Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/parser/xml.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import json |
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2 import logging |
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3 import re |
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4 import uuid |
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5 from math import isinf |
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6 |
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7 import packaging.version |
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8 |
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9 from galaxy.tool_util.deps import requirements |
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10 from galaxy.tool_util.parser.util import ( |
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11 DEFAULT_DELTA, |
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12 DEFAULT_DELTA_FRAC |
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13 ) |
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14 from galaxy.util import ( |
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15 string_as_bool, |
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16 xml_text, |
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17 xml_to_string |
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18 ) |
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19 from .interface import ( |
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20 InputSource, |
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21 PageSource, |
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22 PagesSource, |
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23 TestCollectionDef, |
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24 TestCollectionOutputDef, |
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25 ToolSource, |
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26 ) |
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27 from .output_actions import ToolOutputActionGroup |
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28 from .output_collection_def import dataset_collector_descriptions_from_elem |
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29 from .output_objects import ( |
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30 ToolExpressionOutput, |
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31 ToolOutput, |
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32 ToolOutputCollection, |
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33 ToolOutputCollectionStructure |
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34 ) |
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35 from .stdio import ( |
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36 aggressive_error_checks, |
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37 error_on_exit_code, |
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38 StdioErrorLevel, |
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39 ToolStdioExitCode, |
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40 ToolStdioRegex, |
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41 ) |
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42 |
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43 |
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44 log = logging.getLogger(__name__) |
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45 |
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46 |
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47 class XmlToolSource(ToolSource): |
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48 """ Responsible for parsing a tool from classic Galaxy representation. |
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49 """ |
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50 |
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51 def __init__(self, xml_tree, source_path=None, macro_paths=None): |
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52 self.xml_tree = xml_tree |
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53 self.root = xml_tree.getroot() |
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54 self._source_path = source_path |
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55 self._macro_paths = macro_paths or [] |
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56 self.legacy_defaults = self.parse_profile() == "16.01" |
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57 |
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58 def to_string(self): |
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59 return xml_to_string(self.root) |
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60 |
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61 def parse_version(self): |
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62 return self.root.get("version", None) |
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63 |
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64 def parse_id(self): |
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65 return self.root.get("id") |
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66 |
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67 def parse_tool_module(self): |
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68 root = self.root |
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69 if root.find("type") is not None: |
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70 type_elem = root.find("type") |
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71 module = type_elem.get('module', 'galaxy.tools') |
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72 cls = type_elem.get('class') |
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73 return module, cls |
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74 |
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75 return None |
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76 |
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77 def parse_action_module(self): |
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78 root = self.root |
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79 action_elem = root.find("action") |
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80 if action_elem is not None: |
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81 module = action_elem.get('module') |
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82 cls = action_elem.get('class') |
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83 return module, cls |
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84 else: |
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85 return None |
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86 |
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87 def parse_tool_type(self): |
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88 root = self.root |
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89 if root.get('tool_type', None) is not None: |
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90 return root.get('tool_type') |
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91 |
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92 def parse_name(self): |
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93 return self.root.get("name") |
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94 |
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95 def parse_edam_operations(self): |
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96 edam_ops = self.root.find("edam_operations") |
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97 if edam_ops is None: |
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98 return [] |
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99 return [edam_op.text for edam_op in edam_ops.findall("edam_operation")] |
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100 |
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101 def parse_edam_topics(self): |
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102 edam_topics = self.root.find("edam_topics") |
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103 if edam_topics is None: |
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104 return [] |
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105 return [edam_topic.text for edam_topic in edam_topics.findall("edam_topic")] |
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106 |
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107 def parse_xrefs(self): |
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108 xrefs = self.root.find("xrefs") |
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109 if xrefs is None: |
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110 return [] |
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111 return [dict(value=xref.text.strip(), reftype=xref.attrib['type']) for xref in xrefs.findall("xref") if xref.get("type")] |
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112 |
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113 def parse_description(self): |
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114 return xml_text(self.root, "description") |
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115 |
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116 def parse_is_multi_byte(self): |
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117 return self._get_attribute_as_bool("is_multi_byte", self.default_is_multi_byte) |
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118 |
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119 def parse_display_interface(self, default): |
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120 return self._get_attribute_as_bool("display_interface", default) |
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121 |
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122 def parse_require_login(self, default): |
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123 return self._get_attribute_as_bool("require_login", default) |
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124 |
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125 def parse_request_param_translation_elem(self): |
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126 return self.root.find("request_param_translation") |
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127 |
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128 def parse_command(self): |
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129 command_el = self._command_el |
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130 return ((command_el is not None) and command_el.text) or None |
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131 |
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132 def parse_expression(self): |
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133 """ Return string containing command to run. |
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134 """ |
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135 expression_el = self.root.find("expression") |
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136 if expression_el is not None: |
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137 expression_type = expression_el.get("type") |
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138 if expression_type != "ecma5.1": |
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139 raise Exception("Unknown expression type [%s] encountered" % expression_type) |
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140 return expression_el.text |
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141 return None |
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142 |
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143 def parse_environment_variables(self): |
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144 environment_variables_el = self.root.find("environment_variables") |
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145 if environment_variables_el is None: |
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146 return [] |
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147 |
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148 environment_variables = [] |
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149 for environment_variable_el in environment_variables_el.findall("environment_variable"): |
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150 template = environment_variable_el.text |
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151 inject = environment_variable_el.get("inject") |
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152 if inject: |
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153 assert not template, "Cannot specify inject and environment variable template." |
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154 assert inject in ["api_key"] |
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155 if template: |
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156 assert not inject, "Cannot specify inject and environment variable template." |
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157 definition = { |
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158 "name": environment_variable_el.get("name"), |
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159 "template": template, |
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160 "inject": inject, |
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161 "strip": string_as_bool(environment_variable_el.get("strip", False)), |
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162 } |
