Mercurial > repos > davidvanzessen > argalaxy_tools

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
author rhpvorderman
date Wed, 02 Feb 2022 10:50:01 +0000
parents 7ae6b6b5d890
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
56
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
1 # Copyright (c) 2021 Leiden University Medical Center
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
2 #
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
3 # Permission is hereby granted, free of charge, to any person obtaining a copy
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
4 # of this software and associated documentation files (the "Software"), to deal
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
5 # in the Software without restriction, including without limitation the rights
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
6 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
7 # copies of the Software, and to permit persons to whom the Software is
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
8 # furnished to do so, subject to the following conditions:
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
9 #
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
10 # The above copyright notice and this permission notice shall be included in
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
11 # all copies or substantial portions of the Software.
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
12 #
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
13 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
14 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
15 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
16 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
17 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
18 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
19 # SOFTWARE.
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
20
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
21 import os
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
22 import shutil
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
23 import subprocess
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
24 import tempfile
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
25 from pathlib import Path
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
26 from xml.etree import ElementTree
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
27 from xml.etree.ElementTree import Element
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
28
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
29 import pytest
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
30
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
31 GIT_ROOT = Path(__file__).parent.parent.absolute()
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
32 TEST_DIR = Path(__file__).parent
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
33 TEST_DATA_DIR = TEST_DIR / "data"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
34 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
35 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
36
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
37
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
38 def get_container():
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
39 tool = ElementTree.parse(GIT_ROOT / "complete_immunerepertoire.xml").getroot()
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
40 requirements: Element = tool.find("requirements")
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
41 container = requirements.find("container")
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
42 return container.text
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
43
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
44
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
45 @pytest.fixture(scope="module")
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
46 def imgt_result():
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
47 temp_dir = Path(tempfile.mkdtemp())
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
48 tool_dir = temp_dir / "imgt"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
49 shutil.copytree(GIT_ROOT, tool_dir)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
50 working_dir = temp_dir / "working"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
51 working_dir.mkdir(parents=True)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
52 output_dir = temp_dir / "outputs"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
53 output_dir.mkdir(parents=True)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
54 wrapper = str(tool_dir / "complete.sh")
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
55 sample = CONTROL_NWK377_PB_IGHC_MID1_40nt_2
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
56 input = f"\"ID1\" {sample} {sample} \"ID2\" {sample}"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
57 out_files_path = output_dir / "results"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
58 out_files_path.mkdir(parents=True)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
59 out_file = out_files_path / "result.html"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
60 clonaltype = "none"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
61 gene_selection = dict(species="Homo sapiens functional",
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
62 locus="TRA")
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
63 filterproductive = "yes"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
64 clonality_method = "none"
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
65 cmd = [
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
66 "bash",
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
67 wrapper,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
68 input,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
69 str(out_file),
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
70 str(out_files_path),
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
71 clonaltype,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
72 gene_selection["species"],
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
73 gene_selection["locus"],
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
74 filterproductive,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
75 clonality_method
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
76 ]
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
77 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
78 "-v", f"{sample}:{sample}",
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
79 "-w", str(working_dir),
57
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
80 # Run as current user which allows deletion of files.
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
81 # It also mitigates some security considerations
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
82 "-u", f"{os.getuid()}:{os.getgid()}",
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
83 # Run with default seccomp profile to mitigate mitigation slowdown
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
84 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
33412e85e669 "planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents: 56
diff changeset
85 "--security-opt", "seccomp=unconfined",
56
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
86 get_container()] + cmd
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
87 with open(temp_dir / "stderr", "wt") as stderr_file:
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
88 with open(temp_dir / "stdout", "wt") as stdout_file:
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
89 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
90 stderr=stderr_file, check=True)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
91 yield Path(out_files_path)
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
92
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
93
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
94 def test_check_output(imgt_result):
7ae6b6b5d890 "planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
rhpvorderman
parents:
diff changeset
95 assert imgt_result.exists()