Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/yaml.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 from collections import OrderedDict
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2
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3 import packaging.version
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4
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5 from galaxy.tool_util.deps import requirements
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6 from galaxy.tool_util.parser.util import (
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7 DEFAULT_DELTA,
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8 DEFAULT_DELTA_FRAC
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9 )
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10 from .interface import (
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11 InputSource,
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12 PageSource,
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13 PagesSource,
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14 ToolSource,
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15 )
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16 from .output_collection_def import dataset_collector_descriptions_from_output_dict
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17 from .output_objects import (
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18 ToolOutput,
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19 ToolOutputCollection,
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20 ToolOutputCollectionStructure,
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21 )
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22 from .stdio import error_on_exit_code
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23 from .util import is_dict
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24
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25
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26 class YamlToolSource(ToolSource):
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27
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28 def __init__(self, root_dict, source_path=None):
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29 self.root_dict = root_dict
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30 self._source_path = source_path
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31 self._macro_paths = []
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32
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33 @property
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34 def source_path(self):
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35 return self._source_path
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36
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37 def parse_id(self):
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38 return self.root_dict.get("id")
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39
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40 def parse_version(self):
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41 return self.root_dict.get("version")
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42
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43 def parse_name(self):
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44 return self.root_dict.get("name")
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45
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46 def parse_description(self):
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47 return self.root_dict.get("description", "")
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48
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49 def parse_edam_operations(self):
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50 return self.root_dict.get("edam_operations", [])
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51
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52 def parse_edam_topics(self):
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53 return self.root_dict.get("edam_topics", [])
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54
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55 def parse_xrefs(self):
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56 xrefs = self.root_dict.get("xrefs", [])
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57 return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
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58
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59 def parse_is_multi_byte(self):
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60 return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
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61
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62 def parse_sanitize(self):
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63 return self.root_dict.get("sanitize", True)
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64
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65 def parse_display_interface(self, default):
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66 return self.root_dict.get('display_interface', default)
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67
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68 def parse_require_login(self, default):
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69 return self.root_dict.get('require_login', default)
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70
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71 def parse_command(self):
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72 return self.root_dict.get("command")
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73
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74 def parse_expression(self):
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75 return self.root_dict.get("expression")
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76
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77 def parse_environment_variables(self):
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78 return []
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79
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80 def parse_interpreter(self):
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81 return self.root_dict.get("interpreter")
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82
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83 def parse_version_command(self):
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84 return self.root_dict.get("runtime_version", {}).get("command", None)
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85
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86 def parse_version_command_interpreter(self):
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87 return self.root_dict.get("runtime_version", {}).get("interpreter", None)
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88
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89 def parse_requirements_and_containers(self):
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90 return requirements.parse_requirements_from_dict(self.root_dict)
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91
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92 def parse_input_pages(self):
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93 # All YAML tools have only one page (feature is deprecated)
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94 page_source = YamlPageSource(self.root_dict.get("inputs", {}))
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95 return PagesSource([page_source])
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96
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97 def parse_strict_shell(self):
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98 # TODO: Add ability to disable this.
