def test_serializer_with_record_id():
data_dictionary = [{
"field_name": "patient_id",
"form_name": "demographics",
"field_type": "text"
}, {
"field_name":
"gender",
"form_name":
"demographics",
"field_type":
"radio",
"choices":
"1, female | 2, male | 3, unknown | 4, unspecified | 5, not reported"
}]
data_dictionary = [
RedcapField.from_json(field) for field in data_dictionary
]
project_info = {
'secondary_unique_field': [],
'record_autonumbering_enabled': 0,
'next_record_name': 1,
'repeatable_instruments': [],
}
records = [{
"patient_id": "123",
"gender": "male"
}, {
"patient_id": "456",
"gender": "female"
}]
records = pd.DataFrame(records)
records.fillna('', inplace=True)
encoded_rows = serializer.encode_sheet(data_dictionary, project_info,
records)
encoded_rows = encoded_rows.sort_index(axis=1)
d = {
'patient_id': ["123", "456"],
'redcap_repeat_instrument': ['', ''],
'redcap_repeat_instance': ['', ''],
'gender': ['2', '1']
}
expected = pd.DataFrame(data=d)
expected = expected.sort_index(axis=1)
assert len(encoded_rows) == 2
assert_frame_equal(encoded_rows, expected, check_dtype=False)
def test_serializer_with_repeatable_instrument_and_matching_repeat_instances():
data_dictionary = [
{
"field_name": "patient_id",
"form_name": "demographics",
"field_type": "text"
},
{
"field_name":
"gender",
"form_name":
"demographics",
"field_type":
"radio",
"choices":
"1, female | 2, male | 3, unknown | 4, unspecified | 5, not reported"
},
{
"field_name": "treatment_dx",
"form_name": "treatment",
"field_type": "text",
},
{
"field_name": "treatment",
"form_name": "treatment",
"field_type": "radio",
"choices": "1, chemotherapy | 2, immunotherapy"
},
]
data_dictionary = [
RedcapField.from_json(field) for field in data_dictionary
]
project_info = {
'secondary_unique_field': [],
'record_autonumbering_enabled': 0,
'next_record_name': 1,
'repeatable_instruments': ['treatment'],
}
records = [{
"patient_id": "123",
"gender": "male",
"treatment_dx": "2018-09-01",
"treatment": "chemotherapy"
}, {
"patient_id": "123",
"gender": "male",
"treatment_dx": "2019-09-01",
"treatment": "immunotherapy"
}]
records = pd.DataFrame(records)
records.fillna('', inplace=True)
options = {'matching_repeat_instances': {'0': {'treatment': 7}}}
encoded_rows = serializer.encode_sheet(data_dictionary, project_info,
records, options)
encoded_rows = encoded_rows.sort_index(axis=1)
d = {
'patient_id': ['123', '123', '123'],
'redcap_repeat_instrument': ['', 'treatment', 'treatment'],
'redcap_repeat_instance': ['', 7, 2],
'gender': ['2', '', ''],
'treatment': ['', '1', '2'],
'treatment_dx': ['', '2018-09-01', '2019-09-01']
}
expected = pd.DataFrame(data=d)
expected = expected.sort_index(axis=1)
assert len(encoded_rows) == 3
assert_frame_equal(encoded_rows,
expected,
check_dtype=False,
check_like=True)