Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/shed2tap/base.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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0
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1 from __future__ import print_function
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2
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3 from xml.etree import ElementTree
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4
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5 from six.moves.urllib.request import urlretrieve
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6 from six.moves.urllib.error import URLError
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7 from six import string_types
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8
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9 import os
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10 import tarfile
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11 import zipfile
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12 from ftplib import all_errors as FTPErrors # tuple of exceptions
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13
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14 TOOLSHED_MAP = {
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15 "toolshed": "https://toolshed.g2.bx.psu.edu",
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16 "testtoolshed": "https://testtoolshed.g2.bx.psu.edu",
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17 }
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18
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19
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20 class Dependencies(object):
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21 """ Base class for parsing Tool Shed dependency files.
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22 """
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23
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24 def __init__(
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25 self,
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26 dependencies_file,
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27 repo=None,
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28 package_factory=None,
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29 ):
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30 if package_factory is None:
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31 package_factory = BasePackage
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32 self.repo = repo
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33 self.root = ElementTree.parse(dependencies_file).getroot()
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34 packages = []
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35 dependencies = []
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36 package_els = self.root.findall("package")
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37 assert package_els is not None
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38 for package_el in package_els:
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39 install_els = package_el.findall("install")
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40 readme_els = package_el.findall("readme")
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41 if len(readme_els) > 0:
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42 readme = readme_els[0].text
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43 else:
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44 readme = None
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45 assert len(install_els) in (0, 1)
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46 if len(install_els) == 1:
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47 install_el = install_els[0]
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48 package = package_factory(
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49 self,
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50 package_el,
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51 install_el,
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52 readme=readme
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53 )
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54 packages.append(package)
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55 else:
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56 repository_el = package_el.find("repository")
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57 if repository_el is None:
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58 message = "no repository in package el for %s" % repo
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59 raise AssertionError(message)
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60 dependency = Dependency(self, package_el, repository_el)
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61 dependencies.append(dependency)
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62
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63 self.packages = packages
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64 self.dependencies = dependencies
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65
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66 def single_package(self):
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67 return len(self.packages) == 1
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68
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69 def __repr__(self):
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70 return "Dependencies[for_repo=%s]" % self.repo
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71
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72
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73 class Repo(object):
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74
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75 def __init__(self, **kwds):
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76 for key, value in kwds.iteritems():
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77 setattr(self, key, value)
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78
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79 def recipe_base_name(self):
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80 owner = self.owner.replace("-", "")
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81 name = self.name
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82 name = name.replace("_", "").replace("-", "")
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83 base = "%s_%s" % (owner, name)
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84 return base
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85
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86 @staticmethod
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87 def from_xml(elem):
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88 tool_shed_url = elem.attrib.get("toolshed", None)
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89 if tool_shed_url and ("testtoolshed" in tool_shed_url):
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90 prefix = "testtoolshed"
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91 else:
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92 prefix = "toolshed"
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93 prior = elem.attrib.get("prior_installation_required", False)
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94 return Repo(
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95 prefix=prefix,
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96 name=elem.attrib["name"],
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97 owner=elem.attrib["owner"],
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98 tool_shed_url=tool_shed_url,
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99 changeset_revision=elem.attrib.get("changeset_revision", None),
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100 prior_installation_required=prior,
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101 )
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102
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103 @staticmethod
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104 def from_api(prefix, repo_json):
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105 return Repo(
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106 prefix=prefix,
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107 name=repo_json["name"],
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108 owner=repo_json["owner"],
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109 tool_shed_url=TOOLSHED_MAP[prefix],
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110 )
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111
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112 def get_file(self, path):
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113 try:
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114 url_template = "%s/repos/%s/%s/raw-file/tip/%s"
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115 url = url_template % (
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116 self.tool_shed_url,
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117 self.owner,
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118 self.name,
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119 path
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120 )
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121 path, headers = urlretrieve(url)
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122 return path
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123 except Exception as e:
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124 print(e)
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125 return None
