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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_examples.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import json
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2 import logging
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3 import os
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4 import stat
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5 import sys
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6 from io import BytesIO, StringIO
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7 import pytest
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8 from typing_extensions import Text
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9
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10 import schema_salad.validate
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11
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12 import cwltool.checker
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13 import cwltool.expression as expr
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14 import cwltool.factory
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15 import cwltool.pathmapper
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16 import cwltool.process
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17 import cwltool.workflow
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18 from cwltool.context import RuntimeContext
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19 from cwltool.errors import WorkflowException
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20 from cwltool.main import main
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21 from cwltool.utils import onWindows
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22 from cwltool.resolver import Path
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23 from cwltool.process import CWL_IANA
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24 from cwltool.sandboxjs import JavascriptException
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25 from .util import (get_data, get_main_output, get_windows_safe_factory, subprocess,
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26 needs_docker, working_directory, needs_singularity, temp_dir, windows_needs_docker)
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27
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28 import six
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29
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30 try:
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31 reload
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32 except: # pylint: disable=bare-except
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33 try:
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34 from imp import reload
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35 except:
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36 from importlib import reload
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37
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38 sys.argv = ['']
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39
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40 expression_match = [
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41 ("(foo)", True),
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42 ("(foo.bar)", True),
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43 ("(foo['bar'])", True),
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44 ("(foo[\"bar\"])", True),
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45 ("(foo.bar.baz)", True),
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46 ("(foo['bar'].baz)", True),
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47 ("(foo['bar']['baz'])", True),
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48 ("(foo['b\\'ar']['baz'])", True),
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49 ("(foo['b ar']['baz'])", True),
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50 ("(foo_bar)", True),
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51
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52 ("(foo.[\"bar\"])", False),
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53 ("(.foo[\"bar\"])", False),
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54 ("(foo [\"bar\"])", False),
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55 ("( foo[\"bar\"])", False),
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56 ("(foo[bar].baz)", False),
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57 ("(foo['bar\"].baz)", False),
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58 ("(foo['bar].baz)", False),
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59 ("{foo}", False),
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60 ("(foo.bar", False),
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61 ("foo.bar)", False),
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62 ("foo.b ar)", False),
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63 ("foo.b\'ar)", False),
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64 ("(foo+bar", False),
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65 ("(foo bar", False)
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66 ]
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67
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68
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69 @pytest.mark.parametrize('expression,expected', expression_match)
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70 def test_expression_match(expression, expected):
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71 match = expr.param_re.match(expression)
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72 assert (match is not None) == expected
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73
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74
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75 interpolate_input = {
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76 "foo": {
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77 "bar": {
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78 "baz": "zab1"
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79 },
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80 "b ar": {
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81 "baz": 2
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82 },
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83 "b'ar": {
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84 "baz": True
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85 },
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86 'b"ar': {
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87 "baz": None
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88 }
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89 },
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90 "lst": ["A", "B"]
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91 }
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92
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93 interpolate_parameters = [
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94 ("$(foo)", interpolate_input["foo"]),
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95
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96 ("$(foo.bar)", interpolate_input["foo"]["bar"]),
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97 ("$(foo['bar'])", interpolate_input["foo"]["bar"]),
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98 ("$(foo[\"bar\"])", interpolate_input["foo"]["bar"]),
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99
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100 ("$(foo.bar.baz)", interpolate_input['foo']['bar']['baz']),
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101 ("$(foo['bar'].baz)", interpolate_input['foo']['bar']['baz']),
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102 ("$(foo['bar'][\"baz\"])", interpolate_input['foo']['bar']['baz']),
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103 ("$(foo.bar['baz'])", interpolate_input['foo']['bar']['baz']),
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104
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105 ("$(foo['b\\'ar'].baz)", True),
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106 ("$(foo[\"b'ar\"].baz)", True),
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107 ("$(foo['b\\\"ar'].baz)", None),
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108
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109 ("$(lst[0])", "A"),
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110 ("$(lst[1])", "B"),
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111 ("$(lst.length)", 2),
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112 ("$(lst['length'])", 2),
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113
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114 ("-$(foo.bar)", """-{"baz": "zab1"}"""),
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115 ("-$(foo['bar'])", """-{"baz": "zab1"}"""),
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116 ("-$(foo[\"bar\"])", """-{"baz": "zab1"}"""),
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117
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118 ("-$(foo.bar.baz)", "-zab1"),
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119 ("-$(foo['bar'].baz)", "-zab1"),
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120 ("-$(foo['bar'][\"baz\"])", "-zab1"),
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121 ("-$(foo.bar['baz'])", "-zab1"),
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122
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123 ("-$(foo['b ar'].baz)", "-2"),
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124 ("-$(foo['b\\'ar'].baz)", "-true"),
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125 ("-$(foo[\"b\\'ar\"].baz)", "-true"),
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126 ("-$(foo['b\\\"ar'].baz)", "-null"),
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127
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128 ("$(foo.bar) $(foo.bar)", """{"baz": "zab1"} {"baz": "zab1"}"""),
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129 ("$(foo['bar']) $(foo['bar'])", """{"baz": "zab1"} {"baz": "zab1"}"""),
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130 ("$(foo[\"bar\"]) $(foo[\"bar\"])", """{"baz": "zab1"} {"baz": "zab1"}"""),
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131
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132 ("$(foo.bar.baz) $(foo.bar.baz)", "zab1 zab1"),
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133 ("$(foo['bar'].baz) $(foo['bar'].baz)", "zab1 zab1"),
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134 ("$(foo['bar'][\"baz\"]) $(foo['bar'][\"baz\"])", "zab1 zab1"),
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135 ("$(foo.bar['baz']) $(foo.bar['baz'])", "zab1 zab1"),
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136
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137 ("$(foo['b ar'].baz) $(foo['b ar'].baz)", "2 2"),
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138 ("$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)", "true true"),
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139 ("$(foo[\"b\\'ar\"].baz) $(foo[\"b\\'ar\"].baz)", "true true"),
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140 ("$(foo['b\\\"ar'].baz) $(foo['b\\\"ar'].baz)", "null null")
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141 ]
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142
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143
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144 @pytest.mark.parametrize('pattern,expected', interpolate_parameters)
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145 def test_expression_interpolate(pattern, expected):
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146 assert expr.interpolate(pattern, interpolate_input) == expected
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147
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148 interpolate_bad_parameters = [
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149 ("$(fooz)"),
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150 ("$(foo.barz)"),
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151 ("$(foo['barz'])"),
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152 ("$(foo[\"barz\"])"),
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153
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154 ("$(foo.bar.bazz)"),
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155 ("$(foo['bar'].bazz)"),
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156 ("$(foo['bar'][\"bazz\"])"),
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157 ("$(foo.bar['bazz'])"),
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158
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159 ("$(foo['b\\'ar'].bazz)"),