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163 environment_variables.append( |
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164 definition |
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165 ) |
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166 return environment_variables |
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167 |
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168 def parse_home_target(self): |
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169 target = "job_home" if self.parse_profile() >= "18.01" else "shared_home" |
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170 command_el = self._command_el |
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171 command_legacy = (command_el is not None) and command_el.get("use_shared_home", None) |
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172 if command_legacy is not None: |
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173 target = "shared_home" if string_as_bool(command_legacy) else "job_home" |
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174 return target |
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175 |
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176 def parse_tmp_target(self): |
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177 # Default to not touching TMPDIR et. al. but if job_tmp is set |
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178 # in job_conf then do. This is a very conservative approach that shouldn't |
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179 # break or modify any configurations by default. |
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180 return "job_tmp_if_explicit" |
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181 |
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182 def parse_interpreter(self): |
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183 interpreter = None |
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184 command_el = self._command_el |
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185 if command_el is not None: |
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186 interpreter = command_el.get("interpreter", None) |
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187 if interpreter and not self.legacy_defaults: |
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188 log.warning("Deprecated interpreter attribute on command element is now ignored.") |
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189 interpreter = None |
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190 return interpreter |
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191 |
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192 def parse_version_command(self): |
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193 version_cmd = self.root.find("version_command") |
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194 if version_cmd is not None: |
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195 return version_cmd.text |
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196 else: |
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197 return None |
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198 |
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199 def parse_version_command_interpreter(self): |
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200 if self.parse_version_command() is not None: |
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201 version_cmd = self.root.find("version_command") |
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202 version_cmd_interpreter = version_cmd.get("interpreter", None) |
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203 if version_cmd_interpreter: |
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204 return version_cmd_interpreter |
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205 return None |
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206 |
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207 def parse_parallelism(self): |
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208 parallelism = self.root.find("parallelism") |
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209 parallelism_info = None |
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210 if parallelism is not None and parallelism.get("method"): |
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211 return ParallelismInfo(parallelism) |
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212 return parallelism_info |
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213 |
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214 def parse_interactivetool(self): |
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215 interactivetool_el = self.root.find("entry_points") |
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216 rtt = [] |
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217 if interactivetool_el is None: |
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218 return rtt |
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219 for ep_el in interactivetool_el.findall("entry_point"): |
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220 port = ep_el.find("port") |
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221 assert port is not None, ValueError('A port is required for InteractiveTools') |
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222 port = port.text.strip() |
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223 url = ep_el.find("url") |
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224 if url is not None: |
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225 url = url.text.strip() |
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226 name = ep_el.get('name', None) |
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227 if name: |
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228 name = name.strip() |
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229 requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False)) |
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230 rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain)) |
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231 return rtt |
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232 |
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233 def parse_hidden(self): |
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234 hidden = xml_text(self.root, "hidden") |
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235 if hidden: |
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236 hidden = string_as_bool(hidden) |
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237 return hidden |
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238 |
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239 def parse_redirect_url_params_elem(self): |
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240 return self.root.find("redirect_url_params") |
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241 |
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242 def parse_sanitize(self): |
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243 return self._get_option_value("sanitize", True) |
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244 |
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245 def parse_refresh(self): |
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246 return self._get_option_value("refresh", False) |
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247 |
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248 def _get_option_value(self, key, default): |
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249 root = self.root |
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250 for option_elem in root.findall("options"): |
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251 if key in option_elem.attrib: |
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252 return string_as_bool(option_elem.get(key)) |
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253 return default |
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254 |
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255 @property |
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256 def _command_el(self): |
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257 return self.root.find("command") |
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258 |
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259 def _get_attribute_as_bool(self, attribute, default, elem=None): |
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260 if elem is None: |
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261 elem = self.root |
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262 return string_as_bool(elem.get(attribute, default)) |
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263 |
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264 def parse_requirements_and_containers(self): |
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265 return requirements.parse_requirements_from_xml(self.root) |
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266 |
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267 def parse_input_pages(self): |
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268 return XmlPagesSource(self.root) |
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269 |
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270 def parse_provided_metadata_style(self): |
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271 style = None |
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272 out_elem = self.root.find("outputs") |
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273 if out_elem is not None and "provided_metadata_style" in out_elem.attrib: |
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274 style = out_elem.attrib["provided_metadata_style"] |
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275 |
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276 if style is None: |
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277 style = "legacy" if self.parse_profile() < "17.09" else "default" |
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278 |
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279 assert style in ["legacy", "default"] |
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280 return style |
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281 |
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282 def parse_provided_metadata_file(self): |
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283 provided_metadata_file = "galaxy.json" |
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284 out_elem = self.root.find("outputs") |
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285 if out_elem is not None and "provided_metadata_file" in out_elem.attrib: |
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286 provided_metadata_file = out_elem.attrib["provided_metadata_file"] |
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287 |
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288 return provided_metadata_file |
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289 |
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290 def parse_outputs(self, tool): |
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291 out_elem = self.root.find("outputs") |
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292 outputs = {} |
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293 output_collections = {} |
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294 if out_elem is None: |
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295 return outputs, output_collections |
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296 |
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297 data_dict = {} |
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298 |
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299 def _parse(data_elem, **kwds): |
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300 output_def = self._parse_output(data_elem, tool, **kwds) |
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301 data_dict[output_def.name] = output_def |
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302 return output_def |
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303 |
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304 for _ in out_elem.findall("data"): |
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305 _parse(_) |
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306 |
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307 def _parse_expression(output_elem, **kwds): |
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308 output_def = self._parse_expression_output(output_elem, tool, **kwds) |
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309 output_def.filters = output_elem.findall('filter') |
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310 data_dict[output_def.name] = output_def |
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311 return output_def |
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312 |
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313 def _parse_collection(collection_elem): |
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314 name = collection_elem.get("name") |
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315 label = xml_text(collection_elem, "label") |
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316 default_format = collection_elem.get("format", "data") |
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317 collection_type = collection_elem.get("type", None) |