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126
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127 def __repr__(self):
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128 return "Repository[name=%s,owner=%s]" % (self.name, self.owner)
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129
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130
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131 class Dependency(object):
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132
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133 def __init__(self, dependencies, package_el, repository_el):
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134 self.dependencies = dependencies
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135 self.package_el = package_el
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136 self.repository_el = repository_el
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137 self.repo = Repo.from_xml(repository_el)
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138
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139 def __repr__(self):
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140 temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]"
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141 return temp % (
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142 self.package_el.attrib["name"],
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143 self.package_el.attrib["version"],
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144 self.repository_el.attrib["name"]
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145 )
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146
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147
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148 class BasePackage(object):
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149
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150 def __init__(self, dependencies, package_el, install_el, readme):
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151 self.dependencies = dependencies
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152 self.package_el = package_el
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153 self.install_el = install_el
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154 self.readme = readme
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155 self.all_actions = self.get_all_actions()
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156 self.no_arch_option = self.has_no_achitecture_install()
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157
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158 def get_all_actions(self):
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159 action_or_group = self.install_el[0]
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160 parsed_actions = []
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161 if action_or_group.tag == "actions":
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162 parsed_actions.append(self.parse_actions(action_or_group))
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163 elif action_or_group.tag == "actions_group":
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164 actions_els = action_or_group.findall("actions")
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165 assert actions_els is not None
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166 for actions in actions_els:
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167 parsed_actions.append(self.parse_actions(actions))
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168 action_els = action_or_group.findall("action")
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169 assert action_els is not None
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170 for action in action_els:
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171 for parsed_a in parsed_actions:
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172 parsed_a.actions.append(self.parse_action(action))
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173 return parsed_actions
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174
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175 def has_no_achitecture_install(self):
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176 all_actions = self.all_actions
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177 if len(all_actions) < 2:
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178 return False
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179 else:
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180 last_action = all_actions[-1]
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181 return (not last_action.architecture) and (not last_action.os)
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182
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183 def has_explicit_set_environments(self):
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184 all_actions = self.all_actions
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185 for actions in all_actions:
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186 for action in actions.actions:
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187 if action.explicit_variables:
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188 return True
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189 return False
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190
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191 def has_multiple_set_environments(self):
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192 all_actions = self.all_actions
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193 for actions in all_actions:
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194 count = 0
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195 for action in actions.actions:
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196 if action.explicit_variables:
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197 count += 1
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198 if count > 1:
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199 return True
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200 return False
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201
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202 def parse_actions(self, actions):
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203 os = actions.attrib.get("os", None)
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204 architecture = actions.get("architecture", None)
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205 action_els = actions.findall("action")
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206 assert action_els is not None
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207 parsed_actions = map(self.parse_action, action_els)
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208 action_packages = []
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209 for package in actions.findall("package"):
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210 action_packages.append(self.parse_action_package(package))
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211 return Actions(parsed_actions, os, architecture, action_packages)
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212
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213 def parse_action_package(self, elem):
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214 name = elem.attrib["name"]
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215 version = elem.attrib["version"]
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216 repo = Repo.from_xml(elem.find("repository"))
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217 return ActionPackage(name, version, repo)
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218
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219 def parse_action(self, action):
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220 return BaseAction.from_elem(action, package=self)
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221
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222 def __repr__(self):
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223 actions = self.all_actions
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224 parts = (
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225 self.package_el.attrib["name"],
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226 self.package_el.attrib["version"],
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227 self.dependencies,
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228 actions
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229 )
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230 template = "Install[name=%s,version=%s,dependencies=%s,actions=%s]"
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231 return template % parts
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232
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233
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234 class Actions(object):
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235
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236 def __init__(
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237 self,
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238 actions,
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239 os=None,
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240 architecture=None,
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241 action_packages=[]
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242 ):
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243 self.os = os
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244 self.architecture = architecture
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245 self.actions = actions or []
