Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/shed2tap/base.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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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 import os
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4 import subprocess
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5 import sys
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6 import tarfile
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7 import zipfile
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8 from ftplib import all_errors as FTPErrors # tuple of exceptions
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9 from typing import List
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10 from xml.etree import ElementTree
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11
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12 from galaxy.util import unicodify
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13 from six import iteritems
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14 from six import string_types
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15 from six.moves import map as imap
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16 from six.moves.urllib.error import URLError
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17 from six.moves.urllib.request import urlretrieve
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18
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19
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20 TOOLSHED_MAP = {
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21 "toolshed": "https://toolshed.g2.bx.psu.edu",
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22 "testtoolshed": "https://testtoolshed.g2.bx.psu.edu",
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23 }
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24
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25
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26 class Dependencies(object):
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27 """ Base class for parsing Tool Shed dependency files.
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28 """
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29
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30 def __init__(
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31 self,
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32 dependencies_file,
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33 repo=None,
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34 package_factory=None,
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35 ):
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36 if package_factory is None:
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37 package_factory = BasePackage
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38 self.repo = repo
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39 self.root = ElementTree.parse(dependencies_file).getroot()
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40 packages = []
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41 dependencies = []
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42 package_els = self.root.findall("package")
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43 assert package_els is not None
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44 for package_el in package_els:
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45 install_els = package_el.findall("install")
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46 readme_els = package_el.findall("readme")
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47 if len(readme_els) > 0:
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48 readme = readme_els[0].text
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49 else:
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50 readme = None
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51 assert len(install_els) in (0, 1)
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52 if len(install_els) == 1:
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53 install_el = install_els[0]
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54 package = package_factory(
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55 self,
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56 package_el,
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57 install_el,
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58 readme=readme
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59 )
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60 packages.append(package)
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61 else:
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62 repository_el = package_el.find("repository")
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63 if repository_el is None:
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64 message = "no repository in package el for %s" % repo
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65 raise AssertionError(message)
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66 dependency = Dependency(self, package_el, repository_el)
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67 dependencies.append(dependency)
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68
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69 self.packages = packages
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70 self.dependencies = dependencies
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71
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72 def single_package(self):
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73 return len(self.packages) == 1
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74
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75 def __repr__(self):
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76 return "Dependencies[for_repo=%s]" % self.repo
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77
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78
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79 class Repo(object):
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80
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81 def __init__(self, **kwds):
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82 for key, value in iteritems(kwds):
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83 setattr(self, key, value)
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84
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85 def recipe_base_name(self):
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86 owner = self.owner.replace("-", "")
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87 name = self.name
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88 name = name.replace("_", "").replace("-", "")
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89 base = "%s_%s" % (owner, name)
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90 return base
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91
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92 @staticmethod
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93 def from_xml(elem):
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94 tool_shed_url = elem.attrib.get("toolshed", None)
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95 if tool_shed_url and ("testtoolshed" in tool_shed_url):
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96 prefix = "testtoolshed"
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97 else:
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98 prefix = "toolshed"
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99 prior = elem.attrib.get("prior_installation_required", False)
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100 return Repo(
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101 prefix=prefix,
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102 name=elem.attrib["name"],
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103 owner=elem.attrib["owner"],
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104 tool_shed_url=tool_shed_url,
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105 changeset_revision=elem.attrib.get("changeset_revision", None),
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106 prior_installation_required=prior,
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107 )
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108
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109 @staticmethod
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110 def from_api(prefix, repo_json):
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111 return Repo(
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112 prefix=prefix,
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113 name=repo_json["name"],
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114 owner=repo_json["owner"],
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115 tool_shed_url=TOOLSHED_MAP[prefix],
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116 )
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117
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118 def get_file(self, path):
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119 try:
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120 url_template = "%s/repos/%s/%s/raw-file/tip/%s"
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121 url = url_template % (
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122 self.tool_shed_url,
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123 self.owner,
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124 self.name,
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125 path
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126 )
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127 path, headers = urlretrieve(url)
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128 return path
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129 except Exception as e:
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130 print(e)
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131 return None
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132
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133 def __repr__(self):
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134 return "Repository[name=%s,owner=%s]" % (self.name, self.owner)
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135
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136
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137 class Dependency(object):
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138
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139 def __init__(self, dependencies, package_el, repository_el):
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140 self.dependencies = dependencies
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141 self.package_el = package_el
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142 self.repository_el = repository_el
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143 self.repo = Repo.from_xml(repository_el)
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144
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145 def __repr__(self):
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146 temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]"
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147 return temp % (
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148 self.package_el.attrib["name"],
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149 self.package_el.attrib["version"],
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150 self.repository_el.attrib["name"]
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151 )
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152
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153
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154 class BasePackage(object):
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155
