Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/deps/requirements.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 copy
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2
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3 import six
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4
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5 from galaxy.util import (
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6 asbool,
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7 xml_text,
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8 )
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9 from galaxy.util.oset import OrderedSet
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10
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11
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12 DEFAULT_REQUIREMENT_TYPE = "package"
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13 DEFAULT_REQUIREMENT_VERSION = None
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14
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15
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16 @six.python_2_unicode_compatible
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17 class ToolRequirement(object):
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18 """
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19 Represents an external requirement that must be available for the tool to
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20 run (for example, a program, package, or library). Requirements can
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21 optionally assert a specific version.
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22 """
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23
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24 def __init__(self, name=None, type=None, version=None, specs=[]):
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25 self.name = name
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26 self.type = type
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27 self.version = version
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28 self.specs = specs
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29
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30 def to_dict(self):
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31 specs = [s.to_dict() for s in self.specs]
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32 return dict(name=self.name, type=self.type, version=self.version, specs=specs)
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33
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34 def copy(self):
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35 return copy.deepcopy(self)
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36
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37 @staticmethod
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38 def from_dict(dict):
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39 version = dict.get("version", None)
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40 name = dict.get("name", None)
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41 type = dict.get("type", None)
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42 specs = [RequirementSpecification.from_dict(s) for s in dict.get("specs", [])]
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43 return ToolRequirement(name=name, type=type, version=version, specs=specs)
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44
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45 def __eq__(self, other):
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46 return self.name == other.name and self.type == other.type and self.version == other.version and self.specs == other.specs
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47
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48 def __ne__(self, other):
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49 return not self.__eq__(other)
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50
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51 def __hash__(self):
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52 return hash((self.name, self.type, self.version, frozenset(self.specs)))
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53
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54 def __str__(self):
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55 return "ToolRequirement[%s,version=%s,type=%s,specs=%s]" % (self.name, self.version, self.type, self.specs)
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56
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57 __repr__ = __str__
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58
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59
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60 class RequirementSpecification(object):
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61 """Refine a requirement using a URI."""
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62
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63 def __init__(self, uri, version=None):
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64 self.uri = uri
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65 self.version = version
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66
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67 @property
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68 def specifies_version(self):
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69 return self.version is not None
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70
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71 @property
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72 def short_name(self):
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73 return self.uri.split("/")[-1]
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74
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75 def to_dict(self):
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76 return dict(uri=self.uri, version=self.version)
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77
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78 @staticmethod
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79 def from_dict(dict):
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80 uri = dict.get("uri")
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81 version = dict.get("version", None)
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82 return RequirementSpecification(uri=uri, version=version)
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83
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84 def __eq__(self, other):
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85 return self.uri == other.uri and self.version == other.version
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86
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87 def __ne__(self, other):
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88 return not self.__eq__(other)
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89
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90 def __hash__(self):
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91 return hash((self.uri, self.version))
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92
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93
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94 class ToolRequirements(object):
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95 """
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96 Represents all requirements (packages, env vars) needed to run a tool.
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97 """
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98
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99 def __init__(self, tool_requirements=None):
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100 if tool_requirements:
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101 if not isinstance(tool_requirements, list):
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102 raise ToolRequirementsException('ToolRequirements Constructor expects a list')
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103 self.tool_requirements = OrderedSet([r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements])
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104 else:
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105 self.tool_requirements = OrderedSet()
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106
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107 @staticmethod
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108 def from_list(requirements):
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109 return ToolRequirements(requirements)
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110
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111 @property
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112 def resolvable(self):
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113 return ToolRequirements([r for r in self.tool_requirements if r.type in {'package', 'set_environment'}])
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114
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115 @property
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116 def packages(self):
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117 return ToolRequirements([r for r in self.tool_requirements if r.type == 'package'])
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118
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119 def to_list(self):
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120 return [r.to_dict() for r in self.tool_requirements]
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121
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122 def append(self, requirement):
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123 if not isinstance(requirement, ToolRequirement):
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124 requirement = ToolRequirement.from_dict(requirement)
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125 self.tool_requirements.add(requirement)
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126
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127 def __eq__(self, other):
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128 return len(self.tool_requirements & other.tool_requirements) == len(self.tool_requirements) == len(other.tool_requirements)
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129
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130 def __ne__(self, other):
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131 return not self.__eq__(other)
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132
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133 def __iter__(self):
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134 for r in self.tool_requirements:
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135 yield r
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136
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137 def __getitem__(self, ii):
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138 return list(self.tool_requirements)[ii]
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139
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140 def __len__(self):
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141 return len(self.tool_requirements)
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142
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143 def __hash__(self):
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144 return sum([r.__hash__() for r in self.tool_requirements])
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145
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146 def to_dict(self):
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147 return [r.to_dict() for r in self.tool_requirements]
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148
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149
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150 class ToolRequirementsException(Exception):
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151 pass
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152
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153
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154 DEFAULT_CONTAINER_TYPE = "docker"
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155 DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES = False
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156 DEFAULT_CONTAINER_SHELL = "/bin/sh" # Galaxy assumes bash, but containers are usually thinner.
