Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/tool_builder.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 import subprocess
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2 from planemo import templates
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3
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4
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5 TOOL_TEMPLATE = """<tool id="{{id}}" name="{{name}}" version="{{version}}">
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6 {%- if description %}
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7 <description>{{ description }}</description>
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8 {% endif %}
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9 {%- if macros %}
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10 <macros>
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11 <import>macros.xml</import>
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12 </macros>
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13 <expand macro="requirements" />
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14 <expand macro="stdio" />
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15 {%- if version_command %}
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16 <expand macro="version_command" />
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17 {% endif %}
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18 {%- else %}
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19 <requirements>
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20 {%- for requirement in requirements %}
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21 {{ requirement }}
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22 {%- endfor %}
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23 {%- for container in containers %}
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24 {{ container }}
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25 {%- endfor %}
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26 </requirements>
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27 <stdio>
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28 <exit_code range="1:" />
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29 </stdio>
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30 {%- if version_command %}
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31 <version_command>{{ version_command }}</version_command>
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32 {%- endif %}
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33 {% endif %}
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34 <command><![CDATA[
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35 {%- if command %}
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36 {{ command }}
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37 {%- else %}
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38 TODO: Fill in command template.
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39 {%- endif %}
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40 ]]></command>
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41 <inputs>
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42 {%- for input in inputs %}
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43 {{ input }}
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44 {%- endfor %}
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45 </inputs>
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46 <outputs>
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47 {%- for output in outputs %}
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48 {{ output }}
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49 {%- endfor %}
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50 </outputs>
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51 {%- if tests %}
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52 <tests>
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53 {%- for test in tests %}
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54 <test>
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55 {%- for param in test.params %}
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56 <param name="{{ param[0]}}" value="{{ param[1] }}"/>
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57 {%- endfor %}
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58 {%- for output in test.outputs %}
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59 <output name="{{ output[0] }}" file="{{ output[1] }}"/>
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60 {%- endfor %}
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61 </test>
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62 {%- endfor %}
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63 </tests>
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64 {%- endif %}
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65 <help><![CDATA[
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66 {%- if help %}
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67 {{ help }}
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68 {%- else %}
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69 TODO: Fill in help.
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70 {%- endif %}
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71 ]]></help>
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72 {%- if macros %}
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73 <expand macro="citations" />
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74 {%- else %}
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75 {%- if doi %}
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76 <citations>
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77 {%- for single_doi in doi %}
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78 <citation type="doi">{{ single_doi }}</citation>
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79 {%- endfor %}
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80 </citations>
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81 {%- endif %}
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82 {%- endif %}
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83 </tool>
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84 """
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85
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86 MACROS_TEMPLATE = """<macros>
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87 <xml name="requirements">
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88 <requirements>
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89 {%- for requirement in requirements %}
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90 {{ requirement }}
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91 {%- endfor %}
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92 <yield/>
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93 {%- for container in containers %}
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94 {{ container }}
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95 {%- endfor %}
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96 </requirements>
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97 </xml>
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98 <xml name="stdio">
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99 <stdio>
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100 <exit_code range="1:" />
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101 </stdio>
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102 </xml>
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103 <xml name="citations">
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104 <citations>
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105 {%- for single_doi in doi %}
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106 <citation type="doi">{{ single_doi }}</citation>
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107 {%- endfor %}
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108 <yield />
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109 </citations>
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110 </xml>
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111 {%- if version_command %}
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112 <xml name="version_command">
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113 <version_command>{{ version_command }}</version_command>
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114 </xml>
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115 {%- endif %}
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116 </macros>
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117 """
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118
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119
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120 def build(**kwds):
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121 # Test case to build up from supplied inputs and outputs, ultimately
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122 # ignored unless kwds["test_case"] is truthy.