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246 self.action_packages = action_packages
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247
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248 def first_download(self):
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249 for action in self.actions:
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250 if action.action_type in ["download_by_url", "download_file"]:
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251 return action
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252 return None
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253
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254 def downloads(self):
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255 actions = []
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256 for action in self.actions:
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257 if action.action_type in ["download_by_url", "download_file"]:
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258 actions.append(action)
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259 return actions
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260
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261 def __repr__(self):
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262 platform = ""
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263 if self.os or self.architecture:
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264 platform = "os=%s,arch=%s," % (self.os, self.architecture)
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265 return "Actions[%s%s]" % (platform, map(str, self.actions))
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266
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267 def _indent_extend(self, target, new_entries, indent=" "):
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268 for line in new_entries:
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269 target.append(indent + line)
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270
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271 def to_bash(self):
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272 # Use self.os.title() to match "Linux" or "Darwin" in bash where case matters:
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273 if self.os and self.architecture:
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274 condition = '("%s" == `uname`) && ("%s" == `arch`)' % (self.os.title(), self.architecture)
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275 elif self.os:
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276 condition = '"%s" == `uname`' % self.os.title()
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277 elif self.architecture:
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278 condition = '"%s" == `arch`' % self.architecture
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279 else:
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280 condition = None
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281
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282 install_cmds = []
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283 env_cmds = []
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284
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285 if condition:
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286 # Conditional actions block
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287 install_cmds = [
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288 '#' + '-' * 60,
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289 'if [[ $specifc_action_done == 0 && %s ]]' % condition,
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290 'then',
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291 ' echo "Platform-specific action for os=%s, arch=%s"' % (self.os, self.architecture)]
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292 env_cmds = install_cmds[:]
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293 # TODO - Refactor block indentation?
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294 for action in self.actions:
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295 i_cmds, e_cmds = action.to_bash()
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296 self._indent_extend(install_cmds, i_cmds)
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297 self._indent_extend(env_cmds, e_cmds)
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298 # If we run the action, do not want to run any later actions!
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299 install_cmds.extend([' specifc_action_done=1', 'fi'])
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300 env_cmds.extend([' specifc_action_done=1', 'fi'])
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301 else:
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302 # Non-specific default action...
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303 install_cmds = [
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304 '#' + '-' * 60,
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305 'if [[ $specifc_action_done == 0 ]]',
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306 'then',
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307 ' echo "Non-platform-specific actions"']
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308 env_cmds = install_cmds[:]
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309 for action in self.actions:
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310 i_cmds, e_cmds = action.to_bash()
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311 self._indent_extend(install_cmds, i_cmds)
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312 self._indent_extend(env_cmds, e_cmds)
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313 install_cmds.append('fi')
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314 env_cmds.append('fi')
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315 return install_cmds, env_cmds
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316
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317
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318 class ActionPackage(object):
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319
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320 def __init__(self, name, version, repo):
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321 self.name = name
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322 self.version = version
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323 self.repo = repo
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324
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325
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326 class BaseAction(object):
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327
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328 def __repr__(self):
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329 return "Action[type=%s]" % self.action_type
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330
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331 def same_as(self, other):
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332 if self._keys != other._keys:
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333 return False
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334 else:
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335 for key in self._keys:
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336 if getattr(self, key) != getattr(other, key):
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337 return False
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338
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339 return True
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340
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341 def parse_action_repo(self, elem):
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342 repo_elem = elem.find("repository")
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343 repo = Repo.from_xml(repo_elem)
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344 self.repo = repo
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345
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346 def parse_package_elems(self, elem):
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347 package_els = elem.findall("package")
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348 packages = []
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349 assert package_els is not None
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350 for package_el in package_els:
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351 packages.append(package_el.text)
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352 self.packages = packages
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353
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354 @classmethod
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355 def from_elem(cls, elem, package):
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356 type = elem.attrib["type"]
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357 action_class = actions_by_type[type]
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358 return action_class(elem)
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359
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360 def to_bash(self):
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361 """Return lists of bash shell commands to execute this action.
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362
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363 This method is be implemented by each sub-class, and will
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364 return two list of strings (for ``dep_install.sh`` and
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365 ``env.sh`` respectively).
