def cv_value(rec):
values = []
# if rec["CV_RESULT_NUMERIC"]:
# return number(rec["CV_RESULT_NUMERIC"])
if rec["VALUE_TYPE"] == "valueQuantity":
if rec["VALUE"] not in [0, "0", "", None]:
return (
number(rec["VALUE"].strip()),
rec["UCUM_TYPE"],
"http://unitsofmeasure.org",
rec["UCUM_CODE"],
)
else:
return number(rec["VALUE"])
elif rec["VALUE_TYPE"] == "vcc_custom":
codified_value = rec["VALUE"].strip().replace(" ", "_").upper()
values.append(
(
"http://lifeomic.com/ktb/value/" + codified_value, # system
codified_value, # code
rec["VALUE"], # display
)
)
return values
elif rec["VALUE_TYPE"] == "vcc_custom_ynunk":
return map_ynunk(rec["VALUE"])
else:
return rec["VALUE"]
.select('DX_CODE', lambda x: x)
.fieldmap({
'id': 'ID',
'onset': lambda rec: rec['index_date'] + timedelta(int(rec['DAYS_ADM_INDEX'])),
'code': lambda rec: ('http://hl7.org/fhir/sid/icd-9-cm', rec['DX_CODE']),
'note': lambda rec: join(rec['CARE_SETTING_TEXT'], rec['LOCATION_POINT_OF_CARE']),
'subject': 'subject'
}, True))
observations = (etl.io.csv.fromcsv(resolve('work/Observation.csv'))
.hashjoin(index, lkey='STUDYID', rkey='STUDYID')
.fieldmap({
'id': 'ID',
'date': lambda rec: rec['index_date'] + timedelta(int(rec['DAYS_VIS_INDEX'])),
'code': lambda rec: ('lab-text', rec['NAME'], rec['NAME']),
'value': lambda rec: number(rec['RESULT_VALUE']) if rec['RESULT_VALUE'] else (rec['CODED_NAME'] or None),
'subject': 'subject'
}, True)
.select('value', lambda x: x))
def medications(rec):
group = rec['DRUG_GROUP'].strip('*')
clazz = rec['DRUG_CLASS'].strip('*')
return [
('http://hl7.org/fhir/sid/ndc', rec['NDC_CODE'], rec['DRUG_NAME']),
('urn:oid:2.16.840.1.113883.6.68', rec['GPI_CODE'], rec['DRUG_NAME']),
('drug-class', clazz, clazz),
('drug-group', group, group)
]
med_dispenses = (etl.io.csv.fromcsv(resolve('work/MedicationDispense.csv'))
def index_date(rec):
birth = number(rec['BIRTH_YR'])
index_age = number(rec['INDEX_AGE'])
index_date = str(birth + index_age)
return dateparser('%Y', ISOFormat.DAY)(index_date)
'subject':
'subject'
}, True))
observations = (etl.io.csv.fromcsv(resolve('work/Observation.csv')).hashjoin(
index, lkey='CONTROL_ID', rkey='CONTROL_ID'
).fieldmap(
{
'id':
'ID',
'date':
lambda rec: rec['index_date'] + timedelta(int(rec['DAYS_VIS_INDEX'])),
'code':
lambda rec: ('lab-text', rec['NAME'], rec['NAME']),
'value':
lambda rec: number(rec['RESULT_VALUE']) if rec['RESULT_VALUE'] else
(rec['CODED_NAME'] or None),
'subject':
'subject'
}, True).select('value', lambda x: x))
def medications(rec):
group = rec['DRUG_GROUP'].strip('*')
clazz = rec['DRUG_CLASS'].strip('*')
return [('http://hl7.org/fhir/sid/ndc', rec['NDC_CODE'], rec['DRUG_NAME']),
('urn:oid:2.16.840.1.113883.6.68', rec['GPI_CODE'],
rec['DRUG_NAME']), ('drug-class', clazz, clazz),
('drug-group', group, group)]
def cv_value(rec):
if rec['CV_RESULT_NUMERIC']:
return number(rec['CV_RESULT_NUMERIC'])
return rec['CV_RESULT_CATEGORICAL'] or None