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160 ("$(foo[\"b'ar\"].bazz)"),
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161 ("$(foo['b\\\"ar'].bazz)"),
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162
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163 ("$(lst[O])"), # not "0" the number, but the letter O
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164 ("$(lst[2])"),
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165 ("$(lst.lengthz)"),
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166 ("$(lst['lengthz'])"),
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167
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168 ("-$(foo.barz)"),
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169 ("-$(foo['barz'])"),
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170 ("-$(foo[\"barz\"])"),
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171
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172 ("-$(foo.bar.bazz)"),
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173 ("-$(foo['bar'].bazz)"),
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174 ("-$(foo['bar'][\"bazz\"])"),
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175 ("-$(foo.bar['bazz'])"),
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176
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177 ("-$(foo['b ar'].bazz)"),
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178 ("-$(foo['b\\'ar'].bazz)"),
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179 ("-$(foo[\"b\\'ar\"].bazz)"),
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180 ("-$(foo['b\\\"ar'].bazz)"),
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181 ]
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182
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183 @pytest.mark.parametrize('pattern', interpolate_bad_parameters)
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184 def test_expression_interpolate_failures(pattern):
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185 result = None
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186 try:
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187 result = expr.interpolate(pattern, interpolate_input)
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188 except JavascriptException:
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189 return
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190 assert false, 'Should have produced a JavascriptException, got "{}".'.format(result)
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191
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192
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193 @windows_needs_docker
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194 def test_factory():
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195 factory = get_windows_safe_factory()
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196 echo = factory.make(get_data("tests/echo.cwl"))
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197
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198 assert echo(inp="foo") == {"out": "foo\n"}
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199
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200
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201 def test_factory_bad_outputs():
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202 factory = cwltool.factory.Factory()
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203
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204 with pytest.raises(schema_salad.validate.ValidationException):
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205 factory.make(get_data("tests/echo_broken_outputs.cwl"))
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206
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207
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208 def test_factory_default_args():
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209 factory = cwltool.factory.Factory()
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210
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211 assert factory.runtime_context.use_container is True
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212 assert factory.runtime_context.on_error == "stop"
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213
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214
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215 def test_factory_redefined_args():
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216 runtime_context = RuntimeContext()
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217 runtime_context.use_container = False
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218 runtime_context.on_error = "continue"
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219 factory = cwltool.factory.Factory(runtime_context=runtime_context)
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220
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221 assert factory.runtime_context.use_container is False
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222 assert factory.runtime_context.on_error == "continue"
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223
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224
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225 def test_factory_partial_scatter():
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226 runtime_context = RuntimeContext()
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227 runtime_context.on_error = "continue"
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228 factory = cwltool.factory.Factory(runtime_context=runtime_context)
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229
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230 with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
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231 factory.make(get_data("tests/wf/scatterfail.cwl"))()
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232
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233 err = err_info.value
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234 assert err.out["out"][0]["checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
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235 assert err.out["out"][1] is None
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236 assert err.out["out"][2]["checksum"] == 'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436'
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237
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238
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239 def test_factory_partial_output():
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240 runtime_context = RuntimeContext()
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241 runtime_context.on_error = "continue"
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242 factory = cwltool.factory.Factory(runtime_context=runtime_context)
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243
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244 with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
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245 factory.make(get_data("tests/wf/wffail.cwl"))()
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246
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247 err = err_info.value
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248 assert err.out["out1"]["checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
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249 assert err.out["out2"] is None
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250
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251
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252 def test_scandeps():
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253 obj = {
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254 "id": "file:///example/foo.cwl",
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255 "steps": [
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256 {
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257 "id": "file:///example/foo.cwl#step1",
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258 "inputs": [{
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259 "id": "file:///example/foo.cwl#input1",
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260 "default": {
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261 "class": "File",
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262 "location": "file:///example/data.txt"
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263 }
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264 }],
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265 "run": {
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266 "id": "file:///example/bar.cwl",
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267 "inputs": [{
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268 "id": "file:///example/bar.cwl#input2",
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269 "default": {
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270 "class": "Directory",
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271 "location": "file:///example/data2",
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272 "listing": [{
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273 "class": "File",
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274 "location": "file:///example/data3.txt",
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275 "secondaryFiles": [{
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276 "class": "File",
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277 "location": "file:///example/data5.txt"
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278 }]
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279 }]
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280 },
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281 }, {
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282 "id": "file:///example/bar.cwl#input3",
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283 "default": {
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284 "class": "Directory",
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285 "listing": [{
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286 "class": "File",
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287 "location": "file:///example/data4.txt"
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288 }]
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289 }
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290 }, {
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291 "id": "file:///example/bar.cwl#input4",
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292 "default": {
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293 "class": "File",
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294 "contents": "file literal"
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295 }
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296 }]
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297 }
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298 }
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299 ]
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300 }
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301
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302 def loadref(base, p):
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303 if isinstance(p, dict):
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304 return p
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305 raise Exception("test case can't load things")
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306
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307 scanned_deps = cwltool.process.scandeps(
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308 obj["id"], obj,
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309 {"$import", "run"},
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310 {"$include", "$schemas", "location"},
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311 loadref)
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312
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313 scanned_deps.sort(key=lambda k: k["basename"])
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314
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315 expected_deps = [
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316 {"basename": "bar.cwl",
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317 "nameroot": "bar",
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318 "class": "File",
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319 "format": CWL_IANA,
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320 "nameext": ".cwl",
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321 "location": "file:///example/bar.cwl"},
