comparison tests/test_shm_csr.py @ 90:6809c63d9161 draft

"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"

89:3c9d4d976c47

import shutil
import subprocess
import sys
import tempfile
from pathlib import Path

import pytest

GIT_ROOT = str(Path(__file__).parent.parent.absolute())
TEST_DIR = Path(__file__).parent
TEST_DATA_DIR = TEST_DIR / "data"
VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"


@pytest.fixture(scope="module")
def shm_csr_result():
    temp_dir = tempfile.mktemp()
    shutil.copytree(GIT_ROOT, temp_dir)
    input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
    out_files_path = os.path.join(temp_dir, "results")
    out_file = os.path.join(out_files_path, "result.html")
    infile_name = "input_data"
    functionality = "productive"
    unique = "Sequence.ID"
    naive_output = "no"
    naive_output_ca = "None"

    class_filter = '70_70'
    empty_region_filter = 'FR1'
    fast = 'no'
    cmd = [
        "bash",
        "wrapper.sh",
        input,
        "custom",
        out_file,
        out_files_path,
        infile_name,
        "-",
        functionality,
        unique,
        naive_output,

        filter_unique_count,
        class_filter,
        empty_region_filter,
        fast
    ]
    subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr,
                   check=True)
    yield Path(out_files_path)
    #shutil.rmtree(temp_dir)


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


@pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
def test_results_match_validation(shm_csr_result, filename):
    if filename == "shm_overview.txt":
        # TODO: Fix errors in shm_overview.
        return
    with open(Path(shm_csr_result, filename)) as result_h:
        with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
            for line in result_h:
                assert line == validate_h.readline()


def test_nt_overview(shm_csr_result):
    with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
              ) as result_h:

90:6809c63d9161

import shutil
import subprocess
import sys
import tempfile
from pathlib import Path
from xml.etree import ElementTree
from xml.etree.ElementTree import Element

import pytest

GIT_ROOT = Path(__file__).parent.parent.absolute()
TEST_DIR = Path(__file__).parent
TEST_DATA_DIR = TEST_DIR / "data"
VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"


def get_container():
    tool = ElementTree.parse(GIT_ROOT / "shm_csr.xml").getroot()
    requirements: Element = tool.find("requirements")
    container = requirements.find("container")
    return container.text


@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)
    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"

    class_filter = '70_70'
    empty_region_filter = 'FR1'
    fast = 'no'
    cmd = [
        "bash",
        wrapper,
        input,
        "custom",
        str(out_file),
        str(out_files_path),
        infile_name,
        "-",
        functionality,
        unique,
        naive_output,

        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),
                  # Run as current user which allows deletion of files.
                  # It also mitigates some security considerations
                  "-u", f"{os.getuid()}:{os.getgid()}",
                  # Run with default seccomp profile to mitigate mitigation slowdown
                  # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
                  # This knocks down test runtime from 8 to 6 minutes.
                  "--security-opt", "seccomp=unconfined",
                  # Use a mulled container generated with `planemo mull`
                  "quay.io/biocontainers/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
                  ] + 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()


@pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
def test_results_match_validation(shm_csr_result, filename):
    with open(Path(shm_csr_result, filename)) as result_h:
        with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
            for line in result_h:
                # Skip two faulty lines in shm_overview.
                # TODO: Fix the issue.
                validation_line = validate_h.readline()
                if filename == "shm_overview.txt":
                    if (line.startswith("RGYW (%)") or
                            line.startswith("WRCY (%)")):
                        continue
                assert line == validation_line


def test_nt_overview(shm_csr_result):
    with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
              ) as result_h: