Mercurial > repos > guerler > springsuite

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

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 import logging
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2 import re
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3 import uuid
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4 from collections import OrderedDict
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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_docker_env_pass_through(self):
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183 if self.parse_profile() < "18.01":
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184 return ["GALAXY_SLOTS"]
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185 else:
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186 # Pass home, etc...
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187 return super(XmlToolSource, self).parse_docker_env_pass_through()
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188
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189 def parse_interpreter(self):
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190 interpreter = None
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191 command_el = self._command_el
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192 if command_el is not None:
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193 interpreter = command_el.get("interpreter", None)
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194 if interpreter and not self.legacy_defaults:
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195 log.warning("Deprecated interpreter attribute on command element is now ignored.")
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196 interpreter = None
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197 return interpreter
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198
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199 def parse_version_command(self):
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200 version_cmd = self.root.find("version_command")
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201 if version_cmd is not None:
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202 return version_cmd.text
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203 else:
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204 return None
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205
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206 def parse_version_command_interpreter(self):
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207 if self.parse_version_command() is not None:
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208 version_cmd = self.root.find("version_command")
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209 version_cmd_interpreter = version_cmd.get("interpreter", None)
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210 if version_cmd_interpreter:
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211 return version_cmd_interpreter
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212 return None
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213
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214 def parse_parallelism(self):
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215 parallelism = self.root.find("parallelism")
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216 parallelism_info = None
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217 if parallelism is not None and parallelism.get("method"):
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218 return ParallelismInfo(parallelism)
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219 return parallelism_info
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220
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221 def parse_interactivetool(self):
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222 interactivetool_el = self.root.find("entry_points")
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223 rtt = []
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224 if interactivetool_el is None:
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225 return rtt
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226 for ep_el in interactivetool_el.findall("entry_point"):
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227 port = ep_el.find("port")
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228 assert port is not None, ValueError('A port is required for InteractiveTools')
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229 port = port.text.strip()
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230 url = ep_el.find("url")
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231 if url is not None:
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232 url = url.text.strip()
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233 name = ep_el.get('name', None)
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234 if name:
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235 name = name.strip()
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236 requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False))
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237 rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain))
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238 return rtt
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239
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240 def parse_hidden(self):
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241 hidden = xml_text(self.root, "hidden")
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242 if hidden:
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243 hidden = string_as_bool(hidden)
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244 return hidden
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245
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246 def parse_redirect_url_params_elem(self):
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247 return self.root.find("redirect_url_params")
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248
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249 def parse_sanitize(self):
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250 return self._get_option_value("sanitize", True)
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251
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252 def parse_refresh(self):
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253 return self._get_option_value("refresh", False)
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254
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255 def _get_option_value(self, key, default):
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256 root = self.root
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257 for option_elem in root.findall("options"):
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258 if key in option_elem.attrib:
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259 return string_as_bool(option_elem.get(key))
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260 return default
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261
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262 @property
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263 def _command_el(self):
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264 return self.root.find("command")
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265
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266 def _get_attribute_as_bool(self, attribute, default, elem=None):
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267 if elem is None:
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268 elem = self.root
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269 return string_as_bool(elem.get(attribute, default))
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270
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271 def parse_requirements_and_containers(self):
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272 return requirements.parse_requirements_from_xml(self.root)
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273
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274 def parse_input_pages(self):
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275 return XmlPagesSource(self.root)
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276
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277 def parse_provided_metadata_style(self):
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278 style = None
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279 out_elem = self.root.find("outputs")
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280 if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
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281 style = out_elem.attrib["provided_metadata_style"]
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282
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283 if style is None:
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284 style = "legacy" if self.parse_profile() < "17.09" else "default"
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285
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286 assert style in ["legacy", "default"]
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287 return style
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288
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289 def parse_provided_metadata_file(self):
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290 provided_metadata_file = "galaxy.json"
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291 out_elem = self.root.find("outputs")
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292 if out_elem is not None and "provided_metadata_file" in out_elem.attrib:
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293 provided_metadata_file = out_elem.attrib["provided_metadata_file"]
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294
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295 return provided_metadata_file
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296
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297 def parse_outputs(self, tool):
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298 out_elem = self.root.find("outputs")
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299 outputs = OrderedDict()
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300 output_collections = OrderedDict()
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301 if out_elem is None:
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302 return outputs, output_collections
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303
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304 data_dict = OrderedDict()
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305
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306 def _parse(data_elem, **kwds):
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307 output_def = self._parse_output(data_elem, tool, **kwds)
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308 data_dict[output_def.name] = output_def
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309 return output_def
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310
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311 for _ in out_elem.findall("data"):
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312 _parse(_)
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313
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314 def _parse_expression(output_elem, **kwds):
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315 output_def = self._parse_expression_output(output_elem, tool, **kwds)
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316 output_def.filters = output_elem.findall('filter')
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317 data_dict[output_def.name] = output_def
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318 return output_def
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319
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320 def _parse_collection(collection_elem):
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321 name = collection_elem.get("name")
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322 label = xml_text(collection_elem, "label")
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323 default_format = collection_elem.get("format", "data")
