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haddock3 / data /tests /test_cli_traceback.py

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"""Test haddock3-traceback client."""

import os
import shutil
from pathlib import Path
import tempfile

import pandas as pd
import pytest

from haddock.clis.cli_traceback import (
    main,
    get_steps_without_pdbs,
    subset_traceback,
)

from . import golden_data


@pytest.fixture
def rigid_json():
    """Provide example rigidbody io.json file."""
    return Path(golden_data, "io_rigid.json")


@pytest.fixture
def flexref_json():
    """Provide example flexref io.json file."""
    return Path(golden_data, "io_flexref.json")


@pytest.fixture
def expected_traceback():
    "Provide expected traceback dataframe."
    exp_tr = [["00_topo1", "00_topo2", "1_rigidbody", "1_rigidbody_rank", "4_flexref", "4_flexref_rank"],  # noqa: E501
              ["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_3.pdb", "1", "flexref_1.pdb", "1"],  # noqa: E501
              ["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_1.pdb", "2", "flexref_2.pdb", "2"],  # noqa: E501
              ["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_4.pdb", "3", "-", "-"],  # noqa: E501
              ["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_2.pdb", "4", "-", "-"]]  # noqa: E501
    exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
    return exp_tr_df


def test_main(rigid_json, flexref_json, expected_traceback):
    """Test haddock3-traceback client."""
    with tempfile.TemporaryDirectory() as tmpdir:
        # build fake run_dir
        run_dir = Path(tmpdir, "example_dir")
        step_dirs = [os.path.join(run_dir, "1_rigidbody"),
                     os.path.join(run_dir, "4_flexref")]

        # Loop over directories to be created
        for d in [run_dir, *step_dirs]:
            os.mkdir(d)
        shutil.copy(rigid_json, os.path.join(step_dirs[0], "io.json"))
        shutil.copy(flexref_json, os.path.join(step_dirs[1], "io.json"))

        # create fake, empty pdb files
        for i in range(1, 5):
            open(os.path.join(step_dirs[0], f"rigidbody_{i}.pdb"), "w").close()
        for i in range(1, 3):
            open(os.path.join(step_dirs[1], f"flexref_{i}.pdb"), "w").close()

        # run haddock3-traceback
        main(run_dir)

        # check traceback folder exists
        assert os.path.isdir(os.path.join(run_dir, "traceback"))

        # check traceback files exist
        tr_file = os.path.join(run_dir, "traceback", "traceback.tsv")
        assert os.path.isfile(tr_file)

        obs_tr = pd.read_csv(tr_file, sep="\t", dtype=str)

        assert obs_tr.columns.tolist() == expected_traceback.columns.tolist()
        assert obs_tr.equals(expected_traceback)


def test_analysis():
    """Test traceback on a pure analysis run."""
    # build fake run_dir
    with tempfile.TemporaryDirectory() as tmpdir:
        run_dir = Path(tmpdir, "example_dir")
        step_dirs = [os.path.join(run_dir, "0_topoaa"),
                     os.path.join(run_dir, "1_caprieval")]

        for d in [run_dir, *step_dirs]:
            os.mkdir(d)

        # run haddock3-traceback
        main(run_dir)

        # check traceback folder does not exist
        assert not os.path.isdir(os.path.join(run_dir, "traceback"))


def test_get_steps_without_pdbs():
    """Test get_steps_without_pdbs."""
    with tempfile.TemporaryDirectory() as tmpdir:
        # build fake run_dir
        run_dir = Path(tmpdir)
        steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]
        
        for st in steps:
            os.mkdir(Path(run_dir, st))

        # create fake, empty pdb files
        fake_pdb_path = Path(run_dir, steps[1] , f"rigidbody_1.pdb")
        open(fake_pdb_path, "w").close()

        # get steps without pdbs
        obs_steps = get_steps_without_pdbs(run_dir, steps)

        # check steps without pdbs
        exp_steps = ["0_topoaa", "2_caprieval"]
        assert obs_steps == exp_steps

        # now we remove the fake pdb file
        os.remove(fake_pdb_path)

        # get steps without pdbs
        obs_steps = get_steps_without_pdbs(run_dir, steps)
        exp_steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]
        assert obs_steps == exp_steps


def test_subset_traceback(expected_traceback):
    """Test subset_traceback."""
    with tempfile.TemporaryDirectory() as tmpdir:
        cons_filename = Path(tmpdir, "consensus_example.tsv")
        # subset traceback
        obs_tr = subset_traceback(expected_traceback, cons_filename)
        # assert consensus file exists
        assert cons_filename.exists()
        # check subset
        exp_tr = [["Model", "1_rigidbody_rank", "4_flexref_rank", "Sum-of-Ranks"],  # noqa: E501
                  ["flexref_1.pdb", 1, 1, 2],  # noqa: E501
                  ["flexref_2.pdb", 2, 2, 4]]  # noqa: E501
        exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
        assert obs_tr.columns.tolist() == exp_tr_df.columns.tolist()
        assert obs_tr.equals(exp_tr_df)