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366 """
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367 raise NotImplementedError("No to_bash defined for %r" % self)
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368
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369
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370 def _tar_folders(filename):
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371 archive = tarfile.open(filename, "r", errorlevel=0)
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372 folders = set()
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373 for i in archive.getmembers():
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374 if i.isdir():
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375 folders.add(i.name.rstrip("/"))
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376 else:
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377 folders.add(os.path.split(i.name)[0])
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378 return folders
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379
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380
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381 def _zip_folders(filename):
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382 archive = zipfile.ZipFile(filename, "r")
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383 return set(i.filename.rstrip("/") for i in archive.infolist() if i.filename.endswith("/"))
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384
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385
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386 def _common_prefix(folders):
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387 common_prefix = ""
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388 if len(folders) == 1:
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389 common_prefix = list(folders)[0]
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390 else:
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391 common_prefix = os.path.commonprefix(folders)
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392 assert not os.path.isabs(common_prefix), folders
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393 return common_prefix
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394
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395
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396 def _cache_download(url, filename):
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397 """Returns local path to cached copy of URL using given filename."""
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398 try:
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399 cache = os.environ["DOWNLOAD_CACHE"]
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400 except KeyError:
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401 # TODO - expose this as a command line option
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402 raise ValueError("Dependencies cache location $DOWNLOAD_CACHE not set.")
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403
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404 local = os.path.join(cache, filename)
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405
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406 if not os.path.isfile(local):
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407 # Must download it...
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408 try:
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409 import sys # TODO - log this nicely...
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410 sys.stderr.write("Downloading %s\n" % url)
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411 urlretrieve(url, local)
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412 except URLError:
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413 # Most likely server is down, could be bad URL in XML action:
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414 raise RuntimeError("Unable to download %s" % url)
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415 except FTPErrors:
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416 # Most likely server is down, could be bad URL in XML action:
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417 raise RuntimeError("Unable to download %s" % url)
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418
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419 return local
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420
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421
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422 def _determine_compressed_file_folder(url, downloaded_filename):
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423 """Determine how to decompress the file & its directory structure.
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424
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425 Returns a list of shell commands. Consider this example where the
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426 folder to change to cannot be guessed from the tar-ball filename:
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427
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428 $ curl -o "ncbi-blast-2.2.30+-ia32-linux.tar.gz" \
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429 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-ia32-linux.tar.gz"
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430 $ tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz
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431 $ cd ncbi-blast-2.2.30+
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432
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433 Here it would return:
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434
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435 ['tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz', 'cd ncbi-blast-2.2.30+']
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436
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437 If not cached, this function will download the file to the
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438 $DOWNLOAD_CACHE folder, and then open it / decompress it in
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439 order to find common folder prefix used. This will also verify
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440 how to decompress the file.
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441 """
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442 answer = []
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443 local = _cache_download(url, downloaded_filename)
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444
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445 if tarfile.is_tarfile(local):
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446 folders = _tar_folders(local)
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447 if downloaded_filename.endswith(".tar.gz") or downloaded_filename.endswith(".tgz"):
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448 answer.append('tar -zxvf %s' % downloaded_filename)
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449 elif downloaded_filename.endswith(".tar.bz2"):
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450 answer.append('tar -jxvf %s' % downloaded_filename)
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451 elif downloaded_filename.endswith(".tar"):
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452 answer.extend('tar -xvf %s' % downloaded_filename)
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453 else:
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454 # Quite possibly this file doesn't need decompressing,
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455 # but until we've tested lots of real world tool_dependencies.xml
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456 # files I'd like to check these cases to confirm this.
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457 raise NotImplementedError("How to decompress tar file %s?" % downloaded_filename)
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458 elif zipfile.is_zipfile(local):
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459 if local.endswith('.jar'):
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460 # Do not decompress!
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461 return answer
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462 folders = _zip_folders(local)
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463 answer.append('unzip %s' % downloaded_filename)
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464 elif downloaded_filename.endswith(".dmg"):
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465 # Do not decompress!
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466 return answer
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467 else:
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468 # No compression? Leave as it is?
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469 raise NotImplementedError("What kind of compression is %s using?" % local)
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470
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471 common_prefix = _common_prefix(folders)
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472 if common_prefix:
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473 answer.append('cd "%s"' % common_prefix)
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474
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parents:
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475 return answer
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parents:
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476
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parents:
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477
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478 def _commands_to_download_and_extract(url, target_filename=None):
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479 # TODO - Include checksum validation here?