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324 collection_type = collection_elem.get("type", None)
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325 collection_type_source = collection_elem.get("type_source", None)
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326 collection_type_from_rules = collection_elem.get("type_from_rules", None)
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327 structured_like = collection_elem.get("structured_like", None)
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328 inherit_format = False
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329 inherit_metadata = False
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330 if structured_like:
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331 inherit_format = string_as_bool(collection_elem.get("inherit_format", None))
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332 inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
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333 default_format_source = collection_elem.get("format_source", None)
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334 default_metadata_source = collection_elem.get("metadata_source", "")
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335 filters = collection_elem.findall('filter')
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336
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337 dataset_collector_descriptions = None
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338 if collection_elem.find("discover_datasets") is not None:
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339 dataset_collector_descriptions = dataset_collector_descriptions_from_elem(collection_elem, legacy=False)
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340 structure = ToolOutputCollectionStructure(
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341 collection_type=collection_type,
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342 collection_type_source=collection_type_source,
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343 collection_type_from_rules=collection_type_from_rules,
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344 structured_like=structured_like,
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345 dataset_collector_descriptions=dataset_collector_descriptions,
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346 )
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347 output_collection = ToolOutputCollection(
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348 name,
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349 structure,
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350 label=label,
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351 filters=filters,
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352 default_format=default_format,
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353 inherit_format=inherit_format,
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354 inherit_metadata=inherit_metadata,
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355 default_format_source=default_format_source,
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356 default_metadata_source=default_metadata_source,
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357 )
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358 outputs[output_collection.name] = output_collection
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359
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360 for data_elem in collection_elem.findall("data"):
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361 _parse(
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362 data_elem,
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363 default_format=default_format,
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364 default_format_source=default_format_source,
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365 default_metadata_source=default_metadata_source,
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366 )
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367
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368 for data_elem in collection_elem.findall("data"):
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369 output_name = data_elem.get("name")
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370 data = data_dict[output_name]
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371 assert data
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372 del data_dict[output_name]
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373 output_collection.outputs[output_name] = data
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374 output_collections[name] = output_collection
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375
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376 for out_child in out_elem:
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377 if out_child.tag == "data":
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378 _parse(out_child)
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379 elif out_child.tag == "collection":
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380 _parse_collection(out_child)
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381 elif out_child.tag == "output":
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382 output_type = out_child.get("type")
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383 if output_type == "data":
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diff changeset
384 _parse(out_child)
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diff changeset
385 elif output_type == "collection":
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diff changeset
386 out_child.attrib["type"] = out_child.get("collection_type")
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387 out_child.attrib["type_source"] = out_child.get("collection_type_source")
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388 _parse_collection(out_child)
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diff changeset
389 else:
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390 _parse_expression(out_child)
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diff changeset
391 else:
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392 log.warning("Unknown output tag encountered [%s]" % out_child.tag)
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393
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394 for output_def in data_dict.values():
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395 outputs[output_def.name] = output_def
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396 return outputs, output_collections
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397
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398 def _parse_output(
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399 self,
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400 data_elem,
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401 tool,
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402 default_format="data",
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403 default_format_source=None,
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404 default_metadata_source="",
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405 expression_type=None,
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406 ):
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407 output = ToolOutput(data_elem.get("name"))
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408 output_format = data_elem.get("format", default_format)
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409 auto_format = string_as_bool(data_elem.get("auto_format", "false"))
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410 if auto_format and output_format != "data":
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411 raise ValueError("Setting format and auto_format is not supported at this time.")
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412 elif auto_format:
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413 output_format = "_sniff_"
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414 output.format = output_format
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415 output.change_format = data_elem.findall("change_format")
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416 output.format_source = data_elem.get("format_source", default_format_source)
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417 output.default_identifier_source = data_elem.get("default_identifier_source", 'None')
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418 output.metadata_source = data_elem.get("metadata_source", default_metadata_source)
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419 output.parent = data_elem.get("parent", None)
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420 output.label = xml_text(data_elem, "label")
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421 output.count = int(data_elem.get("count", 1))
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422 output.filters = data_elem.findall('filter')
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423 output.tool = tool
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424 output.from_work_dir = data_elem.get("from_work_dir", None)
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425 output.hidden = string_as_bool(data_elem.get("hidden", ""))
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426 output.actions = ToolOutputActionGroup(output, data_elem.find('actions'))
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427 output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(data_elem, legacy=self.legacy_defaults)
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428 return output
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429
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diff changeset
430 def _parse_expression_output(self, output_elem, tool, **kwds):
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431 output_type = output_elem.get("type")
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432 from_expression = output_elem.get("from")
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433 output = ToolExpressionOutput(
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434 output_elem.get("name"),
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diff changeset
435 output_type,
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diff changeset
436 from_expression,
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437 )
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438 output.path = output_elem.get("value")
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439 output.label = xml_text(output_elem, "label")
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440
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441 output.hidden = string_as_bool(output_elem.get("hidden", ""))
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442 output.actions = ToolOutputActionGroup(output, output_elem.find('actions'))
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443 output.dataset_collector_descriptions = []
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444 return output
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445
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446 def parse_stdio(self):
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447 """
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448 parse error handling from command and stdio tag
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449
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450 returns list of exit codes, list of regexes
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451 - exit_codes contain all non-zero exit codes (:-1 and 1:) if
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452 detect_errors is default (if not legacy), exit_code, or aggressive
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453 - the oom_exit_code if given and detect_errors is exit_code
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454 - exit codes and regexes from the stdio tag
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455 these are prepended to the list, i.e. are evaluated prior to regexes
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456 and exit codes derived from the properties of the command tag.