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322 {"basename": "data.txt",
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323 "nameroot": "data",
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324 "class": "File",
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325 "nameext": ".txt",
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326 "location": "file:///example/data.txt"},
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327 {"basename": "data2",
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328 "class": "Directory",
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329 "location": "file:///example/data2",
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330 "listing": [
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331 {"basename": "data3.txt",
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332 "nameroot": "data3",
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333 "class": "File",
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334 "nameext": ".txt",
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335 "location": "file:///example/data3.txt",
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336 "secondaryFiles": [
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337 {"class": "File",
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338 "basename": "data5.txt",
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339 "location": "file:///example/data5.txt",
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340 "nameext": ".txt",
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341 "nameroot": "data5"
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342 }]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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343 }]
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344 }, {
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345 "basename": "data4.txt",
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346 "nameroot": "data4",
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347 "class": "File",
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348 "nameext": ".txt",
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349 "location": "file:///example/data4.txt"
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350 }]
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351
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352 assert scanned_deps == expected_deps
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353
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354 scanned_deps = cwltool.process.scandeps(
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355 obj["id"], obj,
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356 set(("run"), ),
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357 set(), loadref)
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358
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359 scanned_deps.sort(key=lambda k: k["basename"])
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360
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361 expected_deps = [{
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362 "basename": "bar.cwl",
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363 "nameroot": "bar",
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364 "format": CWL_IANA,
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365 "class": "File",
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366 "nameext": ".cwl",
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367 "location": "file:///example/bar.cwl"
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368 }]
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369
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370 assert scanned_deps == expected_deps
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371
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372 def test_trick_scandeps():
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373 if sys.version_info[0] < 3:
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374 stream = BytesIO()
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375 else:
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376 stream = StringIO()
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377
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378 main(["--print-deps", "--debug", get_data("tests/wf/trick_defaults.cwl")], stdout=stream)
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379 assert json.loads(stream.getvalue())["secondaryFiles"][0]["location"][:2] != "_:"
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380
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381
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382 def test_input_deps():
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383 if sys.version_info[0] < 3:
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384 stream = BytesIO()
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385 else:
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386 stream = StringIO()
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387
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388 main(["--print-input-deps", get_data("tests/wf/count-lines1-wf.cwl"),
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389 get_data("tests/wf/wc-job.json")], stdout=stream)
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guerler
parents:
diff changeset
390
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
391 expected = {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
392 "location": "wc-job.json",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
393 "format": CWL_IANA,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
394 "secondaryFiles": [{"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
395 "location": "whale.txt",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
396 "basename": "whale.txt",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
397 "nameroot": "whale",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
398 "nameext": ".txt"}]}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
399 assert json.loads(stream.getvalue()) == expected
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
400
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
401
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
402 def test_input_deps_cmdline_opts():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
403 if sys.version_info[0] < 3:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
404 stream = BytesIO()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
405 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
406 stream = StringIO()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
407
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
408 main(["--print-input-deps",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
409 get_data("tests/wf/count-lines1-wf.cwl"),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
410 "--file1", get_data("tests/wf/whale.txt")], stdout=stream)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
411 expected = {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
412 "location": "",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
413 "format": CWL_IANA,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
414 "secondaryFiles": [{"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
415 "location": "whale.txt",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
416 "basename": "whale.txt",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
417 "nameroot": "whale",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
418 "nameext": ".txt"}]}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
419 assert json.loads(stream.getvalue()) == expected
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
420
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
421
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
422 def test_input_deps_cmdline_opts_relative_deps_cwd():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
423 if sys.version_info[0] < 3:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
424 stream = BytesIO()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
425 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
426 stream = StringIO()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
427
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
428 data_path = get_data("tests/wf/whale.txt")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
429 main(["--print-input-deps", "--relative-deps", "cwd",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
430 get_data("tests/wf/count-lines1-wf.cwl"),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
431 "--file1", data_path], stdout=stream)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
432
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
433 goal = {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
434 "location": "",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
435 "format": CWL_IANA,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
436 "secondaryFiles": [{"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
437 "location": str(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
438 Path(os.path.relpath(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
439 data_path, os.path.curdir))),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
440 "basename": "whale.txt",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
441 "nameroot": "whale",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
442 "nameext": ".txt"}]}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
443 assert json.loads(stream.getvalue()) == goal
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
444
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
445
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
446 def test_dedupe():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
447 not_deduped = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
448 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
449 "location": "file:///example/a"},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
450 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
451 "location": "file:///example/a"},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
452 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
453 "location": "file:///example/d"},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
454 {"class": "Directory",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
455 "location": "file:///example/c",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
456 "listing": [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
457 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
458 "location": "file:///example/d"}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
459 ]}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
460 ]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
461
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
462 expected = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
463 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
464 "location": "file:///example/a"},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
465 {"class": "Directory",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
466 "location": "file:///example/c",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
467 "listing": [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 {"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
469 "location": "file:///example/d"}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
470 ]}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
471 ]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
472
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
473 assert cwltool.pathmapper.dedup(not_deduped) == expected
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
474
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
475
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
476 record = {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
477 'fields': [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
478 {'type': {'items': 'string', 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
479 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
480 },
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
481 {'type': {'items': 'File', 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
482 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
483 }],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
484 'type': 'record',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
485 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
486 }
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
487
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
488 source_to_sink = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
489 ('0',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
493 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
