comparison tests/test_shm_csr.py @ 98:d714f5ea83d7 draft

planemo upload commit 1a01065a084a817382872154f779b94090a35ebf

97:fbc6307dd83b

    "Ignore virtualenv and git directories to prevent massive tmp folders"
    if os.path.basename(src) in (".venv", ".git"):
        return files
    return ()

@pytest.fixture(scope="module")
def shm_csr_result():
    temp_dir = Path(tempfile.mkdtemp())
    tool_dir = temp_dir / "shm_csr"
    shutil.copytree(
        GIT_ROOT, tool_dir,
        # Ignore .venv and .git directories.

    working_dir = temp_dir / "working"
    working_dir.mkdir(parents=True)
    output_dir = temp_dir / "outputs"
    output_dir.mkdir(parents=True)
    wrapper = str(tool_dir / "wrapper.sh")
    input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
    out_files_path = output_dir / "results"
    out_file = out_files_path / "result.html"
    infile_name = "input_data"
    functionality = "productive"
    unique = "Sequence.ID"
    naive_output = "no"
    naive_output_ca = "None"
    naive_output_cg = "None"
    naive_output_cm = "None"
    naive_output_ce = "None"
    naive_output_all = "None"
    naive_output_igm_naive = "None"
    naive_output_igm_naive_memory = "None"
    filter_unique = "remove"
    filter_unique_count = '2'
    class_filter = '70_70'
    empty_region_filter = 'FR1'
    # Skip baseline and changeo by default. These tools cannot be modified
    # anyway and take most of the test time to execute. The environment
    # variable can be set to "no" on the CI so the code path is tested
    # at the time a PR is ready.
    fast = os.environ.get("SHM_CSR_FAST", "yes")
    cmd = [
        "bash",
        wrapper,
        input,
        "custom",

        naive_output_igm_naive_memory,
        filter_unique,
        filter_unique_count,
        class_filter,
        empty_region_filter,
        fast
    ]
    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                  "--rm",  # Remove container after running
                  "-v", f"{input}:{input}",
                  "-w", str(working_dir),

                  ] + cmd
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)
    yield Path(out_files_path)


def test_check_output(shm_csr_result):
    assert shm_csr_result.exists()

              ) as result_h:
        with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
                  ) as validate_h:
            for line in result_h:
                assert line == validate_h.readline()

98:d714f5ea83d7

    "Ignore virtualenv and git directories to prevent massive tmp folders"
    if os.path.basename(src) in (".venv", ".git"):
        return files
    return ()


def run_shm_csr(
    input=str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2),
    infile_name = "input_data",
    functionality = "productive",
    unique = "Sequence.ID",
    naive_output = "no",
    naive_output_ca = "None",
    naive_output_cg = "None",
    naive_output_cm = "None",
    naive_output_ce = "None",
    naive_output_all = "None",
    naive_output_igm_naive = "None",
    naive_output_igm_naive_memory = "None",
    filter_unique = "remove",
    filter_unique_count = '2',
    class_filter = '70_70',
    empty_region_filter = 'FR1',
    # Skip baseline and changeo by default. These tools cannot be modified
    # anyway and take most of the test time to execute. The environment
    # variable can be set to "no" on the CI so the code path is tested
    # at the time a PR is ready.
    run_changeo = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
    run_baseline = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
):
    temp_dir = Path(tempfile.mkdtemp())
    tool_dir = temp_dir / "shm_csr"
    shutil.copytree(
        GIT_ROOT, tool_dir,
        # Ignore .venv and .git directories.

    working_dir = temp_dir / "working"
    working_dir.mkdir(parents=True)
    output_dir = temp_dir / "outputs"
    output_dir.mkdir(parents=True)
    wrapper = str(tool_dir / "wrapper.sh")
    out_files_path = output_dir / "results"
    out_file = out_files_path / "result.html"
    cmd = [
        "bash",
        wrapper,
        input,
        "custom",

        naive_output_igm_naive_memory,
        filter_unique,
        filter_unique_count,
        class_filter,
        empty_region_filter,
        run_changeo,
        run_baseline
    ]
    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                  "--rm",  # Remove container after running
                  "-v", f"{input}:{input}",
                  "-w", str(working_dir),

                  ] + cmd
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)
    return Path(out_files_path)


@pytest.fixture(scope="module")
def shm_csr_result():
    yield run_shm_csr()


def test_check_output(shm_csr_result):
    assert shm_csr_result.exists()

              ) as result_h:
        with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
                  ) as validate_h:
            for line in result_h:
                assert line == validate_h.readline()


def test_baseline_succeeds():
    run_shm_csr(
        functionality="unproductive",
        empty_region_filter="None",
        filter_unique="no",
        unique="VGene,DGene,JGene,CDR3.IMGT.seq",
        class_filter="101_101_IGA",
        naive_output="yes",
        run_baseline="yes",
        run_changeo="yes",
    )