diff --git a/tests/test_acmc.py b/tests/test_acmc.py index 1653ca1a653db657ee213d37741121e2dd8f36cd..bc7c035797fce5853358cb6ec2cc43ceba55651d 100644 --- a/tests/test_acmc.py +++ b/tests/test_acmc.py @@ -8,7 +8,7 @@ from pathlib import Path import trud import omop import phen -import acmc +import main # setup logging from logging_config import setup_logger @@ -35,29 +35,29 @@ def logger(): def test_phen_init_local_default(tmp_dir, monkeypatch, caplog): with caplog.at_level(logging.DEBUG): - monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "init"]) + monkeypatch.setattr(sys, "argv", ["main.py", "phen", "init"]) # Mock input() to return "yes" to the question about reinitialising the directory monkeypatch.setattr("builtins.input", lambda _: "y") - acmc.main() + main.main() assert "Phenotype initialised successfully" in caplog.text 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", ["acmc.py", "phen", "init", "-d", str(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") - acmc.main() + 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", ["acmc.py", "phen", "init", "-d", str(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") - acmc.main() + main.main() assert "Phenotype initialised successfully" in caplog.text with caplog.at_level(logging.DEBUG): @@ -74,31 +74,31 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog): shutil.copy(source, destination) shutil.copy( phen_path / 'config1.json', phen_path / 'config.json') - monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "validate", "-d", str(phen_path.resolve())]) - acmc.main() + monkeypatch.setattr(sys, "argv", ["main.py", "phen", "validate", "-d", str(phen_path.resolve())]) + main.main() assert "Phenotype validated successfully" in caplog.text # map phenotype with caplog.at_level(logging.DEBUG): - monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read2", "-tr", "-ve"]) - acmc.main() + monkeypatch.setattr(sys, "argv", ["main.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read2", "-tr", "-ve"]) + main.main() assert "Phenotype processed successfully" in caplog.text # publish phenotype with caplog.at_level(logging.DEBUG): - monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "publish", "-d", str(phen_path.resolve())]) - acmc.main() + 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", ["acmc.py", "phen", "copy", "-d", str(phen_path.resolve()), "-td", str(tmp_dir.resolve()), "-v", "v1.0.3"]) - acmc.main() + 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", ["acmc.py", "phen", "diff", "-d", str(phen_path.resolve()), "-old", str(old_path.resolve())]) - acmc.main() + 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