test_acmc.py

import pytest
import argparse
import sys
import shutil
import logging
from pathlib import Path

from acmc import trud, omop, main, logging_config as lc

# setup logging
lc.setup_logger()


@pytest.fixture
def tmp_dir():
    # Setup tmp directory
    temp_dir = Path("./tests/tmp")
    temp_dir.mkdir(parents=True, exist_ok=True)

    # Yield the directory path to the test function
    yield temp_dir

    # Remove the directory after the test finishes
    shutil.rmtree(temp_dir)


@pytest.fixture
def logger():
    logger = logging.getLogger("acmc_logger")
    logger.setLevel(logging.DEBUG)
    stream_handler = logging.StreamHandler(sys.stdout)
    logger.addHandler(stream_handler)


def test_phen_init_local_specified(tmp_dir, monkeypatch, caplog):
    with caplog.at_level(logging.DEBUG):
        phen_path = tmp_dir / "phen"
        monkeypatch.setattr(
            sys, "argv", ["main.py", "phen", "init", "-d", str(phen_path.resolve())]
        )
        # Mock input() to return "yes" to the question about reinitialising the directory
        monkeypatch.setattr("builtins.input", lambda _: "y")
        main.main()
    assert "Phenotype initialised successfully" in caplog.text


# TODO: This test will need to be refactored so that the expected outputs match the config files
# right now it just tests that it runs successfully and does not check the contents of the output
@pytest.mark.parametrize(
    "config_file",
    [
        ("config1.yaml"),  # config.yaml test case
        ("config2.yaml"),  # config.yaml test case
        ("config3.yaml"),  # config.yaml test case
    ],
)
def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
    print(f"Temporary directory: {tmp_dir}")  # Prints path for debugging

    with caplog.at_level(logging.DEBUG):
        phen_path = tmp_dir / "phen"
        phen_path = phen_path.resolve()
        monkeypatch.setattr(
            sys, "argv", ["main.py", "phen", "init", "-d", str(phen_path.resolve())]
        )
        # Mock input() to return "yes" to the question about reinitialising the directory
        monkeypatch.setattr("builtins.input", lambda _: "y")
        main.main()
    assert "Phenotype initialised successfully" in caplog.text

    with caplog.at_level(logging.DEBUG):
        # validate phenotype
        # copy examples across
        shutil.rmtree(phen_path / "codes")
        ex_path = Path("./examples").resolve()
        for item in ex_path.iterdir():
            source = ex_path / item.name
            destination = phen_path / item.name
            if source.is_dir():
                shutil.copytree(source, destination)
            else:
                shutil.copy(source, destination)

        # copy the test file to configuration
        shutil.copy(phen_path / config_file, phen_path / "config.yaml")

        monkeypatch.setattr(
            sys, "argv", ["main.py", "phen", "validate", "-d", str(phen_path.resolve())]
        )
        main.main()
    assert "Phenotype validated successfully" in caplog.text

    # map phenotype
    for code_type in ["read2", "read3"]:
        with caplog.at_level(logging.DEBUG):
            monkeypatch.setattr(
                sys,
                "argv",
                [
                    "main.py",
                    "phen",
                    "map",
                    "-d",
                    str(phen_path.resolve()),
                    "-t",
                    code_type,
                ],
            )
            main.main()
        assert "Phenotype processed successfully" in caplog.text

    # publish phenotype
    with caplog.at_level(logging.DEBUG):
        monkeypatch.setattr(
            sys, "argv", ["main.py", "phen", "publish", "-d", str(phen_path.resolve())]
        )
        main.main()
    assert "Phenotype published successfully" in caplog.text

    # copy phenotype'
    with caplog.at_level(logging.DEBUG):
        monkeypatch.setattr(
            sys,
            "argv",
            [
                "main.py",
                "phen",
                "copy",
                "-d",
                str(phen_path.resolve()),
                "-td",
                str(tmp_dir.resolve()),
                "-v",
                "v1.0.3",
            ],
        )
        main.main()
    assert "Phenotype copied successfully" in caplog.text

    # diff phenotype
    with caplog.at_level(logging.DEBUG):
        old_path = tmp_dir / "v1.0.3"
        monkeypatch.setattr(
            sys,
            "argv",
            [
                "main.py",
                "phen",
                "diff",
                "-d",
                str(phen_path.resolve()),
                "-old",
                str(old_path.resolve()),
            ],
        )
        main.main()
    assert "Phenotypes diff'd successfully" in caplog.text


# TODO: Refactor this test so it is shortened, there's lots of duplicate codes
def test_diff(tmp_dir, monkeypatch, caplog):
    print(f"Temporary directory: {tmp_dir}")  # Prints path for debugging

