def map(self):
try:
id_value = sha256(self.data['concat_elements'].encode('utf-8')).hexdigest()
lufu_diagnostic_report = diagnosticreport.DiagnosticReport();
lufu_diagnostic_report.id = id_value
lufu_diagnostic_report_identifier = self.data['untersuchung_id']
lufu_diagnostic_report.identifier = [identifier.Identifier({"use": "official",
"system": self.systems['lufu_obs_id'],
"value": str(lufu_diagnostic_report_identifier)})]
dt_string = self.data['untersuchungsdatum']+" "+self.data['untersuchungsuhrzeit']
lufu_report_dt = datetime.strftime(datetime.strptime(dt_string, "%Y-%m-%d %H:%M:%S"), '%Y-%m-%dT%H:%M:%S')
lufu_diagnostic_report_date = fhirdate.FHIRDate(lufu_report_dt)
lufu_diagnostic_report.effectiveDateTime = lufu_diagnostic_report_date
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
lufu_diagnostic_report.subject = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
lufu_diagnostic_report.encounter = fhirreference.FHIRReference(jsondict=ref)
rep_code_system_cc = codeableconcept.CodeableConcept()
rep_code_system_cc.coding = [coding.Coding({"system": "https://www.dimdi.de/static/de/klassifikationen/ops",
"code": "1-71",
"display": "Pneumologische Funktionsuntersuchunge"})]
rep_status = 'final'
lufu_diagnostic_report.code = rep_code_system_cc
lufu_diagnostic_report.status = rep_status
conclusion_str = ""
if self.data['beurteilung'] is not None and self.data['beurteilung'] != "":
conclusion_str = conclusion_str + "Beurteilung: "+self.data['beurteilung']
if self.data['anmerkung'] is not None and self.data['anmerkung'] != "":
conclusion_str = conclusion_str + "|\n Anmerkung: "+self.data['anmerkung']
if self.data['empfehlung'] is not None and self.data['empfehlung'] != "":
conclusion_str = conclusion_str + " |\n Empfehlung: "+self.data['empfehlung']
lufu_diagnostic_report.conclusion = conclusion_str
return lufu_diagnostic_report
except KeyError as exc:
self.logger.error(f"In {__name__}: Key {exc} not found in dictionary")
raise
except Exception as exc:
self.logger.error(f"In {__name__}: Error occurred in mapping ({exc})")
raise
def map(self):
try:
obs_status = "preliminary"
obs_meta = meta.Meta()
obs_meta.source = "#sap-ish"
start_dt = None
end_dt = None
if not pd.isna(self.data['admission_dt']):
start_dt = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
if not pd.isna(self.data['discharge_dt']):
end_dt = fhirdate.FHIRDate(
datetime.strftime(self.data['discharge_dt'],
'%Y-%m-%dT%H:%M:%S'))
obs_status = "final"
obs_period = period.Period()
obs_period.start = start_dt
obs_period.end = end_dt
id_value = f"{self.data['encounter_psn']}-dia"
dialysis_observation = miracum_observation.Observation()
dialysis_observation.id = id_value
dialysis_sys = self.systems['p21obs_id']
dialysis_observation.identifier = [
identifier.Identifier({
"system": dialysis_sys,
"value": id_value
})
]
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
dialysis_observation.encounter = fhirreference.FHIRReference(
jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
dialysis_observation.subject = fhirreference.FHIRReference(
jsondict=ref)
dialysis_code = miracum_codeableconcept.CodeableConcept()
obs_code_sys = "https://miracum.org/fhir/CodeSystem/core/observations"
dialysis_code.text = "Intercurrent dialysis"
dialysis_code.coding = [
miracum_coding.Coding({
"system": obs_code_sys,
"code": "intercurrent-dialysis",
"display": "Intercurrent dialysis"
})
]
dialysis_observation.code = dialysis_code
dialysis_observation.valueInteger = self.data['dialysis_hours']
dialysis_observation.status = obs_status
dialysis_observation.effectivePeriod = obs_period
dialysis_observation.meta = obs_meta
id_value = f"{self.data['encounter_psn']}-icu"
icu_observation = miracum_observation.Observation()
icu_observation.id = id_value
icu_sys = self.systems['p21obs_id']
icu_observation.identifier = [
identifier.Identifier({
"system": icu_sys,
"value": id_value
})
]
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
icu_observation.encounter = fhirreference.FHIRReference(
jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
icu_observation.subject = fhirreference.FHIRReference(jsondict=ref)
icu_code = miracum_codeableconcept.CodeableConcept()
icu_code.text = "Days in intensive care unit"
icu_code.coding = [
miracum_coding.Coding({
"system": 'http://loinc.org',
"code": "74200-7",
"display": "Days in intensive care unit",
"version": "2.46"
})
]
icu_observation.code = icu_code
if self.data['icu_days']:
icu_observation.valueQuantity = miracum_quantity.Quantity({
"value":
self.data['icu_days'],
"unit":
"d",