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156 def __init__(self, dependencies, package_el, install_el, readme):
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157 self.dependencies = dependencies
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158 self.package_el = package_el
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159 self.install_el = install_el
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160 self.readme = readme
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161 self.all_actions = self.get_all_actions()
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162 self.no_arch_option = self.has_no_achitecture_install()
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163
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164 def get_all_actions(self):
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165 action_or_group = self.install_el[0]
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166 parsed_actions = []
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167 if action_or_group.tag == "actions":
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168 parsed_actions.append(self.parse_actions(action_or_group))
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169 elif action_or_group.tag == "actions_group":
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170 actions_els = action_or_group.findall("actions")
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171 assert actions_els is not None
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172 for actions in actions_els:
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173 parsed_actions.append(self.parse_actions(actions))
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174 action_els = action_or_group.findall("action")
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175 assert action_els is not None
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176 for action in action_els:
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177 for parsed_a in parsed_actions:
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178 parsed_a.actions.append(self.parse_action(action))
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179 return parsed_actions
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180
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181 def has_no_achitecture_install(self):
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182 all_actions = self.all_actions
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183 if len(all_actions) < 2:
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184 return False
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185 else:
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186 last_action = all_actions[-1]
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187 return (not last_action.architecture) and (not last_action.os)
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188
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189 def has_explicit_set_environments(self):
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190 all_actions = self.all_actions
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191 for actions in all_actions:
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192 for action in actions.actions:
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193 if action.explicit_variables:
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194 return True
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195 return False
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196
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197 def has_multiple_set_environments(self):
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198 all_actions = self.all_actions
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199 for actions in all_actions:
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200 count = 0
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201 for action in actions.actions:
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202 if action.explicit_variables:
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203 count += 1
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204 if count > 1:
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205 return True
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206 return False
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207
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208 def parse_actions(self, actions):
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209 os = actions.attrib.get("os", None)
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210 architecture = actions.get("architecture", None)
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211 action_els = actions.findall("action")
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212 assert action_els is not None
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213 parsed_actions = list(imap(self.parse_action, action_els))
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214 action_packages = []
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215 for package in actions.findall("package"):
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216 action_packages.append(self.parse_action_package(package))
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217 return Actions(parsed_actions, os, architecture, action_packages)
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218
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219 def parse_action_package(self, elem):
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220 name = elem.attrib["name"]
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221 version = elem.attrib["version"]
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222 repo = Repo.from_xml(elem.find("repository"))
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223 return ActionPackage(name, version, repo)
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224
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225 def parse_action(self, action):
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226 return BaseAction.from_elem(action, package=self)
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227
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228 def __repr__(self):
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229 actions = self.all_actions
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230 parts = (
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231 self.package_el.attrib["name"],
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232 self.package_el.attrib["version"],
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233 self.dependencies,
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234 actions
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235 )
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236 template = "Install[name=%s,version=%s,dependencies=%s,actions=%s]"
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237 return template % parts
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238
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239
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240 class Actions(object):
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241
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242 def __init__(
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243 self,
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244 actions,
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245 os=None,
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246 architecture=None,
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247 action_packages=[]
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248 ):
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249 self.os = os
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250 self.architecture = architecture
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251 self.actions = actions or []
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252 self.action_packages = action_packages
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253
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254 def first_download(self):
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255 for action in self.actions:
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256 if action.action_type in ["download_by_url", "download_file"]:
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257 return action
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258 return None
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259
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260 def downloads(self):
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261 actions = []
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262 for action in self.actions:
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263 if action.action_type in ["download_by_url", "download_file"]:
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264 actions.append(action)
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265 return actions
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266
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267 def __repr__(self):
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268 platform = ""
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269 if self.os or self.architecture:
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270 platform = "os=%s,arch=%s," % (self.os, self.architecture)
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271 return "Actions[%s%s]" % (platform, map(str, self.actions))
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272
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273 def _indent_extend(self, target, new_entries, indent=" "):
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274 for line in new_entries:
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275 target.append(indent + line)
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276
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277 def to_bash(self):
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278 # Use self.os.title() to match "Linux" or "Darwin" in bash where case matters:
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279 if self.os and self.architecture:
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280 condition = '("%s" == `uname`) && ("%s" == `arch`)' % (self.os.title(), self.architecture)
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281 elif self.os:
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282 condition = '"%s" == `uname`' % self.os.title()
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283 elif self.architecture:
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284 condition = '"%s" == `arch`' % self.architecture
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285 else:
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286 condition = None
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287
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288 install_cmds = []
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289 env_cmds = []
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290
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291 if condition:
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292 # Conditional actions block
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293 install_cmds = [
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294 '#' + '-' * 60,
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295 'if [[ $specifc_action_done == 0 && %s ]]' % condition,
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296 'then',
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297 ' echo "Platform-specific action for os=%s, arch=%s"' % (self.os, self.architecture)]
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298 env_cmds = install_cmds[:]
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299 # TODO - Refactor block indentation?
