annotate tests/test_imgt.py @ 57:33412e85e669 draft

"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
author rhpvorderman
date Wed, 02 Feb 2022 10:50:01 +0000
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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 tempfile
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25 from pathlib import Path
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26 from xml.etree import ElementTree
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27 from xml.etree.ElementTree import Element
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28
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29 import pytest
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30
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31 GIT_ROOT = Path(__file__).parent.parent.absolute()
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32 TEST_DIR = Path(__file__).parent
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33 TEST_DATA_DIR = TEST_DIR / "data"
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34 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
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35 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
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36
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37
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38 def get_container():
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39 tool = ElementTree.parse(GIT_ROOT / "complete_immunerepertoire.xml").getroot()
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40 requirements: Element = tool.find("requirements")
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41 container = requirements.find("container")
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42 return container.text
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44
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45 @pytest.fixture(scope="module")
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46 def imgt_result():
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47 temp_dir = Path(tempfile.mkdtemp())
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48 tool_dir = temp_dir / "imgt"
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49 shutil.copytree(GIT_ROOT, tool_dir)
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50 working_dir = temp_dir / "working"
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51 working_dir.mkdir(parents=True)
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52 output_dir = temp_dir / "outputs"
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53 output_dir.mkdir(parents=True)
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54 wrapper = str(tool_dir / "complete.sh")
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55 sample = CONTROL_NWK377_PB_IGHC_MID1_40nt_2
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56 input = f"\"ID1\" {sample} {sample} \"ID2\" {sample}"
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57 out_files_path = output_dir / "results"
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58 out_files_path.mkdir(parents=True)
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59 out_file = out_files_path / "result.html"
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60 clonaltype = "none"
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61 gene_selection = dict(species="Homo sapiens functional",
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62 locus="TRA")
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63 filterproductive = "yes"
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64 clonality_method = "none"
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65 cmd = [
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66 "bash",
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67 wrapper,
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68 input,
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69 str(out_file),
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70 str(out_files_path),
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71 clonaltype,
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72 gene_selection["species"],
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73 gene_selection["locus"],
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74 filterproductive,
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75 clonality_method
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76 ]
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77 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
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78 "-v", f"{sample}:{sample}",
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79 "-w", str(working_dir),
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80 # Run as current user which allows deletion of files.
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81 # It also mitigates some security considerations
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82 "-u", f"{os.getuid()}:{os.getgid()}",
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83 # Run with default seccomp profile to mitigate mitigation slowdown
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84 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
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85 "--security-opt", "seccomp=unconfined",
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86 get_container()] + cmd
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87 with open(temp_dir / "stderr", "wt") as stderr_file:
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88 with open(temp_dir / "stdout", "wt") as stdout_file:
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89 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
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90 stderr=stderr_file, check=True)
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91 yield Path(out_files_path)
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92
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93
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94 def test_check_output(imgt_result):
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95 assert imgt_result.exists()