"system":
"http://unitsofmeasure.org",
"code":
"d"
})
icu_observation.status = obs_status
icu_observation.effectivePeriod = obs_period
icu_observation.meta = obs_meta
return [dialysis_observation, icu_observation]
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
except FHIRValidationError:
raise
def map(self):
try:
obs_status = "preliminary"
obs_meta = meta.Meta()
obs_meta.source = "#sap-ish"
start_dt = None
end_dt = None
if not pd.isna(self.data['admission_dt']):
start_dt = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
if not pd.isna(self.data['discharge_dt']):
end_dt = fhirdate.FHIRDate(
datetime.strftime(self.data['discharge_dt'],
'%Y-%m-%dT%H:%M:%S'))
obs_status = "final"
obs_period = period.Period()
obs_period.start = start_dt
obs_period.end = end_dt
id_value = f"{self.data['encounter_psn']}-vent"
vent_observation = miracum_observation.Observation()
vent_observation.id = id_value
vent_observation.identifier = [
identifier.Identifier({
"system": self.systems['p21obs_id'],
"value": id_value
})
]
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
vent_observation.encounter = fhirreference.FHIRReference(
jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
vent_observation.subject = fhirreference.FHIRReference(
jsondict=ref)
ventilation_code = miracum_codeableconcept.CodeableConcept()
ventilation_code.text = "Days on Ventilator"
ventilation_code.coding = [
miracum_coding.Coding({
"system": "http://loinc.org",
"code": "74201-5",
"display": "Days on Ventilator"
})
]
vent_observation.code = ventilation_code
if self.data['vent_days']:
vent_observation.valueQuantity = miracum_quantity.Quantity({
"value":
self.data['vent_days'],
"unit":
"d",
"system":
"http://unitsofmeasure.org",
"code":
"d"
})
vent_observation.status = obs_status
vent_observation.effectivePeriod = obs_period
vent_observation.meta = obs_meta
return vent_observation
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
except FHIRValidationError:
raise
def mapLufuItems2Obs(self, param, items):
sct_code = self.snomed_mapper.codeLookup(str(param))
sct_display = self.snomed_mapper.displayLookup(str(sct_code))
lufu_observation = observation.Observation()
observation_unit = ''
concat_string = self.data['concat_elements'] + param
id_value = sha256(concat_string.encode('utf-8')).hexdigest()
lufu_observation.id = id_value
lufu_observation.identifier = [
identifier.Identifier({
"system": self.systems['lufu_obs_id'],
"value": id_value
})
]
obs_actual_code = codeableconcept.CodeableConcept()
obs_actual_code.coding = [
coding.Coding({
"system": "http://snomed.info/sct",
"code": sct_code,
"display": sct_display,
"version": "0.1"
})
]
# obs category
obs_type_sys = "http://terminology.hl7.org/CodeSystem/observation-category"
code = 'exam'
observation_cat = codeableconcept.CodeableConcept()
observation_cat.coding = [
coding.Coding({
"system": obs_type_sys,
"code": code
})
]
lufu_observation.category = [observation_cat]
lufu_observation.code = obs_actual_code
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
lufu_observation.encounter = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
lufu_observation.subject = fhirreference.FHIRReference(jsondict=ref)
if not pd.isna(self.data['untersuchungsdatum']) and not pd.isna(
self.data['untersuchungsuhrzeit']):
dt_string = self.data['untersuchungsdatum'] + " " + self.data[
'untersuchungsuhrzeit']
obs_datetime = datetime.strptime(dt_string, "%Y-%m-%d %H:%M:%S")
obs_datetime.replace(tzinfo=timezone.utc)
# collect_ts_fhir = datetime.strftime(obs_datetime.astimezone().isoformat(), '%Y-%m-%dT%H:%M:%S')
lufu_observation.effectiveDateTime = fhirdate.FHIRDate(
obs_datetime.astimezone().isoformat())
components = []
for item in items:
if 'actual' in str(item):
obs_component = observation.ObservationComponent()
lufu_value = self.data[item]
lookupParam = item
if ("PRE" not in param) and ("POST" not in param):
lookupParam = str(item).replace("PRE_", "")
loinc_code = self.loinc_mapper.codeLookup(lookupParam)
loinc_display = self.loinc_mapper.displayLookup(loinc_code)
i2b2_code = self.i2b2_mapper.codeLookup(lookupParam)
codings = []
if loinc_code != 'No Code':
codings.append(
coding.Coding({
"system": "http://loinc.org",
"code": loinc_code,
"display": loinc_display,
"version": "2.46"
}))
mask = self.map_table[self.map_table['RELMA'] == loinc_code]
observation_unit = mask['Unit'].values[0]
if i2b2_code != 'No Code':
codings.append(
coding.Coding({
"system": "http://mdr.miracum.org",
"code": i2b2_code,
"version": "0.01"
}))
mask = self.map_table[self.map_table['I2B2 Basecode'] ==
