Gnumed.exporters.gmPatientExporter

35 36 #--------------------------------------------------------

37 - def __init__(self, constraints = None, fileout = None, patient = None):

38 """ 39 Constructs a new instance of exporter 40 41 constraints - Exporter constraints for filtering clinical items 42 fileout - File-like object as target for dumping operations 43 """ 44 if constraints is None: 45 # default constraints to None for complete emr dump 46 self.__constraints = { 47 'since': None, 48 'until': None, 49 'encounters': None, 50 'episodes': None, 51 'issues': None 52 } 53 else: 54 self.__constraints = constraints 55 self.__target = fileout 56 self.__patient = patient 57 self.lab_new_encounter = True 58 self.__filtered_items = []

59 #--------------------------------------------------------

60 - def set_constraints(self, constraints = None):

61 """Sets exporter constraints. 62 63 constraints - Exporter constraints for filtering clinical items 64 """ 65 if constraints is None: 66 # default constraints to None for complete emr dump 67 self.__constraints = { 68 'since': None, 69 'until': None, 70 'encounters': None, 71 'episodes': None, 72 'issues': None 73 } 74 else: 75 self.__constraints = constraints 76 return True

77 #--------------------------------------------------------

78 - def get_constraints(self):

79 """ 80 Retrieve exporter constraints 81 """ 82 return self.__constraints

83 #--------------------------------------------------------

84 - def set_patient(self, patient=None):

85 """ 86 Sets exporter patient 87 88 patient - Patient whose data are to be dumped 89 """ 90 if patient is None: 91 _log.error("can't set None patient for exporter") 92 return 93 self.__patient = patient

94 #--------------------------------------------------------

95 - def set_output_file(self, target=None):

96 """ 97 Sets exporter output file 98 99 @param file_name - The file to dump the EMR to 100 @type file_name - FileType 101 """ 102 self.__target = target

103 #--------------------------------------------------------

104 - def get_patient(self):

105 """ 106 Retrieves patient whose data are to be dumped 107 """ 108 return self.__patient

109 #--------------------------------------------------------

110 - def cleanup(self):

111 """ 112 Exporter class cleanup code 113 """ 114 pass

115 #--------------------------------------------------------

116 - def __dump_vacc_table(self, vacc_regimes):