494 ('1',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 {'items': ['string'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
496 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
497 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
498 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 ('2',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 {'items': ['string'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
502 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
503 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
504 ('3',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505 {'items': ['string'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506 {'items': ['int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
507 False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 ('record 0',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
510 record, record,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
511 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
512 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
513 ('record 1',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 record, {'items': 'string', 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515 False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
516 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
517 ]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
518
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520 @pytest.mark.parametrize('name, source, sink, expected', source_to_sink)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
521 def test_compare_types(name, source, sink, expected):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
522 assert cwltool.workflow.can_assign_src_to_sink(source, sink) == expected, name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
523
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
524
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
525 source_to_sink_strict = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
526 ('0',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
527 ['string', 'null'], ['string', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
528 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
529 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
530 ('1',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
531 ['string'], ['string', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
532 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
533 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
534 ('2',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
535 ['string', 'int'], ['string', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
536 False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
537 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
538 ('3',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
539 {'items': ['string'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
540 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
541 True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
542 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
543 ('4',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
544 {'items': ['string', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
545 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
546 False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
547 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
548 ]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
549
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
550
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
551 @pytest.mark.parametrize('name, source, sink, expected', source_to_sink_strict)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
552 def test_compare_types_strict(name, source, sink, expected):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
553 assert cwltool.workflow.can_assign_src_to_sink(source, sink, strict=True) == expected, name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
554
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
555
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
556 typechecks = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
557 (['string', 'int'], ['string', 'int', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
558 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
559 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
561 (['string', 'int'], ['string', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
562 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
563 "warning"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
564 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
565 (['File', 'int'], ['string', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
566 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
567 "exception"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
568 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
569 ({'items': ['string', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
570 {'items': ['string', 'int', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
571 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
572 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
573 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
574 ({'items': ['string', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
575 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
576 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
577 "warning"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
578 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
579 ({'items': ['File', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
580 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
581 None, None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
582 "exception"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
583 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
584 # check linkMerge when sinktype is not an array
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
585 (['string', 'int'], ['string', 'int', 'null'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
586 "merge_nested", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
587 "exception"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
588 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
589 # check linkMerge: merge_nested
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
590 (['string', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
591 {'items': ['string', 'int', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
592 "merge_nested", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
593 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
594 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
595 (['string', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
596 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
597 "merge_nested", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
598 "warning"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
599 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
600 (['File', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
601 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
602 "merge_nested", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
603 "exception"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
604 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
605 # check linkMerge: merge_nested and sinktype is "Any"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
606 (['string', 'int'], "Any",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
607 "merge_nested", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
608 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
609 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
610 # check linkMerge: merge_flattened
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
611 (['string', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
612 {'items': ['string', 'int', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
613 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
614 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
615 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
616 (['string', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
617 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
618 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
619 "warning"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
620 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
621 (['File', 'int'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
622 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
623 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
624 "exception"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
625 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
626 ({'items': ['string', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
627 {'items': ['string', 'int', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
628 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
629 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
630 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
631 ({'items': ['string', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
632 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
633 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
634 "warning"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
635 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
636 ({'items': ['File', 'int'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
637 {'items': ['string', 'null'], 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
638 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
639 "exception"),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
640 # check linkMerge: merge_flattened and sinktype is "Any"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
641 (['string', 'int'], "Any",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
642 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
643 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
644 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
645 ({'items': ['string', 'int'], 'type': 'array'}, "Any",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
646 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
647 "pass"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
648 ),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
649 # check linkMerge: merge_flattened when srctype is a list
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
650 ([{'items': 'string', 'type': 'array'}],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
651 {'items': 'string', 'type': 'array'},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
652 "merge_flattened", None,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
653 "pass"
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parents:
diff changeset
654 ),
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655 # check valueFrom
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diff changeset
656 ({'items': ['File', 'int'], 'type': 'array'},
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diff changeset
657 {'items': ['string', 'null'], 'type': 'array'},
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parents:
diff changeset
658 "merge_flattened", "special value",
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parents:
diff changeset
659 "pass"
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guerler
parents:
diff changeset
660 )
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parents:
diff changeset
661 ]
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guerler
parents:
diff changeset
662
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parents:
diff changeset
663
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diff changeset
664 @pytest.mark.parametrize('src_type,sink_type,link_merge,value_from,expected_type', typechecks)
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parents:
diff changeset
665 def test_typechecking(src_type, sink_type, link_merge, value_from, expected_type):
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666 assert cwltool.checker.check_types(
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parents:
diff changeset
667 src_type, sink_type, linkMerge=link_merge, valueFrom=value_from
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parents:
diff changeset
668 ) == expected_type
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parents:
diff changeset
669
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diff changeset
670
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parents:
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671 def test_lifting():
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diff changeset
672 # check that lifting the types of the process outputs to the workflow step
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diff changeset
673 # fails if the step 'out' doesn't match.
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parents:
diff changeset
674 factory = cwltool.factory.Factory()
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parents:
diff changeset
675 with pytest.raises(schema_salad.validate.ValidationException):
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diff changeset
676 echo = factory.make(get_data("tests/test_bad_outputs_wf.cwl"))
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diff changeset
677 assert echo(inp="foo") == {"out": "foo\n"}
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parents:
diff changeset
678
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diff changeset
679
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diff changeset
680 def test_malformed_outputs():
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diff changeset
681 # check that tool validation fails if one of the outputs is not a valid CWL type
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parents:
diff changeset
682 factory = cwltool.factory.Factory()
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parents:
diff changeset
683 with pytest.raises(schema_salad.validate.ValidationException):
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diff changeset
684 factory.make(get_data("tests/wf/malformed_outputs.cwl"))()
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parents:
diff changeset
685
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diff changeset
686
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diff changeset
687 def test_separate_without_prefix():
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parents:
diff changeset
688 # check that setting 'separate = false' on an inputBinding without prefix fails the workflow
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parents:
diff changeset
689 factory = cwltool.factory.Factory()
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parents:
diff changeset
690 with pytest.raises(WorkflowException):
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parents:
diff changeset
691 factory.make(get_data("tests/wf/separate_without_prefix.cwl"))()
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parents:
diff changeset
692
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parents:
diff changeset
693
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parents:
diff changeset
694 def test_static_checker():
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diff changeset
695 # check that the static checker raises exception when a source type
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parents:
diff changeset
696 # mismatches its sink type.
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diff changeset
697 factory = cwltool.factory.Factory()
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parents:
diff changeset
698
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diff changeset
699 with pytest.raises(schema_salad.validate.ValidationException):
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diff changeset
700 factory.make(get_data("tests/checker_wf/broken-wf.cwl"))
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parents:
diff changeset
701
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parents:
diff changeset
702 with pytest.raises(schema_salad.validate.ValidationException):
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parents:
diff changeset
703 factory.make(get_data("tests/checker_wf/broken-wf2.cwl"))
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parents:
diff changeset
704
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parents:
diff changeset
705 with pytest.raises(schema_salad.validate.ValidationException):
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guerler
parents:
diff changeset
706 factory.make(get_data("tests/checker_wf/broken-wf3.cwl"))
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guerler
parents:
diff changeset
707
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guerler
parents:
diff changeset
708
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parents:
diff changeset
709 def test_var_spool_cwl_checker1():
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parents:
diff changeset
710 """Confirm that references to /var/spool/cwl are caught."""
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diff changeset
711 stream = StringIO()
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diff changeset
712 streamhandler = logging.StreamHandler(stream)
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diff changeset
713 _logger = logging.getLogger("cwltool")
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parents:
diff changeset
714 _logger.addHandler(streamhandler)
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guerler
parents:
diff changeset
715
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parents:
diff changeset
716 factory = cwltool.factory.Factory()
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parents:
diff changeset
717 try:
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diff changeset
718 factory.make(get_data("tests/non_portable.cwl"))
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guerler
parents:
diff changeset
719 assert "non_portable.cwl:18:4: Non-portable reference to /var/spool/cwl detected" in stream.getvalue()
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diff changeset
720 finally:
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parents:
diff changeset
721 _logger.removeHandler(streamhandler)
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guerler
parents:
diff changeset
722
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guerler
parents:
diff changeset
723
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parents:
diff changeset
724 def test_var_spool_cwl_checker2():
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guerler
parents:
diff changeset
725 """Confirm that references to /var/spool/cwl are caught."""
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guerler
parents:
diff changeset
726 stream = StringIO()
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guerler
parents:
diff changeset
727 streamhandler = logging.StreamHandler(stream)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
728 _logger = logging.getLogger("cwltool")
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guerler
parents:
diff changeset
729 _logger.addHandler(streamhandler)
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guerler
parents:
diff changeset
730
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guerler
parents:
diff changeset
731 factory = cwltool.factory.Factory()
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guerler
parents:
diff changeset
732 try:
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parents:
diff changeset
733 factory.make(get_data("tests/non_portable2.cwl"))
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guerler
parents:
diff changeset
734 assert "non_portable2.cwl:19:4: Non-portable reference to /var/spool/cwl detected" in stream.getvalue()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
735 finally:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
736 _logger.removeHandler(streamhandler)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
737
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
738
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
739 def test_var_spool_cwl_checker3():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
740 """Confirm that references to /var/spool/cwl are caught."""