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300 for action in self.actions:
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301 i_cmds, e_cmds = action.to_bash()
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302 self._indent_extend(install_cmds, i_cmds)
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303 self._indent_extend(env_cmds, e_cmds)
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304 # If we run the action, do not want to run any later actions!
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305 install_cmds.extend([' specifc_action_done=1', 'fi'])
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306 env_cmds.extend([' specifc_action_done=1', 'fi'])
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307 else:
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308 # Non-specific default action...
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309 install_cmds = [
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310 '#' + '-' * 60,
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311 'if [[ $specifc_action_done == 0 ]]',
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312 'then',
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313 ' echo "Non-platform-specific actions"']
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314 env_cmds = install_cmds[:]
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315 for action in self.actions:
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316 i_cmds, e_cmds = action.to_bash()
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317 self._indent_extend(install_cmds, i_cmds)
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318 self._indent_extend(env_cmds, e_cmds)
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319 install_cmds.append('fi')
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320 env_cmds.append('fi')
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321 return install_cmds, env_cmds
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322
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323
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324 class ActionPackage(object):
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325
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326 def __init__(self, name, version, repo):
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327 self.name = name
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328 self.version = version
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329 self.repo = repo
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330
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331
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332 class BaseAction(object):
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333 _keys = [] # type: List[str]
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334 action_type = None # type: str
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335
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336 def __repr__(self):
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337 return "Action[type=%s]" % self.action_type
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338
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339 def same_as(self, other):
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340 if self._keys != other._keys:
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341 return False
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342 else:
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343 for key in self._keys:
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344 if getattr(self, key) != getattr(other, key):
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345 return False
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346
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347 return True
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348
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349 def parse_action_repo(self, elem):
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350 repo_elem = elem.find("repository")
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351 repo = Repo.from_xml(repo_elem)
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352 self.repo = repo
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353
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354 def parse_package_elems(self, elem):
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355 package_els = elem.findall("package")
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356 packages = []
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357 assert package_els is not None
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358 for package_el in package_els:
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359 packages.append(package_el.text)
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360 self.packages = packages
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361
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362 @classmethod
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363 def from_elem(cls, elem, package):
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364 type = elem.attrib["type"]
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365 action_class = actions_by_type[type]
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366 return action_class(elem)
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367
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368 def to_bash(self):
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369 """Return lists of bash shell commands to execute this action.
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370
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371 This method is be implemented by each sub-class, and will
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372 return two list of strings (for ``dep_install.sh`` and
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373 ``env.sh`` respectively).