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99 return True
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100
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101 def parse_stdio(self):
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102 return error_on_exit_code()
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103
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104 def parse_help(self):
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105 return self.root_dict.get("help", None)
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106
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107 def parse_outputs(self, tool):
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108 outputs = self.root_dict.get("outputs", {})
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109 output_defs = []
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110 output_collection_defs = []
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111 for name, output_dict in outputs.items():
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112 output_type = output_dict.get("type", "data")
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113 if output_type == "data":
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114 output_defs.append(self._parse_output(tool, name, output_dict))
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115 elif output_type == "collection":
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116 output_collection_defs.append(self._parse_output_collection(tool, name, output_dict))
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117 else:
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118 message = "Unknown output_type [%s] encountered." % output_type
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119 raise Exception(message)
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120 outputs = OrderedDict()
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121 for output in output_defs:
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122 outputs[output.name] = output
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123 output_collections = OrderedDict()
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124 for output in output_collection_defs:
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125 output_collections[output.name] = output
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126
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127 return outputs, output_collections
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128
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129 def _parse_output(self, tool, name, output_dict):
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130 output = ToolOutput.from_dict(name, output_dict, tool=tool)
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131 return output
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132
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133 def _parse_output_collection(self, tool, name, output_dict):
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134 name = output_dict.get("name")
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135 label = output_dict.get("label")
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136 default_format = output_dict.get("format", "data")
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137 collection_type = output_dict.get("type", None)
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138 collection_type_source = output_dict.get("type_source", None)
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139 structured_like = output_dict.get("structured_like", None)
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140 inherit_format = False
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141 inherit_metadata = False
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142 if structured_like:
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143 inherit_format = output_dict.get("inherit_format", None)
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144 inherit_metadata = output_dict.get("inherit_metadata", None)
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145 default_format_source = output_dict.get("format_source", None)
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146 default_metadata_source = output_dict.get("metadata_source", "")
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147 filters = []
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148 dataset_collector_descriptions = dataset_collector_descriptions_from_output_dict(output_dict)
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149
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150 structure = ToolOutputCollectionStructure(
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151 collection_type=collection_type,
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152 collection_type_source=collection_type_source,
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153 structured_like=structured_like,
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154 dataset_collector_descriptions=dataset_collector_descriptions,
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155 )
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156 output_collection = ToolOutputCollection(
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157 name,
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158 structure,
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159 label=label,
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160 filters=filters,
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161 default_format=default_format,
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162 inherit_format=inherit_format,
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163 inherit_metadata=inherit_metadata,
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164 default_format_source=default_format_source,
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165 default_metadata_source=default_metadata_source,
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166 )
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167 return output_collection
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168
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169 def parse_tests_to_dict(self):
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170 tests = []
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171 rval = dict(
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172 tests=tests
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173 )
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174
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175 for i, test_dict in enumerate(self.root_dict.get("tests", [])):
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176 tests.append(_parse_test(i, test_dict))
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177
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178 return rval
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179
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180 def parse_profile(self):
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181 return self.root_dict.get("profile", "16.04")
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182
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183 def parse_interactivetool(self):
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184 return self.root_dict.get("entry_points", [])
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185
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186 def parse_python_template_version(self):
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187 python_template_version = self.root_dict.get("python_template_version", None)
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188 if python_template_version is not None:
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189 python_template_version = packaging.version.parse(python_template_version)
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190 return python_template_version
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191
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192
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193 def _parse_test(i, test_dict):
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194 inputs = test_dict["inputs"]
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195 if is_dict(inputs):
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196 new_inputs = []
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197 for key, value in inputs.items():
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198 new_inputs.append({"name": key, "value": value, "attributes": {}})
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199 test_dict["inputs"] = new_inputs
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200
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201 outputs = test_dict["outputs"]
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202
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203 new_outputs = []
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204 if is_dict(outputs):
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205 for key, value in outputs.items():
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206 if is_dict(value):
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207 attributes = value
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208 file = attributes.get("file")
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209 else:
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210 file = value
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211 attributes = {}
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212 new_outputs.append({
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213 "name": key,
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214 "value": file,
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215 "attributes": attributes
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216 })
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217 else:
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218 for output in outputs:
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219 name = output["name"]
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220 value = output.get("file", None)
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221 attributes = output
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222 new_outputs.append((name, value, attributes))
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223
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224 for output in new_outputs:
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225 attributes = output["attributes"]
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226 defaults = {
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227 'compare': 'diff',
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228 'lines_diff': 0,
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229 'delta': DEFAULT_DELTA,
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230 'delta_frac': DEFAULT_DELTA_FRAC,
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231 'sort': False,
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232 }
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233 # TODO
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234 attributes["extra_files"] = []
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235 # TODO
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236 attributes["metadata"] = {}
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237 # TODO
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238 assert_list = []
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239 assert_list = __to_test_assert_list(attributes.get("asserts", []))
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240 attributes["assert_list"] = assert_list
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241 _ensure_has(attributes, defaults)
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242
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243 test_dict["outputs"] = new_outputs
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244 # TODO: implement output collections for YAML tools.
