Update Python wf

biobb_wf_godmd/tests/python/biobb_wf_godmd.py

@@ -0,0 +1,138 @@
+import pytest
+import glob
+from pathlib import Path
+from biobb_common.configuration import settings
+from biobb_common.tools import file_utils as fu
+from biobb_common.tools import test_fixtures as fx
+from biobb_structure_utils.utils.extract_chain import extract_chain
+from biobb_structure_utils.utils.remove_molecules import remove_molecules
+from biobb_godmd.godmd.godmd_prep import godmd_prep
+from biobb_godmd.godmd.godmd_run import godmd_run
+from biobb_analysis.ambertools.cpptraj_convert import cpptraj_convert
+
+global_work_dir = None
+
+
+def step0_extract_chain(config, system=None):
+    conf = settings.ConfReader(config, system)
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    extract_chain(**global_paths["step0_extract_chain"], properties=global_prop["step0_extract_chain"])
+
+    assert fx.not_empty(global_paths["step0_extract_chain"]["output_structure_path"])
+    assert fx.equal(global_paths["step0_extract_chain"]["output_structure_path"], f'reference/step0_extract_chain/{Path(global_paths["step0_extract_chain"]["output_structure_path"]).name}')
+
+    global global_work_dir
+    global_work_dir = conf.get_working_dir_path()
+
+
+def step1_extract_chain(config, system=None):
+    conf = settings.ConfReader(config, system)
+    conf.working_dir_path = global_work_dir
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    extract_chain(**global_paths["step1_extract_chain"], properties=global_prop["step1_extract_chain"])
+
+    assert fx.not_empty(global_paths["step1_extract_chain"]["output_structure_path"])
+    assert fx.equal(global_paths["step1_extract_chain"]["output_structure_path"], f'reference/step1_extract_chain/{Path(global_paths["step1_extract_chain"]["output_structure_path"]).name}')
+
+
+def step2_remove_molecules(config, system=None):
+    conf = settings.ConfReader(config, system)
+    conf.working_dir_path = global_work_dir
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    remove_molecules(**global_paths["step2_remove_molecules"], properties=global_prop["step2_remove_molecules"])
+
+    assert fx.not_empty(global_paths["step2_remove_molecules"]["output_molecules_path"])
+    assert fx.equal(global_paths["step2_remove_molecules"]["output_molecules_path"], f'reference/step2_remove_molecules/{Path(global_paths["step2_remove_molecules"]["output_molecules_path"]).name}')
+
+
+def step4_godmd_prep(config, system=None):
+    conf = settings.ConfReader(config, system)
+    conf.working_dir_path = global_work_dir
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    global_paths["step4_godmd_prep"]["input_pdb_target_path"] = global_paths["step1_extract_chain"]["output_structure_path"]
+    godmd_prep(**global_paths["step4_godmd_prep"], properties=global_prop["step4_godmd_prep"])
+
+    assert fx.not_empty(global_paths["step4_godmd_prep"]["output_aln_orig_path"])
+    assert fx.equal(global_paths["step4_godmd_prep"]["output_aln_orig_path"], f'reference/step4_godmd_prep/{Path(global_paths["step4_godmd_prep"]["output_aln_orig_path"]).name}')
+    assert fx.not_empty(global_paths["step4_godmd_prep"]["output_aln_target_path"])
+    assert fx.equal(global_paths["step4_godmd_prep"]["output_aln_target_path"], f'reference/step4_godmd_prep/{Path(global_paths["step4_godmd_prep"]["output_aln_target_path"]).name}')
+
+
+def step5_godmd_run(config, system=None):
+    conf = settings.ConfReader(config, system)
+    conf.working_dir_path = global_work_dir
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    global_paths["step5_godmd_run"]["input_pdb_target_path"] = global_paths["step1_extract_chain"]["output_structure_path"]
+    godmd_run(**global_paths["step5_godmd_run"], properties=global_prop["step5_godmd_run"])
+
+    assert fx.not_empty(global_paths["step5_godmd_run"]["output_log_path"])
+    # assert fx.equal(global_paths["step5_godmd_run"]["output_log_path"], f'reference/step5_godmd_run/{Path(global_paths["step5_godmd_run"]["output_log_path"]).name}')
+    assert fx.not_empty(global_paths["step5_godmd_run"]["output_ene_path"])
+    assert fx.equal(global_paths["step5_godmd_run"]["output_ene_path"], f'reference/step5_godmd_run/{Path(global_paths["step5_godmd_run"]["output_ene_path"]).name}')
+    assert fx.not_empty(global_paths["step5_godmd_run"]["output_trj_path"])
+    assert fx.equal(global_paths["step5_godmd_run"]["output_trj_path"], f'reference/step5_godmd_run/{Path(global_paths["step5_godmd_run"]["output_trj_path"]).name}')
+    assert fx.not_empty(global_paths["step5_godmd_run"]["output_pdb_path"])
+    assert fx.equal(global_paths["step5_godmd_run"]["output_pdb_path"], f'reference/step5_godmd_run/{Path(global_paths["step5_godmd_run"]["output_pdb_path"]).name}')
+
+
+def step6_cpptraj_convert(config, remove=False, system=None):
+    conf = settings.ConfReader(config, system)
+    conf.working_dir_path = global_work_dir
+    global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
+    global_prop = conf.get_prop_dic(global_log=global_log)
+    global_paths = conf.get_paths_dic()
+
+    cpptraj_convert(**global_paths["step6_cpptraj_convert"], properties=global_prop["step6_cpptraj_convert"])
+
+    assert fx.not_empty(global_paths["step6_cpptraj_convert"]["output_cpptraj_path"])
+    assert fx.equal(global_paths["step6_cpptraj_convert"]["output_cpptraj_path"], f'reference/step6_cpptraj_convert/{Path(global_paths["step6_cpptraj_convert"]["output_cpptraj_path"]).name}')
+
+    if remove:
+        tmp_files = [conf.get_working_dir_path()]
+        tmp_files.extend(glob.glob('sandbox_*'))
+        fu.rm_file_list(tmp_files)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step0_extract_chain(config_path, system):
+    step0_extract_chain(config_path, system)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step1_extract_chain(config_path, system):
+    step1_extract_chain(config_path, system)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step2_remove_molecules(config_path, system):
+    step2_remove_molecules(config_path, system)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step4_godmd_prep(config_path, system):
+    step4_godmd_prep(config_path, system)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step5_godmd_run(config_path, system):
+    step5_godmd_run(config_path, system)
+
+
+@pytest.mark.parametrize("system", [None])
+def test_step6_cpptraj_convert(config_path, remove_flag, system):
+    step6_cpptraj_convert(config_path, remove_flag, system)

biobb_wf_godmd/tests/python/conftest.py

@@ -0,0 +1,27 @@
+import pytest
+import shutil
+import os
+
+
+def pytest_addoption(parser):
+    parser.addoption("--config", action="store", default=None, help="Path to the config file")
+    parser.addoption("--remove", action="store_true", default=False, help="Remove working directory after tests")
+
+
+@pytest.fixture
+def config_path(request):
+    return request.config.getoption("--config")
+
+
+@pytest.fixture
+def remove_flag(request):
+    return request.config.getoption("--remove")
+
+
+@pytest.fixture(scope="session", autouse=True)
+def cleanup():
+    yield
+    # This code will run after all tests are completed
+    pycache_dir = os.path.join(os.path.dirname(__file__), '__pycache__')
+    if os.path.exists(pycache_dir):
+        shutil.rmtree(pycache_dir)