	"""Test haddock3-traceback client."""

	import os
	import shutil
	from pathlib import Path
	import tempfile

	import pandas as pd
	import pytest

	from haddock.clis.cli_traceback import (
	main,
	get_steps_without_pdbs,
	subset_traceback,
	)

	from . import golden_data


	@pytest.fixture
	def rigid_json():
	"""Provide example rigidbody io.json file."""
	return Path(golden_data, "io_rigid.json")


	@pytest.fixture
	def flexref_json():
	"""Provide example flexref io.json file."""
	return Path(golden_data, "io_flexref.json")


	@pytest.fixture
	def expected_traceback():
	"Provide expected traceback dataframe."
	exp_tr = [["00_topo1", "00_topo2", "1_rigidbody", "1_rigidbody_rank", "4_flexref", "4_flexref_rank"], # noqa: E501
	["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_3.pdb", "1", "flexref_1.pdb", "1"], # noqa: E501
	["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_1.pdb", "2", "flexref_2.pdb", "2"], # noqa: E501
	["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_4.pdb", "3", "-", "-"], # noqa: E501
	["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_2.pdb", "4", "-", "-"]] # noqa: E501
	exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
	return exp_tr_df


	def test_main(rigid_json, flexref_json, expected_traceback):
	"""Test haddock3-traceback client."""
	with tempfile.TemporaryDirectory() as tmpdir:
	# build fake run_dir
	run_dir = Path(tmpdir, "example_dir")
	step_dirs = [os.path.join(run_dir, "1_rigidbody"),
	os.path.join(run_dir, "4_flexref")]

	# Loop over directories to be created
	for d in [run_dir, *step_dirs]:
	os.mkdir(d)
	shutil.copy(rigid_json, os.path.join(step_dirs[0], "io.json"))
	shutil.copy(flexref_json, os.path.join(step_dirs[1], "io.json"))

	# create fake, empty pdb files
	for i in range(1, 5):
	open(os.path.join(step_dirs[0], f"rigidbody_{i}.pdb"), "w").close()
	for i in range(1, 3):
	open(os.path.join(step_dirs[1], f"flexref_{i}.pdb"), "w").close()

	# run haddock3-traceback
	main(run_dir)

	# check traceback folder exists
	assert os.path.isdir(os.path.join(run_dir, "traceback"))

	# check traceback files exist
	tr_file = os.path.join(run_dir, "traceback", "traceback.tsv")
	assert os.path.isfile(tr_file)

	obs_tr = pd.read_csv(tr_file, sep="\t", dtype=str)

	assert obs_tr.columns.tolist() == expected_traceback.columns.tolist()
	assert obs_tr.equals(expected_traceback)


	def test_analysis():
	"""Test traceback on a pure analysis run."""
	# build fake run_dir
	with tempfile.TemporaryDirectory() as tmpdir:
	run_dir = Path(tmpdir, "example_dir")
	step_dirs = [os.path.join(run_dir, "0_topoaa"),
	os.path.join(run_dir, "1_caprieval")]

	for d in [run_dir, *step_dirs]:
	os.mkdir(d)

	# run haddock3-traceback
	main(run_dir)

	# check traceback folder does not exist
	assert not os.path.isdir(os.path.join(run_dir, "traceback"))


	def test_get_steps_without_pdbs():
	"""Test get_steps_without_pdbs."""
	with tempfile.TemporaryDirectory() as tmpdir:
	# build fake run_dir
	run_dir = Path(tmpdir)
	steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]

	for st in steps:
	os.mkdir(Path(run_dir, st))

	# create fake, empty pdb files
	fake_pdb_path = Path(run_dir, steps[1] , f"rigidbody_1.pdb")
	open(fake_pdb_path, "w").close()

	# get steps without pdbs
	obs_steps = get_steps_without_pdbs(run_dir, steps)

	# check steps without pdbs
	exp_steps = ["0_topoaa", "2_caprieval"]
	assert obs_steps == exp_steps

	# now we remove the fake pdb file
	os.remove(fake_pdb_path)

	# get steps without pdbs
	obs_steps = get_steps_without_pdbs(run_dir, steps)
	exp_steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]
	assert obs_steps == exp_steps


	def test_subset_traceback(expected_traceback):
	"""Test subset_traceback."""
	with tempfile.TemporaryDirectory() as tmpdir:
	cons_filename = Path(tmpdir, "consensus_example.tsv")
	# subset traceback
	obs_tr = subset_traceback(expected_traceback, cons_filename)
	# assert consensus file exists
	assert cons_filename.exists()
	# check subset
	exp_tr = [["Model", "1_rigidbody_rank", "4_flexref_rank", "Sum-of-Ranks"], # noqa: E501
	["flexref_1.pdb", 1, 1, 2], # noqa: E501
	["flexref_2.pdb", 2, 2, 4]] # noqa: E501
	exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
	assert obs_tr.columns.tolist() == exp_tr_df.columns.tolist()
	assert obs_tr.equals(exp_tr_df)