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diff changeset
457 thus more specific regexes of the same or more severe error level
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458 are triggered first.
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459 """
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460
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461 command_el = self._command_el
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462 detect_errors = None
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463 if command_el is not None:
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464 detect_errors = command_el.get("detect_errors")
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465
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466 if detect_errors and detect_errors != "default":
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467 if detect_errors == "exit_code":
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468 oom_exit_code = None
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469 if command_el is not None:
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470 oom_exit_code = command_el.get("oom_exit_code", None)
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471 if oom_exit_code is not None:
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472 int(oom_exit_code)
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473 exit_codes, regexes = error_on_exit_code(out_of_memory_exit_code=oom_exit_code)
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474 elif detect_errors == "aggressive":
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475 exit_codes, regexes = aggressive_error_checks()
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476 else:
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477 raise ValueError("Unknown detect_errors value encountered [%s]" % detect_errors)
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478 elif len(self.root.findall('stdio')) == 0 and not self.legacy_defaults:
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479 exit_codes, regexes = error_on_exit_code()
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480 else:
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481 exit_codes = []
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482 regexes = []
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483
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484 if len(self.root.findall('stdio')) > 0:
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485 parser = StdioParser(self.root)
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486 exit_codes = parser.stdio_exit_codes + exit_codes
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487 regexes = parser.stdio_regexes + regexes
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488
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489 return exit_codes, regexes
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490
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491 def parse_strict_shell(self):
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492 command_el = self._command_el
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493 if packaging.version.parse(self.parse_profile()) < packaging.version.parse('20.09'):
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494 default = "False"
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495 else:
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496 default = "True"
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497 if command_el is not None:
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498 return string_as_bool(command_el.get("strict", default))
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499 else:
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500 return string_as_bool(default)
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501
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502 def parse_help(self):
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503 help_elem = self.root.find('help')
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504 return help_elem.text if help_elem is not None else None
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505
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506 @property
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507 def macro_paths(self):
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508 return self._macro_paths
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509
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diff changeset
510 @property
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511 def source_path(self):
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512 return self._source_path
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513
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514 def parse_tests_to_dict(self):
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515 tests_elem = self.root.find("tests")
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516 tests = []
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517 rval = dict(
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518 tests=tests
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519 )
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520
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521 if tests_elem is not None:
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522 for i, test_elem in enumerate(tests_elem.findall("test")):
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523 tests.append(_test_elem_to_dict(test_elem, i))
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524
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525 return rval
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526
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527 def parse_profile(self):
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528 # Pre-16.04 or default XML defaults
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529 # - Use standard error for error detection.
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530 # - Don't run shells with -e
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531 # - Auto-check for implicit multiple outputs.
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532 # - Auto-check for $param_file.
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533 # - Enable buggy interpreter attribute.
