def __find_or_create_test_type(loinc=None, name=None, pk_lab=None, unit=None, link_obj=None, abbrev=None):
tt = gmPathLab.find_measurement_type(link_obj = link_obj, lab = pk_lab, name = name)
if tt is None:
_log.debug('test type [%s %s (%s)] not found for lab #%s, creating', name, unit, loinc, pk_lab)
tt = gmPathLab.create_measurement_type(link_obj = link_obj, lab = pk_lab, abbrev = gmTools.coalesce(abbrev, name), unit = unit, name = name)
if loinc is None:
return tt
if loinc.strip() == u'':
return tt
if tt['loinc'] is None:
tt['loinc'] = loinc
tt.save(conn = link_obj)
return tt
if tt['loinc'] != loinc:
# raise ValueError('LOINC code mismatch between GM (%s) and HL7 (%s) for result type [%s]' % (tt['loinc'], loinc, name))
_log.error('LOINC code mismatch between GM (%s) and HL7 (%s) for result type [%s]', tt['loinc'], loinc, name)
return tt
def __find_or_create_test_type(loinc=None, name=None, pk_lab=None, unit=None, link_obj=None, abbrev=None):
tt = gmPathLab.find_measurement_type(link_obj = link_obj, lab = pk_lab, name = name)
if tt is None:
_log.debug('test type [%s::%s::%s] not found for lab #%s, creating', name, unit, loinc, pk_lab)
tt = gmPathLab.create_measurement_type(link_obj = link_obj, lab = pk_lab, abbrev = gmTools.coalesce(abbrev, name), unit = unit, name = name)
_log.debug('created as: %s', tt)
if loinc is None:
return tt
if loinc.strip() == '':
return tt
if tt['loinc'] is None:
tt['loinc'] = loinc
tt.save(conn = link_obj)
return tt
if tt['loinc'] != loinc:
# raise ValueError('LOINC code mismatch between GM (%s) and HL7 (%s) for result type [%s]' % (tt['loinc'], loinc, name))
_log.error('LOINC code mismatch between GM (%s) and HL7 (%s) for result type [%s]', tt['loinc'], loinc, name)
return tt
def __handle_8410(self, result_data):
if self.__request is None:
_log.Log(gmLog.lErr, 'Kann Labordaten nicht ohne Zuordnung importieren.')
return False
# skip pseudo results
if len(result_data) == 3:
if ('8410' in result_data and # code
'8411' in result_data and # name
'8412' in result_data): # Abrechnungskennung
_log.Log(gmLog.lInfo, 'skipping billing-only record')
return True
# verify essential fields
# - numeric result
try:
vnum = '\n'.join(result_data['8420'])
except KeyError:
vnum = None
# - alphanumeric result
try:
valpha = '\n'.join(result_data['8480'])
except KeyError:
valpha = None
if (valpha is None) and (vnum is None):
valpha = ''
# - code
try:
vcode = result_data['8410'][0]
except KeyError:
_log.Log(gmLog.lWarn, 'adding default test type code')
# - name
try:
vname = result_data['8411'][0]
except KeyError:
_log.Log(gmLog.lWarn, 'adding default test type name')
# - unit
try:
vunit = result_data['8421'][0]
except KeyError:
vunit = ''
# verify/create test type
status, ttype = gmPathLab.create_measurement_type (
lab=self.__lab_name,
code=vcode, # must be abbrev
name=vname,
unit=vunit
)
if status in [False, None]:
_log.Log(gmLog.lErr, 'cannot create/retrieve test type')
return False
if ttype['comment'] in [None, '']:
ttype['comment'] = 'created [%s] by [$RCSfile: gmLDTimporter.py,v $ $Revision: 1.34 $] from [%s]' % (time.strftime('%Y-%m-%d %H:%M'), self.ldt_filename)
ttype.save_payload()
# try to create test result row
whenfield = 'lab_rxd_when' # FIXME: make this configurable
status, self.__lab_result = gmPathLab.create_lab_result(
patient_id = self.__request.get_patient()[0],
when_field = whenfield,
when = self.__request[whenfield],
test_type = ttype['pk'],
val_num = vnum,
val_alpha = valpha,
unit = vunit,
request = self.__request
)
if status is False:
_log.Log(gmLog.lErr, 'cannot create result record')
_log.Log(gmLog.lInfo, str(result_data)[:500])
return False
# FIXME: make this configurable (whether skipping or duplicating)
if status is None:
_log.Log(gmLog.lData, 'skipping duplicate lab result on import')
_log.Log(gmLog.lData, 'in file: %s' % str(result_data))
return True
# update result record from dict
# - force these to None so we can add in the proper values
self.__lab_result['val_num'] = None
self.__lab_result['val_alpha'] = None
# - preset some fields
self.__lab_result['reviewed'] = 'false'
if self.__ref_group_str != '':
self.__lab_result['ref_group'] = self.__ref_group_str
# - process lines
for line_type in result_data.keys():
# get handler
try:
handle_line = cLDTImporter.__8410line_handler[line_type]
except KeyError:
_log.LogException('no handler for line [%s] in [8410] record' % line_type, sys.exc_info(), verbose=0)
return False
# ignore line
if handle_line is None:
continue
if handle_line(self, result_data) is False:
# FIXME: todo item
_log.Log(gmLog.lErr, 'cannot handle [%s] line' % line_type)
return False
if (self.__lab_result['val_alpha'] is None) and (self.__lab_result['val_num'] is None):
_log.Log(gmLog.lWarn, 'both result fields empty, setting alphanumeric default')
self.__lab_result['val_alpha'] = ''
saved, msg = self.__lab_result.save_payload()
del self.__lab_result
if not saved:
_log.Log(gmLog.lErr, 'kann Laborwert (8410) nicht importieren')
return False
_log.Log(gmLog.lInfo, 'Laborwert (8410) erfolgreich importiert')
return True
def __handle_8410(self, result_data):
if self.__request is None:
_log.Log(gmLog.lErr, 'Kann Labordaten nicht ohne Zuordnung importieren.')