    # init phenotype
    phen_path = tmp_dir / "phen"
    phen_path = phen_path.resolve()
    monkeypatch.setattr(
        sys, "argv", ["main.py", "phen", "init", "-d", str(phen_path.resolve())]
    )
    # Mock input() to return "yes" to the question about reinitialising the directory
    monkeypatch.setattr("builtins.input", lambda _: "y")
    main.main()

    # copy example codes
    shutil.rmtree(phen_path / "codes")
    ex_path = Path("./examples").resolve()
    for item in ex_path.iterdir():
        source = ex_path / item.name
        destination = phen_path / item.name
        if source.is_dir():
            shutil.copytree(source, destination)
        else:
            shutil.copy(source, destination)

    # map phenotype for config 1
    shutil.copy(phen_path / "config1.yaml", phen_path / "config.yaml")
    for code_type in ["read2"]:
        with caplog.at_level(logging.DEBUG):
            monkeypatch.setattr(
                sys,
                "argv",
                [
                    "main.py",
                    "phen",
                    "map",
                    "-d",
                    str(phen_path.resolve()),
                    "-t",
                    code_type,
                ],
            )
            main.main()
    assert "Phenotype processed successfully" in caplog.text

    # publish phenotype
    with caplog.at_level(logging.DEBUG):
        monkeypatch.setattr(
            sys, "argv", ["main.py", "phen", "publish", "-d", str(phen_path.resolve())]
        )
        main.main()
    assert "Phenotype published successfully" in caplog.text

    # copy phenotype'
    with caplog.at_level(logging.DEBUG):
        monkeypatch.setattr(
            sys,
            "argv",
            [
                "main.py",
                "phen",
                "copy",
                "-d",
                str(phen_path.resolve()),
                "-td",
                str(tmp_dir.resolve()),
                "-v",
                "v1.0.3",
            ],
        )
        main.main()
    assert "Phenotype copied successfully" in caplog.text

    # map phenotype example 2
    shutil.copy(phen_path / "config2.yaml", phen_path / "config.yaml")
    for code_type in ["read2", "read3"]:
        with caplog.at_level(logging.DEBUG):
            monkeypatch.setattr(
                sys,
                "argv",
                [
                    "main.py",
                    "phen",
                    "map",
                    "-d",
                    str(phen_path.resolve()),
                    "-t",
                    code_type,
                ],
            )
            main.main()
    assert "Phenotype processed successfully" in caplog.text

    # diff phenotype with v1.0.3
    with caplog.at_level(logging.DEBUG):
        old_path = tmp_dir / "v1.0.3"
        monkeypatch.setattr(
            sys,
            "argv",
            [
                "main.py",
                "phen",
                "diff",
                "-d",
                str(phen_path.resolve()),
                "-old",
                str(old_path.resolve()),
            ],
        )
        main.main()
    assert "Phenotypes diff'd successfully" in caplog.text

    # check changes
    with open(phen_path / "v1.0.3_diff.md", "r") as file:
        content = file.read()
    assert "Removed concepts ['ABDO_PAIN']" in content
    assert "Added concepts ['DID_NOT_ATTEND']" in content
    assert "Added outputs: ['read3.csv']" in content

    # map phenotype with example 3
    shutil.copy(phen_path / "config3.yaml", phen_path / "config.yaml")
    for code_type in ["read2", "read3", "snomed"]:
        with caplog.at_level(logging.DEBUG):
            monkeypatch.setattr(
                sys,
                "argv",
                [
                    "main.py",
                    "phen",
                    "map",
                    "-d",
                    str(phen_path.resolve()),
                    "-t",
                    code_type,
                ],
            )
            main.main()
    assert "Phenotype processed successfully" in caplog.text

    # diff phenotype with v1.0.3
    with caplog.at_level(logging.DEBUG):
        old_path = tmp_dir / "v1.0.3"
        monkeypatch.setattr(
            sys,
            "argv",
            [
                "main.py",
                "phen",
                "diff",
                "-d",
                str(phen_path.resolve()),
                "-old",
                str(old_path.resolve()),
            ],
        )
        main.main()
    assert "Phenotypes diff'd successfully" in caplog.text

    with open(phen_path / "v1.0.3_diff.md", "r") as file:
        content = file.read()
    assert "Removed concepts ['ABDO_PAIN']" in content
    assert "Added concepts ['DEPRESSION', 'DID_NOT_ATTEND', 'HYPERTENSION']" in content
    assert "Added outputs: ['read3.csv', 'snomed.csv']" in content