Mercurial > repos > rhpvorderman > shm_csr

annotate tests/test_shm_csr.py @ 6:ea9d5fc4c001 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
author rhpvorderman
date Wed, 22 Dec 2021 11:29:16 +0000
parents 495a521cf9f2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
1 # Copyright (c) 2021 Leiden University Medical Center
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
2 #
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
3 # Permission is hereby granted, free of charge, to any person obtaining a copy
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
4 # of this software and associated documentation files (the "Software"), to deal
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
5 # in the Software without restriction, including without limitation the rights
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
6 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
7 # copies of the Software, and to permit persons to whom the Software is
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
8 # furnished to do so, subject to the following conditions:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
9 #
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
10 # The above copyright notice and this permission notice shall be included in
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
11 # all copies or substantial portions of the Software.
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
12 #
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
13 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
14 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
15 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
16 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
17 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
18 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
19 # SOFTWARE.
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
20
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
21 import os
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
22 import shutil
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
23 import subprocess
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
24 import sys
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
25 import tempfile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
26 from pathlib import Path
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
27 from xml.etree import ElementTree
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
28 from xml.etree.ElementTree import Element
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
29
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
30 import pytest
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
31
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
32 GIT_ROOT = Path(__file__).parent.parent.absolute()
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
33 TEST_DIR = Path(__file__).parent
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
34 TEST_DATA_DIR = TEST_DIR / "data"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
35 VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
36 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
37
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
38
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
39 def get_container():
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
40 tool = ElementTree.parse(GIT_ROOT / "shm_csr.xml").getroot()
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
41 requirements: Element = tool.find("requirements")
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
42 container = requirements.find("container")
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
43 return container.text
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
44
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
45
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
46 @pytest.fixture(scope="module")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
47 def shm_csr_result():
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
48 temp_dir = Path(tempfile.mkdtemp())
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
49 tool_dir = temp_dir / "shm_csr"
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
50 shutil.copytree(GIT_ROOT, tool_dir)
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
51 working_dir = temp_dir / "working"
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
52 working_dir.mkdir(parents=True)
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
53 output_dir = temp_dir / "outputs"
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
54 output_dir.mkdir(parents=True)
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
55 wrapper = str(tool_dir / "wrapper.sh")
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
56 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
57 out_files_path = output_dir / "results"
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
58 out_file = out_files_path / "result.html"
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
59 infile_name = "input_data"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
60 functionality = "productive"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
61 unique = "Sequence.ID"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
62 naive_output = "no"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
63 naive_output_ca = "None"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
64 naive_output_cg = "None"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
65 naive_output_cm = "None"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
66 naive_output_ce = "None"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
67 naive_output_all = "None"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
68 filter_unique = "remove"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
69 filter_unique_count = '2'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
70 class_filter = '70_70'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
71 empty_region_filter = 'FR1'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
72 fast = 'no'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
73 cmd = [
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
74 "bash",
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
75 wrapper,
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
76 input,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
77 "custom",
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
78 str(out_file),
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
79 str(out_files_path),
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
80 infile_name,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
81 "-",
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
82 functionality,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
83 unique,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
84 naive_output,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
85 naive_output_ca,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
86 naive_output_cg,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
87 naive_output_cm,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
88 naive_output_ce,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
89 naive_output_all,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
90 filter_unique,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
91 filter_unique_count,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
92 class_filter,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
93 empty_region_filter,
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
94 fast
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
95 ]
5
495a521cf9f2 "planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
rhpvorderman
parents: 3
diff changeset
96 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
97 "--rm", # Remove container after running
5
495a521cf9f2 "planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
rhpvorderman
parents: 3
diff changeset
98 "-v", f"{input}:{input}",
495a521cf9f2 "planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
rhpvorderman
parents: 3
diff changeset
99 "-w", str(working_dir),
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
100 # Run as current user which allows deletion of files.
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
101 # It also mitigates some security considerations
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
102 "-u", f"{os.getuid()}:{os.getgid()}",
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
103 # Run with default seccomp profile to mitigate mitigation slowdown
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
104 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
105 # This knocks down test runtime from 8 to 6 minutes.
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
106 "--security-opt", "seccomp=unconfined",
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
107 get_container()] + cmd
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
108 with open(temp_dir / "stderr", "wt") as stderr_file:
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
109 with open(temp_dir / "stdout", "wt") as stdout_file:
5
495a521cf9f2 "planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
rhpvorderman
parents: 3
diff changeset
110 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
3
dced6d52d218 "planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
rhpvorderman
parents: 0
diff changeset
111 stderr=stderr_file, check=True)
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
112 yield Path(out_files_path)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
113
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
114
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
115 def test_check_output(shm_csr_result):
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
116 assert shm_csr_result.exists()
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
117
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
118
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
119 @pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
120 def test_results_match_validation(shm_csr_result, filename):
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
121 with open(Path(shm_csr_result, filename)) as result_h:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
122 with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
123 for line in result_h:
6
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
124 # Skip two faulty lines in shm_overview.
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
125 # TODO: Fix the issue.
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
126 validation_line = validate_h.readline()
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
127 if filename == "shm_overview.txt":
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
128 if (line.startswith("RGYW (%)") or
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
129 line.startswith("WRCY (%)")):
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
130 continue
ea9d5fc4c001 "planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
rhpvorderman
parents: 5
diff changeset
131 assert line == validation_line
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
132
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
133
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
134 def test_nt_overview(shm_csr_result):
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
135 with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
136 ) as result_h:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
137 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
138 ) as validate_h:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
139 for line in result_h:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
140 assert line == validate_h.readline()