117 """ 118 Retrieves string containg ASCII vaccination table 119 """ 120 emr = self.__patient.get_emr() 121 # patient dob 122 patient_dob = self.__patient['dob'] 123 date_length = len(patient_dob.strftime('%x')) + 2 124 125 # dictionary of pairs indication : scheduled vaccination 126 vaccinations4regimes = {} 127 for a_vacc_regime in vacc_regimes: 128 indication = a_vacc_regime['indication'] 129 vaccinations4regimes[indication] = emr.get_scheduled_vaccinations(indications=[indication]) 130 # vaccination regimes count 131 chart_columns = len(vacc_regimes) 132 # foot headers 133 foot_headers = ['last booster', 'next booster'] 134 # string for both: ending of vaccinations; non boosters needed 135 ending_str = '=' 136 137 # chart row count, columns width and vaccination dictionary of pairs indication : given shot 138 column_widths = [] 139 chart_rows = -1 140 vaccinations = {} 141 temp = -1 142 for foot_header in foot_headers: # first column width 143 if len(foot_header) > temp: 144 temp = len(foot_header) 145 column_widths.append(temp) 146 for a_vacc_regime in vacc_regimes: 147 if a_vacc_regime['shots'] > chart_rows: # max_seq -> row count 148 chart_rows = a_vacc_regime['shots'] 149 if (len(a_vacc_regime['l10n_indication'])) > date_length: # l10n indication -> column width 150 column_widths.append(len(a_vacc_regime['l10n_indication'])) 151 else: 152 column_widths.append(date_length) # date -> column width at least 153 vaccinations[a_vacc_regime['indication']] = emr.get_vaccinations(indications=[a_vacc_regime['indication']]) # given shots 4 indication 154 155 # patient dob in top of vaccination chart 156 txt = '\nDOB: %s' %(patient_dob.strftime('%x')) + '\n' 157 158 # vacc chart table headers 159 # top ---- header line 160 for column_width in column_widths: 161 txt += column_width * '-' + '-' 162 txt += '\n' 163 # indication names header line 164 txt += column_widths[0] * ' ' + '|' 165 col_index = 1 166 for a_vacc_regime in vacc_regimes: 167 txt += a_vacc_regime['l10n_indication'] + (column_widths[col_index] - len(a_vacc_regime['l10n_indication'])) * ' ' + '|' 168 col_index += 1 169 txt += '\n' 170 # bottom ---- header line 171 for column_width in column_widths: 172 txt += column_width * '-' + '-' 173 txt += '\n' 174 175 # vacc chart data 176 due_date = None 177 # previously displayed date list 178 prev_displayed_date = [patient_dob] 179 for a_regime in vacc_regimes: 180 prev_displayed_date.append(patient_dob) # initialice with patient dob (useful for due first shot date calculation) 181 # iterate data rows 182 for row_index in range(0, chart_rows): 183 row_header = '#%s' %(row_index+1) 184 txt += row_header + (column_widths[0] - len(row_header)) * ' ' + '|' 185 186 for col_index in range(1, chart_columns+1): 187 indication =vacc_regimes[col_index-1]['indication'] 188 seq_no = vacc_regimes[col_index-1]['shots'] 189 if row_index == seq_no: # had just ended scheduled vaccinations 190 txt += ending_str * column_widths[col_index] + '|' 191 elif row_index < seq_no: # vaccination scheduled 192 try: 193 vacc_date = vaccinations[indication][row_index]['date'] # vaccination given 194 vacc_date_str = vacc_date.strftime('%x') 195 txt += vacc_date_str + (column_widths[col_index] - len(vacc_date_str)) * ' ' + '|' 196 prev_displayed_date[col_index] = vacc_date 197 except: 198 if row_index == 0: # due first shot 199 due_date = prev_displayed_date[col_index] + vaccinations4regimes[indication][row_index]['age_due_min'] # FIXME 'age_due_min' not properly retrieved 200 else: # due any other than first shot 201 due_date = prev_displayed_date[col_index] + vaccinations4regimes[indication][row_index]['min_interval'] 202 txt += '('+ due_date.strftime('%Y-%m-%d') + ')' + (column_widths[col_index] - date_length) * ' ' + '|' 203 prev_displayed_date[col_index] = due_date 204 else: # not scheduled vaccination at that position 205 txt += column_widths[col_index] * ' ' + '|' 206 txt += '\n' # end of scheduled vaccination dates display 207 for column_width in column_widths: # ------ separator line 208 txt += column_width * '-' + '-' 209 txt += '\n' 210 211 # scheduled vaccination boosters (date retrieving) 212 all_vreg_boosters = [] 213 for a_vacc_regime in vacc_regimes: 214 vaccs4indication = vaccinations[a_vacc_regime['indication']] # iterate over vaccinations by indication 215 given_boosters = [] # will contain given boosters for current indication 216 for a_vacc in vaccs4indication: 217 try: 218 if a_vacc['is_booster']: 219 given_boosters.append(a_vacc) 220 except: 221 # not a booster 222 pass 223 if len(given_boosters) > 0: 224 all_vreg_boosters.append(given_boosters[len(given_boosters)-1]) # last of given boosters 225 else: 226 all_vreg_boosters.append(None) 227 228 # next booster in schedule 229 all_next_boosters = [] 230 for a_booster in all_vreg_boosters: 231 all_next_boosters.append(None) 232 # scheduled vaccination boosters (displaying string) 233 cont = 0 234 for a_vacc_regime in vacc_regimes: 235 vaccs = vaccinations4regimes[a_vacc_regime['indication']] 236 if vaccs[len(vaccs)-1]['is_booster'] == False: # booster is not scheduled/needed 237 all_vreg_boosters[cont] = ending_str * column_widths[cont+1] 238 all_next_boosters[cont] = ending_str * column_widths[cont+1] 239 else: 240 indication = vacc_regimes[cont]['indication'] 241 if len(vaccinations[indication]) > vacc_regimes[cont]['shots']: # boosters given 242 all_vreg_boosters[cont] = vaccinations[indication][len(vaccinations[indication])-1]['date'].strftime('%Y-%m-%d') # show last given booster date 243 scheduled_booster = vaccinations4regimes[indication][len(vaccinations4regimes[indication])-1] 244 booster_date = vaccinations[indication][len(vaccinations[indication])-1]['date'] + scheduled_booster['min_interval'] 245 if booster_date < mxDT.today(): 246 all_next_boosters[cont] = '<(' + booster_date.strftime('%Y-%m-%d') + ')>' # next booster is due 247 else: 248 all_next_boosters[cont] = booster_date.strftime('%Y-%m-%d') 249 elif len(vaccinations[indication]) == vacc_regimes[cont]['shots']: # just finished vaccinations, begin boosters 250 all_vreg_boosters[cont] = column_widths[cont+1] * ' ' 251 scheduled_booster = vaccinations4regimes[indication][len(vaccinations4regimes[indication])-1] 252 booster_date = vaccinations[indication][len(vaccinations[indication])-1]['date'] + scheduled_booster['min_interval'] 253 if booster_date < mxDT.today(): 254 all_next_boosters[cont] = '<(' + booster_date.strftime('%Y-%m-%d') + ')>' # next booster is due 255 else: 256 all_next_boosters[cont] = booster_date.strftime('%Y-%m-%d') 257 else: 258 all_vreg_boosters[cont] = column_widths[cont+1] * ' ' # unfinished schedule 259 all_next_boosters[cont] = column_widths[cont+1] * ' ' 260 cont += 1 261 262 # given boosters 263 foot_header = foot_headers[0] 264 col_index = 0 265 txt += foot_header + (column_widths[0] - len(foot_header)) * ' ' + '|' 266 col_index += 1 267 for a_vacc_regime in vacc_regimes: 268 txt += str(all_vreg_boosters[col_index-1]) + (column_widths[col_index] - len(str(all_vreg_boosters[col_index-1]))) * ' ' + '|' 269 col_index += 1 270 txt += '\n' 271 for column_width in column_widths: 272 txt += column_width * '-' + '-' 273 txt += '\n' 274 275 # next booster 276 foot_header = foot_headers[1] 277 col_index = 0 278 txt += foot_header + (column_widths[0] - len(foot_header)) * ' ' + '|' 279 col_index += 1 280 for a_vacc_regime in vacc_regimes: 281 txt += str(all_next_boosters[col_index-1]) + (column_widths[col_index] - len(str(all_next_boosters[col_index-1]))) * ' ' + '|' 282 col_index += 1 283 txt += '\n' 284 for column_width in column_widths: 285 txt += column_width * '-' + '-' 286 txt += '\n' 287 288 self.__target.write(txt)