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534 return self.root.get("profile", "16.01")
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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
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543 def _test_elem_to_dict(test_elem, i):
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544 rval = dict(
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545 outputs=__parse_output_elems(test_elem),
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546 output_collections=__parse_output_collection_elems(test_elem),
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547 inputs=__parse_input_elems(test_elem, i),
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548 expect_num_outputs=test_elem.get("expect_num_outputs"),
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549 command=__parse_assert_list_from_elem(test_elem.find("assert_command")),
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550 command_version=__parse_assert_list_from_elem(test_elem.find("assert_command_version")),
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551 stdout=__parse_assert_list_from_elem(test_elem.find("assert_stdout")),
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552 stderr=__parse_assert_list_from_elem(test_elem.find("assert_stderr")),
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553 expect_exit_code=test_elem.get("expect_exit_code"),
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554 expect_failure=string_as_bool(test_elem.get("expect_failure", False)),
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555 maxseconds=test_elem.get("maxseconds", None),
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556 )
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557 _copy_to_dict_if_present(test_elem, rval, ["num_outputs"])
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558 return rval
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559
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560
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561 def __parse_input_elems(test_elem, i):
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562 __expand_input_elems(test_elem)
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563 return __parse_inputs_elems(test_elem, i)
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564
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565
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566 def __parse_output_elems(test_elem):
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567 outputs = []
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568 for output_elem in test_elem.findall("output"):
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569 name, file, attributes = __parse_output_elem(output_elem)
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570 outputs.append({"name": name, "value": file, "attributes": attributes})
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571 return outputs
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572
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573
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574 def __parse_output_elem(output_elem):
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575 attrib = dict(output_elem.attrib)
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576 name = attrib.pop('name', None)
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577 if name is None:
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578 raise Exception("Test output does not have a 'name'")
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579
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580 file, attributes = __parse_test_attributes(output_elem, attrib, parse_discovered_datasets=True)
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581 return name, file, attributes
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582
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583
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584 def __parse_command_elem(test_elem):
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585 assert_elem = test_elem.find("command")
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586 return __parse_assert_list_from_elem(assert_elem)
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587
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588
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589 def __parse_output_collection_elems(test_elem):
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590 output_collections = []
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591 for output_collection_elem in test_elem.findall("output_collection"):
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592 output_collection_def = __parse_output_collection_elem(output_collection_elem)
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593 output_collections.append(output_collection_def)
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594 return output_collections
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595
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596
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597 def __parse_output_collection_elem(output_collection_elem):
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598 attrib = dict(output_collection_elem.attrib)
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599 name = attrib.pop('name', None)
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600 if name is None:
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diff changeset
601 raise Exception("Test output collection does not have a 'name'")
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602 element_tests = __parse_element_tests(output_collection_elem)
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diff changeset
603 return TestCollectionOutputDef(name, attrib, element_tests).to_dict()
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604
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605
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606 def __parse_element_tests(parent_element):
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607 element_tests = {}
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diff changeset
608 for element in parent_element.findall("element"):
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609 element_attrib = dict(element.attrib)
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610 identifier = element_attrib.pop('name', None)
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611 if identifier is None:
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612 raise Exception("Test primary dataset does not have a 'identifier'")
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613 element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True)
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614 return element_tests
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615
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616
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617 def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False):
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618 assert_list = __parse_assert_list(output_elem)
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619
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620 # Allow either file or value to specify a target file to compare result with
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diff changeset
621 # file was traditionally used by outputs and value by extra files.
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622 file = attrib.pop('file', attrib.pop('value', None))
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623
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624 # File no longer required if an list of assertions was present.
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625 attributes = {}
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626 # Method of comparison
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627 attributes['compare'] = attrib.pop('compare', 'diff').lower()
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628 # Number of lines to allow to vary in logs (for dates, etc)
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629 attributes['lines_diff'] = int(attrib.pop('lines_diff', '0'))
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diff changeset
630 # Allow a file size to vary if sim_size compare
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631 attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA))
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632 attributes['delta_frac'] = float(attrib['delta_frac']) if 'delta_frac' in attrib else DEFAULT_DELTA_FRAC
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633 attributes['sort'] = string_as_bool(attrib.pop('sort', False))
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634 attributes['decompress'] = string_as_bool(attrib.pop('decompress', False))
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parents:
diff changeset
635 extra_files = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
636 if 'ftype' in attrib:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
637 attributes['ftype'] = attrib['ftype']
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
638 for extra in output_elem.findall('extra_files'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
639 extra_files.append(__parse_extra_files_elem(extra))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
640 metadata = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
641 for metadata_elem in output_elem.findall('metadata'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
642 metadata[metadata_elem.get('name')] = metadata_elem.get('value')
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guerler
parents:
diff changeset
643 md5sum = attrib.get("md5", None)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
644 checksum = attrib.get("checksum", None)
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guerler
parents:
diff changeset
645 element_tests = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
646 if parse_elements:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
647 element_tests = __parse_element_tests(output_elem)
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parents:
diff changeset
648
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parents:
diff changeset
649 primary_datasets = {}
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guerler
parents:
diff changeset
650 if parse_discovered_datasets:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
651 for primary_elem in (output_elem.findall("discovered_dataset") or []):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
