test_commands.py

import pytest
import argparse
from unittest.mock import patch, MagicMock

import trud
import omop
import phen
from pathlib import Path
from acmc import trud_install, omop_install, omop_clear, omop_delete, phen_init, phen_validate, phen_map, phen_publish, phen_copy, phen_diff

def test_trud_install():
    with patch("trud.install") as mock_install:
        args = argparse.Namespace(api_key="test_key")
        trud_install(args)
        mock_install.assert_called_once_with("test_key")

def test_omop_install():
    with patch("omop.install") as mock_install:
        args = argparse.Namespace(omop_folder="/path/to/omop")
        omop_install(args)
        mock_install.assert_called_once_with(omop.OMOP_DB_PATH, "/path/to/omop")

def test_omop_clear():
    with patch("omop.clear") as mock_clear:
        args = argparse.Namespace()
        omop_clear(args)
        mock_clear.assert_called_once_with(omop.OMOP_DB_PATH)

def test_omop_delete():
    with patch("omop.delete") as mock_delete:
        args = argparse.Namespace()
        omop_delete(args)
        mock_delete.assert_called_once_with(omop.OMOP_DB_PATH)

def test_phen_init():
    with patch("phen.init") as mock_init:
        args = argparse.Namespace(phen_dir="/path/to/phen")
        phen_init(args)
        mock_init.assert_called_once_with("/path/to/phen")

def test_phen_validate():
    with patch("phen.validate") as mock_validate:
        args = argparse.Namespace(phen_dir="/path/to/phen")
        phen_validate(args)
        mock_validate.assert_called_once_with("/path/to/phen")

def test_phen_map():
    with patch("phen.map") as mock_map:
        args = argparse.Namespace(phen_dir="/path/to/phen", target_coding="icd10_code", translate=True, verify=True)
        phen_map(args)
        mock_map.assert_called_once_with("/path/to/phen", "icd10_code", True, True)

def test_phen_publish():
    with patch("phen.publish") as mock_publish:
        args = argparse.Namespace(phen_dir="/path/to/phen")
        phen_publish(args)
        mock_publish.assert_called_once_with("/path/to/phen")

def test_phen_copy():
    with patch("phen.copy") as mock_copy:
        args = argparse.Namespace(phen_dir="/path/to/phen", target_dir="/path/to/target", version="1.0")
        phen_copy(args)
        mock_copy.assert_called_once_with("/path/to/phen", "/path/to/target", "1.0")

def test_phen_diff():
    with patch("phen.diff") as mock_diff:
        args = argparse.Namespace(phen_dir="/path/to/phen", phen_dir_old="/path/to/old_phen")
        phen_diff(args)
        mock_diff.assert_called_once_with("/path/to/phen", "/path/to/old_phen")

def test_phen_local():
    with patch("phen.diff") as mock_diff:
        args = argparse.Namespace(phen_dir="/path/to/phen", phen_dir_old="/path/to/old_phen")
        phen_diff(args)
        mock_diff.assert_called_once_with("/path/to/phen", "/path/to/old_phen")