=False, order_by=None, episodes=None, issues=None, exclude_potential_abuses=False, exclude_medications=False):
1803 1804 where_parts = ['pk_patient = %(pat)s'] 1805 args = {'pat': self.pk_patient} 1806 1807 if not include_inactive: 1808 where_parts.append('is_currently_active IN (TRUE, NULL)') 1809 1810 if not include_unapproved: 1811 where_parts.append('intake_is_approved_of IN (TRUE, NULL)') 1812 1813 if exclude_potential_abuses: 1814 where_parts.append('harmful_use_type IS NULL') 1815 1816 if exclude_medications: 1817 where_parts.append('harmful_use_type IS NOT NULL') 1818 1819 if order_by is None: 1820 order_by = '' 1821 else: 1822 order_by = 'ORDER BY %s' % order_by 1823 1824 cmd = "SELECT * FROM clin.v_substance_intakes WHERE %s %s" % ( 1825 '\nAND '.join(where_parts), 1826 order_by 1827 ) 1828 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 1829 intakes = [ gmMedication.cSubstanceIntakeEntry(row = {'idx': idx, 'data': r, 'pk_field': 'pk_substance_intake'}) for r in rows ] 1830 1831 if episodes is not None: 1832 intakes = [ i for i in intakes if i['pk_episode'] in episodes ] 1833 1834 if issues is not None: 1835 intakes = [ i for i in intakes if i ['pk_health_issue'] in issues ] 1836 1837 return intakes
1838 1839 #--------------------------------------------------------
1840 - def add_substance_intake(self, pk_component=None, pk_episode=None, pk_drug_product=None, pk_health_issue=None):
1841 pk_enc = self.current_encounter['pk_encounter'] 1842 if pk_episode is None: 1843 pk_episode = gmMedication.create_default_medication_history_episode ( 1844 pk_health_issue = pk_health_issue, 1845 encounter = pk_enc 1846 ) 1847 return gmMedication.create_substance_intake ( 1848 pk_component = pk_component, 1849 pk_encounter = pk_enc, 1850 pk_episode = pk_episode, 1851 pk_drug_product = pk_drug_product 1852 )
1853 1854 #--------------------------------------------------------
1855 - def substance_intake_exists(self, pk_component=None, pk_substance=None, pk_drug_product=None):
1856 return gmMedication.substance_intake_exists ( 1857 pk_component = pk_component, 1858 pk_substance = pk_substance, 1859 pk_identity = self.pk_patient, 1860 pk_drug_product = pk_drug_product 1861 )
1862 1863 #-------------------------------------------------------- 1864 # API: vaccinations 1865 #--------------------------------------------------------
1866 - def add_vaccination(self, episode=None, vaccine=None, batch_no=None):
1867 return gmVaccination.create_vaccination ( 1868 encounter = self.current_encounter['pk_encounter'], 1869 episode = episode, 1870 vaccine = vaccine, 1871 batch_no = batch_no 1872 )
1873 1874 #--------------------------------------------------------
1875 - def get_latest_vaccinations(self, episodes=None, issues=None, atc_indications=None):
1876 """Returns latest given vaccination for each vaccinated indication. 1877 1878 as a dict {'l10n_indication': cVaccination instance} 1879 1880 Note that this will produce duplicate vaccination instances on combi-indication vaccines ! 1881 """ 1882 args = {'pat': self.pk_patient} 1883 where_parts = ['c_v_shots.pk_patient = %(pat)s'] 1884 1885 if (episodes is not None) and (len(episodes) > 0): 1886 where_parts.append('c_v_shots.pk_episode IN %(epis)s') 1887 args['epis'] = tuple(episodes) 1888 1889 if (issues is not None) and (len(issues) > 0): 1890 where_parts.append('c_v_shots.pk_episode IN (select pk from clin.episode where fk_health_issue IN %(issues)s)') 1891 args['issues'] = tuple(issues) 1892 1893 if (atc_indications is not None) and (len(atc_indications) > 0): 1894 where_parts.append('c_v_plv4i.atc_indication IN %(atc_inds)s') 1895 args['atc_inds'] = tuple(atc_indications) 1896 1897 # find the shots 1898 cmd = """ 1899 SELECT 1900 c_v_shots.*, 1901 c_v_plv4i.l10n_indication, 1902 c_v_plv4i.no_of_shots 1903 FROM 1904 clin.v_vaccinations c_v_shots 1905 JOIN clin.v_pat_last_vacc4indication c_v_plv4i ON (c_v_shots.pk_vaccination = c_v_plv4i.pk_vaccination) 1906 WHERE %s 1907 """ % '\nAND '.join(where_parts) 1908 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 1909 1910 # none found 1911 if len(rows) == 0: 1912 return {} 1913 1914 # turn them into vaccinations 1915 # (idx is constant) 1916 vaccs = {} 1917 for shot_row in rows: 1918 vaccs[shot_row['l10n_indication']] = ( 1919 shot_row['no_of_shots'], 1920 gmVaccination.cVaccination(row = {'idx': idx, 'data': shot_row, 'pk_field': 'pk_vaccination'}) 1921 ) 1922 1923 return vaccs
1924 1925 #--------------------------------------------------------
1926 - def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None):
1927 return gmVaccination.get_vaccinations ( 1928 pk_identity = self.pk_patient, 1929 pk_episodes = episodes, 1930 pk_health_issues = issues, 1931 pk_encounters = encounters, 1932 order_by = order_by, 1933 return_pks = False 1934 )
1935 1936 vaccinations = property(get_vaccinations, lambda x:x) 1937 1938 #-------------------------------------------------------- 1939 # old/obsolete: 1940 #--------------------------------------------------------
1941 - def get_scheduled_vaccination_regimes(self, ID=None, indications=None):
1942 """Retrieves vaccination regimes the patient is on. 1943 1944 optional: 1945 * ID - PK of the vaccination regime 1946 * indications - indications we want to retrieve vaccination 1947 regimes for, must be primary language, not l10n_indication 1948 """ 1949 # FIXME: use course, not regime 1950 # retrieve vaccination regimes definitions 1951 cmd = """SELECT distinct on(pk_course) pk_course 1952 FROM clin.v_vaccs_scheduled4pat 1953 WHERE pk_patient=%s""" 1954 rows = gmPG.run_ro_query('historica', cmd, None, self.pk_patient) 1955 if rows is None: 1956 _log.error('cannot retrieve scheduled vaccination courses') 1957 return None 1958 # Instantiate vaccination items and keep cache 1959 for row in rows: 1960 self.__db_cache['vaccinations']['scheduled regimes'].append(gmVaccination.cVaccinationCourse(aPK_obj=row[0])) 1961 1962 # ok, let's constrain our list 1963 filtered_regimes = [] 1964 filtered_regimes.extend(self.__db_cache['vaccinations']['scheduled regimes']) 1965 if ID is not None: 1966 filtered_regimes = [ r for r in filtered_regimes if r['pk_course'] == ID ] 1967 if len(filtered_regimes) == 0: 1968 _log.error('no vaccination course [%s] found for patient [%s]' % (ID, self.pk_patient)) 1969 return [] 1970 else: 1971 return filtered_regimes[0] 1972 if indications is not None: 1973 filtered_regimes = [ r for r in filtered_regimes if r['indication'] in indications ] 1974 1975 return filtered_regimes
1976 #-------------------------------------------------------- 1977 # def get_vaccinated_indications(self): 1978 # """Retrieves patient vaccinated indications list. 1979 # 1980 # Note that this does NOT rely on the patient being on 1981 # some schedule or other but rather works with what the 1982 # patient has ACTUALLY been vaccinated against. This is 1983 # deliberate ! 1984 # """ 1985 # # most likely, vaccinations will be fetched close 1986 # # by so it makes sense to count on the cache being 1987 # # filled (or fill it for nearby use) 1988 # vaccinations = self.get_vaccinations() 1989 # if vaccinations is None: 1990 # _log.error('cannot load vaccinated indications for patient [%s]' % self.pk_patient) 1991 # return (False, [[_('ERROR: cannot retrieve vaccinated indications'), _('ERROR: cannot retrieve vaccinated indications')]]) 1992 # if len(vaccinations) == 0: 1993 # return (True, [[_('no vaccinations recorded'), _('no vaccinations recorded')]]) 1994 # v_indications = [] 1995 # for vacc in vaccinations: 1996 # tmp = [vacc['indication'], vacc['l10n_indication']] 1997 # # remove duplicates 1998 # if tmp in v_indications: 1999 # continue 2000 # v_indications.append(tmp) 2001 # return (True, v_indications) 2002 #--------------------------------------------------------
