| """Test haddock3-analyse client.""" |
| import os |
| import shutil |
| from pathlib import Path |
| import tempfile |
|
|
| import pytest |
|
|
| from haddock.clis.cli_analyse import ( |
| get_cluster_ranking, |
| get_top_ranked_mapping, |
| main, |
| update_capri_dict, |
| zip_top_ranked, |
| ) |
| from haddock.gear.yaml2cfg import read_from_yaml_config |
| from haddock.modules.analysis.caprieval import \ |
| DEFAULT_CONFIG as caprieval_params |
|
|
| from . import golden_data |
|
|
|
|
| @pytest.fixture |
| def default_capri(): |
| """Prot-prot input.""" |
| return read_from_yaml_config(caprieval_params) |
|
|
|
|
| @pytest.fixture |
| def example_capri_clt(): |
| """Provide example capri_clt.tsv filename.""" |
| return Path(golden_data, "capri_clt_example.tsv") |
|
|
|
|
| @pytest.fixture |
| def example_capri_ss(): |
| """Provide example capri_ss.tsv filename.""" |
| return Path(golden_data, "capri_ss_example.tsv") |
|
|
|
|
| def test_update_capri_dict(default_capri): |
| """Test update_capri_dict.""" |
| ext_params = {"reference_fname": "example.pdb"} |
| wrong_ext_params = {"wrong_parameter_name": 32} |
| obs_capri_dict = update_capri_dict(default_capri, ext_params) |
| assert obs_capri_dict["reference_fname"].name == "example.pdb" |
| |
| with pytest.raises(SystemExit): |
| update_capri_dict(default_capri, wrong_ext_params) |
|
|
|
|
| def test_get_cluster_ranking(example_capri_clt): |
| """Test get_cluster_ranking.""" |
| obs_cl_ranking = get_cluster_ranking(example_capri_clt, 5) |
| exp_cl_ranking = { |
| 16: 1, |
| 1: 2, |
| 13: 3, |
| 4: 4, |
| 5: 5, |
| } |
| assert exp_cl_ranking == obs_cl_ranking |
|
|
|
|
| def test_main(example_capri_ss, example_capri_clt, monkeypatch): |
| """Test cli_analyse main.""" |
| with tempfile.TemporaryDirectory() as tmpdir: |
| monkeypatch.chdir(tmpdir) |
| |
| run_dir = "example_dir" |
| if os.path.isdir(run_dir): |
| shutil.rmtree(run_dir) |
| step_name = "2_caprieval" |
| step_dir = Path(run_dir, step_name) |
| os.mkdir(run_dir) |
| os.mkdir(step_dir) |
| shutil.copy(example_capri_ss, Path(step_dir, "capri_ss.tsv")) |
| shutil.copy(example_capri_clt, Path(step_dir, "capri_clt.tsv")) |
|
|
| |
| main( |
| run_dir, |
| [2], |
| 5, |
| format=None, |
| scale=None, |
| is_cleaned=False, |
| inter=False, |
| ) |
|
|
| |
| ana_dir = Path(run_dir, "analysis/") |
| assert os.path.isdir(ana_dir) is True |
|
|
| |
| ana_subdir = Path(ana_dir, f"{step_name}_analysis") |
| html_files = [el for el in os.listdir(ana_subdir) if el.endswith(".html")] |
| assert len(html_files) > 0 |
|
|
|
|
| def test_zip_top_ranked(example_capri_ss, monkeypatch): |
| """Test cli_analyse zip_top_ranked function.""" |
| with tempfile.TemporaryDirectory() as tmpdir: |
| monkeypatch.chdir(tmpdir) |
| |
| rigid_dir = "1_rigidbody" |
| rigid_dir_analysis = "1_rigidbody_analysis" |
| os.mkdir(rigid_dir) |
| os.mkdir(rigid_dir_analysis) |
| |
| shutil.copy(Path(golden_data, "protprot_complex_1.pdb"), Path(rigid_dir, "rigidbody_383.pdb")) |
| monkeypatch.chdir(rigid_dir_analysis) |
| |
| exp_cl_ranking = {1: 2} |
| top_ranked_mapping = get_top_ranked_mapping( |
| example_capri_ss, |
| exp_cl_ranking, |
| ) |
| |
| zip_top_ranked(top_ranked_mapping, "summary", True) |
| assert os.path.isfile("summary.tgz") is True |
|
|
| |
| zip_top_ranked(top_ranked_mapping, "notarchived", False) |
| assert not os.path.isfile("notarchived.tgz") |
| assert os.path.isdir("notarchived") |
| assert len(list(Path("notarchived").glob("*.pdb"))) > 0 |
|
|
|
|
| def test_main_offline(example_capri_ss, example_capri_clt, tmp_path): |
| """Test cli_analyse main in offline mode.""" |
| |
| run_dir = tmp_path / "example_dir" |
| if os.path.isdir(run_dir): |
| shutil.rmtree(run_dir) |
| step_name = "2_caprieval" |
| step_dir = run_dir / step_name |
| os.mkdir(run_dir) |
| os.mkdir(step_dir) |
| shutil.copy(example_capri_ss, step_dir / "capri_ss.tsv") |
| shutil.copy(example_capri_clt, step_dir / "capri_clt.tsv") |
|
|
| |
| main( |
| run_dir, |
| [2], |
| 5, |
| format=None, |
| scale=None, |
| is_cleaned=False, |
| inter=False, |
| offline=True, |
| ) |
|
|
| |
| ana_dir = run_dir / "analysis/" |
| assert ana_dir.is_dir() |
|
|
| |
| assert (run_dir / "data/ui/report.bundle.js").is_file() |
| assert (run_dir / "data/ui/index.css").is_file() |
| assert (ana_dir / "2_caprieval_analysis/plotly_bundle.js").is_file() |
|
|
