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from __future__ import absolute_import, print_function, division
from collections import OrderedDict
from petl.test.failonerror import assert_failonerror
from petl.test.helpers import ieq
from petl.transform.maps import fieldmap, rowmap, rowmapmany
from functools import partial
def test_fieldmap():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65, 51.9))
mappings = OrderedDict()
mappings['subject_id'] = 'id'
mappings['gender'] = 'sex', {'male': 'M', 'female': 'F'}
mappings['age_months'] = 'age', lambda v: v * 12
mappings['bmi'] = lambda rec: rec['weight'] / rec['height'] ** 2
actual = fieldmap(table, mappings)
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2),
(5, '-', 25 * 12, 51.9 / 1.65 ** 2))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
# do it with suffix
actual = fieldmap(table)
actual['subject_id'] = 'id'
actual['gender'] = 'sex', {'male': 'M', 'female': 'F'}
actual['age_months'] = 'age', lambda v: v * 12
actual['bmi'] = '{weight} / {height}**2'
ieq(expect, actual)
# test short rows
table2 = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65))
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2),
(5, '-', 25 * 12, None))
actual = fieldmap(table2, mappings)
ieq(expect, actual)
def test_fieldmap_record_access():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65, 51.9))
mappings = OrderedDict()
mappings['subject_id'] = 'id'
mappings['gender'] = 'sex', {'male': 'M', 'female': 'F'}
mappings['age_months'] = 'age', lambda v: v * 12
mappings['bmi'] = lambda rec: rec.weight / rec.height ** 2
actual = fieldmap(table, mappings)
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2),
(5, '-', 25 * 12, 51.9 / 1.65 ** 2))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
def test_fieldmap_empty():
table = (('foo', 'bar'),)
expect = (('foo', 'baz'),)
mappings = OrderedDict()
mappings['foo'] = 'foo'
mappings['baz'] = 'bar', lambda v: v * 2
actual = fieldmap(table, mappings)
ieq(expect, actual)
def test_fieldmap_headerless():
table = []
expect = []
mappings = OrderedDict()
mappings['foo'] = 'foo'
mappings['baz'] = 'bar', lambda v: v * 2
actual = fieldmap(table, mappings)
ieq(expect, actual)
def test_fieldmap_failonerror():
input_ = (('foo',), ('A',), (1,))
mapper_ = {'bar': ('foo', lambda v: v.lower())}
expect_ = (('bar',), ('a',), (None,))
assert_failonerror(
input_fn=partial(fieldmap, input_, mapper_),
expected_output=expect_)
def test_rowmap():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65, 51.9))
def rowmapper(row):
transmf = {'male': 'M', 'female': 'F'}
return [row[0],
transmf[row[1]] if row[1] in transmf else row[1],
row[2] * 12,
row[4] / row[3] ** 2]
actual = rowmap(table, rowmapper, header=['subject_id', 'gender',
'age_months', 'bmi'])
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2),
(5, '-', 25 * 12, 51.9 / 1.65 ** 2))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
# test short rows
table2 = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65))
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2))
actual = rowmap(table2, rowmapper, header=['subject_id', 'gender',
'age_months', 'bmi'])
ieq(expect, actual)
def test_rowmap_empty():
table = (('id', 'sex', 'age', 'height', 'weight'),)
def rowmapper(row):
transmf = {'male': 'M', 'female': 'F'}
return [row[0],
transmf[row[1]] if row[1] in transmf else row[1],
row[2] * 12,
row[4] / row[3] ** 2]
actual = rowmap(table, rowmapper, header=['subject_id', 'gender',
'age_months', 'bmi'])
expect = (('subject_id', 'gender', 'age_months', 'bmi'),)
ieq(expect, actual)
def test_rowmap_headerless():
table = []
def rowmapper(row):
return row
actual = rowmap(table, rowmapper, header=['subject_id', 'gender'])
expect = []
ieq(expect, actual)
def test_rowmap_failonerror():
input_ = (('foo',), ('A',), (1,), ('B',))
mapper = lambda r: [r[0].lower()]