289 #--------------------------------------------------------

290 - def get_vacc_table(self):

291 """ 292 Iterate over patient scheduled regimes preparing vacc tables dump 293 """ 294 295 emr = self.__patient.get_emr() 296 297 # vaccination regimes 298 all_vacc_regimes = emr.get_scheduled_vaccination_regimes() 299 # Configurable: vacc regimes per displayed table 300 # FIXME: option, post 0.1 ? 301 max_regs_per_table = 4 302 303 # Iterate over patient scheduled regimes dumping in tables of 304 # max_regs_per_table regimes per table 305 reg_count = 0 306 vacc_regimes = [] 307 for total_reg_count in range(0,len(all_vacc_regimes)): 308 if reg_count%max_regs_per_table == 0: 309 if len(vacc_regimes) > 0: 310 self.__dump_vacc_table(vacc_regimes) 311 vacc_regimes = [] 312 reg_count = 0 313 vacc_regimes.append(all_vacc_regimes[total_reg_count]) 314 reg_count += 1 315 if len(vacc_regimes) > 0: 316 self.__dump_vacc_table(vacc_regimes)

317 318 #--------------------------------------------------------

319 - def dump_item_fields(self, offset, item, field_list):

320 """ 321 Dump information related to the fields of a clinical item 322 offset - Number of left blank spaces 323 item - Item of the field to dump 324 fields - Fields to dump 325 """ 326 txt = '' 327 for a_field in field_list: 328 if type(a_field) is not types.UnicodeType: 329 a_field = unicode(a_field, encoding='latin1', errors='replace') 330 txt += u'%s%s%s' % ((offset * u' '), a_field, gmTools.coalesce(item[a_field], u'\n', template_initial = u': %s\n')) 331 return txt

332 #--------------------------------------------------------

333 - def get_allergy_output(self, allergy, left_margin = 0):

334 """ 335 Dumps allergy item data 336 allergy - Allergy item to dump 337 left_margin - Number of spaces on the left margin 338 """ 339 txt = '' 340 txt += left_margin*' ' + _('Allergy') + ': \n' 341 txt += self.dump_item_fields((left_margin+3), allergy, ['allergene', 'substance', 'generic_specific','l10n_type', 'definite', 'reaction']) 342 return txt

343 #--------------------------------------------------------

344 - def get_vaccination_output(self, vaccination, left_margin = 0):

345 """ 346 Dumps vaccination item data 347 vaccination - Vaccination item to dump 348 left_margin - Number of spaces on the left margin 349 """ 350 txt = '' 351 txt += left_margin*' ' + _('Vaccination') + ': \n' 352 txt += self.dump_item_fields((left_margin+3), vaccination, ['l10n_indication', 'vaccine', 'batch_no', 'site', 'narrative']) 353 return txt

354 #--------------------------------------------------------

355 - def get_lab_result_output(self, lab_result, left_margin = 0):

356 """ 357 Dumps lab result item data 358 lab_request - Lab request item to dump 359 left_margin - Number of spaces on the left margin 360 """ 361 txt = '' 362 if self.lab_new_encounter: 363 txt += (left_margin)*' ' + _('Lab result') + ': \n' 364 txt += (left_margin+3) * ' ' + lab_result['unified_name'] + ': ' + lab_result['unified_val']+ ' ' + lab_result['val_unit'] + ' (' + lab_result['material'] + ')' + '\n' 365 return txt

366 #--------------------------------------------------------

367 - def get_item_output(self, item, left_margin = 0):