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374 """
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375 raise NotImplementedError("No to_bash defined for %r" % self)
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376
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377
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378 def _tar_folders(filename):
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379 with tarfile.open(filename, "r", errorlevel=0) as archive:
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380 folders = set()
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381 for i in archive.getmembers():
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382 if i.isdir():
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diff changeset
383 folders.add(i.name.rstrip("/"))
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shellac
parents:
diff changeset
384 else:
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shellac
parents:
diff changeset
385 folders.add(os.path.split(i.name)[0])
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shellac
parents:
diff changeset
386 return list(folders)
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shellac
parents:
diff changeset
387
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shellac
parents:
diff changeset
388
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
389 def _zip_folders(filename):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
390 archive = zipfile.ZipFile(filename, "r")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
391 return list(set(i.filename.rstrip("/") for i in archive.infolist() if i.filename.endswith("/")))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
392
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shellac
parents:
diff changeset
393
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shellac
parents:
diff changeset
394 def _common_prefix(folders):
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shellac
parents:
diff changeset
395 common_prefix = ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
396 if len(folders) == 1:
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shellac
parents:
diff changeset
397 common_prefix = list(folders)[0]
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shellac
parents:
diff changeset
398 else:
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shellac
parents:
diff changeset
399 common_prefix = os.path.commonprefix(folders)
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shellac
parents:
diff changeset
400 assert not os.path.isabs(common_prefix), folders
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shellac
parents:
diff changeset
401 return common_prefix
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shellac
parents:
diff changeset
402
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shellac
parents:
diff changeset
403
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shellac
parents:
diff changeset
404 def _cache_download(url, filename, sha256sum=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
405 """Returns local path to cached copy of URL using given filename."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
406 cache = os.environ.get("DOWNLOAD_CACHE", "./download_cache/")
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shellac
parents:
diff changeset
407 # TODO - expose this as a command line option
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shellac
parents:
diff changeset
408
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shellac
parents:
diff changeset
409 if not os.path.isdir(cache):
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shellac
parents:
diff changeset
410 os.mkdir(cache)
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shellac
parents:
diff changeset
411
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shellac
parents:
diff changeset
412 local = os.path.join(cache, filename)
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shellac
parents:
diff changeset
413
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shellac
parents:
diff changeset
414 if not os.path.isfile(local):
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shellac
parents:
diff changeset
415 # Must download it...
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shellac
parents:
diff changeset
416 try:
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shellac
parents:
diff changeset
417 # TODO - log this nicely...
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shellac
parents:
diff changeset
418 sys.stderr.write("Downloading %s to %r\n" % (url, local))
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shellac
parents:
diff changeset
419 urlretrieve(url, local)
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shellac
parents:
diff changeset
420 except URLError:
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shellac
parents:
diff changeset
421 # Most likely server is down, could be bad URL in XML action:
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shellac
parents:
diff changeset
422 raise RuntimeError("Unable to download %s" % url)
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shellac
parents:
diff changeset
423 except FTPErrors:
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shellac
parents:
diff changeset
424 # Most likely server is down, could be bad URL in XML action:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425 raise RuntimeError("Unable to download %s" % url)
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shellac
parents:
diff changeset
426
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 # Verifying the checksum is slow, only do this on a fresh
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428 # download. Assume locally cached files are already OK.
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shellac
parents:
diff changeset
429 if sha256sum:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 # TODO - log this nicely...
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shellac
parents:
diff changeset
431 sys.stderr.write("Verifying checksum for %s\n" % filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
432 filehash = subprocess.check_output(['shasum', '-a', '256', local])[0:64].strip()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
433 filehash = unicodify(filehash)
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shellac
parents:
diff changeset
434 if filehash != sha256sum:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 raise RuntimeError("Checksum failure for %s, got %r but wanted %r" % (local, filehash, sha256sum))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436
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shellac
parents:
diff changeset
437 return local
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shellac
parents:
diff changeset
438
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shellac
parents:
diff changeset
439
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shellac
parents:
diff changeset
440 def _determine_compressed_file_folder(url, downloaded_filename, target_filename=None, sha256sum=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 """Determine how to decompress the file & its directory structure.