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
741 stream = StringIO()
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guerler
parents:
diff changeset
742 streamhandler = logging.StreamHandler(stream)
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guerler
parents:
diff changeset
743 _logger = logging.getLogger("cwltool")
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guerler
parents:
diff changeset
744 _logger.addHandler(streamhandler)
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guerler
parents:
diff changeset
745
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guerler
parents:
diff changeset
746 factory = cwltool.factory.Factory()
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guerler
parents:
diff changeset
747 try:
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guerler
parents:
diff changeset
748 factory.make(get_data("tests/portable.cwl"))
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guerler
parents:
diff changeset
749 assert "Non-portable reference to /var/spool/cwl detected" not in stream.getvalue()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
750 finally:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
751 _logger.removeHandler(streamhandler)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
752
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
753
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
754 def test_print_dot():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
755 assert main(["--print-dot", get_data('tests/wf/revsort.cwl')]) == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
756
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
757 test_factors = [(""), ("--parallel"), ("--debug"), ("--parallel --debug")]
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guerler
parents:
diff changeset
758
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
759 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
760 def test_js_console_cmd_line_tool(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
761 for test_file in ("js_output.cwl", "js_output_workflow.cwl"):
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guerler
parents:
diff changeset
762 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
763 commands.extend(["--js-console", "--no-container", get_data("tests/wf/" + test_file)])
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guerler
parents:
diff changeset
764 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
765
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guerler
parents:
diff changeset
766 assert "[log] Log message" in stderr
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guerler
parents:
diff changeset
767 assert "[err] Error message" in stderr
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guerler
parents:
diff changeset
768
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
769 assert error_code == 0, stderr
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guerler
parents:
diff changeset
770
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
771 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
772 def test_no_js_console(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
773 for test_file in ("js_output.cwl", "js_output_workflow.cwl"):
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guerler
parents:
diff changeset
774 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
775 commands.extend(["--no-container", get_data("tests/wf/" + test_file)])
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guerler
parents:
diff changeset
776 _, _, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
777
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guerler
parents:
diff changeset
778 assert "[log] Log message" not in stderr
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guerler
parents:
diff changeset
779 assert "[err] Error message" not in stderr
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guerler
parents:
diff changeset
780
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
781
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
782 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
783 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784 def test_cid_file_dir(tmpdir, factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 test_file = "cache_test_workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 cwd = tmpdir.chdir()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
787 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
788 commands.extend(["--cidfile-dir", str(tmpdir), get_data("tests/wf/" + test_file)])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
789 error_code, stdout, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
790 assert "completed success" in stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 assert error_code == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
792 cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*"))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793 assert cidfiles_count == 2
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 cwd.chdir()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795 tmpdir.remove(ignore_errors=True)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800 def test_cid_file_dir_arg_is_file_instead_of_dir(tmpdir, factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 test_file = "cache_test_workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802 bad_cidfile_dir = Text(tmpdir.ensure("cidfile-dir-actually-a-file"))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 commands.extend(["--cidfile-dir", bad_cidfile_dir,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 get_data("tests/wf/" + test_file)])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807 assert "is not a directory, please check it first" in stderr, stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808 assert error_code == 2 or error_code == 1, stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
809 tmpdir.remove(ignore_errors=True)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
814 def test_cid_file_non_existing_dir(tmpdir, factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
815 test_file = "cache_test_workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
816 bad_cidfile_dir = Text(tmpdir.join("cidfile-dir-badpath"))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
818 commands.extend(['--record-container-id',"--cidfile-dir", bad_cidfile_dir,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
819 get_data("tests/wf/" + test_file)])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 assert "directory doesn't exist, please create it first" in stderr, stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
822 assert error_code == 2 or error_code == 1, stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
823 tmpdir.remove(ignore_errors=True)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
824
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828 def test_cid_file_w_prefix(tmpdir, factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 test_file = "cache_test_workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 cwd = tmpdir.chdir()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 commands.extend(['--record-container-id', '--cidfile-prefix=pytestcid',
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 get_data("tests/wf/" + test_file)])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 error_code, stdout, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
836 finally:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837 listing = tmpdir.listdir()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 cwd.chdir()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
839 cidfiles_count = sum(1 for _ in tmpdir.visit(fil="pytestcid*"))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 tmpdir.remove(ignore_errors=True)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
841 assert "completed success" in stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842 assert error_code == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
843 assert cidfiles_count == 2, '{}/n{}'.format(listing, stderr)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848 def test_secondary_files_v1_1(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 test_file = "secondary-files.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850 test_job_file = "secondary-files-job.yml"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
851 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
852 old_umask = os.umask(stat.S_IWOTH) # test run with umask 002
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
854 commands.extend(["--enable-dev",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
855 get_data(os.path.join("tests", test_file)),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 get_data(os.path.join("tests", test_job_file))])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
857 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
858 finally:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
859 assert stat.S_IMODE(os.stat('lsout').st_mode) == 436 # 664 in octal, '-rw-rw-r--'
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860 os.umask(old_umask) # revert back to original umask