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318 collection_type_source = collection_elem.get("type_source", None) |
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319 collection_type_from_rules = collection_elem.get("type_from_rules", None) |
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320 structured_like = collection_elem.get("structured_like", None) |
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321 inherit_format = False |
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322 inherit_metadata = False |
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323 if structured_like: |
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324 inherit_format = string_as_bool(collection_elem.get("inherit_format", None)) |
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325 inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None)) |
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326 default_format_source = collection_elem.get("format_source", None) |
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327 default_metadata_source = collection_elem.get("metadata_source", "") |
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328 filters = collection_elem.findall('filter') |
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329 |
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330 dataset_collector_descriptions = None |
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331 if collection_elem.find("discover_datasets") is not None: |
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332 dataset_collector_descriptions = dataset_collector_descriptions_from_elem(collection_elem, legacy=False) |
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333 structure = ToolOutputCollectionStructure( |
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334 collection_type=collection_type, |
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335 collection_type_source=collection_type_source, |
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336 collection_type_from_rules=collection_type_from_rules, |
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337 structured_like=structured_like, |
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338 dataset_collector_descriptions=dataset_collector_descriptions, |
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339 ) |
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340 output_collection = ToolOutputCollection( |
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341 name, |
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342 structure, |
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343 label=label, |
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344 filters=filters, |
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345 default_format=default_format, |
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346 inherit_format=inherit_format, |
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347 inherit_metadata=inherit_metadata, |
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348 default_format_source=default_format_source, |
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349 default_metadata_source=default_metadata_source, |
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350 ) |
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351 outputs[output_collection.name] = output_collection |
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352 |
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353 for data_elem in collection_elem.findall("data"): |
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354 _parse( |
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355 data_elem, |
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356 default_format=default_format, |
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357 default_format_source=default_format_source, |
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358 default_metadata_source=default_metadata_source, |
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359 ) |
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360 |
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361 for data_elem in collection_elem.findall("data"): |
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362 output_name = data_elem.get("name") |
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363 data = data_dict[output_name] |
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364 assert data |
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365 del data_dict[output_name] |
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366 output_collection.outputs[output_name] = data |
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367 output_collections[name] = output_collection |
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368 |
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369 for out_child in out_elem: |
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370 if out_child.tag == "data": |
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371 _parse(out_child) |
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372 elif out_child.tag == "collection": |
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373 _parse_collection(out_child) |
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374 elif out_child.tag == "output": |
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375 output_type = out_child.get("type") |
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376 if output_type == "data": |
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377 _parse(out_child) |
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378 elif output_type == "collection": |
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379 out_child.attrib["type"] = out_child.get("collection_type") |
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380 out_child.attrib["type_source"] = out_child.get("collection_type_source") |
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381 _parse_collection(out_child) |
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382 else: |
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383 _parse_expression(out_child) |
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384 else: |
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385 log.warning("Unknown output tag encountered [%s]" % out_child.tag) |
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386 |
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387 for output_def in data_dict.values(): |
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388 outputs[output_def.name] = output_def |
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389 return outputs, output_collections |
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390 |
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391 def _parse_output( |
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392 self, |
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393 data_elem, |
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394 tool, |
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395 default_format="data", |
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396 default_format_source=None, |
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397 default_metadata_source="", |
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398 expression_type=None, |
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399 ): |
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400 from_expression = data_elem.get("from") |
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401 output = ToolOutput(data_elem.get("name"), from_expression=from_expression) |
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402 output_format = data_elem.get("format", default_format) |
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403 auto_format = string_as_bool(data_elem.get("auto_format", "false")) |
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404 if auto_format and output_format != "data": |
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405 raise ValueError("Setting format and auto_format is not supported at this time.") |
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406 elif auto_format: |
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407 output_format = "_sniff_" |
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408 output.format = output_format |
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409 output.change_format = data_elem.findall("change_format") |
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410 output.format_source = data_elem.get("format_source", default_format_source) |
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411 output.default_identifier_source = data_elem.get("default_identifier_source", 'None') |
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412 output.metadata_source = data_elem.get("metadata_source", default_metadata_source) |
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413 output.parent = data_elem.get("parent", None) |
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414 output.label = xml_text(data_elem, "label") |
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415 output.count = int(data_elem.get("count", 1)) |
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416 output.filters = data_elem.findall('filter') |
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417 output.tool = tool |
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418 output.from_work_dir = data_elem.get("from_work_dir", None) |
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419 output.hidden = string_as_bool(data_elem.get("hidden", "")) |
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420 output.actions = ToolOutputActionGroup(output, data_elem.find('actions')) |
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421 output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(data_elem, legacy=self.legacy_defaults) |
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422 return output |
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423 |
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424 def _parse_expression_output(self, output_elem, tool, **kwds): |
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425 output_type = output_elem.get("type") |
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426 from_expression = output_elem.get("from") |
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427 output = ToolExpressionOutput( |
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428 output_elem.get("name"), |
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429 output_type, |
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430 from_expression, |
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431 ) |
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432 output.path = output_elem.get("value") |
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433 output.label = xml_text(output_elem, "label") |
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434 |
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435 output.hidden = string_as_bool(output_elem.get("hidden", "")) |
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436 output.actions = ToolOutputActionGroup(output, output_elem.find('actions')) |
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437 output.dataset_collector_descriptions = [] |
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438 return output |
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439 |
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440 def parse_stdio(self): |
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441 """ |
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442 parse error handling from command and stdio tag |
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443 |
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444 returns list of exit codes, list of regexes |
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445 |
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446 - exit_codes contain all non-zero exit codes (:-1 and 1:) if |
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447 detect_errors is default (if not legacy), exit_code, or aggressive |
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448 - the oom_exit_code if given and detect_errors is exit_code |
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449 - exit codes and regexes from the stdio tag |
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450 these are prepended to the list, i.e. are evaluated prior to regexes |
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451 and exit codes derived from the properties of the command tag. |
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452 thus more specific regexes of the same or more severe error level |
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|
453 are triggered first. |
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|
454 |
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455 """ |
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456 |
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457 command_el = self._command_el |
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458 detect_errors = None |
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459 if command_el is not None: |
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460 detect_errors = command_el.get("detect_errors") |
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461 |
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462 if detect_errors and detect_errors != "default": |