i2b2_code]
observation_unit = mask['Unit'].values[0]
if len(codings) > 0:
obs_component_code = codeableconcept.CodeableConcept()
obs_component_code.coding = codings
obs_component.code = obs_component_code
#obs_component.valueDateTime = fhirdate.FHIRDate(collect_ts_fhir)
obs_component.valueQuantity = quantity.Quantity({
"value":
lufu_value,
"unit":
observation_unit,
"system":
"http://unitsofmeasure.org",
"code":
observation_unit
})
lufu_ref_value = self.data[str(item).replace(
'actual', 'target')]
low_ref_value = quantity.Quantity({
"value": lufu_ref_value,
"unit": observation_unit,
"system": "http://unitsofmeasure.org",
"code": observation_unit
})
ref_range = ObservationReferenceRange()
ref_range.low = low_ref_value
ref_range.high = low_ref_value
obs_component.referenceRange = [ref_range]
components.append(obs_component)
lufu_observation.component = components
lufu_observation.status = "final"
lufu_actual_meta = meta.Meta()
lufu_actual_meta.source = "#lufu-cwd"
lufu_observation.meta = lufu_actual_meta
if len(lufu_observation.component) > 0:
return lufu_observation
else:
return []
def map(self):
try:
sub_encounter = mii_encounter_abfall.Encounter()
id_value = sha256(
self.data['concat_elements'].encode('utf-8')).hexdigest()
sub_encounter.id = id_value
sub_encounter.identifier = [
identifier.Identifier({
"use": "usual",
"system": self.systems['subencounter_id'],
"value": id_value
})
]
sub_encounter.status = "in-progress"
enc_class_system = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
sub_encounter.class_fhir = mii_coding.Coding({
"system":
enc_class_system,
"code":
"IMP",
"display":
"inpatient encounter"
})
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
sub_encounter.subject = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
sub_encounter.partOf = fhirreference.FHIRReference(jsondict=ref)
fab_code = self.data['dep_full_code']
service_type = mii_codeableconcept.CodeableConcept()
service_type_sys = "http://terminology.hl7.org/CodeSystem/service-type"
service_type.coding = [
mii_coding.Coding({
"system": service_type_sys,
"code": fab_code,
"display": self._dep_name_lookup(fab_code)
})
]
sub_encounter.serviceType = service_type
enc_period = mii_period.Period()
enc_period.start = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
if not pd.isna(self.data['discharge_dt']):
sub_encounter.status = "finished"
enc_period.end = fhirdate.FHIRDate(
datetime.strftime(self.data['discharge_dt'],
'%Y-%m-%dT%H:%M:%S'))
sub_encounter.period = enc_period
enc_meta = meta.Meta()
enc_meta.source = "#sap-ish"
sub_encounter.meta = enc_meta
sub_encounter.location = []
location_list = []
added_res_loc = 0
res_loc_invalid = 0
for loc_name, loc_am_ts, loc_dc_ts in zip(
self.data['loc_name_set'], self.data['loc_am_ts_set'],
self.data['loc_dc_ts_set']):
new_location = location.Location()
id_value = sha256(loc_name.encode('utf-8')).hexdigest()
new_location.id = id_value
new_location.identifier = [
identifier.Identifier({
"use": "usual",
"system":
"https://diz.mii.de/fhir/CodeSystem/TestOrganisationAbteilungen",
"value": id_value
})
]
new_location.name = loc_name
loc = mii_encounter_abfall.EncounterLocation()
loc.status = 'active'
loc_period = mii_period.Period()
loc_period.start = fhirdate.FHIRDate(
datetime.strftime(loc_am_ts, '%Y-%m-%dT%H:%M:%S'))
if not pd.isna(loc_dc_ts):
loc.status = "completed"
loc_period.end = fhirdate.FHIRDate(
datetime.strftime(loc_dc_ts, '%Y-%m-%dT%H:%M:%S'))
loc.period = loc_period
ref = {"reference": f"Location/{id_value}"}
loc.location = fhirreference.FHIRReference(jsondict=ref)
try:
loc.as_json()
sub_encounter.location.append(loc)
location_list.append(new_location)
added_res_loc += 1
except FHIRValidationError:
self.logger.warning(
"Validation error for created Location resource "
f"(id: {self.data['encounter_psn']})")
res_loc_invalid += 1
return sub_encounter, location_list, added_res_loc, res_loc_invalid
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
def _map_dmpro2medi(self, encounter_ref, patient_ref):
new_medication = []
medication_stm = []
mapping_row = self.ops_drug_mapping[self.ops_drug_mapping['ops_code']
== self.data['ops_kode']]
if not mapping_row.empty:
drug_name = mapping_row['medication'].to_string(index=False)[1:]
drug_atc = mapping_row['atc_code1'].to_string(index=False)[1:]
dosage_text = mapping_row['text'].to_string(index=False)[1:]
ucum_short = mapping_row['ucum_short'].to_string(index=False)[1:]
ucum_full = mapping_row['ucum_full'].to_string(index=False)[1:]
dosage_min = mapping_row['dosage_min'].to_string(index=False)[1:]
