Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/cwltool/tests/test_iwdr.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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-1:000000000000 | 0:4f3585e2f14b |
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1 from pathlib import Path | |
2 from typing import Any | |
3 | |
4 from cwltool.main import main | |
5 | |
6 from .util import ( | |
7 get_data, | |
8 get_main_output, | |
9 get_windows_safe_factory, | |
10 needs_docker, | |
11 needs_singularity, | |
12 windows_needs_docker, | |
13 ) | |
14 | |
15 | |
16 @windows_needs_docker | |
17 def test_newline_in_entry() -> None: | |
18 """Files in a InitialWorkingDirectory are created with a newline character.""" | |
19 factory = get_windows_safe_factory() | |
20 echo = factory.make(get_data("tests/wf/iwdr-entry.cwl")) | |
21 assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"} | |
22 | |
23 | |
24 @needs_docker | |
25 def test_empty_file_creation() -> None: | |
26 """An empty file can be created in InitialWorkingDirectory.""" | |
27 err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")]) | |
28 assert err_code == 0 | |
29 | |
30 | |
31 @needs_docker | |
32 def test_directory_literal_with_real_inputs_inside(tmp_path: Path) -> None: | |
33 """Cope with unmoveable files in the output directory created by Docker+IWDR.""" | |
34 err_code, _, _ = get_main_output( | |
35 [ | |
36 "--out", | |
37 str(tmp_path), | |
38 get_data("tests/iwdr_dir_literal_real_file.cwl"), | |
39 "--example={}".format(get_data("tests/__init__.py")), | |
40 ] | |
41 ) | |
42 assert err_code == 0 | |
43 | |
44 | |
45 @needs_docker | |
46 def test_iwdr_permutations(tmp_path_factory: Any) -> None: | |
47 misc = tmp_path_factory.mktemp("misc") | |
48 fifth = str(tmp_path_factory.mktemp("fifth")) | |
49 sixth = str(tmp_path_factory.mktemp("sixth")) | |
50 seventh = str(tmp_path_factory.mktemp("seventh")) | |
51 eighth = str(tmp_path_factory.mktemp("eighth")) | |
52 first = misc / "first" | |
53 first.touch() | |
54 second = misc / "second" | |
55 second.touch() | |
56 third = misc / "third" | |
57 third.touch() | |
58 fourth = misc / "fourth" | |
59 fourth.touch() | |
60 outdir = str(tmp_path_factory.mktemp("outdir")) | |
61 assert ( | |
62 main( | |
63 [ | |
64 "--outdir", | |
65 outdir, | |
66 "--enable-dev", | |
67 get_data("tests/wf/iwdr_permutations.cwl"), | |
68 "--first", | |
69 str(first), | |
70 "--second", | |
71 str(second), | |
72 "--third", | |
73 str(third), | |
74 "--fourth", | |
75 str(fourth), | |
76 "--fifth", | |
77 fifth, | |
78 "--sixth", | |
79 sixth, | |
80 "--seventh", | |
81 seventh, | |
82 "--eighth", | |
83 eighth, | |
84 ] | |
85 ) | |
86 == 0 | |
87 ) | |
88 | |
89 | |
90 @needs_docker | |
91 def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None: | |
92 misc = tmp_path_factory.mktemp("misc") | |
93 fifth = str(tmp_path_factory.mktemp("fifth")) | |
94 sixth = str(tmp_path_factory.mktemp("sixth")) | |
95 seventh = str(tmp_path_factory.mktemp("seventh")) | |
96 eighth = str(tmp_path_factory.mktemp("eighth")) | |
97 first = misc / "first" | |
98 first.touch() | |
99 second = misc / "second" | |
100 second.touch() | |
101 third = misc / "third" | |