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463 if detect_errors == "exit_code": |
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464 oom_exit_code = None |
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465 if command_el is not None: |
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466 oom_exit_code = command_el.get("oom_exit_code", None) |
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467 if oom_exit_code is not None: |
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468 int(oom_exit_code) |
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469 exit_codes, regexes = error_on_exit_code(out_of_memory_exit_code=oom_exit_code) |
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470 elif detect_errors == "aggressive": |
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471 exit_codes, regexes = aggressive_error_checks() |
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472 else: |
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473 raise ValueError("Unknown detect_errors value encountered [%s]" % detect_errors) |
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474 elif len(self.root.findall('stdio')) == 0 and not self.legacy_defaults: |
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475 exit_codes, regexes = error_on_exit_code() |
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476 else: |
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477 exit_codes = [] |
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478 regexes = [] |
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479 |
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480 if len(self.root.findall('stdio')) > 0: |
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481 parser = StdioParser(self.root) |
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482 exit_codes = parser.stdio_exit_codes + exit_codes |
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483 regexes = parser.stdio_regexes + regexes |
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484 |
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485 return exit_codes, regexes |
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486 |
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487 def parse_strict_shell(self): |
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488 command_el = self._command_el |
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489 if packaging.version.parse(self.parse_profile()) < packaging.version.parse('20.09'): |
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490 default = "False" |
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491 else: |
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492 default = "True" |
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493 if command_el is not None: |
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494 return string_as_bool(command_el.get("strict", default)) |
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495 else: |
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496 return string_as_bool(default) |
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497 |
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498 def parse_help(self): |
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499 help_elem = self.root.find('help') |
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500 return help_elem.text if help_elem is not None else None |
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501 |
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502 @property |
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503 def macro_paths(self): |
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504 return self._macro_paths |
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505 |
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506 @property |
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507 def source_path(self): |
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508 return self._source_path |
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509 |
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510 def parse_tests_to_dict(self): |
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511 tests_elem = self.root.find("tests") |
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512 tests = [] |
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513 rval = dict( |
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514 tests=tests |
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|
515 ) |
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516 |
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517 if tests_elem is not None: |
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518 for i, test_elem in enumerate(tests_elem.findall("test")): |
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519 profile = self.parse_profile() |
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520 tests.append(_test_elem_to_dict(test_elem, i, profile)) |
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521 |
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522 return rval |
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523 |
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524 def parse_profile(self): |
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525 # Pre-16.04 or default XML defaults |
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526 # - Use standard error for error detection. |
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527 # - Don't run shells with -e |
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528 # - Auto-check for implicit multiple outputs. |
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529 # - Auto-check for $param_file. |
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530 # - Enable buggy interpreter attribute. |
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531 return self.root.get("profile", "16.01") |
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532 |
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533 def parse_license(self): |
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534 return self.root.get("license") |
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535 |
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536 def parse_python_template_version(self): |
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537 python_template_version = self.root.get("python_template_version", None) |
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538 if python_template_version is not None: |
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539 python_template_version = packaging.version.parse(python_template_version) |
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540 return python_template_version |
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541 |
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542 def parse_creator(self): |
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543 creators_el = self.root.find("creator") |
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544 if creators_el is None: |
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545 return None |
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546 |
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547 creators = [] |
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548 for creator_el in creators_el: |
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549 creator_as_dict = {} |
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550 if creator_el.tag == "person": |
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551 clazz = "Person" |
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552 elif creator_el.tag == "organization": |
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553 clazz = "Organization" |
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554 else: |
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555 continue |
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556 creator_as_dict["class"] = clazz |
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557 creator_as_dict.update(creator_el.attrib) |
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558 creators.append(creator_as_dict) |
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559 return creators |
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560 |
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561 |
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562 def _test_elem_to_dict(test_elem, i, profile=None): |
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563 rval = dict( |
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564 outputs=__parse_output_elems(test_elem), |
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565 output_collections=__parse_output_collection_elems(test_elem, profile=profile), |
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566 inputs=__parse_input_elems(test_elem, i), |
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567 expect_num_outputs=test_elem.get("expect_num_outputs"), |
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568 command=__parse_assert_list_from_elem(test_elem.find("assert_command")), |
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569 command_version=__parse_assert_list_from_elem(test_elem.find("assert_command_version")), |
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570 stdout=__parse_assert_list_from_elem(test_elem.find("assert_stdout")), |
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571 stderr=__parse_assert_list_from_elem(test_elem.find("assert_stderr")), |
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572 expect_exit_code=test_elem.get("expect_exit_code"), |
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573 expect_failure=string_as_bool(test_elem.get("expect_failure", False)), |
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574 maxseconds=test_elem.get("maxseconds", None), |
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575 ) |
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576 _copy_to_dict_if_present(test_elem, rval, ["num_outputs"]) |
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577 return rval |
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578 |
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579 |
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580 def __parse_input_elems(test_elem, i): |
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581 __expand_input_elems(test_elem) |
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582 return __parse_inputs_elems(test_elem, i) |
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583 |
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584 |
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585 def __parse_output_elems(test_elem): |
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586 outputs = [] |
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587 for output_elem in test_elem.findall("output"): |
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588 name, file, attributes = __parse_output_elem(output_elem) |
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589 outputs.append({"name": name, "value": file, "attributes": attributes}) |
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590 return outputs |
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591 |
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592 |
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593 def __parse_output_elem(output_elem): |
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594 attrib = dict(output_elem.attrib) |
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595 name = attrib.pop('name', None) |
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596 if name is None: |
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597 raise Exception("Test output does not have a 'name'") |
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598 |
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599 file, attributes = __parse_test_attributes(output_elem, attrib, parse_discovered_datasets=True) |
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600 return name, file, attributes |
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601 |
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602 |
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603 def __parse_command_elem(test_elem): |
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604 assert_elem = test_elem.find("command") |
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605 return __parse_assert_list_from_elem(assert_elem) |
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606 |
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607 |
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608 def __parse_output_collection_elems(test_elem, profile=None): |
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609 output_collections = [] |
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610 for output_collection_elem in test_elem.findall("output_collection"): |
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611 output_collection_def = __parse_output_collection_elem(output_collection_elem, profile=profile) |
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612 output_collections.append(output_collection_def) |
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613 return output_collections |
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614 |
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615 |