2003 - def get_vaccinations_old(self, ID=None, indications=None, since=None, until=None, encounters=None, episodes=None, issues=None):
2004 """Retrieves list of vaccinations the patient has received. 2005 2006 optional: 2007 * ID - PK of a vaccination 2008 * indications - indications we want to retrieve vaccination 2009 items for, must be primary language, not l10n_indication 2010 * since - initial date for allergy items 2011 * until - final date for allergy items 2012 * encounters - list of encounters whose allergies are to be retrieved 2013 * episodes - list of episodes whose allergies are to be retrieved 2014 * issues - list of health issues whose allergies are to be retrieved 2015 """ 2016 try: 2017 self.__db_cache['vaccinations']['vaccinated'] 2018 except KeyError: 2019 self.__db_cache['vaccinations']['vaccinated'] = [] 2020 # Important fetch ordering by indication, date to know if a vaccination is booster 2021 cmd= """SELECT * FROM clin.v_pat_vaccinations4indication 2022 WHERE pk_patient=%s 2023 order by indication, date""" 2024 rows, idx = gmPG.run_ro_query('historica', cmd, True, self.pk_patient) 2025 if rows is None: 2026 _log.error('cannot load given vaccinations for patient [%s]' % self.pk_patient) 2027 del self.__db_cache['vaccinations']['vaccinated'] 2028 return None 2029 # Instantiate vaccination items 2030 vaccs_by_ind = {} 2031 for row in rows: 2032 vacc_row = { 2033 'pk_field': 'pk_vaccination', 2034 'idx': idx, 2035 'data': row 2036 } 2037 vacc = gmVaccination.cVaccination(row=vacc_row) 2038 self.__db_cache['vaccinations']['vaccinated'].append(vacc) 2039 # keep them, ordered by indication 2040 try: 2041 vaccs_by_ind[vacc['indication']].append(vacc) 2042 except KeyError: 2043 vaccs_by_ind[vacc['indication']] = [vacc] 2044 2045 # calculate sequence number and is_booster 2046 for ind in vaccs_by_ind.keys(): 2047 vacc_regimes = self.get_scheduled_vaccination_regimes(indications = [ind]) 2048 for vacc in vaccs_by_ind[ind]: 2049 # due to the "order by indication, date" the vaccinations are in the 2050 # right temporal order inside the indication-keyed dicts 2051 seq_no = vaccs_by_ind[ind].index(vacc) + 1 2052 vacc['seq_no'] = seq_no 2053 # if no active schedule for indication we cannot 2054 # check for booster status (eg. seq_no > max_shot) 2055 if (vacc_regimes is None) or (len(vacc_regimes) == 0): 2056 continue 2057 if seq_no > vacc_regimes[0]['shots']: 2058 vacc['is_booster'] = True 2059 del vaccs_by_ind 2060 2061 # ok, let's constrain our list 2062 filtered_shots = [] 2063 filtered_shots.extend(self.__db_cache['vaccinations']['vaccinated']) 2064 if ID is not None: 2065 filtered_shots = filter(lambda shot: shot['pk_vaccination'] == ID, filtered_shots) 2066 if len(filtered_shots) == 0: 2067 _log.error('no vaccination [%s] found for patient [%s]' % (ID, self.pk_patient)) 2068 return None 2069 else: 2070 return filtered_shots[0] 2071 if since is not None: 2072 filtered_shots = filter(lambda shot: shot['date'] >= since, filtered_shots) 2073 if until is not None: 2074 filtered_shots = filter(lambda shot: shot['date'] < until, filtered_shots) 2075 if issues is not None: 2076 filtered_shots = filter(lambda shot: shot['pk_health_issue'] in issues, filtered_shots) 2077 if episodes is not None: 2078 filtered_shots = filter(lambda shot: shot['pk_episode'] in episodes, filtered_shots) 2079 if encounters is not None: 2080 filtered_shots = filter(lambda shot: shot['pk_encounter'] in encounters, filtered_shots) 2081 if indications is not None: 2082 filtered_shots = filter(lambda shot: shot['indication'] in indications, filtered_shots) 2083 return filtered_shots
2084 #--------------------------------------------------------
2085 - def get_scheduled_vaccinations(self, indications=None):
2086 """Retrieves vaccinations scheduled for a regime a patient is on. 2087 2088 The regime is referenced by its indication (not l10n) 2089 2090 * indications - List of indications (not l10n) of regimes we want scheduled 2091 vaccinations to be fetched for 2092 """ 2093 try: 2094 self.__db_cache['vaccinations']['scheduled'] 2095 except KeyError: 2096 self.__db_cache['vaccinations']['scheduled'] = [] 2097 cmd = """SELECT * FROM clin.v_vaccs_scheduled4pat WHERE pk_patient=%s""" 2098 rows, idx = gmPG.run_ro_query('historica', cmd, True, self.pk_patient) 2099 if rows is None: 2100 _log.error('cannot load scheduled vaccinations for patient [%s]' % self.pk_patient) 2101 del self.__db_cache['vaccinations']['scheduled'] 2102 return None 2103 # Instantiate vaccination items 2104 for row in rows: 2105 vacc_row = { 2106 'pk_field': 'pk_vacc_def', 2107 'idx': idx, 2108 'data': row 2109 } 2110 self.__db_cache['vaccinations']['scheduled'].append(gmVaccination.cScheduledVaccination(row = vacc_row)) 2111 2112 # ok, let's constrain our list 2113 if indications is None: 2114 return self.__db_cache['vaccinations']['scheduled'] 2115 filtered_shots = [] 2116 filtered_shots.extend(self.__db_cache['vaccinations']['scheduled']) 2117 filtered_shots = filter(lambda shot: shot['indication'] in indications, filtered_shots) 2118 return filtered_shots
2119 #--------------------------------------------------------
2120 - def get_missing_vaccinations(self, indications=None):
2121 try: 2122 self.__db_cache['vaccinations']['missing'] 2123 except KeyError: 2124 self.__db_cache['vaccinations']['missing'] = {} 2125 # 1) non-booster 2126 self.__db_cache['vaccinations']['missing']['due'] = [] 2127 # get list of (indication, seq_no) tuples 2128 cmd = "SELECT indication, seq_no FROM clin.v_pat_missing_vaccs WHERE pk_patient=%s" 2129 rows = gmPG.run_ro_query('historica', cmd, None, self.pk_patient) 2130 if rows is None: 2131 _log.error('error loading (indication, seq_no) for due/overdue vaccinations for patient [%s]' % self.pk_patient) 2132 return None 2133 pk_args = {'pat_id': self.pk_patient} 2134 if rows is not None: 2135 for row in rows: 2136 pk_args['indication'] = row[0] 2137 pk_args['seq_no'] = row[1] 2138 self.__db_cache['vaccinations']['missing']['due'].append(gmVaccination.cMissingVaccination(aPK_obj=pk_args)) 2139 2140 # 2) boosters 2141 self.__db_cache['vaccinations']['missing']['boosters'] = [] 2142 # get list of indications 2143 cmd = "SELECT indication, seq_no FROM clin.v_pat_missing_boosters WHERE pk_patient=%s" 2144 rows = gmPG.run_ro_query('historica', cmd, None, self.pk_patient) 2145 if rows is None: 2146 _log.error('error loading indications for missing boosters for patient [%s]' % self.pk_patient) 2147 return None 2148 pk_args = {'pat_id': self.pk_patient} 2149 if rows is not None: 2150 for row in rows: 2151 pk_args['indication'] = row[0] 2152 self.__db_cache['vaccinations']['missing']['boosters'].append(gmVaccination.cMissingBooster(aPK_obj=pk_args)) 2153 2154 # if any filters ... 2155 if indications is None: 2156 return self.__db_cache['vaccinations']['missing'] 2157 if len(indications) == 0: 2158 return self.__db_cache['vaccinations']['missing'] 2159 # ... apply them 2160 filtered_shots = { 2161 'due': [], 2162 'boosters': [] 2163 } 2164 for due_shot in self.__db_cache['vaccinations']['missing']['due']: 2165 if due_shot['indication'] in indications: #and due_shot not in filtered_shots['due']: 2166 filtered_shots['due'].append(due_shot) 2167 for due_shot in self.__db_cache['vaccinations']['missing']['boosters']: 2168 if due_shot['indication'] in indications: #and due_shot not in filtered_shots['boosters']: 2169 filtered_shots['boosters'].append(due_shot) 2170 return filtered_shots
