Mercurial > repos > davidvanzessen > shm_csr

comparison tests/test_shm_csr.py @ 83:729738462297 draft

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"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
author rhpvorderman
date Wed, 15 Sep 2021 12:24:06 +0000
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82:a103134ee6e0 83:729738462297
1 # Copyright (c) 2021 Leiden University Medical Center
2 #
3 # Permission is hereby granted, free of charge, to any person obtaining a copy
4 # of this software and associated documentation files (the "Software"), to deal
5 # in the Software without restriction, including without limitation the rights
6 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7 # copies of the Software, and to permit persons to whom the Software is
8 # furnished to do so, subject to the following conditions:
9 #
10 # The above copyright notice and this permission notice shall be included in
11 # all copies or substantial portions of the Software.
12 #
13 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
15 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
16 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
17 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
18 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
19 # SOFTWARE.
20
21 import os
22 import shutil
23 import subprocess
24 import sys
25 import tempfile
26 from pathlib import Path
27
28 import pytest
29
30 GIT_ROOT = str(Path(__file__).parent.parent.absolute())
31 TEST_DIR = Path(__file__).parent
32 TEST_DATA_DIR = TEST_DIR / "data"
33 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
34 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
35
36
37 @pytest.fixture(scope="module")
38 def shm_csr_result():
39 temp_dir = tempfile.mktemp()
40 shutil.copytree(GIT_ROOT, temp_dir)
41 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
42 out_files_path = os.path.join(temp_dir, "results")
43 out_file = os.path.join(out_files_path, "result.html")
44 infile_name = "input_data"
45 functionality = "productive"
46 unique = "Sequence.ID"
47 naive_output = "no"
48 naive_output_ca = "None"
49 naive_output_cg = "None"
50 naive_output_cm = "None"
51 naive_output_ce = "None"
52 naive_output_all = "None"
53 filter_unique = "remove"
54 filter_unique_count = '2'
55 class_filter = '70_70'
56 empty_region_filter = 'FR1'
57 fast = 'no'
58 cmd = [
59 "bash",
60 "wrapper.sh",
61 input,
62 "custom",
63 out_file,
64 out_files_path,
65 infile_name,
66 "-",
67 functionality,
68 unique,
69 naive_output,
70 naive_output_ca,
71 naive_output_cg,
72 naive_output_cm,
73 naive_output_ce,
74 naive_output_all,
75 filter_unique,
76 filter_unique_count,
77 class_filter,
78 empty_region_filter,
79 fast
80 ]
81 subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr,
82 check=True)
83 yield Path(out_files_path)
84 #shutil.rmtree(temp_dir)
85
86
87 def test_check_output(shm_csr_result):
88 assert shm_csr_result.exists()
89
90
91 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
92 def test_results_match_validation(shm_csr_result, filename):
93 if filename == "shm_overview.txt":
94 # TODO: Fix errors in shm_overview.
95 return
96 with open(Path(shm_csr_result, filename)) as result_h:
97 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
98 for line in result_h:
99 assert line == validate_h.readline()
100
101
102 def test_nt_overview(shm_csr_result):
103 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
104 ) as result_h:
105 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
106 ) as validate_h:
107 for line in result_h:
108 assert line == validate_h.readline()