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616 def __parse_output_collection_elem(output_collection_elem, profile=None): |
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617 attrib = dict(output_collection_elem.attrib) |
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618 name = attrib.pop('name', None) |
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619 if name is None: |
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620 raise Exception("Test output collection does not have a 'name'") |
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621 element_tests = __parse_element_tests(output_collection_elem, profile=profile) |
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622 return TestCollectionOutputDef(name, attrib, element_tests).to_dict() |
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623 |
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624 |
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625 def __parse_element_tests(parent_element, profile=None): |
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626 element_tests = {} |
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627 for idx, element in enumerate(parent_element.findall("element")): |
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628 element_attrib = dict(element.attrib) |
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629 identifier = element_attrib.pop('name', None) |
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630 if identifier is None: |
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631 raise Exception("Test primary dataset does not have a 'identifier'") |
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632 element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True, profile=profile) |
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633 if profile and profile >= "20.09": |
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634 element_tests[identifier][1]["expected_sort_order"] = idx |
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635 |
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636 return element_tests |
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637 |
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638 |
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639 def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False, profile=None): |
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640 assert_list = __parse_assert_list(output_elem) |
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641 |
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642 # Allow either file or value to specify a target file to compare result with |
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643 # file was traditionally used by outputs and value by extra files. |
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644 file = attrib.pop('file', attrib.pop('value', None)) |
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645 |
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646 # File no longer required if an list of assertions was present. |
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647 attributes = {} |
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648 |
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649 if 'value_json' in attrib: |
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650 attributes['object'] = json.loads(attrib.pop('value_json')) |
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651 |
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652 # Method of comparison |
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653 attributes['compare'] = attrib.pop('compare', 'diff').lower() |
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654 # Number of lines to allow to vary in logs (for dates, etc) |
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655 attributes['lines_diff'] = int(attrib.pop('lines_diff', '0')) |
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656 # Allow a file size to vary if sim_size compare |
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657 attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA)) |
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658 attributes['delta_frac'] = float(attrib['delta_frac']) if 'delta_frac' in attrib else DEFAULT_DELTA_FRAC |
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659 attributes['sort'] = string_as_bool(attrib.pop('sort', False)) |
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660 attributes['decompress'] = string_as_bool(attrib.pop('decompress', False)) |
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661 extra_files = [] |
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662 if 'ftype' in attrib: |
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663 attributes['ftype'] = attrib['ftype'] |
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664 for extra in output_elem.findall('extra_files'): |
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665 extra_files.append(__parse_extra_files_elem(extra)) |
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666 metadata = {} |
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667 for metadata_elem in output_elem.findall('metadata'): |
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668 metadata[metadata_elem.get('name')] = metadata_elem.get('value') |
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669 md5sum = attrib.get("md5", None) |
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670 checksum = attrib.get("checksum", None) |
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671 element_tests = {} |
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672 if parse_elements: |
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673 element_tests = __parse_element_tests(output_elem, profile=profile) |
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674 |
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675 primary_datasets = {} |
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676 if parse_discovered_datasets: |
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677 for primary_elem in (output_elem.findall("discovered_dataset") or []): |
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678 primary_attrib = dict(primary_elem.attrib) |
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679 designation = primary_attrib.pop('designation', None) |
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680 if designation is None: |
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681 raise Exception("Test primary dataset does not have a 'designation'") |
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682 primary_datasets[designation] = __parse_test_attributes(primary_elem, primary_attrib) |
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683 |
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684 has_checksum = md5sum or checksum |
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685 has_nested_tests = extra_files or element_tests or primary_datasets |
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686 has_object = 'object' in attributes |
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687 if not (assert_list or file or metadata or has_checksum or has_nested_tests or has_object): |
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688 raise Exception("Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)") |
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689 attributes['assert_list'] = assert_list |
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690 attributes['extra_files'] = extra_files |
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691 attributes['metadata'] = metadata |
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692 attributes['md5'] = md5sum |
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693 attributes['checksum'] = checksum |
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694 attributes['elements'] = element_tests |
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695 attributes['primary_datasets'] = primary_datasets |
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696 return file, attributes |
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697 |
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698 |
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699 def __parse_assert_list(output_elem): |
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700 assert_elem = output_elem.find("assert_contents") |
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701 return __parse_assert_list_from_elem(assert_elem) |
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702 |
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703 |
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704 def __parse_assert_list_from_elem(assert_elem): |
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705 assert_list = None |
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706 |
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707 def convert_elem(elem): |
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708 """ Converts and XML element to a dictionary format, used by assertion checking code. """ |
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709 tag = elem.tag |
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710 attributes = dict(elem.attrib) |
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711 converted_children = [] |
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712 for child_elem in elem: |
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713 converted_children.append(convert_elem(child_elem)) |
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714 return {"tag": tag, "attributes": attributes, "children": converted_children} |
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715 if assert_elem is not None: |
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716 assert_list = [] |
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717 for assert_child in list(assert_elem): |
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718 assert_list.append(convert_elem(assert_child)) |
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719 |
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720 return assert_list |
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721 |
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722 |
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723 def __parse_extra_files_elem(extra): |
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724 # File or directory, when directory, compare basename |
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725 # by basename |
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726 attrib = dict(extra.attrib) |
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727 extra_type = attrib.pop('type', 'file') |
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728 extra_name = attrib.pop('name', None) |
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729 assert extra_type == 'directory' or extra_name is not None, \ |
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730 'extra_files type (%s) requires a name attribute' % extra_type |
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731 extra_value, extra_attributes = __parse_test_attributes(extra, attrib) |
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732 return { |
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733 "value": extra_value, |
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734 "name": extra_name, |
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735 "type": extra_type, |
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736 "attributes": extra_attributes |
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737 } |
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738 |
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739 |
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740 def __expand_input_elems(root_elem, prefix=""): |
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741 __append_prefix_to_params(root_elem, prefix) |
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742 |
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743 repeat_elems = root_elem.findall('repeat') |
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744 indices = {} |
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745 for repeat_elem in repeat_elems: |
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746 name = repeat_elem.get("name") |
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747 if name not in indices: |
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748 indices[name] = 0 |
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749 index = 0 |
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750 else: |
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751 index = indices[name] + 1 |
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752 indices[name] = index |
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753 |
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754 new_prefix = __prefix_join(prefix, name, index=index) |
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755 __expand_input_elems(repeat_elem, new_prefix) |
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756 __pull_up_params(root_elem, repeat_elem) |
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757 |
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758 cond_elems = root_elem.findall('conditional') |
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759 for cond_elem in cond_elems: |
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760 new_prefix = __prefix_join(prefix, cond_elem.get("name")) |