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245 test_dict["output_collections"] = []
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246 test_dict["command"] = __to_test_assert_list(test_dict.get("command", []))
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247 test_dict["stdout"] = __to_test_assert_list(test_dict.get("stdout", []))
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248 test_dict["stderr"] = __to_test_assert_list(test_dict.get("stderr", []))
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249 test_dict["expect_exit_code"] = test_dict.get("expect_exit_code", None)
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250 test_dict["expect_failure"] = test_dict.get("expect_exit_code", False)
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251 return test_dict
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252
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253
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254 def __to_test_assert_list(assertions):
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255 def expand_dict_form(item):
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256 key, value = item
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257 new_value = value.copy()
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258 new_value["that"] = key
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259 return new_value
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260
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261 if is_dict(assertions):
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262 assertions = map(expand_dict_form, assertions.items())
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263
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264 assert_list = []
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265 for assertion in assertions:
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266 # TODO: not handling nested assertions correctly,
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267 # not sure these are used though.
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268 children = []
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269 if "children" in assertion:
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270 children = assertion["children"]
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271 del assertion["children"]
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272 assert_dict = dict(
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273 tag=assertion["that"],
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274 attributes=assertion,
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275 children=children,
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276 )
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277 assert_list.append(assert_dict)
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278
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279 return assert_list or None # XML variant is None if no assertions made
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280
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281
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282 class YamlPageSource(PageSource):
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283
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284 def __init__(self, inputs_list):
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285 self.inputs_list = inputs_list
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286
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287 def parse_input_sources(self):
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288 return map(YamlInputSource, self.inputs_list)
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289
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290
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291 class YamlInputSource(InputSource):
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292
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293 def __init__(self, input_dict):
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294 self.input_dict = input_dict
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295
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296 def get(self, key, default=None):
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297 return self.input_dict.get(key, default)
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298
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299 def get_bool(self, key, default):
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300 return self.input_dict.get(key, default)
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301
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302 def parse_input_type(self):
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303 input_type = self.input_dict["type"]
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304 if input_type == "repeat":
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305 return "repeat"
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306 elif input_type == "conditional":
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307 return "conditional"
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308 else:
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309 return "param"
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310
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311 def parse_nested_inputs_source(self):
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312 assert self.parse_input_type() == "repeat"
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313 return YamlPageSource(self.input_dict["blocks"])
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314
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315 def parse_test_input_source(self):
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316 test_dict = self.input_dict.get("test", None)
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317 assert test_dict is not None, "conditional must contain a `test` definition"
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318 return YamlInputSource(test_dict)
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319
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320 def parse_when_input_sources(self):
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321 input_dict = self.input_dict
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322
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323 sources = []
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324 for value, block in input_dict.get("when", {}).items():
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325 if value is True:
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326 value = "true"
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327 elif value is False:
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328 value = "false"
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329 else:
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330 value = str(value)
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331
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332 # str here to lose type information like XML, needed?
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333 if not isinstance(block, list):
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334 block = [block]
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335 case_page_source = YamlPageSource(block)
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336 sources.append((value, case_page_source))
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337 return sources
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338
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339 def parse_static_options(self):
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340 static_options = list()
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341 input_dict = self.input_dict
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342 for index, option in enumerate(input_dict.get("options", {})):
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343 value = option.get("value")
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344 label = option.get("label", value)
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345 selected = option.get("selected", False)
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346 static_options.append((label, value, selected))
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347 return static_options
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348
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349
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350 def _ensure_has(dict, defaults):
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351 for key, value in defaults.items():
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352 if key not in dict:
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353 dict[key] = value