652 primary_attrib = dict(primary_elem.attrib)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
653 designation = primary_attrib.pop('designation', None)
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guerler
parents:
diff changeset
654 if designation is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
655 raise Exception("Test primary dataset does not have a 'designation'")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
656 primary_datasets[designation] = __parse_test_attributes(primary_elem, primary_attrib)
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guerler
parents:
diff changeset
657
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parents:
diff changeset
658 has_checksum = md5sum or checksum
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guerler
parents:
diff changeset
659 has_nested_tests = extra_files or element_tests or primary_datasets
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guerler
parents:
diff changeset
660 if not (assert_list or file or metadata or has_checksum or has_nested_tests):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
661 raise Exception("Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
662 attributes['assert_list'] = assert_list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
663 attributes['extra_files'] = extra_files
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parents:
diff changeset
664 attributes['metadata'] = metadata
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parents:
diff changeset
665 attributes['md5'] = md5sum
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parents:
diff changeset
666 attributes['checksum'] = checksum
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parents:
diff changeset
667 attributes['elements'] = element_tests
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parents:
diff changeset
668 attributes['primary_datasets'] = primary_datasets
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guerler
parents:
diff changeset
669 return file, attributes
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parents:
diff changeset
670
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parents:
diff changeset
671
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parents:
diff changeset
672 def __parse_assert_list(output_elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
673 assert_elem = output_elem.find("assert_contents")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
674 return __parse_assert_list_from_elem(assert_elem)
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guerler
parents:
diff changeset
675
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guerler
parents:
diff changeset
676
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parents:
diff changeset
677 def __parse_assert_list_from_elem(assert_elem):
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parents:
diff changeset
678 assert_list = None
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parents:
diff changeset
679
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guerler
parents:
diff changeset
680 def convert_elem(elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
681 """ Converts and XML element to a dictionary format, used by assertion checking code. """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
682 tag = elem.tag
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
683 attributes = dict(elem.attrib)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
684 converted_children = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
685 for child_elem in elem:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
686 converted_children.append(convert_elem(child_elem))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
687 return {"tag": tag, "attributes": attributes, "children": converted_children}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
688 if assert_elem is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
689 assert_list = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
690 for assert_child in list(assert_elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
691 assert_list.append(convert_elem(assert_child))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
692
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parents:
diff changeset
693 return assert_list
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parents:
diff changeset
694
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parents:
diff changeset
695
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parents:
diff changeset
696 def __parse_extra_files_elem(extra):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
697 # File or directory, when directory, compare basename
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
698 # by basename
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guerler
parents:
diff changeset
699 attrib = dict(extra.attrib)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
700 extra_type = attrib.pop('type', 'file')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
701 extra_name = attrib.pop('name', None)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
702 assert extra_type == 'directory' or extra_name is not None, \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
703 'extra_files type (%s) requires a name attribute' % extra_type
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
704 extra_value, extra_attributes = __parse_test_attributes(extra, attrib)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
705 return {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
706 "value": extra_value,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
707 "name": extra_name,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
708 "type": extra_type,
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guerler
parents:
diff changeset
709 "attributes": extra_attributes
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parents:
diff changeset
710 }
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guerler
parents:
diff changeset
711
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
712
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guerler
parents:
diff changeset
713 def __expand_input_elems(root_elem, prefix=""):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
714 __append_prefix_to_params(root_elem, prefix)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
715
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guerler
parents:
diff changeset
716 repeat_elems = root_elem.findall('repeat')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
717 indices = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
718 for repeat_elem in repeat_elems:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
719 name = repeat_elem.get("name")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
720 if name not in indices:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
721 indices[name] = 0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
722 index = 0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
723 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
724 index = indices[name] + 1
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
725 indices[name] = index
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
726
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
727 new_prefix = __prefix_join(prefix, name, index=index)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
728 __expand_input_elems(repeat_elem, new_prefix)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
729 __pull_up_params(root_elem, repeat_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
730
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
731 cond_elems = root_elem.findall('conditional')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
732 for cond_elem in cond_elems:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
733 new_prefix = __prefix_join(prefix, cond_elem.get("name"))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
734 __expand_input_elems(cond_elem, new_prefix)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
735 __pull_up_params(root_elem, cond_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
736
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
737 section_elems = root_elem.findall('section')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
738 for section_elem in section_elems:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
739 new_prefix = __prefix_join(prefix, section_elem.get("name"))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
740 __expand_input_elems(section_elem, new_prefix)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
741 __pull_up_params(root_elem, section_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
742
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
743
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
744 def __append_prefix_to_params(elem, prefix):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
745 for param_elem in elem.findall('param'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
746 param_elem.set("name", __prefix_join(prefix, param_elem.get("name")))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
747
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
748
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
749 def __pull_up_params(parent_elem, child_elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
750 for param_elem in child_elem.findall('param'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
751 parent_elem.append(param_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
752
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
753
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
754 def __prefix_join(prefix, name, index=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
755 name = name if index is None else "%s_%d" % (name, index)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
756 return name if not prefix else "%s|%s" % (prefix, name)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
757
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
758
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
759 def _copy_to_dict_if_present(elem, rval, attributes):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
760 for attribute in attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
761 if attribute in elem.attrib:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
762 rval[attribute] = elem.get(attribute)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
763 return rval
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
764
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
765
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
766 def __parse_inputs_elems(test_elem, i):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
767 raw_inputs = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
