Mercurial > repos > davidvanzessen > shm_csr
view tests/test_shm_csr.py @ 92:cf8ad181628f draft
planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c
author | rhpvorderman |
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date | Mon, 12 Dec 2022 12:32:44 +0000 |
parents | 6809c63d9161 |
children | 8fcf31272f6e |
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# Copyright (c) 2021 Leiden University Medical Center # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import os 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" naive_output_cg = "None" naive_output_cm = "None" naive_output_ce = "None" naive_output_all = "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", str(out_file), str(out_files_path), infile_name, "-", functionality, unique, naive_output, naive_output_ca, naive_output_cg, naive_output_cm, naive_output_ce, naive_output_all, 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), # 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: with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt") ) as validate_h: for line in result_h: assert line == validate_h.readline()