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480 if target_filename:
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481 downloaded_filename = target_filename
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482 else:
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483 downloaded_filename = os.path.split(url)[-1]
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484 if "?" in downloaded_filename:
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parents:
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485 downloaded_filename = downloaded_filename[:downloaded_filename.index("?")]
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486 if "#" in downloaded_filename:
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487 downloaded_filename = downloaded_filename[:downloaded_filename.index("#")]
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488
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489 # Curl is present on Mac OS X, can we assume it will be on Linux?
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490 # Cannot assume that wget will be on Mac OS X.
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491 answer = [
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492 'if [[ -f "%s" ]]' % downloaded_filename,
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493 'then',
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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494 ' echo "Reusing existing %s"' % downloaded_filename,
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495 'elif [[ -f "$DOWNLOAD_CACHE/%s" ]]' % downloaded_filename,
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496 'then',
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497 ' echo "Reusing cached %s"' % downloaded_filename,
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498 ' ln -s "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, downloaded_filename),
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499 'else',
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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500 ' echo "Downloading %s"' % downloaded_filename,
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501 ' curl -L -o "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, url),
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502 ' ln -s "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, downloaded_filename),
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503 'fi',
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parents:
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504 ]
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505 answer.extend(_determine_compressed_file_folder(url, downloaded_filename))
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506 return answer, []
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parents:
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507
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508
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509 class DownloadByUrlAction(BaseAction):
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510 action_type = "download_by_url"
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511 _keys = ["url"]
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512
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513 def __init__(self, elem):
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514 self.url = elem.text.strip()
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515 assert self.url
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diff changeset
516
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517 def to_bash(self):
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518 # See class DownloadByUrl in Galaxy,
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519 # lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
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520 # Do we need to worry about target_filename here?
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521 return _commands_to_download_and_extract(self.url)
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parents:
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522
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diff changeset
523
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524 class DownloadFileAction(BaseAction):
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525 action_type = "download_file"
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diff changeset
526 _keys = ["url", "extract"]
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527
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diff changeset
528 def __init__(self, elem):
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529 self.url = elem.text.strip()
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530 self.extract = asbool(elem.attrib.get("extract", False))
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531
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532 def to_bash(self):
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533 if self.extract:
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534 return _commands_to_download_and_extract(self.url)
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535 else:
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536 return ['wget %s' % self.url], []
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537
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diff changeset
538
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539 class DownloadBinary(BaseAction):
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540 action_type = "download_binary"
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541 _keys = ["url_template", "target_directory"]
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542
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543 def __init__(self, elem):
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544 self.url_template = elem.text
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545 assert self.url_template
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546 self.target_directory = elem.get('target_directory', None)
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547
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548
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549 class ShellCommandAction(BaseAction):
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550 action_type = "shell_command"
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551 _keys = ["command"]
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552
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553 def __init__(self, elem):
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554 self.command = elem.text
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555
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556 def to_bash(self):
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557 return [self.command], []
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558
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559
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560 class TemplateShellCommandAction(BaseAction):
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561 action_type = "template_command"
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562 _keys = ["language", "command"]
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563
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564 def __init__(self, elem):
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565 self.command = elem.text
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566 self.language = elem.get('language', 'cheetah').lower()
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567 assert self.command
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568 assert self.language == "cheetah"
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569
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570
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571 class MoveFileAction(BaseAction):
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572 action_type = "move_file"
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573 _keys = ["move_file"]
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574
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575 def __init__(self, elem):
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576 self.source = elem.find("source").text
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577 self.destination = elem.find("destination").text
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578
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579 def to_bash(self):
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580 return ["mv %s %s" % (self.source, self.destination)], []
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581
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582
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583 class MoveDirectoryFilesAction(BaseAction):
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584 action_type = "move_directory_files"
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585 _keys = ["source_directory", "destination_directory"]
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586
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587 def __init__(self, elem):
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588 source_directory = elem.find("source_directory").text
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589 destination_directory = elem.find("destination_directory").text
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parents:
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590 self.source_directory = source_directory
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parents:
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591 self.destination_directory = destination_directory
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592
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593 def to_bash(self):
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parents:
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594 return ["mv %s/* %s/" % (self.source_directory, self.destination_directory)], []
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parents:
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595
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596
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597 class SetEnvironmentAction(BaseAction):
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598 action_type = "set_environment"
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599 _keys = ["variables"]
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600
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parents:
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601 def __init__(self, elem):
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602 variables = []
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603 var_els = elem.findall("environment_variable")
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604 assert var_els is not None
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parents:
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605 for ev_elem in var_els:
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606 var = SetVariable(ev_elem)
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parents:
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607 variables.append(var)
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parents:
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608 self.variables = variables
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parents:
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609 assert self.variables
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parents:
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610
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parents:
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611 def to_bash(self):
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parents:
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612 answer = []
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613 for var in self.variables:
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614 # Expand $INSTALL_DIR here?