2171 2172 #------------------------------------------------------------------ 2173 # API: encounters 2174 #------------------------------------------------------------------
2175 - def _get_current_encounter(self):
2176 return self.__encounter
2177
2178 - def _set_current_encounter(self, encounter):
2179 # first ever setting ? -> fast path 2180 if self.__encounter is None: 2181 _log.debug('first setting of active encounter in this clinical record instance') 2182 encounter.lock(exclusive = False) # lock new 2183 self.__encounter = encounter 2184 gmDispatcher.send('current_encounter_switched') 2185 return True 2186 2187 # real switch -> slow path 2188 _log.debug('switching of active encounter') 2189 # fail if the currently active encounter has unsaved changes 2190 if self.__encounter.is_modified(): 2191 gmTools.compare_dict_likes(self.__encounter, encounter, 'modified enc in client', 'enc to switch to') 2192 _log.error('current in client: %s', self.__encounter) 2193 raise ValueError('unsaved changes in active encounter [%s], cannot switch to another one [%s]' % ( 2194 self.__encounter['pk_encounter'], 2195 encounter['pk_encounter'] 2196 )) 2197 2198 prev_enc = self.__encounter 2199 encounter.lock(exclusive = False) # lock new 2200 self.__encounter = encounter 2201 prev_enc.unlock(exclusive = False) # unlock old 2202 gmDispatcher.send('current_encounter_switched') 2203 2204 return True
2205 2206 current_encounter = property(_get_current_encounter, _set_current_encounter) 2207 active_encounter = property(_get_current_encounter, _set_current_encounter) 2208 2209 #--------------------------------------------------------
2210 - def __setup_active_encounter(self):
2211 _log.debug('setting up active encounter for identity [%s]', self.pk_patient) 2212 2213 # log access to patient record (HIPAA, for example) 2214 _delayed_execute(self.log_access, action = 'pulling chart for identity [%s]' % self.pk_patient) 2215 2216 # cleanup (not async, because we don't want recent encounters 2217 # to become the active one just because they are recent) 2218 self.remove_empty_encounters() 2219 2220 # activate very recent encounter if available 2221 if self.__activate_very_recent_encounter(): 2222 return 2223 2224 fairly_recent_enc = self.__get_fairly_recent_encounter() 2225 2226 # create new encounter for the time being 2227 self.start_new_encounter() 2228 2229 if fairly_recent_enc is None: 2230 return 2231 2232 # but check whether user wants to continue a "fairly recent" one 2233 gmDispatcher.send ( 2234 signal = 'ask_for_encounter_continuation', 2235 new_encounter = self.__encounter, 2236 fairly_recent_encounter = fairly_recent_enc 2237 )
2238 2239 #------------------------------------------------------------------
2240 - def __activate_very_recent_encounter(self):
2241 """Try to attach to a "very recent" encounter if there is one. 2242 2243 returns: 2244 False: no "very recent" encounter 2245 True: success 2246 """ 2247 cfg_db = gmCfg.cCfgSQL() 2248 min_ttl = cfg_db.get2 ( 2249 option = 'encounter.minimum_ttl', 2250 workplace = _here.active_workplace, 2251 bias = 'user', 2252 default = '1 hour 30 minutes' 2253 ) 2254 cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = ( 2255 SELECT pk_encounter 2256 FROM clin.v_most_recent_encounters 2257 WHERE 2258 pk_patient = %s 2259 and 2260 last_affirmed > (now() - %s::interval) 2261 ORDER BY 2262 last_affirmed DESC 2263 LIMIT 1 2264 )""" 2265 enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, min_ttl]}], get_col_idx = True) 2266 2267 # none found 2268 if len(enc_rows) == 0: 2269 _log.debug('no <very recent> encounter (younger than [%s]) found' % min_ttl) 2270 return False 2271 2272 _log.debug('"very recent" encounter [%s] found and re-activated' % enc_rows[0]['pk_encounter']) 2273 2274 # attach to existing 2275 self.current_encounter = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) 2276 return True
2277 2278 #------------------------------------------------------------------
2279 - def __get_fairly_recent_encounter(self):
2280 cfg_db = gmCfg.cCfgSQL() 2281 min_ttl = cfg_db.get2 ( 2282 option = 'encounter.minimum_ttl', 2283 workplace = _here.active_workplace, 2284 bias = 'user', 2285 default = '1 hour 30 minutes' 2286 ) 2287 max_ttl = cfg_db.get2 ( 2288 option = 'encounter.maximum_ttl', 2289 workplace = _here.active_workplace, 2290 bias = 'user', 2291 default = '6 hours' 2292 ) 2293 2294 # do we happen to have a "fairly recent" candidate ? 2295 cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = ( 2296 SELECT pk_encounter 2297 FROM clin.v_most_recent_encounters 2298 WHERE 2299 pk_patient=%s 2300 AND 2301 last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) 2302 ORDER BY 2303 last_affirmed DESC 2304 LIMIT 1 2305 )""" 2306 enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True) 2307 2308 # none found 2309 if len(enc_rows) == 0: 2310 _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) 2311 return None 2312 2313 _log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter']) 2314 return gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
2315 2316 # #------------------------------------------------------------------ 2317 # def __check_for_fairly_recent_encounter(self): 2318 # 2319 # cfg_db = gmCfg.cCfgSQL() 2320 # min_ttl = cfg_db.get2 ( 2321 # option = u'encounter.minimum_ttl', 2322 # workplace = _here.active_workplace, 2323 # bias = u'user', 2324 # default = u'1 hour 30 minutes' 2325 # ) 2326 # max_ttl = cfg_db.get2 ( 2327 # option = u'encounter.maximum_ttl', 2328 # workplace = _here.active_workplace, 2329 # bias = u'user', 2330 # default = u'6 hours' 2331 # ) 2332 # 2333 # # do we happen to have a "fairly recent" candidate ? 2334 # cmd = gmEMRStructItems.SQL_get_encounters % u"""pk_encounter = ( 2335 # SELECT pk_encounter 2336 # FROM clin.v_most_recent_encounters 2337 # WHERE 2338 # pk_patient=%s 2339 # AND 2340 # last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) 2341 # ORDER BY 2342 # last_affirmed DESC 2343 # LIMIT 1 2344 # )""" 2345 # enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True) 2346 # 2347 # # none found 2348 # if len(enc_rows) == 0: 2349 # _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) 2350 # return 2351 # 2352 # _log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter']) 2353 # fairly_recent_enc = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) 2354 # gmDispatcher.send(u'ask_for_encounter_continuation', current = self.__encounter, fairly_recent_encounter = fairly_recent_enc) 2355 2356 # #------------------------------------------------------------------ 2357 # def __activate_fairly_recent_encounter(self, allow_user_interaction=True): 2358 # """Try to attach to a "fairly recent" encounter if there is one. 2359 # 2360 # returns: 2361 # False: no "fairly recent" encounter, create new one 2362 # True: success 2363 # """ 2364 # if _func_ask_user is None: 2365 # _log.debug('cannot ask user for guidance, not looking for fairly recent encounter') 2366 # return False 2367 # 2368 # if not allow_user_interaction: 2369 # _log.exception('user interaction not desired, not looking for fairly recent encounter') 2370 # return False 2371 # 2372 # cfg_db = gmCfg.cCfgSQL() 2373 # min_ttl = cfg_db.get2 ( 2374 # option = u'encounter.minimum_ttl', 2375 # workplace = _here.active_workplace, 2376 # bias = u'user', 2377 # default = u'1 hour 30 minutes' 2378 # ) 2379 # max_ttl = cfg_db.get2 ( 2380 # option = u'encounter.maximum_ttl', 2381 # workplace = _here.active_workplace, 2382 # bias = u'user', 2383 # default = u'6 hours' 2384 # ) 2385 # cmd = u""" 2386 # SELECT pk_encounter 2387 # FROM clin.v_most_recent_encounters 2388 # WHERE 2389 # pk_patient=%s 2390 # AND 2391 # last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) 2392 # ORDER BY 2393 # last_affirmed DESC""" 2394 # enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}]) 2395 # # none found 2396 # if len(enc_rows) == 0: 2397 # _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) 2398 # return False 2399 # 2400 # _log.debug('"fairly recent" encounter [%s] found', enc_rows[0][0]) 2401 # 2402 # encounter = gmEMRStructItems.cEncounter(aPK_obj=enc_rows[0][0]) 2403 # # ask user whether to attach or not 2404 # cmd = u""" 2405 # SELECT title, firstnames, lastnames, gender, dob 2406 # FROM dem.v_all_persons WHERE pk_identity=%s""" 2407 # pats, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}]) 2408 # pat = pats[0] 2409 # pat_str = u'%s %s %s (%s), %s [#%s]' % ( 2410 # gmTools.coalesce(pat[0], u'')[:5], 2411 # pat[1][:15], 2412 # pat[2][:15], 2413 # pat[3], 2414 # gmDateTime.pydt_strftime(pat[4], '%Y %b %d'), 2415 # self.pk_patient 2416 # ) 2417 # msg = _( 2418 # '%s\n' 2419 # '\n' 2420 # "This patient's chart was worked on only recently:\n" 2421 # '\n' 2422 # ' %s %s - %s (%s)\n' 2423 # '\n' 2424 # ' Reason for Encounter:\n' 2425 # ' %s\n' 2426 # ' Assessment of Encounter:\n' 2427 # ' %s\n' 2428 # '\n' 2429 # 'Do you want to continue that consultation\n' 2430 # 'or do you want to start a new one ?\n' 2431 # ) % ( 2432 # pat_str, 2433 # gmDateTime.pydt_strftime(encounter['started'], '%Y %b %d'), 2434 # gmDateTime.pydt_strftime(encounter['started'], '%H:%M'), gmDateTime.pydt_strftime(encounter['last_affirmed'], '%H:%M'), 2435 # encounter['l10n_type'], 2436 # gmTools.coalesce(encounter['reason_for_encounter'], _('none given')), 2437 # gmTools.coalesce(encounter['assessment_of_encounter'], _('none given')), 2438 # ) 2439 # attach = False 2440 # try: 2441 # attach = _func_ask_user(msg = msg, caption = _('Starting patient encounter'), encounter = encounter) 2442 # except: 2443 # _log.exception('cannot ask user for guidance, not attaching to existing encounter') 2444 # return False 2445 # if not attach: 2446 # return False 2447 # 2448 # # attach to existing 2449 # self.current_encounter = encounter 2450 # _log.debug('"fairly recent" encounter re-activated') 2451 # return True 2452 2453 #------------------------------------------------------------------
2454 - def start_new_encounter(self):
2455 cfg_db = gmCfg.cCfgSQL() 2456 enc_type = cfg_db.get2 ( 2457 option = 'encounter.default_type', 2458 workplace = _here.active_workplace, 2459 bias = 'user' 2460 ) 2461 if enc_type is None: 2462 enc_type = gmEMRStructItems.get_most_commonly_used_encounter_type() 2463 if enc_type is None: 2464 enc_type = 'in surgery' 2465 enc = gmEMRStructItems.create_encounter(fk_patient = self.pk_patient, enc_type = enc_type) 2466 enc['pk_org_unit'] = _here['pk_org_unit'] 2467 enc.save() 2468 self.current_encounter = enc 2469 _log.debug('new encounter [%s] activated', enc['pk_encounter'])
2470 2471 #------------------------------------------------------------------
2472 - def get_encounters(self, since=None, until=None, id_list=None, episodes=None, issues=None, skip_empty=False, order_by=None, max_encounters=None):
2473 """Retrieves patient's encounters. 2474 2475 id_list - PKs of encounters to fetch 2476 since - initial date for encounter items, DateTime instance 2477 until - final date for encounter items, DateTime instance 2478 episodes - PKs of the episodes the encounters belong to (many-to-many relation) 2479 issues - PKs of the health issues the encounters belong to (many-to-many relation) 2480 skip_empty - do NOT return those which do not have any of documents/clinical items/RFE/AOE 2481 2482 NOTE: if you specify *both* issues and episodes 2483 you will get the *aggregate* of all encounters even 2484 if the episodes all belong to the health issues listed. 2485 IOW, the issues broaden the episode list rather than 2486 the episode list narrowing the episodes-from-issues 2487 list. 2488 Rationale: If it was the other way round it would be 2489 redundant to specify the list of issues at all. 2490 """ 2491 # if issues are given, translate them to their episodes 2492 if (issues is not None) and (len(issues) > 0): 2493 # - find episodes corresponding to the health issues in question 2494 cmd = "SELECT distinct pk_episode FROM clin.v_pat_episodes WHERE pk_health_issue in %(issue_pks)s AND pk_patient = %(pat)s" 2495 args = {'issue_pks': tuple(issues), 'pat': self.pk_patient} 2496 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) 2497 epis4issues_pks = [ r['pk_episode'] for r in rows ] 2498 if episodes is None: 2499 episodes = [] 2500 episodes.extend(epis4issues_pks) 2501 2502 if (episodes is not None) and (len(episodes) > 0): 2503 # since the episodes to filter by belong to the patient in question so will 2504 # the encounters found with them - hence we don't need a WHERE on the patient ... 2505 # but, better safe than sorry ... 2506 args = {'epi_pks': tuple(episodes), 'pat': self.pk_patient} 2507 cmd = "SELECT distinct fk_encounter FROM clin.clin_root_item WHERE fk_episode IN %(epi_pks)s AND fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" 2508 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) 2509 encs4epis_pks = [ r['fk_encounter'] for r in rows ] 2510 if id_list is None: 2511 id_list = [] 2512 id_list.extend(encs4epis_pks) 2513 2514 where_parts = ['c_vpe.pk_patient = %(pat)s'] 2515 args = {'pat': self.pk_patient} 2516 2517 if skip_empty: 2518 where_parts.append("""NOT ( 2519 gm.is_null_or_blank_string(c_vpe.reason_for_encounter) 2520 AND 2521 gm.is_null_or_blank_string(c_vpe.assessment_of_encounter) 2522 AND 2523 NOT EXISTS ( 2524 SELECT 1 FROM clin.v_pat_items c_vpi WHERE c_vpi.pk_patient = %(pat)s AND c_vpi.pk_encounter = c_vpe.pk_encounter 2525 UNION ALL 2526 SELECT 1 FROM blobs.v_doc_med b_vdm WHERE b_vdm.pk_patient = %(pat)s AND b_vdm.pk_encounter = c_vpe.pk_encounter 2527 ))""") 2528 2529 if since is not None: 2530 where_parts.append('c_vpe.started >= %(start)s') 2531 args['start'] = since 2532 2533 if until is not None: 