# exceptions in rowmappers do not generate an output row
expect_ = (('foo',), ('a',), ('b',))
assert_failonerror(
input_fn=partial(rowmap, input_, mapper, header=('foo',)),
expected_output=expect_)
def test_recordmap():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65, 51.9))
def recmapper(rec):
transmf = {'male': 'M', 'female': 'F'}
return [rec['id'],
transmf[rec['sex']] if rec['sex'] in transmf else rec['sex'],
rec['age'] * 12,
rec['weight'] / rec['height'] ** 2]
actual = rowmap(table, recmapper, header=['subject_id', 'gender',
'age_months', 'bmi'])
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2),
(5, '-', 25 * 12, 51.9 / 1.65 ** 2))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
# test short rows
table2 = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65))
expect = (('subject_id', 'gender', 'age_months', 'bmi'),
(1, 'M', 16 * 12, 62.0 / 1.45 ** 2),
(2, 'F', 19 * 12, 55.4 / 1.34 ** 2),
(3, 'F', 17 * 12, 74.4 / 1.78 ** 2),
(4, 'M', 21 * 12, 45.2 / 1.33 ** 2))
actual = rowmap(table2, recmapper, header=['subject_id', 'gender',
'age_months', 'bmi'])
ieq(expect, actual)
def test_rowmapmany():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, '-', 17, 1.78, 74.4),
(4, 'male', 21, 1.33))
def rowgenerator(row):
transmf = {'male': 'M', 'female': 'F'}
yield [row[0], 'gender',
transmf[row[1]] if row[1] in transmf else row[1]]
yield [row[0], 'age_months', row[2] * 12]
yield [row[0], 'bmi', row[4] / row[3] ** 2]
actual = rowmapmany(table, rowgenerator, header=['subject_id', 'variable',
'value'])
expect = (('subject_id', 'variable', 'value'),
(1, 'gender', 'M'),
(1, 'age_months', 16 * 12),
(1, 'bmi', 62.0 / 1.45 ** 2),
(2, 'gender', 'F'),
(2, 'age_months', 19 * 12),
(2, 'bmi', 55.4 / 1.34 ** 2),
(3, 'gender', '-'),
(3, 'age_months', 17 * 12),
(3, 'bmi', 74.4 / 1.78 ** 2),
(4, 'gender', 'M'),
(4, 'age_months', 21 * 12))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
def test_rowmapmany_failonerror():
input_ = (('foo',), ('A',), (1,), ('B',))
mapper = lambda r: [r[0].lower()]
expect_ = (('foo',), ('a',), ('b',),)
assert_failonerror(
input_fn=partial(rowmapmany, input_, mapper, header=('foo',)),
expected_output=expect_)
def test_recordmapmany():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, '-', 17, 1.78, 74.4),
(4, 'male', 21, 1.33))
def rowgenerator(rec):
transmf = {'male': 'M', 'female': 'F'}
yield [rec['id'], 'gender',
transmf[rec['sex']] if rec['sex'] in transmf else rec['sex']]
yield [rec['id'], 'age_months', rec['age'] * 12]
yield [rec['id'], 'bmi', rec['weight'] / rec['height'] ** 2]
actual = rowmapmany(table, rowgenerator, header=['subject_id', 'variable',
'value'])
expect = (('subject_id', 'variable', 'value'),
(1, 'gender', 'M'),
(1, 'age_months', 16 * 12),
(1, 'bmi', 62.0 / 1.45 ** 2),
(2, 'gender', 'F'),
(2, 'age_months', 19 * 12),
(2, 'bmi', 55.4 / 1.34 ** 2),
(3, 'gender', '-'),
(3, 'age_months', 17 * 12),
(3, 'bmi', 74.4 / 1.78 ** 2),
(4, 'gender', 'M'),
(4, 'age_months', 21 * 12))
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
def test_recordmapmany_headerless():
table = []
def duplicate(rec):
yield rec
yield rec
actual = rowmapmany(table, duplicate, header=['subject_id', 'variable'])
expect = []
ieq(expect, actual)
ieq(expect, actual) # can iteratate twice?
def test_fieldmap_untrusted():
table = (('id', 'sex', 'age', 'height', 'weight'),
(1, 'male', 16, 1.45, 62.0),
(2, 'female', 19, 1.34, 55.4),
(3, 'female', 17, 1.78, 74.4),
(4, 'male', 21, 1.33, 45.2),
(5, '-', 25, 1.65, 51.9))
expect = (('subject_id', 'bmi'),
(1, 62.0 / 1.45 ** 2),
(2, 55.4 / 1.34 ** 2),
(3, 74.4 / 1.78 ** 2),
(4, 45.2 / 1.33 ** 2),
(5, 51.9 / 1.65 ** 2))
# do it with suffix
actual = fieldmap(table, trusted=True)
actual['subject_id'] = 'id'
actual['bmi'] = '{weight} / {height}**2'
ieq(expect, actual)
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