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157
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158
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159 @six.python_2_unicode_compatible
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160 class ContainerDescription(object):
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161
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162 def __init__(
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163 self,
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164 identifier=None,
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165 type=DEFAULT_CONTAINER_TYPE,
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166 resolve_dependencies=DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES,
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167 shell=DEFAULT_CONTAINER_SHELL,
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168 ):
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169 # Force to lowercase because container image names must be lowercase
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170 self.identifier = identifier.lower() if identifier else None
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171 self.type = type
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172 self.resolve_dependencies = resolve_dependencies
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173 self.shell = shell
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174 self.explicit = False
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175
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176 def to_dict(self, *args, **kwds):
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177 return dict(
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178 identifier=self.identifier,
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179 type=self.type,
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180 resolve_dependencies=self.resolve_dependencies,
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181 shell=self.shell,
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182 )
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183
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184 @staticmethod
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185 def from_dict(dict):
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186 identifier = dict["identifier"]
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187 type = dict.get("type", DEFAULT_CONTAINER_TYPE)
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188 resolve_dependencies = dict.get("resolve_dependencies", DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES)
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189 shell = dict.get("shell", DEFAULT_CONTAINER_SHELL)
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190 return ContainerDescription(
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191 identifier=identifier,
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192 type=type,
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193 resolve_dependencies=resolve_dependencies,
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194 shell=shell,
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195 )
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196
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197 def __str__(self):
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198 return "ContainerDescription[identifier=%s,type=%s]" % (self.identifier, self.type)
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199
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200
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201 def parse_requirements_from_dict(root_dict):
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202 requirements = root_dict.get("requirements", [])
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203 containers = root_dict.get("containers", [])
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204 return ToolRequirements.from_list(requirements), [ContainerDescription.from_dict(c) for c in containers]
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205
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206
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207 def parse_requirements_from_xml(xml_root):
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208 """
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209
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210 >>> from galaxy.util import parse_xml_string
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211 >>> def load_requirements(contents):
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212 ... contents_document = '''<tool><requirements>%s</requirements></tool>'''
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213 ... root = parse_xml_string(contents_document % contents)
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214 ... return parse_requirements_from_xml(root)
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215 >>> reqs, containers = load_requirements('''<requirement>bwa</requirement>''')
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216 >>> reqs[0].name
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217 'bwa'
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218 >>> reqs[0].version is None
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219 True
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220 >>> reqs[0].type
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221 'package'
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222 >>> reqs, containers = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''')
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223 >>> reqs[0].name
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224 'cufflinks'
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225 >>> reqs[0].version
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226 '1.3.3'
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227 >>> reqs[0].type
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228 'binary'
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229 """
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230 requirements_elem = xml_root.find("requirements")
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231
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232 requirement_elems = []
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233 if requirements_elem is not None:
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234 requirement_elems = requirements_elem.findall('requirement')
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235
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236 requirements = ToolRequirements()
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237 for requirement_elem in requirement_elems:
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238 name = xml_text(requirement_elem)
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239 type = requirement_elem.get("type", DEFAULT_REQUIREMENT_TYPE)
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240 version = requirement_elem.get("version", DEFAULT_REQUIREMENT_VERSION)
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241 requirement = ToolRequirement(name=name, type=type, version=version)
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242 requirements.append(requirement)
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243
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244 container_elems = []
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245 if requirements_elem is not None:
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246 container_elems = requirements_elem.findall('container')
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247
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248 containers = [container_from_element(c) for c in container_elems]
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249
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250 return requirements, containers
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251
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252
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253 def container_from_element(container_elem):
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254 identifier = xml_text(container_elem)
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255 type = container_elem.get("type", DEFAULT_CONTAINER_TYPE)
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256 resolve_dependencies = asbool(container_elem.get("resolve_dependencies", DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES))
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257 shell = container_elem.get("shell", DEFAULT_CONTAINER_SHELL)
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258 container = ContainerDescription(
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259 identifier=identifier,
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260 type=type,
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261 resolve_dependencies=resolve_dependencies,
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262 shell=shell,
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263 )
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264 return container