Mercurial > repos > davidvanzessen > shm_csr

annotate tests/test_shm_csr.py @ 98:d714f5ea83d7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents 84e9e5c8c101
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
1 # Copyright (c) 2021 Leiden University Medical Center
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
2 #
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
3 # Permission is hereby granted, free of charge, to any person obtaining a copy
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
4 # of this software and associated documentation files (the "Software"), to deal
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
5 # in the Software without restriction, including without limitation the rights
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
6 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
7 # copies of the Software, and to permit persons to whom the Software is
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
8 # furnished to do so, subject to the following conditions:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
9 #
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
10 # The above copyright notice and this permission notice shall be included in
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
11 # all copies or substantial portions of the Software.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
12 #
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
13 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
14 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
15 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
16 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
17 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
18 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
19 # SOFTWARE.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
20
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
21 import os
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
22 import shutil
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
23 import subprocess
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
24 import sys
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
25 import tempfile
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
26 from pathlib import Path
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
27 from xml.etree import ElementTree
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
28 from xml.etree.ElementTree import Element
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
29
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
30 import pytest
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
31
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
32 GIT_ROOT = Path(__file__).parent.parent.absolute()
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
33 TEST_DIR = Path(__file__).parent
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
34 TEST_DATA_DIR = TEST_DIR / "data"
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
35 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
36 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
37
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
38
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
39 def get_container():
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
40 tool = ElementTree.parse(GIT_ROOT / "shm_csr.xml").getroot()
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
41 requirements: Element = tool.find("requirements")
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
42 container = requirements.find("container")
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
43 return container.text
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
44
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
45
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
46 def ignore_files(src, files):
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
47 "Ignore virtualenv and git directories to prevent massive tmp folders"
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
48 if os.path.basename(src) in (".venv", ".git"):
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
49 return files
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
50 return ()
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
51
98
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
52
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
53 def run_shm_csr(
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
54 input=str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2),
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
55 infile_name = "input_data",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
56 functionality = "productive",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
57 unique = "Sequence.ID",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
58 naive_output = "no",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
59 naive_output_ca = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
60 naive_output_cg = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
61 naive_output_cm = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
62 naive_output_ce = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
63 naive_output_all = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
64 naive_output_igm_naive = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
65 naive_output_igm_naive_memory = "None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
66 filter_unique = "remove",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
67 filter_unique_count = '2',
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
68 class_filter = '70_70',
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
69 empty_region_filter = 'FR1',
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
70 # Skip baseline and changeo by default. These tools cannot be modified
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
71 # anyway and take most of the test time to execute. The environment
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
72 # variable can be set to "no" on the CI so the code path is tested
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
73 # at the time a PR is ready.
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
74 run_changeo = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
75 run_baseline = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
76 ):
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
77 temp_dir = Path(tempfile.mkdtemp())
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
78 tool_dir = temp_dir / "shm_csr"
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
79 shutil.copytree(
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
80 GIT_ROOT, tool_dir,
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
81 # Ignore .venv and .git directories.
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
82 ignore=ignore_files)
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
83 working_dir = temp_dir / "working"
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
84 working_dir.mkdir(parents=True)
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
85 output_dir = temp_dir / "outputs"
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
86 output_dir.mkdir(parents=True)
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
87 wrapper = str(tool_dir / "wrapper.sh")
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
88 out_files_path = output_dir / "results"
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
89 out_file = out_files_path / "result.html"
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
90 cmd = [
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
91 "bash",
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
92 wrapper,
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
93 input,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
94 "custom",
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
95 str(out_file),
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
96 str(out_files_path),
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
97 infile_name,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
98 "-",
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
99 functionality,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
100 unique,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
101 naive_output,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
102 naive_output_ca,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
103 naive_output_cg,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
104 naive_output_cm,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
105 naive_output_ce,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
106 naive_output_all,
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
107 naive_output_igm_naive,
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
108 naive_output_igm_naive_memory,
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
109 filter_unique,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
110 filter_unique_count,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
111 class_filter,
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
112 empty_region_filter,
98
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
113 run_changeo,
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
114 run_baseline
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
115 ]
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
116 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
117 "--rm", # Remove container after running
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
118 "-v", f"{input}:{input}",
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
119 "-w", str(working_dir),
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
120 # Run as current user which allows deletion of files.
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
121 # It also mitigates some security considerations
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
122 "-u", f"{os.getuid()}:{os.getgid()}",
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
123 # Run with default seccomp profile to mitigate mitigation slowdown
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
124 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
125 # This knocks down test runtime from 8 to 6 minutes.
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
126 "--security-opt", "seccomp=unconfined",
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
127 # Use a mulled container generated with `planemo mull`
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
128 "quay.io/biocontainers/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
129 ] + cmd
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
130 with open(temp_dir / "stderr", "wt") as stderr_file:
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
131 with open(temp_dir / "stdout", "wt") as stdout_file:
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
132 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
133 stderr=stderr_file, check=True)
98
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
134 return Path(out_files_path)
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
135
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
136
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
137 @pytest.fixture(scope="module")
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
138 def shm_csr_result():
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
139 yield run_shm_csr()
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
140
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
141
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
142 def test_check_output(shm_csr_result):
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
143 assert shm_csr_result.exists()
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
144
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
145
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
146 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
147 def test_results_match_validation(shm_csr_result, filename):
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
148 with open(Path(shm_csr_result, filename)) as result_h:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
149 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
150 for line in result_h:
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
151 # Skip two faulty lines in shm_overview.
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
152 # TODO: Fix the issue.
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
153 validation_line = validate_h.readline()
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
154 if filename == "shm_overview.txt":
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
155 if (line.startswith("RGYW (%)") or
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
156 line.startswith("WRCY (%)")):
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
157 continue
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 83
diff changeset
158 assert line == validation_line
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
159
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
160
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
161 def test_nt_overview(shm_csr_result):
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
162 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
163 ) as result_h:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
164 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
165 ) as validate_h:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
166 for line in result_h:
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents:
diff changeset
167 assert line == validate_h.readline()
98
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
168
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
169
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
170 def test_baseline_succeeds():
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
171 run_shm_csr(
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
172 functionality="unproductive",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
173 empty_region_filter="None",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
174 filter_unique="no",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
175 unique="VGene,DGene,JGene,CDR3.IMGT.seq",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
176 class_filter="101_101_IGA",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
177 naive_output="yes",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
178 run_baseline="yes",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
179 run_changeo="yes",
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents: 94
diff changeset
180 )