Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/tests/test_ext.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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0
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1 from __future__ import absolute_import
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2
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3 import os
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4 import shutil
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5 import tempfile
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6 import sys
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7 import re
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8 from io import StringIO
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9
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10 import pytest
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11
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12 from cwltool.main import main
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13 import cwltool.process
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14
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15
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16 from .util import get_data, needs_docker, temp_dir, windows_needs_docker
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17
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18
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19 @needs_docker
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20 def test_missing_enable_ext():
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21 # Require that --enable-ext is provided.
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22 assert main([get_data('tests/wf/listing_deep.cwl'), get_data('tests/listing-job.yml')]) != 0
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23
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24 @needs_docker
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25 def test_listing_deep():
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26 params = ["--enable-ext", get_data('tests/wf/listing_deep.cwl'),
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27 get_data('tests/listing-job.yml')]
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28 assert main(params) == 0
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29
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30 @needs_docker
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31 def test_cwltool_options():
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32 try:
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33 opt = os.environ.get("CWLTOOL_OPTIONS")
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34 os.environ["CWLTOOL_OPTIONS"] = "--enable-ext"
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35 params = [get_data('tests/wf/listing_deep.cwl'),
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36 get_data('tests/listing-job.yml')]
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37 assert main(params) == 0
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38 finally:
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39 if opt is not None:
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40 os.environ["CWLTOOL_OPTIONS"] = opt
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41 else:
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42 del os.environ["CWLTOOL_OPTIONS"]
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43
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44 @needs_docker
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45 def test_listing_shallow():
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46 # This fails on purpose, because it tries to access listing in a subdirectory
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47 # the same way that listing_deep does, but it shouldn't be expanded.
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48 params = ["--enable-ext", get_data('tests/wf/listing_shallow.cwl'),
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49 get_data('tests/listing-job.yml')]
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50 assert main(params) != 0
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51
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52 @needs_docker
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53 def test_listing_none():
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54 # This fails on purpose, because it tries to access listing but it shouldn't be there.
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55 params = ["--enable-ext", get_data('tests/wf/listing_none.cwl'),
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56 get_data('tests/listing-job.yml')]
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57 assert main(params) != 0
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58
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59 @needs_docker
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60 def test_listing_v1_0():
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61 # Default behavior in 1.0 is deep expansion.
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62 assert main([get_data('tests/wf/listing_v1_0.cwl'), get_data('tests/listing-job.yml')]) == 0
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63
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64 @pytest.mark.skip(reason="This is not the default behaviour yet")
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65 @needs_docker
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66 def test_listing_v1_1():
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67 # Default behavior in 1.1 will be no expansion
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68 assert main([get_data('tests/wf/listing_v1_1.cwl'), get_data('tests/listing-job.yml')]) != 0
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69
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70 @needs_docker
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71 def test_double_overwrite(tmpdir):
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72 with temp_dir() as tmp:
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73 tmp_name = os.path.join(tmp, "value")
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74
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75 before_value, expected_value = "1", "3"
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76
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77 with open(tmp_name, "w") as f:
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78 f.write(before_value)
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79
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80 assert main(["--enable-ext", "--outdir", str(tmpdir),
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81 get_data('tests/wf/mut2.cwl'), "-a", tmp_name]) == 0
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82
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83 with open(tmp_name, "r") as f:
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84 actual_value = f.read()
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85
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86 assert actual_value == expected_value
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87
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88 @needs_docker
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89 def test_disable_file_overwrite_without_ext():
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90 with temp_dir() as tmp:
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91 with temp_dir() as out:
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92 tmp_name = os.path.join(tmp, "value")
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93 out_name = os.path.join(out, "value")
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94
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95 before_value, expected_value = "1", "2"
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96
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97 with open(tmp_name, "w") as f:
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98 f.write(before_value)
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99
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100 assert main(["--outdir", out, get_data('tests/wf/updateval.cwl'), "-r", tmp_name]) == 0
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101
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102 with open(tmp_name, "r") as f:
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103 tmp_value = f.read()
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104 with open(out_name, "r") as f:
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105 out_value = f.read()
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106