2534 where_parts.append('c_vpe.last_affirmed <= %(end)s') 2535 args['end'] = since 2536 2537 if (id_list is not None) and (len(id_list) > 0): 2538 where_parts.append('c_vpe.pk_encounter IN %(enc_pks)s') 2539 args['enc_pks'] = tuple(id_list) 2540 2541 if order_by is None: 2542 order_by = 'c_vpe.started' 2543 2544 if max_encounters is None: 2545 limit = '' 2546 else: 2547 limit = 'LIMIT %s' % max_encounters 2548 2549 cmd = """ 2550 SELECT * FROM clin.v_pat_encounters c_vpe 2551 WHERE 2552 %s 2553 ORDER BY %s %s 2554 """ % ( 2555 ' AND '.join(where_parts), 2556 order_by, 2557 limit 2558 ) 2559 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2560 encounters = [ gmEMRStructItems.cEncounter(row = {'data': r, 'idx': idx, 'pk_field': 'pk_encounter'}) for r in rows ] 2561 2562 # we've got the encounters, start filtering 2563 filtered_encounters = [] 2564 filtered_encounters.extend(encounters) 2565 2566 if (episodes is not None) and (len(episodes) > 0): 2567 # since the episodes to filter by belong to the patient in question so will 2568 # the encounters found with them - hence we don't need a WHERE on the patient ... 2569 # but, better safe than sorry ... 2570 args = {'epi_pks': tuple(episodes), 'pat': self.pk_patient} 2571 cmd = "SELECT distinct fk_encounter FROM clin.clin_root_item WHERE fk_episode IN %(epi_pks)s AND fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" 2572 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) 2573 encs4epis_pks = [ r['fk_encounter'] for r in rows ] 2574 filtered_encounters = [ enc for enc in filtered_encounters if enc['pk_encounter'] in encs4epis_pks ] 2575 2576 return filtered_encounters
2577 2578 #--------------------------------------------------------
2579 - def get_first_encounter(self, issue_id=None, episode_id=None):
2580 """Retrieves first encounter for a particular issue and/or episode. 2581 2582 issue_id - First encounter associated health issue 2583 episode - First encounter associated episode 2584 """ 2585 if issue_id is None: 2586 issues = None 2587 else: 2588 issues = [issue_id] 2589 2590 if episode_id is None: 2591 episodes = None 2592 else: 2593 episodes = [episode_id] 2594 2595 encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started', max_encounters = 1) 2596 if len(encounters) == 0: 2597 return None 2598 2599 return encounters[0]
2600 2601 first_encounter = property(get_first_encounter, lambda x:x) 2602 2603 #--------------------------------------------------------
2604 - def get_earliest_care_date(self):
2605 args = {'pat': self.pk_patient} 2606 cmd = """ 2607 SELECT MIN(earliest) FROM ( 2608 ( 2609 SELECT MIN(episode_modified_when) AS earliest FROM clin.v_pat_episodes WHERE pk_patient = %(pat)s 2610 2611 ) UNION ALL ( 2612 2613 SELECT MIN(modified_when) AS earliest FROM clin.v_health_issues WHERE pk_patient = %(pat)s 2614 2615 ) UNION ALL ( 2616 2617 SELECT MIN(modified_when) AS earliest FROM clin.encounter WHERE fk_patient = %(pat)s 2618 2619 ) UNION ALL ( 2620 2621 SELECT MIN(started) AS earliest FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s 2622 2623 ) UNION ALL ( 2624 2625 SELECT MIN(modified_when) AS earliest FROM clin.v_pat_items WHERE pk_patient = %(pat)s 2626 2627 ) UNION ALL ( 2628 2629 SELECT MIN(modified_when) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s 2630 2631 ) UNION ALL ( 2632 2633 SELECT MIN(last_confirmed) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s 2634 2635 ) 2636 ) AS candidates""" 2637 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2638 return rows[0][0]
2639 2640 earliest_care_date = property(get_earliest_care_date, lambda x:x) 2641 2642 #--------------------------------------------------------
2643 - def get_most_recent_care_date(self):
2644 encounters = self.get_encounters(order_by = 'started DESC', max_encounters = 1) 2645 if len(encounters) == 0: 2646 return None 2647 return encounters[0]['last_affirmed']
2648 2649 most_recent_care_date = property(get_most_recent_care_date) 2650 2651 #--------------------------------------------------------
2652 - def get_last_encounter(self, issue_id=None, episode_id=None):
2653 """Retrieves last encounter for a concrete issue and/or episode 2654 2655 issue_id - Last encounter associated health issue 2656 episode_id - Last encounter associated episode 2657 """ 2658 if issue_id is None: 2659 issues = None 2660 else: 2661 issues = [issue_id] 2662 2663 if episode_id is None: 2664 episodes = None 2665 else: 2666 episodes = [episode_id] 2667 2668 encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started DESC', max_encounters = 1) 2669 if len(encounters) == 0: 2670 return None 2671 2672 return encounters[0]
2673 2674 last_encounter = property(get_last_encounter, lambda x:x) 2675 2676 #------------------------------------------------------------------
2677 - def get_encounter_stats_by_type(self, cover_period=None):
2678 args = {'pat': self.pk_patient, 'range': cover_period} 2679 where_parts = ['pk_patient = %(pat)s'] 2680 if cover_period is not None: 2681 where_parts.append('last_affirmed > now() - %(range)s') 2682 2683 cmd = """ 2684 SELECT l10n_type, count(1) AS frequency 2685 FROM clin.v_pat_encounters 2686 WHERE 2687 %s 2688 GROUP BY l10n_type 2689 ORDER BY frequency DESC 2690 """ % ' AND '.join(where_parts) 2691 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2692 return rows
2693 2694 #------------------------------------------------------------------
2695 - def get_last_but_one_encounter(self, issue_id=None, episode_id=None):
2696 2697 args = {'pat': self.pk_patient} 2698 2699 if (issue_id is None) and (episode_id is None): 2700 cmd = """ 2701 SELECT * FROM clin.v_pat_encounters 2702 WHERE pk_patient = %(pat)s 2703 ORDER BY started DESC 2704 LIMIT 2 2705 """ 2706 else: 2707 where_parts = [] 2708 2709 if issue_id is not None: 2710 where_parts.append('pk_health_issue = %(issue)s') 2711 args['issue'] = issue_id 2712 2713 if episode_id is not None: 2714 where_parts.append('pk_episode = %(epi)s') 2715 args['epi'] = episode_id 2716 2717 cmd = """ 2718 SELECT * 2719 FROM clin.v_pat_encounters 2720 WHERE 2721 pk_patient = %%(pat)s 2722 AND 2723 pk_encounter IN ( 2724 SELECT distinct pk_encounter 2725 FROM clin.v_narrative 2726 WHERE 2727 %s 2728 ) 2729 ORDER BY started DESC 2730 LIMIT 2 2731 """ % ' AND '.join(where_parts) 2732 2733 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2734 2735 if len(rows) == 0: 2736 return None 2737 2738 # just one encounter within the above limits 2739 if len(rows) == 1: 2740 # is it the current encounter ? 2741 if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: 2742 # yes 2743 return None 2744 # no 2745 return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) 2746 2747 # more than one encounter 2748 if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: 2749 return gmEMRStructItems.cEncounter(row = {'data': rows[1], 'idx': idx, 'pk_field': 'pk_encounter'}) 2750 2751 return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
2752 2753 last_but_one_encounter = property(get_last_but_one_encounter, lambda x:x) 2754 2755 #------------------------------------------------------------------
2756 - def remove_empty_encounters(self):
