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
logger = 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


def test_phen_workflow(tmp_dir, monkeypatch, caplog):
    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)

        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", "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

    # 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