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107 assert tmp_value == before_value
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108 assert out_value == expected_value
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109
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110 @needs_docker
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111 def test_disable_dir_overwrite_without_ext():
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112 with temp_dir() as tmp:
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113 with temp_dir() as out:
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114
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115 assert main(["--outdir", out, get_data('tests/wf/updatedir.cwl'), "-r", tmp]) == 0
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116
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117 assert not os.listdir(tmp)
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118 assert os.listdir(out)
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119
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120 @needs_docker
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121 def test_disable_file_creation_in_outdir_with_ext():
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122 with temp_dir() as tmp:
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123 with temp_dir() as out:
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124
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125 tmp_name = os.path.join(tmp, "value")
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126 out_name = os.path.join(out, "value")
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127
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128 before_value, expected_value = "1", "2"
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129
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130 with open(tmp_name, "w") as f:
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131 f.write(before_value)
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132
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133 params = ["--enable-ext", "--leave-outputs", "--outdir",
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134 out, get_data('tests/wf/updateval_inplace.cwl'), "-r", tmp_name]
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135 assert main(params) == 0
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136
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137 with open(tmp_name, "r") as f:
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138 tmp_value = f.read()
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139
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140 assert tmp_value == expected_value
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141 assert not os.path.exists(out_name)
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142
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143 @needs_docker
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144 def test_disable_dir_creation_in_outdir_with_ext():
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145 with temp_dir() as tmp:
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146 with temp_dir() as out:
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147 params = ["--enable-ext", "--leave-outputs", "--outdir",
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148 out, get_data('tests/wf/updatedir_inplace.cwl'), "-r", tmp]
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149 assert main(params) == 0
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150
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151 assert os.listdir(tmp)
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152 assert not os.listdir(out)
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153
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154 @needs_docker
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155 def test_write_write_conflict():
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156 with temp_dir('tmp') as tmp:
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157 tmp_name = os.path.join(tmp, "value")
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158
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159 before_value, expected_value = "1", "2"
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160
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161 with open(tmp_name, "w") as f:
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162 f.write(before_value)
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163
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164 assert main(["--enable-ext", get_data('tests/wf/mut.cwl'), "-a", tmp_name]) != 0
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165
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166 with open(tmp_name, "r") as f:
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167 tmp_value = f.read()
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168
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169 assert tmp_value == expected_value
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170
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171 @pytest.mark.skip(reason="This test is non-deterministic")
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172 def test_read_write_conflict():
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173 with temp_dir('tmp') as tmp:
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174 tmp_name = os.path.join(tmp, "value")
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175
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176 with open(tmp_name, "w") as f:
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177 f.write("1")
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178
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179 assert main(["--enable-ext", get_data('tests/wf/mut3.cwl'), "-a", tmp_name]) != 0
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180
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181 @needs_docker
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182 def test_require_prefix_networkaccess():
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183 assert main(["--enable-ext", get_data('tests/wf/networkaccess.cwl')]) == 0
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184 assert main([get_data('tests/wf/networkaccess.cwl')]) != 0
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185 assert main(["--enable-ext", get_data('tests/wf/networkaccess-fail.cwl')]) != 0
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186
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187 @needs_docker
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188 def test_require_prefix_workreuse(tmpdir):
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189 assert main(["--enable-ext", '--outdir', str(tmpdir), get_data('tests/wf/workreuse.cwl')]) == 0
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190 assert main([get_data('tests/wf/workreuse.cwl')]) != 0
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191 assert main(["--enable-ext", get_data('tests/wf/workreuse-fail.cwl')]) != 0
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192
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193 @windows_needs_docker
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194 def test_require_prefix_timelimit():
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195 assert main(["--enable-ext", get_data('tests/wf/timelimit.cwl')]) == 0
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196 assert main([get_data('tests/wf/timelimit.cwl')]) != 0
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197 assert main(["--enable-ext", get_data('tests/wf/timelimit-fail.cwl')]) != 0
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198
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199 def test_warn_large_inputs():
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200 was = cwltool.process.FILE_COUNT_WARNING
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201 try:
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202 stream = StringIO()
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203
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204 cwltool.process.FILE_COUNT_WARNING = 3
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205 main([get_data('tests/wf/listing_v1_0.cwl'), get_data('tests/listing2-job.yml')],
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206 stderr=stream)
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207
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208 assert "Recursive directory listing has resulted in a large number of File" in re.sub("\n *", " ", stream.getvalue())
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209 finally:
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210 cwltool.process.FILE_COUNT_WARNING = was