def parse_date(text, month=None, day=None, complete_date_bool=False):
if len(text) == 5:
dt = datetime.fromordinal(
datetime(1900, 1, 1).toordinal() + int(text) - 2
).date()
parser = dateparser("%Y-%m-%d", ISOFormat.DAY)
date_string = str(dt)
elif len(text) < 4:
return None
elif month and day and text:
parser = dateparser("%m/%d/%Y", ISOFormat.DAY)
date_string = "{0}/{1}/{2}".format(month, day, text)
elif day and text:
parser = dateparser("%Y", ISOFormat.YEAR)
date_string = "{0}".format(text)
elif month and text and not day:
parser = dateparser("%m/%Y", ISOFormat.MONTH)
date_string = "{0}/{1}".format(month, text)
elif not complete_date_bool:
parser = dateparser("%Y", ISOFormat.YEAR)
date_string = "{0}".format(text)
else:
parser = dateparser("%m/%d/%Y", ISOFormat.DAY)
date_string = "{0}".format(text)
return parser(date_string)
'ASIAN': ('http://hl7.org/fhir/v3/Race', '2028-9', 'Asian'),
'BLACK OR AFRICAN AMERICAN': ('http://hl7.org/fhir/v3/Race', '2054-5', 'Black or African American'),
'HISPANIC OR LATINO': ('http://hl7.org/fhir/v3/Race', '2106-3', 'White'),
'WHITE': ('http://hl7.org/fhir/v3/Race', '2106-3', 'White'),
'NATIVE HAWAIIAN AND OTHER PACIFIC ISLANDER': ('http://hl7.org/fhir/v3/Race', '2076-8', 'Native Hawaiian or Other Pacific Islander')
}.get(race, None)
patients = (etl.io.csv.fromcsv(resolve('work/Patient.csv'))
.fieldmap({
'id': 'ID',
'STUDYID': 'STUDYID',
'subject_id': ('STUDYID', lambda x: 'CASE-' + x),
'race': ('RACE', map_race),
'gender': ('SEX', {'F': 'female', 'M': 'male'}),
'birth_date': ('BIRTH_YR', year),
'index_date': ('INDEX_YEAR', dateparser('%Y', ISOFormat.DAY)),
'tag': lambda rec: ('subject-type', 'case')
}, True))
index = (patients
.cut('STUDYID', 'id', 'index_date')
.rename('id', 'subject'))
procedures = (etl.io.csv.fromcsv(resolve('work/Procedure.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: ('http://www.ama-assn.org/go/cpt', rec['PROC_CODE'], rec['NAME'].strip('" ')),
'subject': 'subject'
}, True))
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)
def sample_date(text):
parser = dateparser("%m/%d/%y %H:%M", ISOFormat.DAY)
return parser(text)
from datetime import timedelta
import petl as etl
import math
from fhir_petl.fhir import to_json
from fhir_petl.util import resolve, mkdirp, number, year, dateparser, ISOFormat
from datetime import datetime
date = dateparser("%m/%d/%y", ISOFormat.DAY)
def map_race(race):
return {
"Asian": ("http://hl7.org/fhir/v3/Race", "2028-9", "Asian"),
"Black": ("http://hl7.org/fhir/v3/Race", "2054-5", "Black or African American"),
"African American": (
"http://hl7.org/fhir/v3/Race",
"2054-5",
"Black or African American",
),
"White": ("http://hl7.org/fhir/v3/Race", "2106-3", "White"),
"Other": ("http://hl7.org/fhir/v3/Race", "2131-1", "Other Race"),
"Unknown": ("http://hl7.org/fhir/v3/NullFlavor", "UNK", "Unknown"),
"Native American / Alaskan": (
"http://hl7.org/fhir/v3/Race",
"1002-5",
"American Indian or Alaska Native",
),
"Native Hawaiian / Pacific Islander": (
"http://hl7.org/fhir/v3/Race",
"2076-8",
"Native Hawaiian or Other Pacific Islander",
def test_dateparser():
year = util.dateparser('%Y', util.ISOFormat.YEAR)
assert year('1994').isoformat() == '1994'
second = util.dateparser('%Y', util.ISOFormat.SECOND)
assert second('1994').isoformat() == '1994-01-01T00:00:00'
from datetime import timedelta
import petl as etl
from fhir_petl.fhir import to_json
from fhir_petl.util import resolve, mkdirp, number, year, dateparser, ISOFormat
date = dateparser('%Y-%m-%d %H:%M:%S', ISOFormat.DAY)
def map_race(race):
return {
'ASIAN': ('http://hl7.org/fhir/v3/Race', '2028-9', 'Asian'),
'BLACK':
('http://hl7.org/fhir/v3/Race', '2054-5', 'Black or African American'),
'HISPANIC/LATINO': ('http://hl7.org/fhir/v3/Race', '2106-3', 'White'),
'WHITE': ('http://hl7.org/fhir/v3/Race', '2106-3', 'White'),
'NATIVE HAWAIIAN/PACIFIC ISLANDER':
('http://hl7.org/fhir/v3/Race', '2076-8',
'Native Hawaiian or Other Pacific Islander')
}.get(race, None)
def sample_date(text):
parser = dateparser('%m/%d/%y %H:%M', ISOFormat.DAY)
return parser(text)
def birth_date(rec):
sample_age = timedelta(int(rec['Age (Sample)']) * 365.25)
return sample_date(rec['SAMPLE_DATE']) - sample_age