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123 test_case = TestCase()
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124
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125 command = _find_command(kwds)
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126
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127 _handle_help(kwds)
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128
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129 # process raw inputs
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130 inputs = kwds.get("input", [])
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131 del kwds["input"]
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132 inputs = list(map(Input, inputs or []))
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133
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134 # alternatively process example inputs
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135 example_inputs = kwds["example_input"]
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136 del kwds["example_input"]
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137 for i, input_file in enumerate(example_inputs or []):
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138 name = "input%d" % (i + 1)
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139 inputs.append(Input(input_file, name=name))
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140 test_case.params.append((name, input_file))
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141 command = _replace_file_in_command(command, input_file, name)
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142
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143 # handle raw outputs (from_work_dir ones) as well as named_outputs
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144 outputs = kwds.get("output", [])
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145 del kwds["output"]
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146 outputs = list(map(Output, outputs or []))
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147
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148 named_outputs = kwds.get("named_output", [])
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149 del kwds["named_output"]
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150 for named_output in (named_outputs or []):
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151 outputs.append(Output(name=named_output))
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152
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153 # handle example outputs
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154 example_outputs = kwds["example_output"]
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155 del kwds["example_output"]
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156 for i, output_file in enumerate(example_outputs or []):
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157 name = "output%d" % (i + 1)
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158 from_path = output_file
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159 if output_file in command:
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160 # Actually found the file in the command, assume it can
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161 # be specified directly and skip from_work_dir.
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162 from_path = None
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163 output = Output(name=name, from_path=from_path)
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164 outputs.append(output)
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165 test_case.outputs.append((name, output_file))
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166 command = _replace_file_in_command(command, output_file, output.name)
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167
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168 kwds["inputs"] = inputs
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169 kwds["outputs"] = outputs
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170
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171 # handle requirements and containers
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172 _handle_requirements(kwds)
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173
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174 kwds["command"] = command
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175
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176 # finally wrap up tests
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177 tests, test_files = _handle_tests(kwds, test_case)
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178 kwds["tests"] = tests
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179
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180 # Render tool content from template.
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181 contents = _render(kwds)
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182
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183 macro_contents = None
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184 if kwds["macros"]:
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185 macro_contents = _render(kwds, MACROS_TEMPLATE)
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186
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187 return ToolDescription(contents, macro_contents, test_files)
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188
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189
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190 def _render(kwds, template_str=TOOL_TEMPLATE):
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191 """ Apply supplied template variables to TOOL_TEMPLATE to generate
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192 the final tool.
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193 """
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194 return templates.render(template_str, **kwds)
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195
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196
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197 def _replace_file_in_command(command, specified_file, name):
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198 """ Replace example file with cheetah variable name in supplied command
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199 or command template. Be sure to quote the name.
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200 """
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201 # TODO: check if the supplied variant was single quoted already.
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202 if '"%s"' % specified_file in command:
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203 # Sample command already wrapped filename in double quotes
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204 command = command.replace(specified_file, '$%s' % name)
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205 else:
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206 # In case of spaces, best to wrap filename in double quotes
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207 command = command.replace(specified_file, '"$%s"' % name)
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208 return command
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209
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210
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211 def _handle_help(kwds):
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212 """ Convert supplied help parameters into a help variable for template.
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213 If help_text is supplied, use as is. If help is specified from a command,
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214 run the command and use that help text.
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215 """
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216 help_text = kwds.get("help_text")
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217 if not help_text:
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218 help_from_command = kwds.get("help_from_command")
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219 if help_from_command:
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220 p = subprocess.Popen(
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221 help_from_command,
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222 shell=True,
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223 stdout=subprocess.PIPE,
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224 stderr=subprocess.STDOUT
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225 )
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226 help_text = p.communicate()[0]
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227
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228 del kwds["help_text"]
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229 del kwds["help_from_command"]
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230
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231 kwds["help"] = help_text
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232
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233
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234 def _handle_tests(kwds, test_case):
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235 """ Given state built up from handling rest of arguments (test_case) and
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236 supplied kwds - build tests for template and corresponding test files.