dosage_max = mapping_row['dosage_max'].to_string(index=False)[1:]
combi_product = mapping_row['medication_combi'].to_string(
index=False)
# generate medication statement resources
new_medication = medication.Medication()
id_value = str(self.data['encounter_psn']) + '_' + str(
self.data['procedure_nr']) + '_med'
#id_value = f"{drug_name}"
#id_value = sha256(id_value.encode('utf-8')).hexdigest()
new_medication.id = id_value
new_medication.identifier = [
identifier.Identifier({
"system": self.systems['med_id'],
"value": id_value
})
]
atc_cc = codeableconcept.CodeableConcept()
atc_cc.coding = [
coding.Coding({
"system": "http://fhir.de/CodeSystem/dimdi/atc",
"code": drug_atc,
"version": "ATC/DDD Version 2020",
"display": drug_name
})
]
new_medication.code = atc_cc
new_medication.status = "active"
med_meta = meta.Meta()
med_meta.source = "#sap-ish"
new_medication.meta = med_meta
substances = [drug_name]
if combi_product:
substances = drug_name.split('-')
ingredients = []
if substances != ["UNKLAR"]:
for substance in substances:
mapping_row2 = self.drug_unii_mapping[
self.drug_unii_mapping['Substanzangabe_aus_OPS-Code']
== substance]
substance_unii = mapping_row2[
'Substanz_fuer_Dosisberechnung_UNII-number'].to_string(
index=False)[1:]
substance_ask = mapping_row2[
'Substanz_fuer_Dosisberechnung_ASK-Nr'].to_string(
index=False)[1:]
substance_cas = mapping_row2[
'Substanz_fuer_Dosisberechnung_CAS-Nummer'].to_string(
index=False)[1:]
ingredient = medication.MedicationIngredient()
ingredient_cc = codeableconcept.CodeableConcept()
ingredient_cc.coding = [
coding.Coding({
"system": "http://fdasis.nlm.nih.gov",
"code": substance_unii,
"display": substance
})
]
ingredient_cc.coding += [
coding.Coding({
"system": "http://fhir.de/CodeSystem/ask",
"code": substance_ask,
"display": substance
})
]
ingredient_cc.coding += [
coding.Coding({
"system": "urn:oid:2.16.840.1.113883.6.61",
"code": substance_cas,
"display": substance
})
]
ingredient.itemCodeableConcept = ingredient_cc
ingredients.append(ingredient)
new_medication.ingredient = ingredients
# generate medication statement resources
id_value = str(self.data['encounter_psn']) + '_' + str(
self.data['procedure_nr']) + '_med_stat'
#id_value = f"{self.data['concat_elements']}-medication"
#id_value = sha256(id_value.encode('utf-8')).hexdigest()
medication_stm = medicationstatement.MedicationStatement()
medication_stm.id = id_value
medication_stm.identifier = [
identifier.Identifier({
"system": self.systems['med_stm_id'],
"value": id_value
})
]
med_meta = meta.Meta()
med_meta.source = "#sap-ish"
medication_stm.meta = med_meta
ref = {"reference": f"Medication/{new_medication.id}"}
medication_ref = fhirreference.FHIRReference(jsondict=ref)
medication_stm.medicationReference = medication_ref
medication_stm.context = encounter_ref
medication_stm.subject = patient_ref
#medication_stm.partOf =
medication_stm.status = "active"
if not pd.isna(self.data['admission_dt']):
med_period = period.Period()
med_period.start = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
if not pd.isna(self.data['discharge_dt']):
med_period.end = fhirdate.FHIRDate(
datetime.strftime(self.data['discharge_dt'],
'%Y-%m-%dT%H:%M:%S'))
medication_stm.status = "completed"
medication_stm.effectivePeriod = med_period
new_dosage = dosage.Dosage()
new_dosage.text = dosage_text
dose_range = range.Range()
if dosage_min != "NaN":
dose_range.low = quantity.Quantity({
"value":
float(dosage_min.replace(',', '.')),
"unit":
ucum_full,
"system":
"http://unitsofmeasure.org",
"code":
ucum_short
})
if dosage_max != "NaN":
dose_range.high = quantity.Quantity({
"value":
float(dosage_max.replace(',', '.')),
"unit":
ucum_full,
"system":
"http://unitsofmeasure.org",
"code":
ucum_short
})
dose_rate = dosage.DosageDoseAndRate()
dose_rate.doseRange = dose_range
new_dosage.doseAndRate = [dose_rate]
#method, route, site
medication_stm.dosage = [new_dosage]
return [new_medication, medication_stm]
def map(self):
try:
new_medication = []
medication_stm = []
#id_value = sha256(self.data['concat_elements'].encode('utf-8')).hexdigest()
id_value = str(self.data['encounter_psn']) + '_' + str(
self.data['procedure_nr'])
pat_procedure = mii_procedure.Procedure()
pat_procedure.id = id_value
pat_procedure.identifier = [
identifier.Identifier({
"system": self.systems['prod_id'],
"value": id_value
})
]
pat_procedure.status = "completed"
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
encounter_ref = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
patient_ref = fhirreference.FHIRReference(jsondict=ref)