768 for param_elem in test_elem.findall("param"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
769 raw_inputs.append(__parse_param_elem(param_elem, i))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
770
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
771 return raw_inputs
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
772
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
773
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
774 def __parse_param_elem(param_elem, i=0):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
775 attrib = dict(param_elem.attrib)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
776 if 'values' in attrib:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
777 value = attrib['values'].split(',')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
778 elif 'value' in attrib:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
779 value = attrib['value']
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
780 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
781 value = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
782 children_elem = param_elem
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
783 if children_elem is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784 # At this time, we can assume having children only
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 # occurs on DataToolParameter test items but this could
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 # change and would cause the below parsing to change
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
787 # based upon differences in children items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
788 attrib['metadata'] = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
789 attrib['composite_data'] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
790 attrib['edit_attributes'] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 # Composite datasets need to be renamed uniquely
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
792 composite_data_name = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793 for child in children_elem:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 if child.tag == 'composite_data':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795 file_name = child.get("value")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796 attrib['composite_data'].append(file_name)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797 if composite_data_name is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798 # Generate a unique name; each test uses a
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 # fresh history.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800 composite_data_name = '_COMPOSITE_RENAMED_t%d_%s' \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 % (i, uuid.uuid1().hex)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802 elif child.tag == 'metadata':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 attrib['metadata'][child.get("name")] = child.get("value")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 elif child.tag == 'edit_attributes':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 attrib['edit_attributes'].append(child)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 elif child.tag == 'collection':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807 attrib['collection'] = TestCollectionDef.from_xml(child, __parse_param_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808 if composite_data_name:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
809 # Composite datasets need implicit renaming;
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810 # inserted at front of list so explicit declarations
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811 # take precedence
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 attrib['edit_attributes'].insert(0, {'type': 'name', 'value': composite_data_name})
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 name = attrib.pop('name')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
814 return {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
815 "name": name,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
816 "value": value,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817 "attributes": attrib
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
818 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
819
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 class StdioParser(object):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
822
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
823 def __init__(self, root):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
824 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825 self.stdio_exit_codes = list()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 self.stdio_regexes = list()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828 # We should have a single <stdio> element, but handle the case for
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 # multiples.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 # For every stdio element, add all of the exit_code and regex
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831 # subelements that we find:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 for stdio_elem in (root.findall('stdio')):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 self.parse_stdio_exit_codes(stdio_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 self.parse_stdio_regexes(stdio_elem)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 except Exception:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
836 log.exception("Exception in parse_stdio!")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 def parse_stdio_exit_codes(self, stdio_elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
839 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 Parse the tool's <stdio> element's <exit_code> subelements.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
841 This will add all of those elements, if any, to self.stdio_exit_codes.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
843 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844 # Look for all <exit_code> elements. Each exit_code element must
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845 # have a range/value.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 # Exit-code ranges have precedence over a single exit code.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847 # So if there are value and range attributes, we use the range
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848 # attribute. If there is neither a range nor a value, then print
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 # a warning and skip to the next.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850 for exit_code_elem in (stdio_elem.findall("exit_code")):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
851 exit_code = ToolStdioExitCode()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
852 # Each exit code has an optional description that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853 # part of the "desc" or "description" attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
854 exit_code.desc = exit_code_elem.get("desc")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
855 if exit_code.desc is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 exit_code.desc = exit_code_elem.get("description")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
857 # Parse the error level:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
858 exit_code.error_level = (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
859 self.parse_error_level(exit_code_elem.get("level")))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860 code_range = exit_code_elem.get("range", "")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 if code_range is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
862 code_range = exit_code_elem.get("value", "")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
863 if code_range is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 log.warning("Tool stdio exit codes must have a range or value")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
866 # Parse the range. We look for:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 # :Y
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868 # X:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 # X:Y - Split on the colon. We do not allow a colon
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 # without a beginning or end, though we could.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871 # Also note that whitespace is eliminated.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 # TODO: Turn this into a single match - it should be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873 # more efficient.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874 code_range = re.sub(r"\s", "", code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 code_ranges = re.split(r":", code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876 if (len(code_ranges) == 2):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877 if (code_ranges[0] is None or '' == code_ranges[0]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 exit_code.range_start = float("-inf")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880 exit_code.range_start = int(code_ranges[0])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 if (code_ranges[1] is None or '' == code_ranges[1]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882 exit_code.range_end = float("inf")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 exit_code.range_end = int(code_ranges[1])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 # If we got more than one colon, then ignore the exit code.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 elif (len(code_ranges) > 2):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 log.warning("Invalid tool exit_code range %s - ignored"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
888 % code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
889 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
890 # Else we have a singular value. If it's not an integer, then
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
891 # we'll just write a log message and skip this exit_code.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
892 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
893 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
894 exit_code.range_start = int(code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
895 except Exception:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
896 log.error(code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