2757 _log.debug('removing empty encounters for pk_identity [%s]', self.pk_patient) 2758 cfg_db = gmCfg.cCfgSQL() 2759 ttl = cfg_db.get2 ( 2760 option = 'encounter.ttl_if_empty', 2761 workplace = _here.active_workplace, 2762 bias = 'user', 2763 default = '1 week' 2764 ) 2765 # # FIXME: this should be done async 2766 cmd = "SELECT clin.remove_old_empty_encounters(%(pat)s::INTEGER, %(ttl)s::INTERVAL)" 2767 args = {'pat': self.pk_patient, 'ttl': ttl} 2768 try: 2769 rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True) 2770 except: 2771 _log.exception('error deleting empty encounters') 2772 return False 2773 2774 if not rows[0][0]: 2775 _log.debug('no encounters deleted (less than 2 exist)') 2776 2777 return True
2778 2779 #------------------------------------------------------------------ 2780 # API: measurements / test results 2781 #------------------------------------------------------------------
2782 - def get_most_recent_results_for_patient(self, no_of_results=1):
2783 return gmPathLab.get_most_recent_results_for_patient ( 2784 no_of_results = no_of_results, 2785 patient = self.pk_patient 2786 )
2787 2788 #------------------------------------------------------------------
2789 - def get_most_recent_results_in_loinc_group(self, loincs=None, no_of_results=1, consider_meta_type=False):
2790 return gmPathLab.get_most_recent_results_in_loinc_group ( 2791 loincs = loincs, 2792 no_of_results = no_of_results, 2793 consider_meta_type = consider_meta_type, 2794 patient = self.pk_patient 2795 )
2796 2797 #------------------------------------------------------------------
2798 - def get_most_recent_results_for_test_type(self, test_type=None, no_of_results=1):
2799 return gmPathLab.get_most_recent_results_for_test_type ( 2800 test_type = test_type, 2801 no_of_results = no_of_results, 2802 patient = self.pk_patient 2803 )
2804 2805 #------------------------------------------------------------------
2806 - def get_most_recent_result_for_test_types(self, pk_test_types=None):
2807 return gmPathLab.get_most_recent_result_for_test_types ( 2808 pk_test_types = pk_test_types, 2809 pk_patient = self.pk_patient 2810 )
2811 2812 #------------------------------------------------------------------
2813 - def get_result_at_timestamp(self, timestamp=None, test_type=None, loinc=None, tolerance_interval='12 hours'):
2814 return gmPathLab.get_result_at_timestamp ( 2815 timestamp = timestamp, 2816 test_type = test_type, 2817 loinc = loinc, 2818 tolerance_interval = tolerance_interval, 2819 patient = self.pk_patient 2820 )
2821 2822 #------------------------------------------------------------------
2823 - def get_results_for_day(self, timestamp=None, order_by=None):
2824 return gmPathLab.get_results_for_day ( 2825 timestamp = timestamp, 2826 patient = self.pk_patient, 2827 order_by = order_by 2828 )
2829 2830 #------------------------------------------------------------------
2831 - def get_results_for_issue(self, pk_health_issue=None, order_by=None):
2832 return gmPathLab.get_results_for_issue ( 2833 pk_health_issue = pk_health_issue, 2834 order_by = order_by 2835 )
2836 2837 #------------------------------------------------------------------
2838 - def get_results_for_episode(self, pk_episode=None):
2839 return gmPathLab.get_results_for_episode(pk_episode = pk_episode)
2840 2841 #------------------------------------------------------------------
2842 - def get_unsigned_results(self, order_by=None):
2843 if order_by is None: 2844 order_by = '' 2845 else: 2846 order_by = 'ORDER BY %s' % order_by 2847 cmd = """ 2848 SELECT * FROM clin.v_test_results 2849 WHERE 2850 pk_patient = %%(pat)s 2851 AND 2852 reviewed IS FALSE 2853 %s""" % order_by 2854 args = {'pat': self.pk_patient} 2855 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2856 return [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ]
2857 2858 #------------------------------------------------------------------ 2859 # FIXME: use psyopg2 dbapi extension of named cursors - they are *server* side !
2860 - def get_test_types_for_results(self, order_by=None, unique_meta_types=False):
2861 """Retrieve data about test types for which this patient has results.""" 2862 if order_by is None: 2863 order_by = '' 2864 else: 2865 order_by = 'ORDER BY %s' % order_by 2866 2867 if unique_meta_types: 2868 cmd = """ 2869 SELECT * FROM clin.v_test_types c_vtt 2870 WHERE c_vtt.pk_test_type IN ( 2871 SELECT DISTINCT ON (c_vtr1.pk_meta_test_type) c_vtr1.pk_test_type 2872 FROM clin.v_test_results c_vtr1 2873 WHERE 2874 c_vtr1.pk_patient = %%(pat)s 2875 AND 2876 c_vtr1.pk_meta_test_type IS NOT NULL 2877 UNION ALL 2878 SELECT DISTINCT ON (c_vtr2.pk_test_type) c_vtr2.pk_test_type 2879 FROM clin.v_test_results c_vtr2 2880 WHERE 2881 c_vtr2.pk_patient = %%(pat)s 2882 AND 2883 c_vtr2.pk_meta_test_type IS NULL 2884 ) 2885 %s""" % order_by 2886 else: 2887 cmd = """ 2888 SELECT * FROM clin.v_test_types c_vtt 2889 WHERE c_vtt.pk_test_type IN ( 2890 SELECT DISTINCT ON (c_vtr.pk_test_type) c_vtr.pk_test_type 2891 FROM clin.v_test_results c_vtr 2892 WHERE c_vtr.pk_patient = %%(pat)s 2893 ) 2894 %s""" % order_by 2895 2896 args = {'pat': self.pk_patient} 2897 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 2898 return [ gmPathLab.cMeasurementType(row = {'pk_field': 'pk_test_type', 'idx': idx, 'data': r}) for r in rows ]
2899 2900 #------------------------------------------------------------------
2901 - def get_dates_for_results(self, tests=None, reverse_chronological=True):
2902 """Get the dates for which we have results.""" 2903 where_parts = ['pk_patient = %(pat)s'] 2904 args = {'pat': self.pk_patient} 2905 2906 if tests is not None: 2907 where_parts.append('pk_test_type IN %(tests)s') 2908 args['tests'] = tuple(tests) 2909 2910 cmd = """ 2911 SELECT DISTINCT ON (clin_when_day) 2912 clin_when_day, 2913 is_reviewed 2914 FROM ( 2915 SELECT 2916 date_trunc('day', clin_when) 2917 AS clin_when_day, 2918 bool_and(reviewed) 2919 AS is_reviewed 2920 FROM ( 2921 SELECT 2922 clin_when, 2923 reviewed, 2924 pk_patient, 2925 pk_test_result 2926 FROM clin.v_test_results 2927 WHERE %s 2928 ) 2929 AS patient_tests 2930 GROUP BY clin_when_day 2931 ) 2932 AS grouped_days 2933 ORDER BY clin_when_day %s 2934 """ % ( 2935 ' AND '.join(where_parts), 2936 gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') 2937 ) 2938 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 2939 return rows
2940 2941 #------------------------------------------------------------------
2942 - def get_issues_or_episodes_for_results(self, tests=None):
2943 """Get the issues/episodes for which we have results.""" 2944 where_parts = ['pk_patient = %(pat)s'] 2945 args = {'pat': self.pk_patient} 2946 2947 if tests is not None: 2948 where_parts.append('pk_test_type IN %(tests)s') 2949 args['tests'] = tuple(tests) 2950 where = ' AND '.join(where_parts) 2951 cmd = """ 2952 SELECT * FROM (( 2953 -- issues, each including all it"s episodes 2954 SELECT 2955 health_issue AS problem, 2956 pk_health_issue, 2957 NULL::integer AS pk_episode, 2958 1 AS rank 2959 FROM clin.v_test_results 2960 WHERE pk_health_issue IS NOT NULL AND %s 2961 GROUP BY pk_health_issue, problem 2962 ) UNION ALL ( 2963 -- episodes w/o issue 2964 SELECT 2965 episode AS problem, 2966 NULL::integer AS pk_health_issue, 2967 pk_episode, 2968 2 AS rank 2969 FROM clin.v_test_results 2970 WHERE pk_health_issue IS NULL AND %s 2971 GROUP BY pk_episode, problem 2972 )) AS grouped_union 2973 ORDER BY rank, problem 2974 """ % (where, where) 2975 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 2976 return rows