pat_procedure.encounter = encounter_ref
pat_procedure.subject = patient_ref
category = mii_codeableconcept.CodeableConcept()
category.coding = [
mii_coding.Coding({
"system": "http://snomed.info/sct",
"code": "387713003"
})
]
pat_procedure.category = category
procedure_code = mii_codeableconcept.CodeableConcept()
procedure_code.coding = [
mii_coding.Coding({
"system": "http://fhir.de/CodeSystem/dimdi/ops",
"code": self.data['ops_kode'],
"version": self.data['ops_version']
})
]
pat_procedure.code = procedure_code
if self.data['ops_kode'][0] == '6':
[new_medication, medication_stm
] = self._map_dmpro2medi(encounter_ref, patient_ref)
if not pd.isna(self.data['ops_datum']):
ops_datum_fhir = datetime.strftime(self.data['ops_datum'],
'%Y-%m-%dT%H:%M:%S')
pat_procedure.performedDateTime = fhirdate.FHIRDate(
ops_datum_fhir)
if self.data['lokalisation']:
pat_procedure.bodySite = []
snomed_ver = "http://snomed.info/sct/900000000000207008/version/20200309"
if self.data['lokalisation'] == 'L' or self.data[
'lokalisation'] == 'B':
left_body_part = mii_codeableconcept.CodeableConcept()
left_body_part.coding = [
mii_coding.Coding({
"system": "http://snomed.info/sct",
"code": "31156008",
"display": '''Structure of left half
of body (body structure)''',
"version": snomed_ver
})
]
pat_procedure.bodySite.append(left_body_part)
if self.data['lokalisation'] == 'R' or self.data[
'lokalisation'] == 'B':
right_body_part = mii_codeableconcept.CodeableConcept()
right_body_part.coding = [
mii_coding.Coding({
"system": "http://snomed.info/sct",
"code": "85421007",
"display": '''Structure of right half
of body (body structure)''',
"version": snomed_ver
})
]
pat_procedure.bodySite.append(right_body_part)
pro_meta = meta.Meta()
pro_meta.source = "#sap-ish"
pat_procedure.meta = pro_meta
return [pat_procedure, new_medication, medication_stm]
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
def map(self, lufu_section):
try:
ops_code = 'No OPS Code'
ops_text = 'No OPS Code Text'
if lufu_section == 'B':
ops_code = '1-710'
ops_text = self.procedure_mapper.codeLookup(ops_code)
else:
ops_code = '1-71'
ops_text = self.procedure_mapper.codeLookup(ops_code)
id_value = sha256(
(str(lufu_section) +
self.data['concat_elements']).encode('utf-8')).hexdigest()
lufu_procedure = procedure.Procedure()
#lufu_procedure_system = ''
lufu_procedure_identifier = id_value
lufu_procedure.identifier = [
identifier.Identifier({
"use": "official",
"system": self.systems['prod_id'],
"value": lufu_procedure_identifier
})
]
lufu_procedure.id = id_value
lufu_procedure_identifier_perf_date = fhirdate.FHIRDate(
datetime.strftime(
datetime.strptime(self.data['untersuchungsdatum'],
'%d.%m.%Y %H:%M:%S'),
'%Y-%m-%dT%H:%M:%S'))
lufu_procedure.performedDateTime = lufu_procedure_identifier_perf_date
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
lufu_procedure.subject = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
lufu_procedure.encounter = fhirreference.FHIRReference(
jsondict=ref)
rep_code_system_cc = codeableconcept.CodeableConcept()
rep_code_system_cc.coding = [
coding.Coding({
"system":
"https://www.dimdi.de/static/de/klassifikationen/ops",
"code": ops_code,
"display": ops_text
})
]
rep_status = 'completed'
lufu_procedure.code = rep_code_system_cc
lufu_procedure.status = rep_status
return lufu_procedure
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
except Exception as exc:
self.logger.error(
f"In {__name__}: Error occurred in mapping ({exc})")
raise
def map(self):
try:
pat_encounter = mii_encounter_verfall.Encounter()
pat_encounter.id = self.data['encounter_psn']
identifier_type = mii_codeableconcept.CodeableConcept()
identifier_type.coding = [
mii_coding.Coding({
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "VN"
})
]
pat_encounter.identifier = [
mii_identifier.Identifier({
"use":
"usual",
"system":
self.systems['encounter_id'],
"value":
self.data['encounter_psn'],
"assigner": {
"reference": "Organization/1111"
},
"type":
identifier_type.as_json()
})
]
enc_class_system = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
pat_encounter.class_fhir = mii_coding.Coding({
"system":
enc_class_system,
"code":
"IMP",
"display":
"inpatient encounter"
})
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
pat_encounter.subject = fhirreference.FHIRReference(jsondict=ref)
enc_period = mii_period.Period()
pat_encounter.status = "in-progress"
if not pd.isna(self.data['admission_dt']):
enc_period.start = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
pat_encounter.period = enc_period