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shellac
parents:
diff changeset
442
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shellac
parents:
diff changeset
443 Returns a list of shell commands. Consider this example where the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
444 folder to change to cannot be guessed from the tar-ball filename:
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shellac
parents:
diff changeset
445
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shellac
parents:
diff changeset
446 $ curl -o "ncbi-blast-2.2.30+-ia32-linux.tar.gz" \
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shellac
parents:
diff changeset
447 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-ia32-linux.tar.gz"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448 $ tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz
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shellac
parents:
diff changeset
449 $ cd ncbi-blast-2.2.30+
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shellac
parents:
diff changeset
450
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
451 Here it would return:
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shellac
parents:
diff changeset
452
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 ['tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz', 'cd ncbi-blast-2.2.30+']
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shellac
parents:
diff changeset
454
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455 If not cached, this function will download the file to the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 $DOWNLOAD_CACHE folder, and then open it / decompress it in
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457 order to find common folder prefix used. This will also verify
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 how to decompress the file, and the checksum if given.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 """
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shellac
parents:
diff changeset
460 answer = []
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shellac
parents:
diff changeset
461
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shellac
parents:
diff changeset
462 local = _cache_download(url, downloaded_filename, sha256sum)
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shellac
parents:
diff changeset
463
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 if not target_filename:
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shellac
parents:
diff changeset
465 target_filename = downloaded_filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467 if tarfile.is_tarfile(local):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468 folders = _tar_folders(local)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 if target_filename.endswith((".tar.gz", ".tgz")):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 answer.append('tar -zxvf %s' % target_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 elif target_filename.endswith(".tar.bz2"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 answer.append('tar -jxvf %s' % target_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 elif target_filename.endswith(".tar"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 answer.extend('tar -xvf %s' % target_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 # Quite possibly this file doesn't need decompressing,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 # but until we've tested lots of real world tool_dependencies.xml
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 # files I'd like to check these cases to confirm this.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 raise NotImplementedError("How to decompress tar file %s?" % target_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 elif zipfile.is_zipfile(local):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 if target_filename.endswith(".jar"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 # Do not decompress!
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483 return answer
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 folders = _zip_folders(local)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485 answer.append('unzip %s' % target_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 elif target_filename.endswith(".dmg"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 # Do not decompress!
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 return answer
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
489 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490 # No compression? Leave as it is?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491 raise NotImplementedError("What kind of compression is %s using?" % local)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
492
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shellac
parents:
diff changeset
493 common_prefix = _common_prefix(folders)
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shellac
parents:
diff changeset
494 if common_prefix:
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shellac
parents:
diff changeset
495 answer.append('cd "%s"' % common_prefix)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
496
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497 return answer
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
498
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500 def _commands_and_downloaded_file(url, target_filename=None, sha256sum=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
501 # We preserve the filename from the URL in the cache.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
502 # i.e. We do NOT use the target_filename in the cache.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 # This because some Galaxy recipes normalise platform specific downloads
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 # to use a single target filename, which would therefore break checksums etc
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505 # e.g. tests/data/repos/package_1/tool_dependencies.xml
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
506 downloaded_filename = os.path.split(url)[-1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
507 if "?" in downloaded_filename:
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shellac
parents:
diff changeset
508 downloaded_filename = downloaded_filename[:downloaded_filename.index("?")]
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shellac
parents:
diff changeset
509 if "#" in downloaded_filename:
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shellac
parents:
diff changeset
510 downloaded_filename = downloaded_filename[:downloaded_filename.index("#")]
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shellac
parents:
diff changeset
511
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shellac
parents:
diff changeset
512 if not target_filename:
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shellac
parents:
diff changeset
513 target_filename = downloaded_filename
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shellac
parents:
diff changeset
514
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shellac
parents:
diff changeset
515 # Curl is present on Mac OS X, can we assume it will be on Linux?
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shellac
parents:
diff changeset
516 # Cannot assume that wget will be on Mac OS X.
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shellac
parents:
diff changeset
517 answer = [
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parents:
diff changeset
518 'if [[ -f "%s" ]]' % target_filename,
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shellac
parents:
diff changeset
519 'then',
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shellac
parents:
diff changeset
520 ' echo "Reusing existing %s"' % target_filename,
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shellac
parents:
diff changeset
521 'elif [[ -f "$DOWNLOAD_CACHE/%s" ]]' % downloaded_filename,
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shellac
parents:
diff changeset
522 'then',
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parents:
diff changeset
523 ' echo "Reusing cached %s"' % downloaded_filename,
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shellac
parents:
diff changeset
524 ' cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
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shellac
parents:
diff changeset
525 'else',
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shellac
parents:
diff changeset
526 ' echo "Downloading %s"' % downloaded_filename,
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shellac
parents:
diff changeset
527 ' curl -L -o "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, url),
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shellac
parents:
diff changeset
528 ' cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
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shellac
parents:
diff changeset
529 ]
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shellac
parents:
diff changeset
530 if sha256sum:
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shellac
parents:
diff changeset
531 # This is inserted into the if-else for a fresh download only.