102 third.touch() | |
103 fourth = misc / "fourth" | |
104 fourth.touch() | |
105 outdir = str(tmp_path_factory.mktemp("outdir")) | |
106 assert ( | |
107 main( | |
108 [ | |
109 "--outdir", | |
110 outdir, | |
111 "--enable-ext", | |
112 "--enable-dev", | |
113 "--overrides", | |
114 get_data("tests/wf/iwdr_permutations_inplace.yml"), | |
115 get_data("tests/wf/iwdr_permutations.cwl"), | |
116 "--first", | |
117 str(first), | |
118 "--second", | |
119 str(second), | |
120 "--third", | |
121 str(third), | |
122 "--fourth", | |
123 str(fourth), | |
124 "--fifth", | |
125 fifth, | |
126 "--sixth", | |
127 sixth, | |
128 "--seventh", | |
129 seventh, | |
130 "--eighth", | |
131 eighth, | |
132 ] | |
133 ) | |
134 == 0 | |
135 ) | |
136 | |
137 | |
138 @needs_singularity | |
139 def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None: | |
140 misc = tmp_path_factory.mktemp("misc") | |
141 fifth = str(tmp_path_factory.mktemp("fifth")) | |
142 sixth = str(tmp_path_factory.mktemp("sixth")) | |
143 seventh = str(tmp_path_factory.mktemp("seventh")) | |
144 eighth = str(tmp_path_factory.mktemp("eighth")) | |
145 first = misc / "first" | |
146 first.touch() | |
147 second = misc / "second" | |
148 second.touch() | |
149 third = misc / "third" | |
150 third.touch() | |
151 fourth = misc / "fourth" | |
152 fourth.touch() | |
153 outdir = str(tmp_path_factory.mktemp("outdir")) | |
154 assert ( | |
155 main( | |
156 [ | |
157 "--outdir", | |
158 outdir, | |
159 "--enable-dev", | |
160 "--singularity", | |
161 get_data("tests/wf/iwdr_permutations.cwl"), | |
162 "--first", | |
163 str(first), | |
164 "--second", | |
165 str(second), | |
166 "--third", | |
167 str(third), | |
168 "--fourth", | |
169 str(fourth), | |
170 "--fifth", | |
171 fifth, | |
172 "--sixth", | |
173 sixth, | |
174 "--seventh", | |
175 seventh, | |
176 "--eighth", | |
177 eighth, | |
178 ] | |
179 ) | |
180 == 0 | |
181 ) | |
182 | |
183 | |
184 @needs_singularity | |
185 def test_iwdr_permutations_singularity_inplace(tmp_path_factory: Any) -> None: | |
186 misc = tmp_path_factory.mktemp("misc") | |
187 fifth = str(tmp_path_factory.mktemp("fifth")) | |
188 sixth = str(tmp_path_factory.mktemp("sixth")) | |
189 seventh = str(tmp_path_factory.mktemp("seventh")) | |
190 eighth = str(tmp_path_factory.mktemp("eighth")) | |
191 first = misc / "first" | |
192 first.touch() | |
193 second = misc / "second" | |
194 second.touch() | |
195 third = misc / "third" | |
196 third.touch() | |
197 fourth = misc / "fourth" | |
198 fourth.touch() | |
199 outdir = str(tmp_path_factory.mktemp("outdir")) | |
200 assert ( | |
201 main( | |
202 [ | |
203 "--outdir", | |
204 outdir, | |
205 "--singularity", | |
206 "--enable-ext", | |
207 "--enable-dev", | |
208 "--overrides", | |
209 get_data("tests/wf/iwdr_permutations_inplace.yml"), | |
210 get_data("tests/wf/iwdr_permutations.cwl"), | |
211 "--first", | |
212 str(first), | |
213 "--second", | |
214 str(second), | |
215 "--third", | |
216 str(third), | |
217 "--fourth", | |
218 str(fourth), | |
219 "--fifth", | |
220 fifth, | |
221 "--sixth", | |
222 sixth, | |
223 "--seventh", | |
224 seventh, | |
225 "--eighth", | |
226 eighth, | |
227 ] | |
228 ) | |
229 == 0 | |
230 ) |