368 """ 369 Obtains formatted clinical item output dump 370 item - The clinical item to dump 371 left_margin - Number of spaces on the left margin 372 """ 373 txt = '' 374 if isinstance(item, gmAllergy.cAllergy): 375 txt += self.get_allergy_output(item, left_margin) 376 # elif isinstance(item, gmVaccination.cVaccination): 377 # txt += self.get_vaccination_output(item, left_margin) 378 # elif isinstance(item, gmPathLab.cLabResult): 379 # txt += self.get_lab_result_output(item, left_margin) 380 # self.lab_new_encounter = False 381 return txt

382 #--------------------------------------------------------

383 - def __fetch_filtered_items(self):

384 """ 385 Retrieve patient clinical items filtered by multiple constraints 386 """ 387 if not self.__patient.connected: 388 return False 389 emr = self.__patient.get_emr() 390 filtered_items = [] 391 filtered_items.extend(emr.get_allergies( 392 since=self.__constraints['since'], 393 until=self.__constraints['until'], 394 encounters=self.__constraints['encounters'], 395 episodes=self.__constraints['episodes'], 396 issues=self.__constraints['issues'])) 397 # try: 398 # filtered_items.extend(emr.get_vaccinations( 399 # since=self.__constraints['since'], 400 # until=self.__constraints['until'], 401 # encounters=self.__constraints['encounters'], 402 # episodes=self.__constraints['episodes'], 403 # issues=self.__constraints['issues'])) 404 # except: 405 # _log.error("vaccination error? outside regime") 406 407 # filtered_items.extend(emr.get_lab_results( 408 # since=self.__constraints['since'], 409 # until=self.__constraints['until'], 410 # encounters=self.__constraints['encounters'], 411 # episodes=self.__constraints['episodes'], 412 # issues=self.__constraints['issues'])) 413 self.__filtered_items = filtered_items 414 return True

415 #--------------------------------------------------------

416 - def get_allergy_summary(self, allergy, left_margin = 0):

417 """ 418 Dumps allergy item data summary 419 allergy - Allergy item to dump 420 left_margin - Number of spaces on the left margin 421 """ 422 txt = _('%sAllergy: %s, %s (noted %s)\n') % ( 423 left_margin * u' ', 424 allergy['descriptor'], 425 gmTools.coalesce(allergy['reaction'], _('unknown reaction')), 426 allergy['date'].strftime('%x') 427 ) 428 # txt = left_margin * ' ' \ 429 # + _('Allergy') + ': ' \ 430 # + allergy['descriptor'] + u', ' \ 431 # + gmTools.coalesce(allergy['reaction'], _('unknown reaction')) ' ' \ 432 # + _('(noted %s)') % allergy['date'].strftime('%x') \ 433 # + '\n' 434 return txt

435 #--------------------------------------------------------

436 - def get_vaccination_summary(self, vaccination, left_margin = 0):

437 """ 438 Dumps vaccination item data summary 439 vaccination - Vaccination item to dump 440 left_margin - Number of spaces on the left margin 441 """ 442 txt = left_margin*' ' + _('Vaccination') + ': ' + vaccination['l10n_indication'] + ', ' + \ 443 vaccination['narrative'] + '\n' 444 return txt

445 #--------------------------------------------------------

446 - def get_lab_result_summary(self, lab_result, left_margin = 0):

447 """ 448 Dumps lab result item data summary 449 lab_request - Lab request item to dump 450 left_margin - Number of spaces on the left margin 451 """ 452 txt = '' 453 if self.lab_new_encounter: 454 txt += (left_margin+3)*' ' + _('Lab') + ': ' + \ 455 lab_result['unified_name'] + '-> ' + lab_result['unified_val'] + \ 456 ' ' + lab_result['val_unit']+ '\n' + '(' + lab_result['req_when'].strftime('%Y-%m-%d') + ')' 457 return txt

458 #--------------------------------------------------------

459 - def get_item_summary(self, item, left_margin = 0):

460 """ 461 Obtains formatted clinical item summary dump 462 item - The clinical item to dump 463 left_margin - Number of spaces on the left margin 464 """ 465 txt = '' 466 if isinstance(item, gmAllergy.cAllergy): 467 txt += self.get_allergy_summary(item, left_margin) 468 # elif isinstance(item, gmVaccination.cVaccination): 469 # txt += self.get_vaccination_summary(item, left_margin) 470 # elif isinstance(item, gmPathLab.cLabResult) and \ 471 # True: 472 # #(item['relevant'] == True or item['abnormal'] == True): 473 # txt += self.get_lab_result_summary(item, left_margin) 474 # self.lab_new_encounter = False 475 return txt

476 #--------------------------------------------------------

477 - def refresh_historical_tree(self, emr_tree):

