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)
		shutil.copy( phen_path / 'config1.json', phen_path / 'config.json')	
		
		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