if not pd.isna(self.data['discharge_dt']):
enc_period.end = fhirdate.FHIRDate(
datetime.strftime(self.data['discharge_dt'],
'%Y-%m-%dT%H:%M:%S'))
pat_encounter.status = "finished"
pat_encounter.extension = []
if self.data['admission_reason']:
admission_reason_obj = self._admission_reason_lookup(
self.data['admission_reason'])
admission_reason_coding = mii_coding.Coding({
"system":
self.systems['admission_reason'],
"code":
self.data['admission_reason'],
"display":
admission_reason_obj[0]
})
admission_ext = extension.Extension({
"url":
self.systems['admission_reason_url'],
"valueCoding":
admission_reason_coding.as_json()
})
pat_encounter.extension.append(admission_ext)
if self.data['discharge_reason']:
discharge_reason_obj = self._discharge_reason_lookup(
self.data['discharge_reason'])
discharge_reason_cc = mii_codeableconcept.CodeableConcept()
discharge_reason_cc.coding = [
mii_coding.Coding({
"system":
self.systems['discharge_reason'],
"code":
self.data['discharge_reason'],
"display":
discharge_reason_obj[0]
})
]
discharge_ext = extension.Extension({
"url":
self.systems['discharge_reason_url'],
"valueCodeableConcept":
discharge_reason_cc.as_json()
})
pat_encounter.extension.append(discharge_ext)
discharge_dispo = mii_codeableconcept.CodeableConcept()
discharge_dispo_sys = "http://terminology.hl7.org/CodeSystem/discharge-disposition"
discharge_dispo.coding = [
mii_coding.Coding({
"system": discharge_dispo_sys,
"code": discharge_reason_obj[1],
"display": discharge_reason_obj[2]
})
]
hospitalization_encounter = mii_encounter_verfall.EncounterHospitalization(
)
hospitalization_encounter.dischargeDisposition = discharge_dispo
pat_encounter.hospitalization = hospitalization_encounter
diagnosis_use = mii_codeableconcept.CodeableConcept()
diag_use_sys = "http://terminology.hl7.org/CodeSystem/diagnosis-role"
diagnosis_use.coding = [
mii_coding.Coding({
"system": diag_use_sys,
"code": "billing"
})
]
if self.data['ranked_cond_ref']:
pat_encounter.diagnosis = []
for condition_ref in self.data['ranked_cond_ref']:
cond_diagnosis = mii_encounter_verfall.EncounterDiagnosis()
cond_diagnosis.condition = condition_ref[0]
cond_diagnosis.rank = condition_ref[1]
cond_diagnosis.use = diagnosis_use
pat_encounter.diagnosis.append(cond_diagnosis)
enc_meta = meta.Meta()
enc_meta.source = "#sap-ish"
pat_encounter.meta = enc_meta
return pat_encounter
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
def map(self):
try:
id_value = str(
self.data['result_id']
) #2sha256(self.data['concat_elements'].encode('utf-8')).hexdigest()
lab_observation = mii_observation.Observation()
lab_observation.id = id_value
identifier_type = mii_codeableconcept.CodeableConcept()
identifier_type.coding = [
mii_coding.Coding({
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR"
})
]
lab_observation.identifier = [
mii_identifier.Identifier({
"system": self.systems['lab_id'],
"value": id_value,
"assigner": {
"reference": "Organization/1111"
},
"type": identifier_type.as_json()
})
]
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
lab_observation.encounter = fhirreference.FHIRReference(
jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
lab_observation.subject = fhirreference.FHIRReference(jsondict=ref)
lab_observation.status = "final"
if not pd.isna(self.data['collect_ts']):
collect_ts_fhir = datetime.strftime(self.data['collect_ts'],
'%Y-%m-%dT%H:%M:%S')
lab_observation.effectiveDateTime = fhirdate.FHIRDate(
collect_ts_fhir)
if not pd.isna(self.data['value_num']):
if (self.data['loinc_code']
and self.data['loinc_code'] != 'noLoinc'
and self.data['value_unit']):
if self.data['value_unit'] == '10E12/L':
self.data['value_unit'] = '10*6/uL'
elif self.data['value_unit'] == '10E9/L':
self.data['value_unit'] = '10*3/uL'
elif self.data['value_unit'] == 'mE/l':
self.data['value_unit'] = 'm[IU]/L'
elif (self.data['value_unit'] == 'ug/l'
or self.data['value_unit'] == 'µg/l'):
self.data['value_unit'] = 'ng/mL'
if self.loinc_url:
result = self._convert_loinc()
#print(f"{self.data['loinc_code']} {self.data['value_num']} {self.data['value_unit']}")
#print(result)
if result and isinstance(
result, list) and not 'error' in result[0]:
if result[0]['loinc'] and result[0][
'value'] and result[0]['unit']:
self.data['loinc_code'] = result[0]['loinc']
self.data['value_num'] = result[0]['value']
self.data['value_unit'] = result[0]['unit']
self.data['value_unit'] = self.data[
'value_unit'].replace("'", "''")
#else:
# print(f"{self.data['loinc_code']} {self.data['value_num']} {self.data['value_unit']}")
# print(result)
if (self.data['value_comp'] == '!='