478 """ 479 checks a emr_tree constructed with this.get_historical_tree() 480 and sees if any new items need to be inserted. 481 """ 482 #TODO , caching eliminates tree update time, so don't really need this 483 self._traverse_health_issues( emr_tree, self._update_health_issue_branch)

484 #--------------------------------------------------------

485 - def get_historical_tree( self, emr_tree):

486 self._traverse_health_issues( emr_tree, self._add_health_issue_branch)

487 #--------------------------------------------------------

488 - def _traverse_health_issues(self, emr_tree, health_issue_action):

489 """ 490 Retrieves patient's historical in form of a wx tree of health issues 491 -> episodes 492 -> encounters 493 Encounter object is associated with item to allow displaying its information 494 """ 495 # variable initialization 496 # this protects the emrBrowser from locking up in a paint event, e.g. in 497 # some configurations which want to use emrBrowser, but don't stop tabbing 498 # to emr browser when no patient selected. the effect is to displace a cNull instance 499 # which is a sane representation when no patient is selected. 500 if not self.__fetch_filtered_items(): 501 return 502 emr = self.__patient.get_emr() 503 unlinked_episodes = emr.get_episodes(issues = [None]) 504 h_issues = [] 505 h_issues.extend(emr.get_health_issues(id_list = self.__constraints['issues'])) 506 # build the tree 507 # unlinked episodes 508 if len(unlinked_episodes) > 0: 509 h_issues.insert(0, { 510 'description': _('Unattributed episodes'), 511 'pk_health_issue': None 512 }) 513 # existing issues 514 for a_health_issue in h_issues: 515 health_issue_action( emr_tree, a_health_issue) 516 517 emr_tree.SortChildren(emr_tree.GetRootItem())

518 #--------------------------------------------------------

519 - def _add_health_issue_branch( self, emr_tree, a_health_issue):

520 """appends to a wx emr_tree , building wx treenodes from the health_issue make this reusable for non-collapsing tree updates""" 521 emr = self.__patient.get_emr() 522 root_node = emr_tree.GetRootItem() 523 issue_node = emr_tree.AppendItem(root_node, a_health_issue['description']) 524 emr_tree.SetPyData(issue_node, a_health_issue) 525 episodes = emr.get_episodes(id_list=self.__constraints['episodes'], issues = [a_health_issue['pk_health_issue']]) 526 for an_episode in episodes: 527 self._add_episode_to_tree( emr, emr_tree, issue_node,a_health_issue, an_episode) 528 emr_tree.SortChildren(issue_node)

529 #--------------------------------------------------------

530 - def _add_episode_to_tree( self, emr , emr_tree, issue_node, a_health_issue, an_episode):

531 episode_node = emr_tree.AppendItem(issue_node, an_episode['description']) 532 emr_tree.SetPyData(episode_node, an_episode) 533 if an_episode['episode_open']: 534 emr_tree.SetItemBold(issue_node, True) 535 536 encounters = self._get_encounters( an_episode, emr ) 537 self._add_encounters_to_tree( encounters, emr_tree, episode_node ) 538 emr_tree.SortChildren(episode_node) 539 return episode_node

540 #--------------------------------------------------------

541 - def _add_encounters_to_tree( self, encounters, emr_tree, episode_node):

542 for an_encounter in encounters: 543 # label = u'%s: %s' % (an_encounter['started'].strftime('%Y-%m-%d'), an_encounter['l10n_type']) 544 label = u'%s: %s' % ( 545 an_encounter['started'].strftime('%Y-%m-%d'), 546 gmTools.unwrap ( 547 gmTools.coalesce ( 548 gmTools.coalesce ( 549 gmTools.coalesce ( 550 an_encounter.get_latest_soap ( # soAp 551 soap_cat = 'a', 552 episode = emr_tree.GetPyData(episode_node)['pk_episode'] 553 ), 554 an_encounter['assessment_of_encounter'] # or AOE 555 ), 556 an_encounter['reason_for_encounter'] # or RFE 557 ), 558 an_encounter['l10n_type'] # or type 559 ), 560 max_length = 40 561 ) 562 ) 563 encounter_node_id = emr_tree.AppendItem(episode_node, label) 564 emr_tree.SetPyData(encounter_node_id, an_encounter)

565 #--------------------------------------------------------

566 - def _get_encounters ( self, an_episode, emr ):

567 encounters = emr.get_encounters ( 568 episodes = [an_episode['pk_episode']] 569 ) 570 return encounters

571 #--------------------------------------------------------

572 - def _update_health_issue_branch(self, emr_tree, a_health_issue):