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shellac
parents:
diff changeset
532 # Note double space between checksum and filename:
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shellac
parents:
diff changeset
533 answer.append(' echo "%s %s" | shasum -a 256 -c -' % (sha256sum, target_filename))
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parents:
diff changeset
534 answer.append('fi')
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parents:
diff changeset
535
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shellac
parents:
diff changeset
536 return answer, downloaded_filename
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shellac
parents:
diff changeset
537
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shellac
parents:
diff changeset
538
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parents:
diff changeset
539 def _commands_to_download_and_extract(url, target_filename=None, sha256sum=None):
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shellac
parents:
diff changeset
540 answer, downloaded_filename = _commands_and_downloaded_file(url, target_filename, sha256sum)
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shellac
parents:
diff changeset
541 # Now should we unpack the tar-ball etc?
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shellac
parents:
diff changeset
542 answer.extend(_determine_compressed_file_folder(url, downloaded_filename, target_filename, sha256sum))
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parents:
diff changeset
543 return answer, []
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shellac
parents:
diff changeset
544
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shellac
parents:
diff changeset
545
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parents:
diff changeset
546 class DownloadByUrlAction(BaseAction):
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parents:
diff changeset
547 action_type = "download_by_url"
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parents:
diff changeset
548 _keys = ["url"]
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parents:
diff changeset
549
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parents:
diff changeset
550 def __init__(self, elem):
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parents:
diff changeset
551 self.url = elem.text.strip()
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shellac
parents:
diff changeset
552 assert self.url
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parents:
diff changeset
553 self.sha256sum = elem.attrib.get("sha256sum", None)
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shellac
parents:
diff changeset
554 self.target_filename = elem.attrib.get("target_filename", None)
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shellac
parents:
diff changeset
555
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parents:
diff changeset
556 def to_bash(self):
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shellac
parents:
diff changeset
557 # See class DownloadByUrl in Galaxy,
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shellac
parents:
diff changeset
558 # lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
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parents:
diff changeset
559 return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)
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shellac
parents:
diff changeset
560
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shellac
parents:
diff changeset
561
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parents:
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562 class DownloadFileAction(BaseAction):
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parents:
diff changeset
563 action_type = "download_file"
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parents:
diff changeset
564 _keys = ["url", "extract"]
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shellac
parents:
diff changeset
565
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shellac
parents:
diff changeset
566 def __init__(self, elem):
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parents:
diff changeset
567 self.url = elem.text.strip()
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parents:
diff changeset
568 self.extract = asbool(elem.attrib.get("extract", False))
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shellac
parents:
diff changeset
569 self.sha256sum = elem.attrib.get("sha256sum", None)
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parents:
diff changeset
570 self.target_filename = elem.attrib.get("target_filename", None)
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parents:
diff changeset
571
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parents:
diff changeset
572 def to_bash(self):
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parents:
diff changeset
573 if self.extract:
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shellac
parents:
diff changeset
574 return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)
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parents:
diff changeset
575 else:
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shellac
parents:
diff changeset
576 commands, downloaded_file = _commands_and_downloaded_file(self.url, self.target_filename, self.sha256sum)
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shellac
parents:
diff changeset
577 return commands, []
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shellac
parents:
diff changeset
578
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shellac
parents:
diff changeset
579
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parents:
diff changeset
580 class DownloadBinary(BaseAction):
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shellac
parents:
diff changeset
581 action_type = "download_binary"
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shellac
parents:
diff changeset
582 _keys = ["url_template", "target_directory"]
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shellac
parents:
diff changeset
583
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shellac
parents:
diff changeset
584 def __init__(self, elem):
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shellac
parents:
diff changeset
585 self.url_template = elem.text
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shellac
parents:
diff changeset
586 assert self.url_template
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shellac
parents:
diff changeset
587 self.target_directory = elem.get('target_directory', None)
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shellac
parents:
diff changeset
588
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shellac
parents:
diff changeset
589
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shellac
parents:
diff changeset
590 class ShellCommandAction(BaseAction):
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shellac
parents:
diff changeset
591 action_type = "shell_command"
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shellac
parents:
diff changeset
592 _keys = ["command"]
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shellac
parents:
diff changeset
593
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shellac
parents:
diff changeset
594 def __init__(self, elem):
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shellac
parents:
diff changeset
595 self.command = elem.text
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shellac
parents:
diff changeset
596
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shellac
parents:
diff changeset
597 def to_bash(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 # Galaxy would run each action from the same temp
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
599 # working directory - possible that tool_dependencies.xml
