Python dateparser Examples

Example #1

File: etl.py Project: lifeomic/fhir-petl

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)

Example #2

        '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))

Example #3

File: etl.py Project: mattphillipsphd/fhir-petl

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)

Example #4

File: etl.py Project: lifeomic/fhir-petl

def sample_date(text):
    parser = dateparser("%m/%d/%y %H:%M", ISOFormat.DAY)
    return parser(text)

Example #5

File: etl.py Project: lifeomic/fhir-petl

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",

Example #6

File: util_test.py Project: mattphillipsphd/fhir-petl

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'

Example #7

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