Mercurial > repos > davidvanzessen > shm_csr

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

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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
author rhpvorderman
date Tue, 25 Jan 2022 11:28:29 +0000
parents 729738462297
children cf8ad181628f
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1 # Copyright (c) 2021 Leiden University Medical Center
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2 #
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3 # Permission is hereby granted, free of charge, to any person obtaining a copy
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4 # of this software and associated documentation files (the "Software"), to deal
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5 # in the Software without restriction, including without limitation the rights
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6 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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7 # copies of the Software, and to permit persons to whom the Software is
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8 # furnished to do so, subject to the following conditions:
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9 #
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10 # The above copyright notice and this permission notice shall be included in
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11 # all copies or substantial portions of the Software.
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12 #
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13 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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14 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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15 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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16 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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17 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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18 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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19 # SOFTWARE.
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20
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21 import os
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22 import shutil
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23 import subprocess
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24 import sys
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25 import tempfile
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26 from pathlib import Path
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27 from xml.etree import ElementTree
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28 from xml.etree.ElementTree import Element
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29
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30 import pytest
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31
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32 GIT_ROOT = Path(__file__).parent.parent.absolute()
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33 TEST_DIR = Path(__file__).parent
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34 TEST_DATA_DIR = TEST_DIR / "data"
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35 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
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36 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
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37
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38
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39 def get_container():
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40 tool = ElementTree.parse(GIT_ROOT / "shm_csr.xml").getroot()
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41 requirements: Element = tool.find("requirements")
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42 container = requirements.find("container")
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43 return container.text
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45
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46 @pytest.fixture(scope="module")
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47 def shm_csr_result():
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48 temp_dir = Path(tempfile.mkdtemp())
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49 tool_dir = temp_dir / "shm_csr"
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50 shutil.copytree(GIT_ROOT, tool_dir)
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51 working_dir = temp_dir / "working"
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52 working_dir.mkdir(parents=True)
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53 output_dir = temp_dir / "outputs"
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54 output_dir.mkdir(parents=True)
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55 wrapper = str(tool_dir / "wrapper.sh")
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56 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
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57 out_files_path = output_dir / "results"
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58 out_file = out_files_path / "result.html"
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59 infile_name = "input_data"
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60 functionality = "productive"
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61 unique = "Sequence.ID"
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62 naive_output = "no"
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63 naive_output_ca = "None"
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64 naive_output_cg = "None"
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65 naive_output_cm = "None"
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66 naive_output_ce = "None"
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67 naive_output_all = "None"
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68 filter_unique = "remove"
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69 filter_unique_count = '2'
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70 class_filter = '70_70'
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71 empty_region_filter = 'FR1'
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72 fast = 'no'
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73 cmd = [
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74 "bash",
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75 wrapper,
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76 input,
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77 "custom",
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78 str(out_file),
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79 str(out_files_path),
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80 infile_name,
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81 "-",
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82 functionality,
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83 unique,
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84 naive_output,
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85 naive_output_ca,
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86 naive_output_cg,
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87 naive_output_cm,
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88 naive_output_ce,
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89 naive_output_all,
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90 filter_unique,
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91 filter_unique_count,
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92 class_filter,
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93 empty_region_filter,
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94 fast
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95 ]
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96 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
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97 "--rm", # Remove container after running
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98 "-v", f"{input}:{input}",
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99 "-w", str(working_dir),
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100 # Run as current user which allows deletion of files.
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101 # It also mitigates some security considerations
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102 "-u", f"{os.getuid()}:{os.getgid()}",
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103 # Run with default seccomp profile to mitigate mitigation slowdown
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104 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
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105 # This knocks down test runtime from 8 to 6 minutes.
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106 "--security-opt", "seccomp=unconfined",
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107 # Use a mulled container generated with `planemo mull`
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108 "quay.io/biocontainers/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
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109 ] + cmd
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110 with open(temp_dir / "stderr", "wt") as stderr_file:
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111 with open(temp_dir / "stdout", "wt") as stdout_file:
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112 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
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113 stderr=stderr_file, check=True)
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114 yield Path(out_files_path)
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115
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116
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117 def test_check_output(shm_csr_result):
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118 assert shm_csr_result.exists()
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119
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120
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121 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
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122 def test_results_match_validation(shm_csr_result, filename):
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123 with open(Path(shm_csr_result, filename)) as result_h:
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124 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
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125 for line in result_h:
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126 # Skip two faulty lines in shm_overview.
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127 # TODO: Fix the issue.
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128 validation_line = validate_h.readline()
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129 if filename == "shm_overview.txt":
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130 if (line.startswith("RGYW (%)") or
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131 line.startswith("WRCY (%)")):
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132 continue
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133 assert line == validation_line
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134
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135
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136 def test_nt_overview(shm_csr_result):
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137 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
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138 ) as result_h:
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139 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
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140 ) as validate_h:
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141 for line in result_h:
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142 assert line == validate_h.readline()