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shellac
parents:
diff changeset
600 # shell_command could change $PWD so reset this:
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shellac
parents:
diff changeset
601 return ["pushd . > /dev/null", self.command, "popd > /dev/null"], []
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shellac
parents:
diff changeset
602
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shellac
parents:
diff changeset
603
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604 class TemplateShellCommandAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 action_type = "template_command"
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shellac
parents:
diff changeset
606 _keys = ["language", "command"]
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shellac
parents:
diff changeset
607
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 def __init__(self, elem):
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shellac
parents:
diff changeset
609 self.command = elem.text
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shellac
parents:
diff changeset
610 self.language = elem.get('language', 'cheetah').lower()
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shellac
parents:
diff changeset
611 assert self.command
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shellac
parents:
diff changeset
612 assert self.language == "cheetah"
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shellac
parents:
diff changeset
613
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shellac
parents:
diff changeset
614
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shellac
parents:
diff changeset
615 class MoveFileAction(BaseAction):
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shellac
parents:
diff changeset
616 action_type = "move_file"
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parents:
diff changeset
617 _keys = ["move_file"]
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shellac
parents:
diff changeset
618
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shellac
parents:
diff changeset
619 def __init__(self, elem):
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shellac
parents:
diff changeset
620 self.source = elem.find("source").text
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shellac
parents:
diff changeset
621 self.destination = elem.find("destination").text
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shellac
parents:
diff changeset
622
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shellac
parents:
diff changeset
623 def to_bash(self):
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shellac
parents:
diff changeset
624 return ["mv %s %s" % (self.source, self.destination)], []
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shellac
parents:
diff changeset
625
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shellac
parents:
diff changeset
626
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
627 class MoveDirectoryFilesAction(BaseAction):
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shellac
parents:
diff changeset
628 action_type = "move_directory_files"
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shellac
parents:
diff changeset
629 _keys = ["source_directory", "destination_directory"]
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shellac
parents:
diff changeset
630
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shellac
parents:
diff changeset
631 def __init__(self, elem):
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shellac
parents:
diff changeset
632 source_directory = elem.find("source_directory").text
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parents:
diff changeset
633 destination_directory = elem.find("destination_directory").text
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parents:
diff changeset
634 self.source_directory = source_directory
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parents:
diff changeset
635 self.destination_directory = destination_directory
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parents:
diff changeset
636
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diff changeset
637 def to_bash(self):
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parents:
diff changeset
638 return ["mv %s/* %s/" % (self.source_directory, self.destination_directory)], []
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parents:
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639
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parents:
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640
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parents:
diff changeset
641 class SetEnvironmentAction(BaseAction):
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parents:
diff changeset
642 action_type = "set_environment"
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parents:
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643 _keys = ["variables"]
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parents:
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644
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645 def __init__(self, elem):
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646 variables = []
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647 var_els = elem.findall("environment_variable")
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648 assert var_els is not None
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649 for ev_elem in var_els:
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650 var = SetVariable(ev_elem)
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parents:
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651 variables.append(var)
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parents:
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652 self.variables = variables
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parents:
diff changeset
653 assert self.variables
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parents:
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654
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parents:
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655 def to_bash(self):
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656 answer = []
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657 for var in self.variables:
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parents:
diff changeset
658 # Expand $INSTALL_DIR here?
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parents:
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659 if var.action == "set_to":
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parents:
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660 answer.append('export %s=%s' % (var.name, var.raw_value))
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parents:
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661 elif var.action == "prepend_to":
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parents:
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662 answer.append('export %s=%s:$%s' % (var.name, var.raw_value, var.name))
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parents:
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663 elif var.action == "append_to":
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parents:
diff changeset
664 answer.append('export %s=$%s:%s' % (var.name, var.name, var.raw_value))
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665 else:
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666 raise ValueError("Undefined environment variable action %r" % var.action)
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parents:
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667 return answer, answer # Actions needed in env.sh here!