573 emr = self.__patient.get_emr() 574 root_node = emr_tree.GetRootItem() 575 id, cookie = emr_tree.GetFirstChild(root_node) 576 found = False 577 while id.IsOk(): 578 if emr_tree.GetItemText(id) == a_health_issue['description']: 579 found = True 580 break 581 id,cookie = emr_tree.GetNextChild( root_node, cookie) 582 583 if not found: 584 _log.error("health issue %s should exist in tree already", a_health_issue['description'] ) 585 return 586 issue_node = id 587 episodes = emr.get_episodes(id_list=self.__constraints['episodes'], issues = [a_health_issue['pk_health_issue']]) 588 589 #check for removed episode and update tree 590 tree_episodes = {} 591 id_episode, cookie = emr_tree.GetFirstChild(issue_node) 592 while id_episode.IsOk(): 593 tree_episodes[ emr_tree.GetPyData(id_episode)['pk_episode'] ]= id_episode 594 id_episode,cookie = emr_tree.GetNextChild( issue_node, cookie) 595 596 existing_episode_pk = [ e['pk_episode'] for e in episodes] 597 missing_tree_pk = [ pk for pk in tree_episodes.keys() if pk not in existing_episode_pk] 598 for pk in missing_tree_pk: 599 emr_tree.Remove( tree_episodes[pk] ) 600 601 added_episode_pk = [pk for pk in existing_episode_pk if pk not in tree_episodes.keys()] 602 add_episodes = [ e for e in episodes if e['pk_episode'] in added_episode_pk] 603 604 #check for added episodes and update tree 605 for an_episode in add_episodes: 606 node = self._add_episode_to_tree( emr, emr_tree, issue_node, a_health_issue, an_episode) 607 tree_episodes[an_episode['pk_episode']] = node 608 609 for an_episode in episodes: 610 # found episode, check for encounter change 611 try: 612 #print "getting id_episode of ", an_episode['pk_episode'] 613 id_episode = tree_episodes[an_episode['pk_episode']] 614 except: 615 import pdb 616 pdb.set_trace() 617 # get a map of encounters in the tree by pk_encounter as key 618 tree_enc = {} 619 id_encounter, cookie = emr_tree.GetFirstChild(id_episode) 620 while id_encounter.IsOk(): 621 tree_enc[ emr_tree.GetPyData(id_encounter)['pk_encounter'] ] = id_encounter 622 id_encounter,cookie = emr_tree.GetNextChild(id_episode, cookie) 623 624 # remove encounters in tree not in existing encounters in episode 625 # encounters = self._get_encounters( a_health_issue, an_episode, emr ) 626 encounters = self._get_encounters( an_episode, emr ) 627 existing_enc_pk = [ enc['pk_encounter'] for enc in encounters] 628 missing_enc_pk = [ pk for pk in tree_enc.keys() if pk not in existing_enc_pk] 629 for pk in missing_enc_pk: 630 emr_tree.Remove( tree_enc[pk] ) 631 632 # check for added encounter 633 added_enc_pk = [ pk for pk in existing_enc_pk if pk not in tree_enc.keys() ] 634 add_encounters = [ enc for enc in encounters if enc['pk_encounter'] in added_enc_pk] 635 if add_encounters != []: 636 #print "DEBUG found encounters to add" 637 self._add_encounters_to_tree( add_encounters, emr_tree, id_episode)

638 #--------------------------------------------------------

639 - def get_summary_info(self, left_margin = 0):

640 """ 641 Dumps patient EMR summary 642 """ 643 txt = '' 644 for an_item in self.__filtered_items: 645 txt += self.get_item_summary(an_item, left_margin) 646 return txt

647 #--------------------------------------------------------

648 - def get_episode_summary (self, episode, left_margin = 0):

649 """Dumps episode specific data""" 650 emr = self.__patient.get_emr() 651 encs = emr.get_encounters(episodes = [episode['pk_episode']]) 652 if encs is None: 653 txt = left_margin * ' ' + _('Error retrieving encounters for episode\n%s') % str(episode) 654 return txt 655 no_encs = len(encs) 656 if no_encs == 0: 657 txt = left_margin * ' ' + _('There are no encounters for this episode.') 658 return txt 659 if episode['episode_open']: 660 status = _('active') 661 else: 662 status = _('finished') 663 first_encounter = emr.get_first_encounter(episode_id = episode['pk_episode']) 664 last_encounter = emr.get_last_encounter(episode_id = episode['pk_episode']) 665 txt = _( 666 '%sEpisode "%s" [%s]\n' 667 '%sEncounters: %s (%s - %s)\n' 668 '%sLast worked on: %s\n' 669 ) % ( 670 left_margin * ' ', episode['description'], status, 671 left_margin * ' ', no_encs, first_encounter['started'].strftime('%m/%Y'), last_encounter['last_affirmed'].strftime('%m/%Y'), 672 left_margin * ' ', last_encounter['last_affirmed'].strftime('%Y-%m-%d %H:%M') 673 ) 674 return txt

675 #--------------------------------------------------------

676 - def get_encounter_info(self, episode, encounter, left_margin = 0):