2977 2978 #------------------------------------------------------------------
2979 - def get_test_results(self, encounters=None, episodes=None, tests=None, order_by=None):
2980 return gmPathLab.get_test_results ( 2981 pk_patient = self.pk_patient, 2982 encounters = encounters, 2983 episodes = episodes, 2984 order_by = order_by 2985 )
2986 #------------------------------------------------------------------
2987 - def get_test_results_by_date(self, encounter=None, episodes=None, tests=None, reverse_chronological=True):
2988 2989 where_parts = ['pk_patient = %(pat)s'] 2990 args = {'pat': self.pk_patient} 2991 2992 if tests is not None: 2993 where_parts.append('pk_test_type IN %(tests)s') 2994 args['tests'] = tuple(tests) 2995 2996 if encounter is not None: 2997 where_parts.append('pk_encounter = %(enc)s') 2998 args['enc'] = encounter 2999 3000 if episodes is not None: 3001 where_parts.append('pk_episode IN %(epis)s') 3002 args['epis'] = tuple(episodes) 3003 3004 cmd = """ 3005 SELECT * FROM clin.v_test_results 3006 WHERE %s 3007 ORDER BY clin_when %s, pk_episode, unified_name 3008 """ % ( 3009 ' AND '.join(where_parts), 3010 gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') 3011 ) 3012 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 3013 3014 tests = [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ] 3015 3016 return tests
3017 #------------------------------------------------------------------
3018 - def add_test_result(self, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None):
3019 3020 try: 3021 epi = int(episode) 3022 except: 3023 epi = episode['pk_episode'] 3024 3025 try: 3026 type = int(type) 3027 except: 3028 type = type['pk_test_type'] 3029 3030 tr = gmPathLab.create_test_result ( 3031 link_obj = link_obj, 3032 encounter = self.current_encounter['pk_encounter'], 3033 episode = epi, 3034 type = type, 3035 intended_reviewer = intended_reviewer, 3036 val_num = val_num, 3037 val_alpha = val_alpha, 3038 unit = unit 3039 ) 3040 3041 return tr
3042 3043 #------------------------------------------------------------------
3044 - def get_labs_as_org_units(self):
3045 where = 'pk_org_unit IN (%s)' % """ 3046 SELECT DISTINCT fk_org_unit FROM clin.test_org WHERE pk IN ( 3047 SELECT DISTINCT pk_test_org FROM clin.v_test_results where pk_patient = %(pat)s 3048 )""" 3049 args = {'pat': self.pk_patient} 3050 cmd = gmOrganization._SQL_get_org_unit % where 3051 rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) 3052 return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
3053 3054 #------------------------------------------------------------------
3055 - def _get_best_gfr_or_crea(self):
3056 3057 measured_gfr = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_gfr_quantity, no_of_results = 1) 3058 crea = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_creatinine_quantity, no_of_results = 1) 3059 3060 if (measured_gfr is None) and (crea is None): 3061 return None 3062 3063 if (measured_gfr is not None) and (crea is None): 3064 return measured_gfr 3065 3066 # from here, Crea cannot be None anymore 3067 if measured_gfr is None: 3068 eGFR = self.calculator.eGFR 3069 if eGFR.numeric_value is None: 3070 return crea 3071 return eGFR 3072 3073 # from here, measured_gfr cannot be None anymore, either 3074 two_weeks = pydt.timedelta(weeks = 2) 3075 gfr_too_old = (crea['clin_when'] - measured_gfr['clin_when']) > two_weeks 3076 if not gfr_too_old: 3077 return measured_gfr 3078 3079 # from here, measured_gfr is considered too 3080 # old, so attempt a more timely estimate 3081 eGFR = self.calculator.eGFR 3082 if eGFR.numeric_value is None: 3083 # return crea since we cannot get a 3084 # better estimate for some reason 3085 return crea 3086 3087 return eGFR
3088 3089 best_gfr_or_crea = property(_get_best_gfr_or_crea, lambda x:x) 3090 3091 #------------------------------------------------------------------
3092 - def _get_bmi(self):
3093 return self.calculator.bmi
3094 3095 bmi = property(_get_bmi, lambda x:x) 3096 3097 #------------------------------------------------------------------
3098 - def _get_dynamic_hints(self):
3099 return gmAutoHints.get_hints_for_patient(pk_identity = self.pk_patient, pk_encounter = self.current_encounter['pk_encounter'])
3100 3101 dynamic_hints = property(_get_dynamic_hints, lambda x:x) 3102 3103 #------------------------------------------------------------------ 3104 #------------------------------------------------------------------ 3105 #------------------------------------------------------------------
3106 - def get_lab_request(self, pk=None, req_id=None, lab=None):
3107 # FIXME: verify that it is our patient ? ... 3108 req = gmPathLab.cLabRequest(aPK_obj=pk, req_id=req_id, lab=lab) 3109 return req
3110 #------------------------------------------------------------------
3111 - def add_lab_request(self, lab=None, req_id=None, encounter_id=None, episode_id=None):
3112 if encounter_id is None: 3113 encounter_id = self.current_encounter['pk_encounter'] 3114 status, data = gmPathLab.create_lab_request( 3115 lab=lab, 3116 req_id=req_id, 3117 pat_id=self.pk_patient, 3118 encounter_id=encounter_id, 3119 episode_id=episode_id 3120 ) 3121 if not status: 3122 _log.error(str(data)) 3123 return None 3124 return data
3125 3126 #============================================================ 3127 # main 3128 #------------------------------------------------------------ 3129 if __name__ == "__main__": 3130 3131 if len(sys.argv) == 1: 3132 sys.exit() 3133 3134 if sys.argv[1] != 'test': 3135 sys.exit() 3136 3137 from Gnumed.pycommon import gmLog2 3138 3139 from Gnumed.business import gmPraxis 3140 branches = gmPraxis.get_praxis_branches() 3141 praxis = gmPraxis.gmCurrentPraxisBranch(branches[0]) 3142
3143 - def _do_delayed(*args, **kwargs):
3144 print(args) 3145 print(kwargs) 3146 args[0](*args[1:], **kwargs)
3147 3148 set_delayed_executor(_do_delayed) 3149 3150 #-----------------------------------------
3151 - def test_allergy_state():
3152 emr = cClinicalRecord(aPKey=1) 3153 state = emr.allergy_state 3154 print("allergy state is:", state) 3155 3156 print("setting state to 0") 3157 emr.allergy_state = 0 3158 3159 print("setting state to None") 3160 emr.allergy_state = None 3161 3162 print("setting state to 'abc'") 3163 emr.allergy_state = 'abc'
3164 3165 #-----------------------------------------
3166 - def test_get_test_names():
3167 emr = cClinicalRecord(aPKey = 6) 3168 rows = emr.get_test_types_for_results(unique_meta_types = True) 3169 print("test result names:", len(rows))
3170 # for row in rows: 3171 # print row 3172 3173 #-----------------------------------------
3174 - def test_get_dates_for_results():
3175 emr = cClinicalRecord(aPKey=12) 3176 rows = emr.get_dates_for_results() 3177 print("test result dates:") 3178 for row in rows: 3179 print(row)
3180 3181 #-----------------------------------------
3182 - def test_get_measurements():
3183 emr = cClinicalRecord(aPKey=12) 3184 rows, idx = emr.get_measurements_by_date() 3185 print("test results:") 3186 for row in rows: 3187 print(row)