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761 __expand_input_elems(cond_elem, new_prefix) |
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762 __pull_up_params(root_elem, cond_elem) |
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763 |
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764 section_elems = root_elem.findall('section') |
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765 for section_elem in section_elems: |
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766 new_prefix = __prefix_join(prefix, section_elem.get("name")) |
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767 __expand_input_elems(section_elem, new_prefix) |
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768 __pull_up_params(root_elem, section_elem) |
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769 |
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770 |
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771 def __append_prefix_to_params(elem, prefix): |
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772 for param_elem in elem.findall('param'): |
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773 param_elem.set("name", __prefix_join(prefix, param_elem.get("name"))) |
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774 |
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775 |
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776 def __pull_up_params(parent_elem, child_elem): |
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777 for param_elem in child_elem.findall('param'): |
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778 parent_elem.append(param_elem) |
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779 |
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780 |
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781 def __prefix_join(prefix, name, index=None): |
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782 name = name if index is None else "%s_%d" % (name, index) |
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783 return name if not prefix else f"{prefix}|{name}" |
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784 |
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785 |
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786 def _copy_to_dict_if_present(elem, rval, attributes): |
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787 for attribute in attributes: |
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788 if attribute in elem.attrib: |
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789 rval[attribute] = elem.get(attribute) |
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790 return rval |
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791 |
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792 |
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793 def __parse_inputs_elems(test_elem, i): |
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794 raw_inputs = [] |
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795 for param_elem in test_elem.findall("param"): |
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796 raw_inputs.append(__parse_param_elem(param_elem, i)) |
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797 |
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|
798 return raw_inputs |
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799 |
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800 |
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801 def __parse_param_elem(param_elem, i=0): |
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802 attrib = dict(param_elem.attrib) |
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803 if 'values' in attrib: |
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804 value = attrib['values'].split(',') |
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805 elif 'value' in attrib: |
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806 value = attrib['value'] |
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807 elif 'value_json' in attrib: |
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808 value = json.loads(attrib['value_json']) |
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809 else: |
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810 value = None |
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811 |
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812 children_elem = param_elem |
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813 if children_elem is not None: |
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814 # At this time, we can assume having children only |
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815 # occurs on DataToolParameter test items but this could |
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816 # change and would cause the below parsing to change |
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817 # based upon differences in children items |
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818 attrib['metadata'] = {} |
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819 attrib['composite_data'] = [] |
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820 attrib['edit_attributes'] = [] |
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821 # Composite datasets need to be renamed uniquely |
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822 composite_data_name = None |
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823 for child in children_elem: |
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824 if child.tag == 'composite_data': |
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825 file_name = child.get("value") |
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826 attrib['composite_data'].append(file_name) |
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827 if composite_data_name is None: |
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828 # Generate a unique name; each test uses a |
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829 # fresh history. |
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830 composite_data_name = '_COMPOSITE_RENAMED_t%d_%s' \ |
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831 % (i, uuid.uuid1().hex) |
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832 elif child.tag == 'metadata': |
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833 attrib['metadata'][child.get("name")] = child.get("value") |
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834 elif child.tag == 'edit_attributes': |
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835 attrib['edit_attributes'].append(child) |
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836 elif child.tag == 'collection': |
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837 attrib['collection'] = TestCollectionDef.from_xml(child, __parse_param_elem) |
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838 if composite_data_name: |
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839 # Composite datasets need implicit renaming; |
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840 # inserted at front of list so explicit declarations |
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841 # take precedence |
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842 attrib['edit_attributes'].insert(0, {'type': 'name', 'value': composite_data_name}) |
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843 name = attrib.pop('name') |
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844 return { |
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845 "name": name, |
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846 "value": value, |
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847 "attributes": attrib |
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848 } |
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849 |
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850 |
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851 class StdioParser: |
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852 |
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853 def __init__(self, root): |
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854 try: |
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855 self.stdio_exit_codes = list() |
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856 self.stdio_regexes = list() |
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857 |
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858 # We should have a single <stdio> element, but handle the case for |
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859 # multiples. |
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860 # For every stdio element, add all of the exit_code and regex |
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861 # subelements that we find: |
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862 for stdio_elem in (root.findall('stdio')): |
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863 self.parse_stdio_exit_codes(stdio_elem) |
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864 self.parse_stdio_regexes(stdio_elem) |
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865 except Exception: |
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866 log.exception("Exception in parse_stdio!") |
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867 |
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868 def parse_stdio_exit_codes(self, stdio_elem): |
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869 """ |
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870 Parse the tool's <stdio> element's <exit_code> subelements. |
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871 This will add all of those elements, if any, to self.stdio_exit_codes. |
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872 """ |
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873 try: |
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874 # Look for all <exit_code> elements. Each exit_code element must |
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875 # have a range/value. |
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876 # Exit-code ranges have precedence over a single exit code. |
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877 # So if there are value and range attributes, we use the range |
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878 # attribute. If there is neither a range nor a value, then print |
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879 # a warning and skip to the next. |
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880 for exit_code_elem in (stdio_elem.findall("exit_code")): |
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881 exit_code = ToolStdioExitCode() |
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882 # Each exit code has an optional description that can be |
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883 # part of the "desc" or "description" attributes: |
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884 exit_code.desc = exit_code_elem.get("desc") |
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885 if exit_code.desc is None: |
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886 exit_code.desc = exit_code_elem.get("description") |
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887 # Parse the error level: |
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888 exit_code.error_level = ( |
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889 self.parse_error_level(exit_code_elem.get("level"))) |
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890 code_range = exit_code_elem.get("range", "") |
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891 if code_range is None: |
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|
892 code_range = exit_code_elem.get("value", "") |
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|
893 if code_range is None: |
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|
894 log.warning("Tool stdio exit codes must have a range or value") |
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parents:
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|
895 continue |
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parents:
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|
896 # Parse the range. We look for: |
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|
897 # :Y |
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|
898 # X: |
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|
899 # X:Y - Split on the colon. We do not allow a colon |
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shellac
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|
900 # without a beginning or end, though we could. |
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|
901 # Also note that whitespace is eliminated. |
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shellac
parents:
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|
902 # TODO: Turn this into a single match - it should be |
4f3585e2f14b
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|
903 # more efficient. |
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|
904 code_range = re.sub(r"\s", "", code_range) |
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|
905 code_ranges = re.split(r":", code_range) |
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|
906 if (len(code_ranges) == 2): |
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|
907 if (code_ranges[0] is None or '' == code_ranges[0]): |
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|