897 log.warning("Invalid range start for tool's exit_code %s: exit_code ignored" % code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
898 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
899 exit_code.range_end = exit_code.range_start
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
900 # TODO: Check if we got ">", ">=", "<", or "<=":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
901 # Check that the range, regardless of how we got it,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
902 # isn't bogus. If we have two infinite values, then
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
903 # the start must be -inf and the end must be +inf.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
904 # So at least warn about this situation:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
905 if isinf(exit_code.range_start) and isinf(exit_code.range_end):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
906 log.warning("Tool exit_code range %s will match on all exit codes" % code_range)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
907 self.stdio_exit_codes.append(exit_code)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
908 except Exception:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
909 log.exception("Exception in parse_stdio_exit_codes!")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
910
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
911 def parse_stdio_regexes(self, stdio_elem):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
912 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
913 Look in the tool's <stdio> elem for all <regex> subelements
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
914 that define how to look for warnings and fatal errors in
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
915 stdout and stderr. This will add all such regex elements
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
916 to the Tols's stdio_regexes list.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
917 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
918 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
919 # Look for every <regex> subelement. The regular expression
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
920 # will have "match" and "source" (or "src") attributes.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
921 for regex_elem in (stdio_elem.findall("regex")):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
922 # TODO: Fill in ToolStdioRegex
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
923 regex = ToolStdioRegex()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
924 # Each regex has an optional description that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
925 # part of the "desc" or "description" attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
926 regex.desc = regex_elem.get("desc")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
927 if regex.desc is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
928 regex.desc = regex_elem.get("description")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
929 # Parse the error level
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
930 regex.error_level = (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
931 self.parse_error_level(regex_elem.get("level")))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
932 regex.match = regex_elem.get("match", "")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
933 if regex.match is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
934 # TODO: Convert the offending XML element to a string
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
935 log.warning("Ignoring tool's stdio regex element %s - "
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
936 "the 'match' attribute must exist")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
937 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
938 # Parse the output sources. We look for the "src", "source",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
939 # and "sources" attributes, in that order. If there is no
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
940 # such source, then the source defaults to stderr & stdout.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
941 # Look for a comma and then look for "err", "error", "out",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
942 # and "output":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
943 output_srcs = regex_elem.get("src")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
944 if output_srcs is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
945 output_srcs = regex_elem.get("source")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
946 if output_srcs is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
947 output_srcs = regex_elem.get("sources")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
948 if output_srcs is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
949 output_srcs = "output,error"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
950 output_srcs = re.sub(r"\s", "", output_srcs)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
951 src_list = re.split(r",", output_srcs)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
952 # Just put together anything to do with "out", including
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
953 # "stdout", "output", etc. Repeat for "stderr", "error",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
954 # and anything to do with "err". If neither stdout nor
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
955 # stderr were specified, then raise a warning and scan both.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
956 for src in src_list:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
957 if re.search("both", src, re.IGNORECASE):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
958 regex.stdout_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
959 regex.stderr_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
960 if re.search("out", src, re.IGNORECASE):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
961 regex.stdout_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
962 if re.search("err", src, re.IGNORECASE):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
963 regex.stderr_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
964 if (not regex.stdout_match and not regex.stderr_match):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
965 log.warning("Tool id %s: unable to determine if tool "
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
966 "stream source scanning is output, error, "
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
967 "or both. Defaulting to use both." % self.id)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
968 regex.stdout_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
969 regex.stderr_match = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
970 self.stdio_regexes.append(regex)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
971 except Exception:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
972 log.exception("Exception in parse_stdio_exit_codes!")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
973
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
974 # TODO: This method doesn't have to be part of the Tool class.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
975 def parse_error_level(self, err_level):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
976 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
977 Parses error level and returns error level enumeration. If
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
978 unparsable, returns 'fatal'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
979 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
980 return_level = StdioErrorLevel.FATAL
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
981 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
982 if err_level:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
983 if (re.search("log", err_level, re.IGNORECASE)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
984 return_level = StdioErrorLevel.LOG
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
985 elif (re.search("qc", err_level, re.IGNORECASE)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
986 return_level = StdioErrorLevel.QC
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
987 elif (re.search("warning", err_level, re.IGNORECASE)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
988 return_level = StdioErrorLevel.WARNING
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
989 elif (re.search("fatal_oom", err_level, re.IGNORECASE)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
990 return_level = StdioErrorLevel.FATAL_OOM
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
991 elif (re.search("fatal", err_level, re.IGNORECASE)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
992 return_level = StdioErrorLevel.FATAL
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
993 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
994 log.debug("Tool %s: error level %s did not match log/warning/fatal" %
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
995 (self.id, err_level))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
996 except Exception:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
997 log.exception("Exception in parse_error_level")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
998 return return_level
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
999
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1000
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1001 class XmlPagesSource(PagesSource):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1002
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1003 def __init__(self, root):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1004 self.input_elem = root.find("inputs")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1005 page_sources = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1006 if self.input_elem is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1007 pages_elem = self.input_elem.findall("page")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1008 for page in (pages_elem or [self.input_elem]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1009 page_sources.append(XmlPageSource(page))
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1010 super(XmlPagesSource, self).__init__(page_sources)
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1011
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1012 @property
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1013 def inputs_defined(self):
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1014 return self.input_elem is not None
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1015