677 """ 678 Dumps encounter specific data (rfe, aoe and soap) 679 """ 680 emr = self.__patient.get_emr() 681 # general 682 txt = (' ' * left_margin) + '#%s: %s - %s %s' % ( 683 encounter['pk_encounter'], 684 encounter['started'].strftime('%Y-%m-%d %H:%M'), 685 encounter['last_affirmed'].strftime('%H:%M (%Z)'), 686 encounter['l10n_type'] 687 ) 688 if (encounter['assessment_of_encounter'] is not None) and (len(encounter['assessment_of_encounter']) > 0): 689 txt += ' "%s"' % encounter['assessment_of_encounter'] 690 txt += '\n\n' 691 692 # rfe/aoe 693 txt += (' ' * left_margin) + '%s: %s\n' % (_('RFE'), encounter['reason_for_encounter']) 694 txt += (' ' * left_margin) + '%s: %s\n' % (_('AOE'), encounter['assessment_of_encounter']) 695 696 # soap 697 soap_cat_labels = { 698 's': _('Subjective'), 699 'o': _('Objective'), 700 'a': _('Assessment'), 701 'p': _('Plan'), 702 None: _('Administrative') 703 } 704 eol_w_margin = '\n' + (' ' * (left_margin+3)) 705 for soap_cat in 'soap': 706 soap_cat_narratives = emr.get_clin_narrative ( 707 episodes = [episode['pk_episode']], 708 encounters = [encounter['pk_encounter']], 709 soap_cats = [soap_cat] 710 ) 711 if soap_cat_narratives is None: 712 continue 713 if len(soap_cat_narratives) == 0: 714 continue 715 txt += (' ' * left_margin) + soap_cat_labels[soap_cat] + ':\n' 716 for soap_entry in soap_cat_narratives: 717 txt += gmTools.wrap ( 718 '%s %.8s: %s\n' % ( 719 soap_entry['date'].strftime('%d.%m. %H:%M'), 720 soap_entry['provider'], 721 soap_entry['narrative'] 722 ), 75 723 ) 724 725 # txt += ( 726 # (' ' * (left_margin+3)) + 727 # soap_entry['date'].strftime('%H:%M %.8s: ') % soap_entry['provider'] + 728 # soap_entry['narrative'].replace('\n', eol_w_margin) + 729 # '\n' 730 # ) 731 #FIXME: add diagnoses 732 733 # items 734 for an_item in self.__filtered_items: 735 if an_item['pk_encounter'] == encounter['pk_encounter']: 736 txt += self.get_item_output(an_item, left_margin) 737 return txt

738 #--------------------------------------------------------

739 - def dump_historical_tree(self):

740 """Dumps patient's historical in form of a tree of health issues 741 -> episodes 742 -> encounters 743 -> clinical items 744 """ 745 746 # fecth all values 747 self.__fetch_filtered_items() 748 emr = self.__patient.get_emr() 749 750 # dump clinically relevant items summary 751 for an_item in self.__filtered_items: 752 self.__target.write(self.get_item_summary(an_item, 3)) 753 754 # begin with the tree 755 h_issues = [] 756 h_issues.extend(emr.get_health_issues(id_list = self.__constraints['issues'])) 757 # unlinked episodes 758 unlinked_episodes = emr.get_episodes(issues = [None]) 759 if len(unlinked_episodes) > 0: 760 h_issues.insert(0, {'description':_('Unattributed episodes'), 'pk_health_issue':None}) 761 for a_health_issue in h_issues: 762 self.__target.write('\n' + 3*' ' + 'Health Issue: ' + a_health_issue['description'] + '\n') 763 episodes = emr.get_episodes(id_list=self.__constraints['episodes'], issues = [a_health_issue['pk_health_issue']]) 764 for an_episode in episodes: 765 self.__target.write('\n' + 6*' ' + 'Episode: ' + an_episode['description'] + '\n') 766 if a_health_issue['pk_health_issue'] is None: 767 issues = None 768 else: 769 issues = [a_health_issue['pk_health_issue']] 770 encounters = emr.get_encounters ( 771 since = self.__constraints['since'], 772 until = self.__constraints['until'], 773 id_list = self.__constraints['encounters'], 774 episodes = [an_episode['pk_episode']], 775 issues = issues 776 ) 777 for an_encounter in encounters: 778 # title 779 self.lab_new_encounter = True 780 self.__target.write( 781 '\n %s %s: %s - %s (%s)\n' % ( 782 _('Encounter'), 783 an_encounter['l10n_type'], 784 an_encounter['started'].strftime('%A, %Y-%m-%d %H:%M'), 785 an_encounter['last_affirmed'].strftime('%m-%d %H:%M'), 786 an_encounter['assessment_of_encounter'] 787 ) 788 ) 789 self.__target.write(self.get_encounter_info(an_episode, an_encounter, 12))