or self.data['value_comp'] == '='
or self.data['value_comp'] == '=='):
self.data['value_comp'] = None
lab_quantity = mii_quantity.Quantity({
"value":
self.data['value_num'],
"unit":
self.data['value_unit'],
"comparator":
self.data['value_comp'],
"system":
"http://unitsofmeasure.org",
"code":
self.data['value_unit']
})
lab_observation.valueQuantity = lab_quantity
elif self.data['value_text']:
lab_observation.valueString = self.data['value_text']
lab_code = codeableconcept.CodeableConcept()
lab_code.coding = [
coding.Coding({
"system": "http://loinc.org",
"code": self.data['loinc_code']
})
]
lab_observation.code = lab_code
if not pd.isna(self.data['ref_high_num']) and not pd.isna(
self.data['ref_low_num']):
reference_range = mii_observation.ObservationReferenceRange()
reference_range.high = quantity.Quantity({
"value":
self.data['ref_high_num'],
"unit":
self.data['value_unit'],
"system":
"http://unitsofmeasure.org",
"code":
self.data['value_unit']
})
reference_range.low = quantity.Quantity({
"value":
self.data['ref_low_num'],
"unit":
self.data['value_unit'],
"system":
"http://unitsofmeasure.org",
"code":
self.data['value_unit']
})
lab_observation.referenceRange = [reference_range]
lab_method = codeableconcept.CodeableConcept()
lab_method.coding = [
coding.Coding({
"system": "http://methodConcept",
"display": self.data['method']
})
]
lab_observation.method = lab_method
lab_meta = meta.Meta()
lab_meta.source = "#laboratory"
lab_observation.meta = lab_meta
lab_cat = mii_codeableconcept.CodeableConcept()
lab_cat_sys = "http://terminology.hl7.org/CodeSystem/observation-category"
lab_cat.coding = [
mii_coding.Coding({
"system": lab_cat_sys,
"display": "Laboratory",
"code": "laboratory"
})
]
lab_observation.category = lab_cat
#lab_annotation = annotation_model.Annotation({"text": note})
#lab_observation.note = [lab_annotation]
if self.data['int_flag']:
if self.data['int_flag'] == "N":
int_flag_long = "Normal"
elif self.data['int_flag'] == "L":
int_flag_long = "Low"
elif self.data['int_flag'] == "H":
int_flag_long = "High"
else:
int_flag_long = "Unknown"
lab_interpretation = codeableconcept.CodeableConcept()
lab_int_sys = "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"
lab_interpretation.coding = [
coding.Coding({
"system": lab_int_sys,
"code": self.data['int_flag'],
"display": int_flag_long
})
]
lab_observation.interpretation = [lab_interpretation]
return lab_observation
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
except FHIRValidationError:
raise
def map(self):
try:
id_value = str(self.data['encounter_psn']) + '_' + str(
self.data['diagnosis_nr'])
#sha256(self.data['concat_elements'].encode('utf-8')).hexdigest()
icd_condition = mii_condition.Condition()
icd_condition.id = id_value
icd_condition.identifier = [
identifier.Identifier({
"system": self.systems['condition_id'],
"value": id_value
})
]
clinic_status = codeableconcept.CodeableConcept()
clinic_status.coding = [
coding.Coding({
"system":
"http://terminology.hl7.org/CodeSystem/condition-clinical",
"code": "active"
})
]
icd_condition.clinicalStatus = clinic_status
full_code = self.data['code']
if self.data['sec_code']:
full_code = self.data['code'] + " " + self.data['sec_code']
condition_coding = mii_coding.Coding()
condition_coding.system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm"
condition_coding.code = full_code
condition_coding.version = self.data['code_ver']
if self.data['sec_code']:
main_cross_ext = extension.Extension()
main_cross_ext.url = "http://fhir.de/StructureDefinition/icd-10-gm-haupt-kreuz"
main_cross_ext.valueCoding = coding.Coding({
"system":
condition_coding.system,
"version":
self.data['code_ver'],
"code":
re.sub(r"[+†]", "", self.data['code'])
})
condition_coding.extension = [main_cross_ext]
if '!' in self.data['sec_code']:
excl_ext = extension.Extension()
excl_ext.url = "http://fhir.de/StructureDefinition/icd-10-gm-ausrufezeichen"
excl_ext.valueCoding = coding.Coding({
"system":
condition_coding.system,
"version":
self.data['code_ver'],
"code":
re.sub(r"!", "", self.data['sec_code'])
})
condition_coding.extension.append(excl_ext)
if '*' in self.data['sec_code']:
star_ext = extension.Extension()
star_ext.url = "http://fhir.de/StructureDefinition/icd-10-gm-stern"
star_ext.valueCoding = coding.Coding({
"system":
condition_coding.system,
"version":
self.data['code_ver'],
"code":
re.sub(r"\*", "", self.data['sec_code'])
})
condition_coding.extension.append(star_ext)
condition_code = mii_codeableconcept.CodeableConcept()
condition_code.coding = [condition_coding]
