Mercurial > repos > rhpvorderman > shm_csr

annotate tests/test_shm_csr.py @ 4:c8f02bce10d0 draft

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"planemo upload commit 05326cc2233eb0fa8beaf4198bd7c1519f2a0bf9"
author rhpvorderman
date Mon, 15 Nov 2021 14:04:10 +0000
parents dced6d52d218
children 495a521cf9f2
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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
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28 import pytest
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29
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30 GIT_ROOT = str(Path(__file__).parent.parent.absolute())
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31 TEST_DIR = Path(__file__).parent
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32 TEST_DATA_DIR = TEST_DIR / "data"
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33 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
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34 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
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35
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36
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37 @pytest.fixture(scope="module")
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38 def shm_csr_result():
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39 temp_dir = Path(tempfile.mkdtemp())
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40 tool_dir = temp_dir / "shm_csr"
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41 shutil.copytree(GIT_ROOT, tool_dir)
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42 working_dir = temp_dir / "working"
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43 working_dir.mkdir(parents=True)
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44 output_dir = temp_dir / "outputs"
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45 output_dir.mkdir(parents=True)
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46 wrapper = str(tool_dir / "wrapper.sh")
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47 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
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48 out_files_path = output_dir / "results"
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49 out_file = out_files_path / "result.html"
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50 infile_name = "input_data"
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51 functionality = "productive"
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52 unique = "Sequence.ID"
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53 naive_output = "no"
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54 naive_output_ca = "None"
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55 naive_output_cg = "None"
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56 naive_output_cm = "None"
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57 naive_output_ce = "None"
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58 naive_output_all = "None"
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59 filter_unique = "remove"
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60 filter_unique_count = '2'
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61 class_filter = '70_70'
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62 empty_region_filter = 'FR1'
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63 fast = 'no'
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64 cmd = [
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65 "bash",
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66 wrapper,
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67 input,
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68 "custom",
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69 str(out_file),
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70 str(out_files_path),
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71 infile_name,
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72 "-",
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73 functionality,
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74 unique,
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75 naive_output,
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76 naive_output_ca,
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77 naive_output_cg,
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78 naive_output_cm,
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79 naive_output_ce,
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80 naive_output_all,
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81 filter_unique,
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82 filter_unique_count,
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83 class_filter,
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84 empty_region_filter,
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85 fast
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86 ]
3
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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(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 #shutil.rmtree(temp_dir)
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93
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94
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95 def test_check_output(shm_csr_result):
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96 assert shm_csr_result.exists()
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97
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98
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99 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
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100 def test_results_match_validation(shm_csr_result, filename):
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101 if filename == "shm_overview.txt":
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102 # TODO: Fix errors in shm_overview.
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103 return
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104 with open(Path(shm_csr_result, filename)) as result_h:
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105 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
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106 for line in result_h:
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107 assert line == validate_h.readline()
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108
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109
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110 def test_nt_overview(shm_csr_result):
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111 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
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112 ) as result_h:
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113 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
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114 ) as validate_h:
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115 for line in result_h:
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rhpvorderman
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diff changeset
116 assert line == validate_h.readline()