790 #--------------------------------------------------------

791 - def dump_clinical_record(self):

792 """ 793 Dumps in ASCII format patient's clinical record 794 """ 795 emr = self.__patient.get_emr() 796 if emr is None: 797 _log.error('cannot get EMR text dump') 798 print(_( 799 'An error occurred while retrieving a text\n' 800 'dump of the EMR for the active patient.\n\n' 801 'Please check the log file for details.' 802 )) 803 return None 804 self.__target.write('\nOverview\n') 805 self.__target.write('--------\n') 806 self.__target.write("1) Allergy status (for details, see below):\n\n") 807 for allergy in emr.get_allergies(): 808 self.__target.write(" " + allergy['descriptor'] + "\n\n") 809 self.__target.write("2) Vaccination status (* indicates booster):\n") 810 # self.get_vacc_table() 811 self.__target.write("\n3) Historical:\n\n") 812 self.dump_historical_tree() 813 814 try: 815 emr.cleanup() 816 except: 817 print "error cleaning up EMR"

818 #--------------------------------------------------------

819 - def dump_med_docs(self):

820 """ 821 Dumps patient stored medical documents 822 823 """ 824 doc_folder = self.__patient.get_document_folder() 825 826 self.__target.write('\n4) Medical documents: (date) reference - type "comment"\n') 827 self.__target.write(' object - comment') 828 829 docs = doc_folder.get_documents() 830 for doc in docs: 831 self.__target.write('\n\n (%s) %s - %s "%s"' % ( 832 doc['clin_when'].strftime('%Y-%m-%d'), 833 doc['ext_ref'], 834 doc['l10n_type'], 835 doc['comment']) 836 ) 837 parts = doc.get_parts() 838 for part in parts: 839 self.__target.write('\n %s - %s' % ( 840 part['seq_idx'], 841 part['obj_comment']) 842 ) 843 self.__target.write('\n\n')

844 #--------------------------------------------------------

845 - def dump_demographic_record(self, all = False):

846 """ 847 Dumps in ASCII format some basic patient's demographic data 848 """ 849 if self.__patient is None: 850 _log.error('cannot get Demographic export') 851 print(_( 852 'An error occurred while Demographic record export\n' 853 'Please check the log file for details.' 854 )) 855 return None 856 857 self.__target.write('\n\n\nDemographics') 858 self.__target.write('\n------------\n') 859 self.__target.write(' Id: %s \n' % self.__patient['pk_identity']) 860 cont = 0 861 for name in self.__patient.get_names(): 862 if cont == 0: 863 self.__target.write(' Name (Active): %s, %s\n' % (name['firstnames'], name['lastnames']) ) 864 else: 865 self.__target.write(' Name %s: %s, %s\n' % (cont, name['firstnames'], name['lastnames'])) 866 cont += 1 867 self.__target.write(' Gender: %s\n' % self.__patient['gender']) 868 self.__target.write(' Title: %s\n' % self.__patient['title']) 869 self.__target.write(' Dob: %s\n' % self.__patient.get_formatted_dob(format = '%Y-%m-%d')) 870 self.__target.write(' Medical age: %s\n' % self.__patient.get_medical_age())

871 #--------------------------------------------------------

872 - def dump_constraints(self):

873 """ 874 Dumps exporter filtering constraints 875 """ 876 self.__first_constraint = True 877 if not self.__constraints['since'] is None: 878 self.dump_constraints_header() 879 self.__target.write('\nSince: %s' % self.__constraints['since'].strftime('%Y-%m-%d')) 880 881 if not self.__constraints['until'] is None: 882 self.dump_constraints_header() 883 self.__target.write('\nUntil: %s' % self.__constraints['until'].strftime('%Y-%m-%d')) 884 885 if not self.__constraints['encounters'] is None: 886 self.dump_constraints_header() 887 self.__target.write('\nEncounters: ') 888 for enc in self.__constraints['encounters']: 889 self.__target.write(str(enc) + ' ') 890 891 if not self.__constraints['episodes'] is None: 892 self.dump_constraints_header() 893 self.__target.write('\nEpisodes: ') 894 for epi in self.__constraints['episodes']: 895 self.__target.write(str(epi) + ' ') 896 897 if not self.__constraints['issues'] is None: 898 self.dump_constraints_header() 899 self.__target.write('\nIssues: ') 900 for iss in self.__constraints['issues']: 901 self.__target.write(str(iss) + ' ')

902 #--------------------------------------------------------

903 - def dump_constraints_header(self):

904 """ 905 Dumps constraints header 906 """ 907 if self.__first_constraint == True: 908 self.__target.write('\nClinical items dump constraints\n') 909 self.__target.write('-'*(len(head_txt)-2)) 910 self.__first_constraint = False

Source Code for Module Gnumed.exporters.gmPatientExporter