3188 3189 #-----------------------------------------
3190 - def test_get_test_results_by_date():
3191 emr = cClinicalRecord(aPKey=12) 3192 tests = emr.get_test_results_by_date() 3193 print("test results:") 3194 for test in tests: 3195 print(test)
3196 3197 #-----------------------------------------
3198 - def test_get_statistics():
3199 emr = cClinicalRecord(aPKey=12) 3200 for key, item in emr.get_statistics().items(): 3201 print(key, ":", item)
3202 3203 #-----------------------------------------
3204 - def test_get_problems():
3205 emr = cClinicalRecord(aPKey=12) 3206 3207 probs = emr.get_problems() 3208 print("normal probs (%s):" % len(probs)) 3209 for p in probs: 3210 print('%s (%s)' % (p['problem'], p['type'])) 3211 3212 probs = emr.get_problems(include_closed_episodes=True) 3213 print("probs + closed episodes (%s):" % len(probs)) 3214 for p in probs: 3215 print('%s (%s)' % (p['problem'], p['type'])) 3216 3217 probs = emr.get_problems(include_irrelevant_issues=True) 3218 print("probs + issues (%s):" % len(probs)) 3219 for p in probs: 3220 print('%s (%s)' % (p['problem'], p['type'])) 3221 3222 probs = emr.get_problems(include_closed_episodes=True, include_irrelevant_issues=True) 3223 print("probs + issues + epis (%s):" % len(probs)) 3224 for p in probs: 3225 print('%s (%s)' % (p['problem'], p['type']))
3226 3227 #-----------------------------------------
3228 - def test_add_test_result():
3229 emr = cClinicalRecord(aPKey=12) 3230 tr = emr.add_test_result ( 3231 episode = 1, 3232 intended_reviewer = 1, 3233 type = 1, 3234 val_num = 75, 3235 val_alpha = 'somewhat obese', 3236 unit = 'kg' 3237 ) 3238 print(tr)
3239 3240 #-----------------------------------------
3241 - def test_get_most_recent_episode():
3242 emr = cClinicalRecord(aPKey=12) 3243 print(emr.get_most_recent_episode(issue = 2))
3244 3245 #-----------------------------------------
3246 - def test_get_almost_recent_encounter():
3247 emr = cClinicalRecord(aPKey=12) 3248 print(emr.get_last_encounter(issue_id=2)) 3249 print(emr.get_last_but_one_encounter(issue_id=2))
3250 3251 #-----------------------------------------
3252 - def test_get_encounters():
3253 emr = cClinicalRecord(aPKey = 5) 3254 print(emr.get_first_encounter(episode_id = 1638)) 3255 print(emr.get_last_encounter(episode_id = 1638))
3256 3257 #-----------------------------------------
3258 - def test_get_issues():
3259 emr = cClinicalRecord(aPKey = 12) 3260 for issue in emr.health_issues: 3261 print(issue['description'])
3262 3263 #-----------------------------------------
3264 - def test_get_dx():
3265 emr = cClinicalRecord(aPKey = 12) 3266 for dx in emr.candidate_diagnoses: 3267 print(dx)
3268 3269 #-----------------------------------------
3270 - def test_get_meds():
3271 emr = cClinicalRecord(aPKey=12) 3272 for med in emr.get_current_medications(): 3273 print(med)
3274 3275 #-----------------------------------------
3276 - def test_get_abuses():
3277 emr = cClinicalRecord(aPKey=12) 3278 for med in emr.abused_substances: 3279 print(med.format(single_line = True))
3280 3281 #-----------------------------------------
3282 - def test_is_allergic_to():
3283 emr = cClinicalRecord(aPKey = 12) 3284 print(emr.is_allergic_to(atcs = tuple(sys.argv[2:]), inns = tuple(sys.argv[2:]), product_name = sys.argv[2]))
3285 3286 #-----------------------------------------
3287 - def test_get_as_journal():
3288 emr = cClinicalRecord(aPKey = 12) 3289 for journal_line in emr.get_as_journal(): 3290 #print journal_line.keys() 3291 print('%(date)s %(modified_by)s %(soap_cat)s %(narrative)s' % journal_line) 3292 print("")
3293 3294 #-----------------------------------------
3295 - def test_get_most_recent():
3296 emr = cClinicalRecord(aPKey=12) 3297 print(emr.get_most_recent_results_for_test_type())
3298 3299 #-----------------------------------------
3300 - def test_episodes():
3301 emr = cClinicalRecord(aPKey=12) 3302 print("episodes:", emr.episodes) 3303 print("unlinked:", emr.unlinked_episodes)
3304 3305 #-----------------------------------------
3306 - def test_format_as_journal():
3307 emr = cClinicalRecord(aPKey=12) 3308 from Gnumed.business.gmPerson import cPatient 3309 pat = cPatient(aPK_obj = 12) 3310 print(emr.format_as_journal(left_margin = 1, patient = pat))
3311 3312 #-----------------------------------------
3313 - def test_smoking():
3314 emr = cClinicalRecord(aPKey=12) 3315 #print emr.is_or_was_smoker 3316 smoking, details = emr.smoking_status 3317 print('status:', smoking) 3318 print('details:') 3319 print(details) 3320 emr.smoking_status = (True, {'comment': '2', 'last_confirmed': gmDateTime.pydt_now_here()}) 3321 print(emr.smoking_status) 3322 print(emr.alcohol_status) 3323 print(emr.drugs_status)
3324 3325 #----------------------------------------- 3326 3327 #test_allergy_state() 3328 #test_is_allergic_to() 3329 3330 #test_get_test_names() 3331 #test_get_dates_for_results() 3332 #test_get_measurements() 3333 #test_get_test_results_by_date() 3334 #test_get_statistics() 3335 #test_get_problems() 3336 #test_add_test_result() 3337 #test_get_most_recent_episode() 3338 #test_get_almost_recent_encounter() 3339 #test_get_meds() 3340 #test_get_as_journal() 3341 #test_get_most_recent() 3342 #test_episodes() 3343 #test_format_as_journal() 3344 #test_smoking() 3345 #test_get_abuses() 3346 #test_get_encounters() 3347 #test_get_issues() 3348 #test_get_dx() 3349 3350 emr = cClinicalRecord(aPKey = 12) 3351 3352 # # Vacc regimes 3353 # vacc_regimes = emr.get_scheduled_vaccination_regimes(indications = ['tetanus']) 3354 # print '\nVaccination regimes: ' 3355 # for a_regime in vacc_regimes: 3356 # pass 3357 # #print a_regime 3358 # vacc_regime = emr.get_scheduled_vaccination_regimes(ID=10) 3359 # #print vacc_regime 3360 3361 # # vaccination regimes and vaccinations for regimes 3362 # scheduled_vaccs = emr.get_scheduled_vaccinations(indications = ['tetanus']) 3363 # print 'Vaccinations for the regime:' 3364 # for a_scheduled_vacc in scheduled_vaccs: 3365 # pass 3366 # #print ' %s' %(a_scheduled_vacc) 3367 3368 # # vaccination next shot and booster 3369 v1 = emr.vaccinations 3370 print(v1) 3371 v2 = gmVaccination.get_vaccinations(pk_identity = 12, return_pks = True) 3372 print(v2) 3373 for v in v1: 3374 if v['pk_vaccination'] not in v2: 3375 print('ERROR') 3376 3377 # for a_vacc in vaccinations: 3378 # print '\nVaccination %s , date: %s, booster: %s, seq no: %s' %(a_vacc['batch_no'], a_vacc['date'].strftime('%Y-%m-%d'), a_vacc['is_booster'], a_vacc['seq_no']) 3379 3380 # # first and last encounters 3381 # first_encounter = emr.get_first_encounter(issue_id = 1) 3382 # print '\nFirst encounter: ' + str(first_encounter) 3383 # last_encounter = emr.get_last_encounter(episode_id = 1) 3384 # print '\nLast encounter: ' + str(last_encounter) 3385 # print '' 3386 3387 #dump = record.get_missing_vaccinations() 3388 #f = io.open('vaccs.lst', 'wb') 3389 #if dump is not None: 3390 # print "=== due ===" 3391 # f.write(u"=== due ===\n") 3392 # for row in dump['due']: 3393 # print row 3394 # f.write(repr(row)) 3395 # f.write(u'\n') 3396 # print "=== overdue ===" 3397 # f.write(u"=== overdue ===\n") 3398 # for row in dump['overdue']: 3399 # print row 3400 # f.write(repr(row)) 3401 # f.write(u'\n') 3402 #f.close() 3403