908 exit_code.range_start = float("-inf") |
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|
909 else: |
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|
910 exit_code.range_start = int(code_ranges[0]) |
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|
911 if (code_ranges[1] is None or '' == code_ranges[1]): |
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shellac
parents:
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|
912 exit_code.range_end = float("inf") |
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|
913 else: |
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|
914 exit_code.range_end = int(code_ranges[1]) |
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|
915 # If we got more than one colon, then ignore the exit code. |
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|
916 elif (len(code_ranges) > 2): |
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|
917 log.warning("Invalid tool exit_code range %s - ignored" |
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|
918 % code_range) |
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|
919 continue |
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|
920 # Else we have a singular value. If it's not an integer, then |
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|
921 # we'll just write a log message and skip this exit_code. |
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|
922 else: |
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|
923 try: |
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|
924 exit_code.range_start = int(code_range) |
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|
925 except Exception: |
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|
926 log.error(code_range) |
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|
927 log.warning("Invalid range start for tool's exit_code %s: exit_code ignored" % code_range) |
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|
928 continue |
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|
929 exit_code.range_end = exit_code.range_start |
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|
930 # TODO: Check if we got ">", ">=", "<", or "<=": |
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|
931 # Check that the range, regardless of how we got it, |
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|
932 # isn't bogus. If we have two infinite values, then |
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|
933 # the start must be -inf and the end must be +inf. |
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|
934 # So at least warn about this situation: |
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shellac
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|
935 if isinf(exit_code.range_start) and isinf(exit_code.range_end): |
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shellac
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|
936 log.warning("Tool exit_code range %s will match on all exit codes" % code_range) |
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|
937 self.stdio_exit_codes.append(exit_code) |
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938 except Exception: |
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|
939 log.exception("Exception in parse_stdio_exit_codes!") |
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shellac
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|
940 |
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shellac
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|
941 def parse_stdio_regexes(self, stdio_elem): |
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shellac
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|
942 """ |
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shellac
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|
943 Look in the tool's <stdio> elem for all <regex> subelements |
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|
944 that define how to look for warnings and fatal errors in |
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shellac
parents:
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|
945 stdout and stderr. This will add all such regex elements |
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shellac
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|
946 to the Tols's stdio_regexes list. |
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shellac
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|
947 """ |
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|
948 try: |
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shellac
parents:
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|
949 # Look for every <regex> subelement. The regular expression |
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shellac
parents:
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|
950 # will have "match" and "source" (or "src") attributes. |
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shellac
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|
951 for regex_elem in (stdio_elem.findall("regex")): |
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shellac
parents:
diff
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|
952 # TODO: Fill in ToolStdioRegex |
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shellac
parents:
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|
953 regex = ToolStdioRegex() |
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shellac
parents:
diff
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|
954 # Each regex has an optional description that can be |
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shellac
parents:
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|
955 # part of the "desc" or "description" attributes: |
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shellac
parents:
diff
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|
956 regex.desc = regex_elem.get("desc") |
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shellac
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|
957 if regex.desc is None: |
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shellac
parents:
diff
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|
958 regex.desc = regex_elem.get("description") |
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shellac
parents:
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|
959 # Parse the error level |
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shellac
parents:
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|
960 regex.error_level = ( |
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shellac
parents:
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|
961 self.parse_error_level(regex_elem.get("level"))) |
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shellac
parents:
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|
962 regex.match = regex_elem.get("match", "") |
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|
963 if regex.match is None: |
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shellac
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|
964 # TODO: Convert the offending XML element to a string |
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shellac
parents:
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|
965 log.warning("Ignoring tool's stdio regex element %s - " |
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|
966 "the 'match' attribute must exist") |
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shellac
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|
967 continue |
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shellac
parents:
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|
968 # Parse the output sources. We look for the "src", "source", |
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shellac
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|
969 # and "sources" attributes, in that order. If there is no |
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shellac
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|
970 # such source, then the source defaults to stderr & stdout. |
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shellac
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|
971 # Look for a comma and then look for "err", "error", "out", |
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shellac
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|
972 # and "output": |
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|
973 output_srcs = regex_elem.get("src") |
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shellac
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|
974 if output_srcs is None: |
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shellac
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|
975 output_srcs = regex_elem.get("source") |
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976 if output_srcs is None: |
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shellac
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|
977 output_srcs = regex_elem.get("sources") |
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shellac
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|
978 if output_srcs is None: |
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shellac
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|
979 output_srcs = "output,error" |
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980 output_srcs = re.sub(r"\s", "", output_srcs) |
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|
981 src_list = re.split(r",", output_srcs) |
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shellac
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|
982 # Just put together anything to do with "out", including |
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|
983 # "stdout", "output", etc. Repeat for "stderr", "error", |
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shellac
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|
984 # and anything to do with "err". If neither stdout nor |
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shellac
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|
985 # stderr were specified, then raise a warning and scan both. |
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|
986 for src in src_list: |
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|
987 if re.search("both", src, re.IGNORECASE): |
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parents:
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|
988 regex.stdout_match = True |
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shellac
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|
989 regex.stderr_match = True |
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|
990 if re.search("out", src, re.IGNORECASE): |
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|
991 regex.stdout_match = True |
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|
992 if re.search("err", src, re.IGNORECASE): |
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|
993 regex.stderr_match = True |
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shellac
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|
994 if (not regex.stdout_match and not regex.stderr_match): |
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shellac
parents:
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|
995 log.warning("Tool id %s: unable to determine if tool " |
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shellac
parents:
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|
996 "stream source scanning is output, error, " |
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shellac
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|
997 "or both. Defaulting to use both." % self.id) |
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parents:
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|
998 regex.stdout_match = True |
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999 regex.stderr_match = True |
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1000 self.stdio_regexes.append(regex) |
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1001 except Exception: |
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1002 log.exception("Exception in parse_stdio_exit_codes!") |
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1003 |
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1004 # TODO: This method doesn't have to be part of the Tool class. |
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1005 def parse_error_level(self, err_level): |
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1006 """ |
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1007 Parses error level and returns error level enumeration. If |
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1008 unparsable, returns 'fatal' |
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1009 """ |
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1010 return_level = StdioErrorLevel.FATAL |
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1011 try: |
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1012 if err_level: |
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1013 if (re.search("log", err_level, re.IGNORECASE)): |
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1014 return_level = StdioErrorLevel.LOG |
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1015 elif (re.search("qc", err_level, re.IGNORECASE)): |
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1016 return_level = StdioErrorLevel.QC |