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237 """
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238 test_files = []
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239 if kwds["test_case"]:
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240 tests = [test_case]
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241 test_files.extend(map(lambda x: x[1], test_case.params))
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242 test_files.extend(map(lambda x: x[1], test_case.outputs))
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243 else:
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244 tests = []
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245 return tests, test_files
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246
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247
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248 def _handle_requirements(kwds):
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249 """ Convert requirements and containers specified from the command-line
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250 into abstract format for consumption by the template.
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251 """
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252 requirements = kwds["requirement"]
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253 del kwds["requirement"]
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254 requirements = map(Requirement, requirements or [])
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255
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256 container = kwds["container"]
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257 del kwds["container"]
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258 containers = map(Container, container or [])
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259
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260 kwds["requirements"] = requirements
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261 kwds["containers"] = containers
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262
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263
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264 def _find_command(kwds):
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265 """ Find base command from supplied arguments or just return None if no
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266 such command was supplied (template will just replace this with TODO
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267 item).
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268 """
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269 command = kwds.get("command")
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270 if not command:
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271 command = kwds.get("example_command", None)
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272 if command:
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273 del kwds["example_command"]
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274 return command
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275
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276
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277 class ToolDescription(object):
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278
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279 def __init__(self, contents, macro_contents, test_files):
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280 self.contents = contents
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281 self.macro_contents = macro_contents
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282 self.test_files = test_files
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283
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284
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285 class Input(object):
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286
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287 def __init__(self, input_description, name=None):
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288 parts = input_description.split(".")
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289 name = name or parts[0]
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290 if len(parts) > 0:
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291 datatype = ".".join(parts[1:])
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292 else:
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293 datatype = "data"
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294
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295 self.name = name
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296 self.datatype = datatype
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297
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298 def __str__(self):
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299 template = '<param type="data" name="{0}" format="{1}" />'
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300 return template.format(self.name, self.datatype)
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301
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302
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303 class Output(object):
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304
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305 def __init__(self, from_path=None, name=None):
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306 if from_path:
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307 parts = from_path.split(".")
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308 name = name or parts[0]
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309 if len(parts) > 1:
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310 datatype = ".".join(parts[1:])
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311 else:
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312 datatype = "data"
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313 else:
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314 name = name
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315 datatype = "data"
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316
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317 self.name = name
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318 self.datatype = datatype
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319 self.from_path = from_path
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320
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321 def __str__(self):
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322 if self.from_path:
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323 return self._from_path_str()
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324 else:
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325 return self._named_str()
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326
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327 def _from_path_str(self):
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328 template = '<data name="{0}" format="{1}" from_work_dir="{2}" />'
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329 return template.format(self.name, self.datatype, self.from_path)
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330
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331 def _named_str(self):
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332 template = '<data name="{0}" format="{1}" />'
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333 return template.format(self.name, self.datatype)
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334
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335
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336 class Requirement(object):
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337
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338 def __init__(self, requirement):
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339 parts = requirement.split("@", 1)
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340 if len(parts) > 1:
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341 name = parts[0]
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342 version = "@".join(parts[1:])
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343 else:
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344 name = parts[0]
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345 version = None
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346 self.name = name
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347 self.version = version
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348
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349 def __str__(self):
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350 base = '<requirement type="package"{0}>{1}</requirement>'
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351 if self.version is not None:
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352 attrs = ' version="{0}"'.format(self.version)
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353 else:
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354 attrs = ''
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355 return base.format(attrs, self.name)
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356
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357
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358 class Container(object):
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359
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360 def __init__(self, image_id):
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361 self.type = "docker"
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362 self.image_id = image_id
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363
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364 def __str__(self):
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365 template = '<container type="{0}">{1}</container>'
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366 return template.format(self.type, self.image_id)
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367
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368
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369 class TestCase(object):
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370
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371 def __init__(self):
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372 self.params = []
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373 self.outputs = []