File size: 4,937 Bytes
5631464 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 | """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"
# when an invalid parameter is provided, it should exit
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)
# build fake run_dir
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"))
# run haddock3-analyse
main(
run_dir,
[2],
5,
format=None,
scale=None,
is_cleaned=False,
inter=False,
)
# check analysis directory exists
ana_dir = Path(run_dir, "analysis/")
assert os.path.isdir(ana_dir) is True
# check whether there are some html files
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)
# build fake run_dir
rigid_dir = "1_rigidbody"
rigid_dir_analysis = "1_rigidbody_analysis"
os.mkdir(rigid_dir)
os.mkdir(rigid_dir_analysis)
# fill rigidbody directory with one file
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,
)
# Archive version
zip_top_ranked(top_ranked_mapping, "summary", True)
assert os.path.isfile("summary.tgz") is True
# Non-Archived version
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."""
# build fake run_dir
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")
# run haddock3-analyse
main(
run_dir,
[2],
5,
format=None,
scale=None,
is_cleaned=False,
inter=False,
offline=True,
)
# check analysis directory exists
ana_dir = run_dir / "analysis/"
assert ana_dir.is_dir()
# check whether there are js and css files
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()
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