icd_condition.code = condition_code
# todo: what value of the data mart should be mapped?
icd_condition.onsetString = '2002-01-01'
ref = {"reference": f"Encounter/{self.data['encounter_psn']}"}
icd_condition.encounter = fhirreference.FHIRReference(jsondict=ref)
ref = {"reference": f"Patient/{self.data['patient_psn']}"}
icd_condition.subject = fhirreference.FHIRReference(jsondict=ref)
if not pd.isna(self.data['admission_dt']):
icd_condition.recordedDate = fhirdate.FHIRDate(
datetime.strftime(self.data['admission_dt'],
'%Y-%m-%dT%H:%M:%S'))
if self.data['loc']:
icd_condition.bodySite = []
if self.data['loc'] == "L" or self.data['loc'] == "B":
left_body_part = mii_codeableconcept.CodeableConcept()
icd_loc_sys = "http://fhir.de/CodeSystem/kbv/s_icd_seitenlokalisation"
left_body_part.coding = [
mii_coding.Coding({
"system": icd_loc_sys,
"code": "L",
"display": "links"
})
]
icd_condition.bodySite.append(left_body_part)
if self.data['loc'] == "R" or self.data['loc'] == "B":
right_body_part = mii_codeableconcept.CodeableConcept()
icd_loc_sys = "http://fhir.de/CodeSystem/kbv/s_icd_seitenlokalisation"
right_body_part.coding = [
mii_coding.Coding({
"system": icd_loc_sys,
"code": "R",
"display": "rechts"
})
]
icd_condition.bodySite.append(right_body_part)
rank = 2
if self.data['diag_type'] == 1:
rank = 1
icd_meta = meta.Meta()
icd_meta.source = "#sap-ish"
icd_condition.meta = icd_meta
return [icd_condition, rank]
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise
def map(self):
try:
inpatient = mii_patient.Patient()
inpatient.id = self.data['patient_psn']
identifier_type = mii_codeableconcept.CodeableConcept()
identifier_type.coding = [
mii_coding.Coding({
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR"
})
]
inpatient.identifier = [
mii_identifier_pat.Identifier({
"use":
"official",
"system":
self.systems['patient_id'],
"value":
self.data['patient_psn'],
"assigner": {
"reference": "Organization/1111"
},
"type":
identifier_type.as_json()
})
]
if self.data['insurance_id']:
insurance_id_type = mii_codeableconcept.CodeableConcept()
insurance_type_sys = "http://fhir.de/CodeSystem/identifier-type-de-basis"
insurance_id_type.coding = [
mii_coding.Coding({
"system":
insurance_type_sys,
"code":
"GKV",
"display":
"Gesetzliche Krankenversicherung"
})
]
gkv_sys = "http://fhir.de/NamingSystem/gkv/kvid-10"
identifier_type.coding = [
mii_coding.Coding({
"system":
"http://fhir.de/CodeSystem/identifier-type-de-basi",
"code": "GKV"
})
]
inpatient.identifier.append(
mii_identifier_pat.Identifier({
"use":
"official",
"system":
gkv_sys,
"type":
insurance_id_type.as_json(),
"value":
self.data['insurance_id'],
"assigner": {
"reference": "Organization/1111"
}
}))
if self.data['gender'] == 'm':
gender_code = "male"
elif self.data['gender'] == 'w':
gender_code = "female"
elif self.data['gender'] == 'x':
gender_code = "other"
else:
gender_code = "unknown"
inpatient.gender = gender_code
inpatient.birthDate = fhirdate.FHIRDate(
str(self.data['birth_date']))
inpatient.deceasedBoolean = False
if self.data['deceased_flag']:
inpatient.deceasedBoolean = True
inpatient.address = mii_address.Address({
"city":
self.data['city'],
"postalCode":
self.data['postal_code'],
"line":
self.data['street'],
"country":
self.data['country'],
"type":
""
})
inpatient.name = [
mii_humanname.HumanName({
"use": 'official',
"family": self.data['family_name'],
"given": [self.data['given_name']]
})
]
pat_meta = meta.Meta()
pat_meta.source = "#sap-ish"
inpatient.meta = pat_meta
return inpatient
except KeyError as exc:
self.logger.error(
f"In {__name__}: Key {exc} not found in dictionary")
raise