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1016
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1017 class XmlPageSource(PageSource):
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1018
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1019 def __init__(self, parent_elem):
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1020 self.parent_elem = parent_elem
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1021
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1022 def parse_display(self):
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1023 display_elem = self.parent_elem.find("display")
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1024 if display_elem is not None:
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1025 display = xml_to_string(display_elem)
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1026 else:
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1027 display = None
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1028 return display
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1029
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1030 def parse_input_sources(self):
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1031 return map(XmlInputSource, self.parent_elem)
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1032
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1033
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1034 class XmlInputSource(InputSource):
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1035
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1036 def __init__(self, input_elem):
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1037 self.input_elem = input_elem
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1038 self.input_type = self.input_elem.tag
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1039
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1040 def parse_input_type(self):
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1041 return self.input_type
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1042
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1043 def elem(self):
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1044 return self.input_elem
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1045
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1046 def get(self, key, value=None):
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1047 return self.input_elem.get(key, value)
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1048
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1049 def get_bool(self, key, default):
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1050 return string_as_bool(self.get(key, default))
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1051
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1052 def parse_label(self):
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1053 return xml_text(self.input_elem, "label")
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1054
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1055 def parse_help(self):
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1056 return xml_text(self.input_elem, "help")
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1057
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1058 def parse_sanitizer_elem(self):
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1059 return self.input_elem.find("sanitizer")
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1060
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1061 def parse_validator_elems(self):
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1062 return self.input_elem.findall("validator")
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1063
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1064 def parse_dynamic_options_elem(self):
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1065 """ Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
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1066 if appropriate.
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1067 """
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1068 options_elem = self.input_elem.find('options')
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1069 return options_elem
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1070
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1071 def parse_static_options(self):
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1072 static_options = list()
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1073 elem = self.input_elem
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1074 for option in elem.findall("option"):
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1075 value = option.get("value")
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1076 selected = string_as_bool(option.get("selected", False))
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1077 static_options.append((option.text or value, value, selected))
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1078 return static_options
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1079
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1080 def parse_optional(self, default=None):
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1081 """ Return boolean indicating whether parameter is optional. """
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1082 elem = self.input_elem
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1083 if self.get('type') == "data_column":
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1084 # Allow specifing force_select for backward compat., but probably
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1085 # should use optional going forward for consistency with other
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1086 # parameters.
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1087 if "force_select" in elem.attrib:
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1088 force_select = string_as_bool(elem.get("force_select"))
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1089 else:
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1090 force_select = not string_as_bool(elem.get("optional", False))
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1091 return not force_select
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1092
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1093 if default is None:
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1094 default = self.default_optional
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1095 return self.get_bool("optional", default)
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1096
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1097 def parse_conversion_tuples(self):
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1098 elem = self.input_elem
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1099 conversions = []
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1100 for conv_elem in elem.findall("conversion"):
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1101 name = conv_elem.get("name") # name for commandline substitution
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1102 conv_extensions = conv_elem.get("type") # target datatype extension
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1103 conversions.append((name, conv_extensions))
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1104 return conversions
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1105
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1106 def parse_nested_inputs_source(self):
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1107 elem = self.input_elem
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1108 return XmlPageSource(elem)
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1109
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1110 def parse_test_input_source(self):
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1111 elem = self.input_elem
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1112 input_elem = elem.find("param")
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1113 assert input_elem is not None, "<conditional> must have a child <param>"
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1114 return XmlInputSource(input_elem)
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1115
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1116 def parse_when_input_sources(self):
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1117 elem = self.input_elem
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1118
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1119 sources = []
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1120 for case_elem in elem.findall("when"):
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1121 value = case_elem.get("value")
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1122 case_page_source = XmlPageSource(case_elem)
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1123 sources.append((value, case_page_source))
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1124 return sources
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1125
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1126
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1127 class ParallelismInfo(object):
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1128 """
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1129 Stores the information (if any) for running multiple instances of the tool in parallel
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1130 on the same set of inputs.
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1131 """
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1132
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1133 def __init__(self, tag):
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1134 self.method = tag.get('method')
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1135 if isinstance(tag, dict):
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1136 items = tag.items()
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1137 else:
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1138 items = tag.attrib.items()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1139 self.attributes = dict([item for item in items if item[0] != 'method'])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1140 if len(self.attributes) == 0:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1141 # legacy basic mode - provide compatible defaults
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1142 self.attributes['split_size'] = 20
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1143 self.attributes['split_mode'] = 'number_of_parts'