test_bpc_redcap_export_mapping.py

import pytest
from unittest import mock

import pandas as pd
import synapseclient

from geniesp import bpc_redcap_export_mapping as bpc_export


@pytest.fixture
def mock_syn():
    yield mock.Mock(spec=synapseclient.Synapse)


def test_that_get_drug_variable_names_gets_expected_list():
    var_names = bpc_export.get_drug_variable_names()
    assert var_names == [
        "drugs_drug_1",
        "drugs_drug_oth1",
        "drugs_drug_2",
        "drugs_drug_oth2",
        "drugs_drug_3",
        "drugs_drug_oth3",
        "drugs_drug_4",
        "drugs_drug_oth4",
        "drugs_drug_5",
        "drugs_drug_oth5",
    ]


def test_get_mapping_data_calls_grs_if_use_grs_is_true(mock_syn):
    with mock.patch.object(mock_syn, "get") as mock_get, mock.patch.object(
        pd, "read_csv"
    ):
        bpc_export.get_mapping_data(
            syn=mock_syn, synid_file_grs="synGRS", synid_file_dd="synDD", use_grs=True
        )
        mock_get.assert_called_with("synGRS")


def test_get_mapping_data_calls_dd_if_use_grs_is_false(mock_syn):
    with mock.patch.object(mock_syn, "get") as mock_get, mock.patch.object(
        pd, "read_csv"
    ):
        bpc_export.get_mapping_data(
            syn=mock_syn, synid_file_grs="synGRS", synid_file_dd="synDD", use_grs=False
        )
        mock_get.assert_called_with("synDD")


@pytest.mark.parametrize(
    "input_mapping, var_names, output_mapping",
    [
        (
            pd.DataFrame(
                {
                    "Variable / Field Name": ["drugs_drug_1", "drugs_drug_2"],
                    "Choices, Calculations, OR Slider Labels": [
                        "D001, Aspirin | D002, Ibuprofen | D003, Paracetamol",
                        "D004, Tylenol |",
                    ],
                }
            ),
            ["drugs_drug_1", "drugs_drug_2"],
            {
                "Aspirin": "D001",
                "Ibuprofen": "D002",
                "Paracetamol": "D003",
                "Tylenol": "D004",
            },
        ),
        (
            pd.DataFrame(
                {
                    "Variable / Field Name": ["drugs_drug_1"],
                    "Choices, Calculations, OR Slider Labels": ["D001, Aspirin|"],
                }
            ),
            ["drugs_drug_1"],
            {"Aspirin": "D001"},
        ),
        (
            pd.DataFrame(
                {
                    "Variable / Field Name": ["ethnicity"],
                    "Choices, Calculations, OR Slider Labels": ["1"],
                }
            ),
            ["drugs_drug_1"],
            {},
        ),
        (
            pd.DataFrame(
                {
                    "Variable / Field Name": ["drugs_drug_1"],
                    "Choices, Calculations, OR Slider Labels": [
                        "D001, Aspirin (alternative) | D002, Ibuprofen | D003, Paracetamol"
                    ],
                    "extra_column" : ["test1"]
                }
            ),
            ["drugs_drug_1"],
            {"Aspirin": "D001", "Ibuprofen": "D002", "Paracetamol": "D003"},
        ),
    ],
    ids=[
        "multiple_drug_vars",
        "empty_split",
        "nothing_to_parse",
        "parenthesis_split",
    ],
)
def test_that_parse_drug_mappings(input_mapping, var_names, output_mapping):
    result = bpc_export.parse_drug_mappings(mapping=input_mapping, var_names=var_names)
    assert result == output_mapping