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 assert "completed success" in stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
862 assert error_code == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
863
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
866 def test_secondary_files_v1_0(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 test_file = "secondary-files-string-v1.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868 test_job_file = "secondary-files-job.yml"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 old_umask = os.umask(stat.S_IWOTH) # test run with umask 002
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 commands.extend([
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873 get_data(os.path.join("tests", test_file)),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874 get_data(os.path.join("tests", test_job_file))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 ])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877 finally:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 assert stat.S_IMODE(os.stat('lsout').st_mode) == 436 # 664 in octal, '-rw-rw-r--'
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 os.umask(old_umask) # revert back to original umask
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880 assert "completed success" in stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 assert error_code == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 def test_wf_without_container(tmpdir, factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 test_file = "hello-workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
888 with temp_dir("cwltool_cache") as cache_dir:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
889 commands = factor.split()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
890 commands.extend(["--cachedir", cache_dir, "--outdir", str(tmpdir),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
891 get_data("tests/wf/" + test_file),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
892 "--usermessage",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
893 "hello"])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
894 error_code, _, stderr = get_main_output(commands)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
895
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
896 assert "completed success" in stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
897 assert error_code == 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
898
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
899
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
900 @needs_docker
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
901 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
902 def test_issue_740_fixed(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
903 test_file = "cache_test_workflow.cwl"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
904 with temp_dir("cwltool_cache") as cache_dir:
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guerler
parents:
diff changeset
905 commands = factor.split()
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guerler
parents:
diff changeset
906 commands.extend(["--cachedir", cache_dir, get_data("tests/wf/" + test_file)])
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guerler
parents:
diff changeset
907 error_code, _, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
908
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guerler
parents:
diff changeset
909 assert "completed success" in stderr
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guerler
parents:
diff changeset
910 assert error_code == 0
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guerler
parents:
diff changeset
911
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guerler
parents:
diff changeset
912 commands = factor.split()
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guerler
parents:
diff changeset
913 commands.extend(["--cachedir", cache_dir, get_data("tests/wf/" + test_file)])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
914 error_code, _, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
915
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guerler
parents:
diff changeset
916 assert "Output of job will be cached in" not in stderr
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guerler
parents:
diff changeset
917 assert error_code == 0, stderr
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guerler
parents:
diff changeset
918
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guerler
parents:
diff changeset
919
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guerler
parents:
diff changeset
920 @needs_docker
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guerler
parents:
diff changeset
921 def test_compute_checksum():
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guerler
parents:
diff changeset
922 runtime_context = RuntimeContext()
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guerler
parents:
diff changeset
923 runtime_context.compute_checksum = True
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guerler
parents:
diff changeset
924 runtime_context.use_container = onWindows()
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guerler
parents:
diff changeset
925 factory = cwltool.factory.Factory(runtime_context=runtime_context)
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guerler
parents:
diff changeset
926 echo = factory.make(get_data("tests/wf/cat-tool.cwl"))
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guerler
parents:
diff changeset
927 output = echo(
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guerler
parents:
diff changeset
928 file1={"class": "File",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
929 "location": get_data("tests/wf/whale.txt")},
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guerler
parents:
diff changeset
930 reverse=False)
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guerler
parents:
diff changeset
931 assert output['output']["checksum"] == "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"
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guerler
parents:
diff changeset
932
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guerler
parents:
diff changeset
933
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guerler
parents:
diff changeset
934 @needs_docker
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guerler
parents:
diff changeset
935 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
936 def test_no_compute_chcksum(tmpdir, factor):
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guerler
parents:
diff changeset
937 test_file = "tests/wf/wc-tool.cwl"
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guerler
parents:
diff changeset
938 job_file = "tests/wf/wc-job.json"
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guerler
parents:
diff changeset
939 commands = factor.split()
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guerler
parents:
diff changeset
940 commands.extend(["--no-compute-checksum", "--outdir", str(tmpdir),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
941 get_data(test_file), get_data(job_file)])
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guerler
parents:
diff changeset
942 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
943 assert "completed success" in stderr
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guerler
parents:
diff changeset
944 assert error_code == 0
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guerler
parents:
diff changeset
945 assert "checksum" not in stdout
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guerler
parents:
diff changeset
946
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guerler
parents:
diff changeset
947
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guerler
parents:
diff changeset
948 @pytest.mark.parametrize("factor", test_factors)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
949 def test_bad_userspace_runtime(factor):
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guerler
parents:
diff changeset
950 test_file = "tests/wf/wc-tool.cwl"
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guerler
parents:
diff changeset
951 job_file = "tests/wf/wc-job.json"
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guerler
parents:
diff changeset
952 commands = factor.split()
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guerler
parents:
diff changeset
953 commands.extend([
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parents:
diff changeset
954 "--user-space-docker-cmd=quaquioN", "--default-container=debian",
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guerler
parents:
diff changeset
955 get_data(test_file), get_data(job_file)])
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guerler
parents:
diff changeset
956 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
957 assert "or quaquioN is missing or broken" in stderr, stderr
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guerler
parents:
diff changeset
958 assert error_code == 1
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guerler
parents:
diff changeset
959
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guerler
parents:
diff changeset
960 @windows_needs_docker
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guerler