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parents:
diff changeset
615 if var.action == "set_to":
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616 answer.append('export %s=%s' % (var.name, var.raw_value))
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617 elif var.action == "prepend_to":
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618 answer.append('export %s=%s:$%s' % (var.name, var.raw_value, var.name))
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619 elif var.action == "append_to":
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620 answer.append('export %s=$%s:%s' % (var.name, var.name, var.raw_value))
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621 else:
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parents:
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622 raise ValueError("Undefined environment variable action %r" % var.action)
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623 return answer, answer # Actions needed in env.sh here!
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parents:
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624
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parents:
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625
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parents:
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626 class ChmodAction(BaseAction):
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627 action_type = "chmod"
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parents:
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628 _keys = ["mods"]
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parents:
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629
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630 def __init__(self, elem):
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631 mods = []
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632 file_els = elem.findall("file")
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parents:
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633 assert file_els is not None
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parents:
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634 for mod_elem in file_els:
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635 mod = {}
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parents:
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636 mod["mode"] = mod_elem.attrib["mode"]
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637 mod["target"] = mod_elem.text
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638 mods.append(mod)
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639 self.mods = mods
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640 assert self.mods
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641
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642 def to_bash(self):
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643 return ["chmod %s %s" % (m["mode"], m["target"]) for m in self.mods], []
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644
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645
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646 class MakeInstallAction(BaseAction):
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647 action_type = "make_install"
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648 _keys = []
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649
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650 def __init__(self, elem):
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651 pass
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652
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653 def to_bash(self):
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654 return ["make install"], []
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diff changeset
655
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656
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657 class AutoconfAction(BaseAction):
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658 action_type = "autoconf"
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659 _keys = ["options"]
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660
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661 def __init__(self, elem):
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662 self.options = elem.text
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diff changeset
663
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664 def to_bash(self):
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665 if self.options:
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666 raise NotImplementedError("Options with action autoconf not implemented yet.")
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667 return ['./configure', 'make', 'make install'], []
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668
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669
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670 class ChangeDirectoryAction(BaseAction):
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671 action_type = "change_directory"
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672 _keys = ["directory"]
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673
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674 def __init__(self, elem):
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675 self.directory = elem.text
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676 assert self.directory
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677
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678 def to_bash(self):
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679 return ["cd %s" % self.directory], []
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680
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681
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682 class MakeDirectoryAction(BaseAction):
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683 action_type = "make_directory"
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684 _keys = ["directory"]
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diff changeset
685
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686 def __init__(self, elem):
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687 self.directory = elem.text
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parents:
diff changeset
688
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689 def to_bash(self):
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690 return ["mkdir -p %s" % self.directory], []
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691
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692
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693 class SetupPerlEnvironmentAction(BaseAction):
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694 action_type = "setup_perl_environment"
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diff changeset
695 _keys = ["repo", "packages"]
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696
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diff changeset
697 def __init__(self, elem):
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diff changeset
698 self.parse_action_repo(elem)
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diff changeset
699 self.parse_package_elems(elem)
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diff changeset
700
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701
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702 class SetupRubyEnvironmentAction(BaseAction):
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diff changeset
703 action_type = "setup_ruby_environment"
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diff changeset
704 _keys = ["repo", "packages"]
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diff changeset
705
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parents:
diff changeset
706 def __init__(self, elem):
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diff changeset
707 self.parse_action_repo(elem)
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diff changeset
708 self.parse_package_elems(elem)
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parents:
diff changeset
709
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parents:
diff changeset
710
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711 class SetupPythonEnvironmentAction(BaseAction):
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diff changeset