return False
# skip pseudo results
if len(result_data) == 3:
if (result_data.has_key('8410') and # code
result_data.has_key('8411') and # name
result_data.has_key('8412')): # Abrechnungskennung
_log.Log(gmLog.lInfo, 'skipping billing-only record')
return True
# verify essential fields
# - numeric result
try:
vnum = '\n'.join(result_data['8420'])
except KeyError:
vnum = None
# - alphanumeric result
try:
valpha = '\n'.join(result_data['8480'])
except KeyError:
valpha = None
if (valpha is None) and (vnum is None):
valpha = ''
# - code
try:
vcode = result_data['8410'][0]
except KeyError:
_log.Log(gmLog.lWarn, 'adding default test type code')
# - name
try:
vname = result_data['8411'][0]
except KeyError:
_log.Log(gmLog.lWarn, 'adding default test type name')
# - unit
try:
vunit = result_data['8421'][0]
except KeyError:
vunit = ''
# verify/create test type
status, ttype = gmPathLab.create_measurement_type (
lab=self.__lab_name,
code=vcode, # must be abbrev
name=vname,
unit=vunit
)
if status in [False, None]:
_log.Log(gmLog.lErr, 'cannot create/retrieve test type')
return False
if ttype['comment'] in [None, '']:
ttype['comment'] = 'created [%s] by [$RCSfile: gmLDTimporter.py,v $ $Revision: 1.34 $] from [%s]' % (time.strftime('%Y-%m-%d %H:%M'), self.ldt_filename)
ttype.save_payload()
# try to create test result row
whenfield = 'lab_rxd_when' # FIXME: make this configurable
status, self.__lab_result = gmPathLab.create_lab_result(
patient_id = self.__request.get_patient()[0],
when_field = whenfield,
when = self.__request[whenfield],
test_type = ttype['pk'],
val_num = vnum,
val_alpha = valpha,
unit = vunit,
request = self.__request
)
if status is False:
_log.Log(gmLog.lErr, 'cannot create result record')
_log.Log(gmLog.lInfo, str(result_data)[:500])
return False
# FIXME: make this configurable (whether skipping or duplicating)
if status is None:
_log.Log(gmLog.lData, 'skipping duplicate lab result on import')
_log.Log(gmLog.lData, 'in file: %s' % str(result_data))
return True
# update result record from dict
# - force these to None so we can add in the proper values
self.__lab_result['val_num'] = None
self.__lab_result['val_alpha'] = None
# - preset some fields
self.__lab_result['reviewed'] = 'false'
if self.__ref_group_str != '':
self.__lab_result['ref_group'] = self.__ref_group_str
# - process lines
for line_type in result_data.keys():
# get handler
try:
handle_line = cLDTImporter.__8410line_handler[line_type]
except KeyError:
_log.LogException('no handler for line [%s] in [8410] record' % line_type, sys.exc_info(), verbose=0)
return False
# ignore line
if handle_line is None:
continue
if handle_line(self, result_data) is False:
# FIXME: todo item
_log.Log(gmLog.lErr, 'cannot handle [%s] line' % line_type)
return False
if (self.__lab_result['val_alpha'] is None) and (self.__lab_result['val_num'] is None):
_log.Log(gmLog.lWarn, 'both result fields empty, setting alphanumeric default')
self.__lab_result['val_alpha'] = ''
saved, msg = self.__lab_result.save_payload()
del self.__lab_result
if not saved:
_log.Log(gmLog.lErr, 'kann Laborwert (8410) nicht importieren')
return False
_log.Log(gmLog.lInfo, 'Laborwert (8410) erfolgreich importiert')
return True