Mercurial > repos > davidvanzessen > shm_csr
view tests/test_shm_csr.py @ 85:a539d14d66b6 draft
"planemo upload commit 95767c430ea956636f95ec28bb749a84eabe0156"
author | rhpvorderman |
---|---|
date | Wed, 27 Oct 2021 09:41:34 +0000 |
parents | 729738462297 |
children | 6809c63d9161 |
line wrap: on
line source
# 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 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" 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' fast = 'no' cmd = [ "bash", "wrapper.sh", input, "custom", out_file, 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 ] 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: with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt") ) as validate_h: for line in result_h: assert line == validate_h.readline()