712 action_type = "setup_python_environment"
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
713 _keys = ["repo", "packages"]
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
714
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parents:
diff changeset
715 def __init__(self, elem):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
716 self.parse_action_repo(elem)
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diff changeset
717 self.parse_package_elems(elem)
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diff changeset
718
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parents:
diff changeset
719
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diff changeset
720 class SetupVirtualenvAction(BaseAction):
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parents:
diff changeset
721 action_type = "setup_virtualenv"
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parents:
diff changeset
722 _keys = ["use_requirements_file", "python", "requirements"]
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parents:
diff changeset
723
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parents:
diff changeset
724 def __init__(self, elem):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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diff changeset
725 use_reqs = elem.attrib.get("use_requirements_file", "True")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
726 self.use_requirements_file = asbool(use_reqs)
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diff changeset
727 self.python = elem.get('python', 'python')
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parents:
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728 self.requirements = elem.text or 'requirements.txt'
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parents:
diff changeset
729
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parents:
diff changeset
730
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parents:
diff changeset
731 class SetupREnvironmentAction(BaseAction):
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parents:
diff changeset
732 action_type = "setup_r_environment"
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parents:
diff changeset
733 _keys = ["repo", "packages"]
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parents:
diff changeset
734
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parents:
diff changeset
735 def __init__(self, elem):
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parents:
diff changeset
736 self.parse_action_repo(elem)
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parents:
diff changeset
737 self.parse_package_elems(elem)
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parents:
diff changeset
738
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parents:
diff changeset
739
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
740 class SetEnvironmentForInstallAction(BaseAction):
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parents:
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741 action_type = "set_environment_for_install"
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parents:
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742
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parents:
diff changeset
743 def __init__(self, elem):
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parents:
diff changeset
744 pass
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bcclaywell
parents:
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745
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746 def to_bash(self):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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747 # TODO - How could we resolve/check the dependencies?
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parents:
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748 return ['echo "WARNING: Assuming packages already installed!"'], []
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parents:
diff changeset
749
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bcclaywell
parents:
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750
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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751 class SetVariable(object):
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parents:
diff changeset
752
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parents:
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753 def __init__(self, elem):
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parents:
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754 self.action = elem.attrib["action"]
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parents:
diff changeset
755 self.name = elem.attrib["name"]
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parents:
diff changeset
756 self.raw_value = elem.text
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parents:
diff changeset
757
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bcclaywell
parents:
diff changeset
758
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bcclaywell
parents:
diff changeset
759 truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
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bcclaywell
parents:
diff changeset
760 falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
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parents:
diff changeset
761
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bcclaywell
parents:
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762
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parents:
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763 def asbool(obj):
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parents:
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764 if isinstance(obj, string_types):
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parents:
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765 obj = obj.strip().lower()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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766 if obj in truthy:
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bcclaywell
parents:
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767 return True
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768 elif obj in falsy:
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769 return False
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770 else:
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771 raise ValueError("String is not true/false: %r" % obj)
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772 return bool(obj)
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773
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774
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775 action_classes = [
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776 DownloadByUrlAction,
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777 DownloadFileAction,
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778 DownloadBinary,
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779 ShellCommandAction,
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780 TemplateShellCommandAction,
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781 MoveFileAction,
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782 MoveDirectoryFilesAction,
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783 SetEnvironmentAction,
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784 ChmodAction,
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785 MakeInstallAction,
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786 AutoconfAction,
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787 ChangeDirectoryAction,
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788 MakeDirectoryAction,
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789 SetupPerlEnvironmentAction,
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790 SetupRubyEnvironmentAction,
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791 SetupPythonEnvironmentAction,
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792 SetupVirtualenvAction,
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793 SetupREnvironmentAction,
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794 SetEnvironmentForInstallAction,
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795 ]
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796
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797 actions_by_type = dict(map(lambda c: (c.action_type, c), action_classes))