parents:
diff changeset
961 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
962 def test_bad_basecommand(factor):
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guerler
parents:
diff changeset
963 test_file = "tests/wf/missing-tool.cwl"
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guerler
parents:
diff changeset
964 commands = factor.split()
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guerler
parents:
diff changeset
965 commands.extend([get_data(test_file)])
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guerler
parents:
diff changeset
966 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
967 assert "'neenooGo' not found" in stderr, stderr
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guerler
parents:
diff changeset
968 assert error_code == 1
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guerler
parents:
diff changeset
969
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guerler
parents:
diff changeset
970
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guerler
parents:
diff changeset
971 @needs_docker
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guerler
parents:
diff changeset
972 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
973 def test_bad_basecommand_docker(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
974 test_file = "tests/wf/missing-tool.cwl"
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guerler
parents:
diff changeset
975 commands = factor.split()
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guerler
parents:
diff changeset
976 commands.extend(
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guerler
parents:
diff changeset
977 ["--debug", "--default-container", "debian", get_data(test_file)])
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guerler
parents:
diff changeset
978 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
979 assert "permanentFail" in stderr, stderr
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guerler
parents:
diff changeset
980 assert error_code == 1
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guerler
parents:
diff changeset
981
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guerler
parents:
diff changeset
982 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
983 def test_v1_0_position_expression(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
984 test_file = "tests/echo-position-expr.cwl"
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guerler
parents:
diff changeset
985 test_job = "tests/echo-position-expr-job.yml"
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guerler
parents:
diff changeset
986 commands = factor.split()
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guerler
parents:
diff changeset
987 commands.extend(
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guerler
parents:
diff changeset
988 ['--debug', get_data(test_file), get_data(test_job)])
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guerler
parents:
diff changeset
989 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
990 assert "is not int" in stderr, stderr
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guerler
parents:
diff changeset
991 assert error_code == 1
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guerler
parents:
diff changeset
992
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guerler
parents:
diff changeset
993
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guerler
parents:
diff changeset
994 @windows_needs_docker
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guerler
parents:
diff changeset
995 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
996 def test_optional_numeric_output_0(factor):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
997 test_file = "tests/wf/optional-numerical-output-0.cwl"
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guerler
parents:
diff changeset
998 commands = factor.split()
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guerler
parents:
diff changeset
999 commands.extend([get_data(test_file)])
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guerler
parents:
diff changeset
1000 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
1001
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guerler
parents:
diff changeset
1002 assert "completed success" in stderr
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guerler
parents:
diff changeset
1003 assert error_code == 0
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guerler
parents:
diff changeset
1004 assert json.loads(stdout)['out'] == 0
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guerler
parents:
diff changeset
1005
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guerler
parents:
diff changeset
1006 @pytest.mark.parametrize("factor", test_factors)
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guerler
parents:
diff changeset
1007 @windows_needs_docker
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guerler
parents:
diff changeset
1008 def test_env_filtering(factor):
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guerler
parents:
diff changeset
1009 test_file = "tests/env.cwl"
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guerler
parents:
diff changeset
1010 commands = factor.split()
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guerler
parents:
diff changeset
1011 commands.extend([get_data(test_file)])
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guerler
parents:
diff changeset
1012 error_code, stdout, stderr = get_main_output(commands)
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guerler
parents:
diff changeset
1013
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parents:
diff changeset
1014 process = subprocess.Popen(["sh", "-c", r"""getTrueShellExeName() {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1015 local trueExe nextTarget 2>/dev/null
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1016 trueExe=$(ps -o comm= $$) || return 1
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guerler
parents:
diff changeset
1017 [ "${trueExe#-}" = "$trueExe" ] || trueExe=${trueExe#-}
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guerler
parents:
diff changeset
1018 [ "${trueExe#/}" != "$trueExe" ] || trueExe=$([ -n "$ZSH_VERSION" ] && which -p "$trueExe" || which "$trueExe")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1019 while nextTarget=$(readlink "$trueExe"); do trueExe=$nextTarget; done
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guerler
parents:
diff changeset
1020 printf '%s\n' "$(basename "$trueExe")"
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guerler
parents:
diff changeset
1021 } ; getTrueShellExeName"""], stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1022 sh_name, sh_name_err = process.communicate()
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guerler
parents:
diff changeset
1023 sh_name = sh_name.decode('utf-8').strip()
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guerler
parents:
diff changeset
1024
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guerler
parents:
diff changeset
1025 assert "completed success" in stderr, (error_code, stdout, stderr)
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guerler
parents:
diff changeset
1026 assert error_code == 0, (error_code, stdout, stderr)
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guerler
parents:
diff changeset
1027 if onWindows():
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1028 target = 5
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1029 elif sh_name == "dash":
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1030 target = 4
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1031 else: # bash adds "SHLVL" and "_" environment variables
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1032 target = 6
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1033 result = json.loads(stdout)['env_count']
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1034 details = ''
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1035 if result != target:
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1036 _, details, _ = get_main_output(["--quiet", get_data("tests/env2.cwl")])
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1037 print(sh_name)
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1038 print(sh_name_err)
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1039 print(details)
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1040 assert result == target, (error_code, sh_name, sh_name_err, details, stdout, stderr)
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1041
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1042 @windows_needs_docker
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1043 def test_v1_0_arg_empty_prefix_separate_false():
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1044 test_file = "tests/arg-empty-prefix-separate-false.cwl"
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1045 error_code, stdout, stderr = get_main_output(
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1046 ['--debug', get_data(test_file), "--echo"])
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1047 assert "completed success" in stderr
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1048 assert error_code == 0