Mercurial > repos > davidvanzessen > shm_csr

annotate tests/test_shm_csr.py @ 94:84e9e5c8c101 draft

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"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
author rhpvorderman
date Fri, 24 Mar 2023 16:58:28 +0000
parents 8fcf31272f6e
children d714f5ea83d7
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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 def ignore_files(src, files):
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47 "Ignore virtualenv and git directories to prevent massive tmp folders"
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48 if os.path.basename(src) in (".venv", ".git"):
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49 return files
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50 return ()
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51
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52 @pytest.fixture(scope="module")
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53 def shm_csr_result():
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54 temp_dir = Path(tempfile.mkdtemp())
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55 tool_dir = temp_dir / "shm_csr"
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56 shutil.copytree(
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57 GIT_ROOT, tool_dir,
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58 # Ignore .venv and .git directories.
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59 ignore=ignore_files)
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60 working_dir = temp_dir / "working"
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61 working_dir.mkdir(parents=True)
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62 output_dir = temp_dir / "outputs"
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63 output_dir.mkdir(parents=True)
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64 wrapper = str(tool_dir / "wrapper.sh")
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65 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
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66 out_files_path = output_dir / "results"
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67 out_file = out_files_path / "result.html"
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68 infile_name = "input_data"
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69 functionality = "productive"
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70 unique = "Sequence.ID"
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71 naive_output = "no"
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72 naive_output_ca = "None"
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73 naive_output_cg = "None"
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74 naive_output_cm = "None"
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75 naive_output_ce = "None"
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76 naive_output_all = "None"
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77 naive_output_igm_naive = "None"
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78 naive_output_igm_naive_memory = "None"
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79 filter_unique = "remove"
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80 filter_unique_count = '2'
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81 class_filter = '70_70'
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82 empty_region_filter = 'FR1'
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83 # Skip baseline and changeo by default. These tools cannot be modified
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84 # anyway and take most of the test time to execute. The environment
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85 # variable can be set to "no" on the CI so the code path is tested
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86 # at the time a PR is ready.
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87 fast = os.environ.get("SHM_CSR_FAST", "yes")
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88 cmd = [
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89 "bash",
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90 wrapper,
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91 input,
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92 "custom",
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93 str(out_file),
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94 str(out_files_path),
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95 infile_name,
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96 "-",
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97 functionality,
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98 unique,
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99 naive_output,
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100 naive_output_ca,
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101 naive_output_cg,
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102 naive_output_cm,
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103 naive_output_ce,
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104 naive_output_all,
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105 naive_output_igm_naive,
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106 naive_output_igm_naive_memory,
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107 filter_unique,
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108 filter_unique_count,
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109 class_filter,
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110 empty_region_filter,
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111 fast
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112 ]
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113 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
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114 "--rm", # Remove container after running
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115 "-v", f"{input}:{input}",
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116 "-w", str(working_dir),
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117 # Run as current user which allows deletion of files.
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118 # It also mitigates some security considerations
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119 "-u", f"{os.getuid()}:{os.getgid()}",
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120 # Run with default seccomp profile to mitigate mitigation slowdown
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121 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
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122 # This knocks down test runtime from 8 to 6 minutes.
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123 "--security-opt", "seccomp=unconfined",
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124 # Use a mulled container generated with `planemo mull`
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125 "quay.io/biocontainers/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
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126 ] + cmd
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127 with open(temp_dir / "stderr", "wt") as stderr_file:
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128 with open(temp_dir / "stdout", "wt") as stdout_file:
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129 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
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130 stderr=stderr_file, check=True)
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131 yield Path(out_files_path)
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132
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133
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134 def test_check_output(shm_csr_result):
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135 assert shm_csr_result.exists()
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136
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137
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138 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
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139 def test_results_match_validation(shm_csr_result, filename):
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140 with open(Path(shm_csr_result, filename)) as result_h:
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141 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
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142 for line in result_h:
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143 # Skip two faulty lines in shm_overview.
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144 # TODO: Fix the issue.
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145 validation_line = validate_h.readline()
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146 if filename == "shm_overview.txt":
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147 if (line.startswith("RGYW (%)") or
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148 line.startswith("WRCY (%)")):
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149 continue
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150 assert line == validation_line
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151
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152
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153 def test_nt_overview(shm_csr_result):
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154 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
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155 ) as result_h:
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156 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
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157 ) as validate_h:
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158 for line in result_h:
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159 assert line == validate_h.readline()