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1017 elif (re.search("warning", err_level, re.IGNORECASE)): |
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1018 return_level = StdioErrorLevel.WARNING |
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1019 elif (re.search("fatal_oom", err_level, re.IGNORECASE)): |
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1020 return_level = StdioErrorLevel.FATAL_OOM |
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1021 elif (re.search("fatal", err_level, re.IGNORECASE)): |
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1022 return_level = StdioErrorLevel.FATAL |
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1023 else: |
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1024 log.debug("Tool %s: error level %s did not match log/warning/fatal" % |
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1025 (self.id, err_level)) |
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1026 except Exception: |
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1027 log.exception("Exception in parse_error_level") |
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1028 return return_level |
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1029 |
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1030 |
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1031 class XmlPagesSource(PagesSource): |
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1032 |
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1033 def __init__(self, root): |
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1034 self.input_elem = root.find("inputs") |
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1035 page_sources = [] |
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1036 if self.input_elem is not None: |
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1037 pages_elem = self.input_elem.findall("page") |
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1038 for page in (pages_elem or [self.input_elem]): |
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1039 page_sources.append(XmlPageSource(page)) |
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1040 super().__init__(page_sources) |
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1041 |
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1042 @property |
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1043 def inputs_defined(self): |
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1044 return self.input_elem is not None |
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1045 |
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1046 |
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1047 class XmlPageSource(PageSource): |
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1048 |
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1049 def __init__(self, parent_elem): |
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1050 self.parent_elem = parent_elem |
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1051 |
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1052 def parse_display(self): |
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1053 display_elem = self.parent_elem.find("display") |
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1054 if display_elem is not None: |
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1055 display = xml_to_string(display_elem) |
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1056 else: |
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1057 display = None |
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1058 return display |
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1059 |
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1060 def parse_input_sources(self): |
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1061 return map(XmlInputSource, self.parent_elem) |
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1062 |
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1063 |
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1064 class XmlInputSource(InputSource): |
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1065 |
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1066 def __init__(self, input_elem): |
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1067 self.input_elem = input_elem |
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1068 self.input_type = self.input_elem.tag |
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1069 |
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1070 def parse_input_type(self): |
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1071 return self.input_type |
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1072 |
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1073 def elem(self): |
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1074 return self.input_elem |
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1075 |
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1076 def get(self, key, value=None): |
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1077 return self.input_elem.get(key, value) |
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1078 |
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1079 def get_bool(self, key, default): |
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1080 return string_as_bool(self.get(key, default)) |
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1081 |
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1082 def parse_label(self): |
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1083 return xml_text(self.input_elem, "label") |
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1084 |
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1085 def parse_help(self): |
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1086 return xml_text(self.input_elem, "help") |
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1087 |
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1088 def parse_sanitizer_elem(self): |
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1089 return self.input_elem.find("sanitizer") |
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1090 |
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1091 def parse_validator_elems(self): |
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1092 return self.input_elem.findall("validator") |
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1093 |
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1094 def parse_dynamic_options_elem(self): |
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1095 """ Return a galaxy.tools.parameters.dynamic_options.DynamicOptions |
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1096 if appropriate. |
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1097 """ |
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1098 options_elem = self.input_elem.find('options') |
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1099 return options_elem |
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1100 |
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1101 def parse_static_options(self): |
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1102 static_options = list() |
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1103 elem = self.input_elem |
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1104 for option in elem.findall("option"): |
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1105 value = option.get("value") |
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1106 selected = string_as_bool(option.get("selected", False)) |
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1107 static_options.append((option.text or value, value, selected)) |
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1108 return static_options |
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1109 |
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1110 def parse_optional(self, default=None): |
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1111 """ Return boolean indicating whether parameter is optional. """ |
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1112 elem = self.input_elem |
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1113 if self.get('type') == "data_column": |
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1114 # Allow specifing force_select for backward compat., but probably |
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1115 # should use optional going forward for consistency with other |
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1116 # parameters. |
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1117 if "force_select" in elem.attrib: |
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1118 force_select = string_as_bool(elem.get("force_select")) |
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1119 else: |
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1120 force_select = not string_as_bool(elem.get("optional", False)) |
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1121 return not force_select |
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1122 |
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1123 if default is None: |
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1124 default = self.default_optional |
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1125 return self.get_bool("optional", default) |
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1126 |
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1127 def parse_conversion_tuples(self): |
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1128 elem = self.input_elem |
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1129 conversions = [] |
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1130 for conv_elem in elem.findall("conversion"): |
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1131 name = conv_elem.get("name") # name for commandline substitution |
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1132 conv_extensions = conv_elem.get("type") # target datatype extension |
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1133 conversions.append((name, conv_extensions)) |
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1134 return conversions |
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1135 |
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1136 def parse_nested_inputs_source(self): |
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1137 elem = self.input_elem |
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1138 return XmlPageSource(elem) |
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1139 |
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1140 def parse_test_input_source(self): |
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1141 elem = self.input_elem |
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1142 input_elem = elem.find("param") |
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1143 assert input_elem is not None, "<conditional> must have a child <param>" |
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1144 return XmlInputSource(input_elem) |
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1145 |
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1146 def parse_when_input_sources(self): |
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1147 elem = self.input_elem |
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1148 |
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1149 sources = [] |
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1150 for case_elem in elem.findall("when"): |
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1151 value = case_elem.get("value") |
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1152 case_page_source = XmlPageSource(case_elem) |
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1153 sources.append((value, case_page_source)) |
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1154 return sources |
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1155 |
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1156 |
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1157 class ParallelismInfo: |
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1158 """ |
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1159 Stores the information (if any) for running multiple instances of the tool in parallel |
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1160 on the same set of inputs. |
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1161 """ |
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1162 |
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1163 def __init__(self, tag): |
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1164 self.method = tag.get('method') |
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1165 if isinstance(tag, dict): |
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1166 items = tag.items() |
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1167 else: |
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1168 items = tag.attrib.items() |
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1169 self.attributes = dict([item for item in items if item[0] != 'method']) |
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1170 if len(self.attributes) == 0: |
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1171 # legacy basic mode - provide compatible defaults |
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1172 self.attributes['split_size'] = 20 |
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1173 self.attributes['split_mode'] = 'number_of_parts' |