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668
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669
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670 class ChmodAction(BaseAction):
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parents:
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671 action_type = "chmod"
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parents:
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672 _keys = ["mods"]
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parents:
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673
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diff changeset
674 def __init__(self, elem):
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parents:
diff changeset
675 mods = []
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parents:
diff changeset
676 file_els = elem.findall("file")
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parents:
diff changeset
677 assert file_els is not None
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parents:
diff changeset
678 for mod_elem in file_els:
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parents:
diff changeset
679 mod = {}
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parents:
diff changeset
680 mod["mode"] = mod_elem.attrib["mode"]
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diff changeset
681 mod["target"] = mod_elem.text
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parents:
diff changeset
682 mods.append(mod)
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parents:
diff changeset
683 self.mods = mods
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parents:
diff changeset
684 assert self.mods
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parents:
diff changeset
685
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parents:
diff changeset
686 def to_bash(self):
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parents:
diff changeset
687 return ["chmod %s %s" % (m["mode"], m["target"]) for m in self.mods], []
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parents:
diff changeset
688
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parents:
diff changeset
689
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parents:
diff changeset
690 class MakeInstallAction(BaseAction):
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parents:
diff changeset
691 action_type = "make_install"
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parents:
diff changeset
692 _keys = [] # type: List[str]
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parents:
diff changeset
693
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parents:
diff changeset
694 def __init__(self, elem):
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shellac
parents:
diff changeset
695 pass
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parents:
diff changeset
696
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parents:
diff changeset
697 def to_bash(self):
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shellac
parents:
diff changeset
698 return ["make install"], []
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parents:
diff changeset
699
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parents:
diff changeset
700
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parents:
diff changeset
701 class AutoconfAction(BaseAction):
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shellac
parents:
diff changeset
702 action_type = "autoconf"
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shellac
parents:
diff changeset
703 _keys = ["options"]
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shellac
parents:
diff changeset
704
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shellac
parents:
diff changeset
705 def __init__(self, elem):
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shellac
parents:
diff changeset
706 self.options = elem.text
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shellac
parents:
diff changeset
707
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shellac
parents:
diff changeset
708 def to_bash(self):
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shellac
parents:
diff changeset
709 if self.options:
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shellac
parents:
diff changeset
710 raise NotImplementedError("Options with action autoconf not implemented yet.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711 return ['./configure', 'make', 'make install'], []
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shellac
parents:
diff changeset
712
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shellac
parents:
diff changeset
713
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shellac
parents:
diff changeset
714 class ChangeDirectoryAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 action_type = "change_directory"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716 _keys = ["directory"]
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shellac
parents:
diff changeset
717
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
718 def __init__(self, elem):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 self.directory = elem.text
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 assert self.directory
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shellac
parents:
diff changeset
721
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 def to_bash(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 return ["cd %s" % self.directory], []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 class MakeDirectoryAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727 action_type = "make_directory"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 _keys = ["directory"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 def __init__(self, elem):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 self.directory = elem.text
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 def to_bash(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 return ["mkdir -p %s" % self.directory], []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 class SetupPerlEnvironmentAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 action_type = "setup_perl_environment"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 _keys = ["repo", "packages"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 def __init__(self, elem):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 self.parse_action_repo(elem)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 self.parse_package_elems(elem)
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shellac
parents:
diff changeset
744
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shellac
parents:
diff changeset
745
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 class SetupRubyEnvironmentAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 action_type = "setup_ruby_environment"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 _keys = ["repo", "packages"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 def __init__(self, elem):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 self.parse_action_repo(elem)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 self.parse_package_elems(elem)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 class SetupPythonEnvironmentAction(BaseAction):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 action_type = "setup_python_environment"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 _keys = ["repo", "packages"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 def __init__(self, elem):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 self.parse_action_repo(elem)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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761 self.parse_package_elems(elem)
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762
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763
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764 class SetupVirtualenvAction(BaseAction):
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765 action_type = "setup_virtualenv"
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766 _keys = ["use_requirements_file", "python", "requirements"]
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767
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768 def __init__(self, elem):
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769 use_reqs = elem.attrib.get("use_requirements_file", "True")
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770 self.use_requirements_file = asbool(use_reqs)
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771 self.python = elem.get('python', 'python')
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772 self.requirements = elem.text or 'requirements.txt'
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773
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774
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775 class SetupREnvironmentAction(BaseAction):
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776 action_type = "setup_r_environment"
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777 _keys = ["repo", "packages"]
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778
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779 def __init__(self, elem):
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780 self.parse_action_repo(elem)
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781 self.parse_package_elems(elem)
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782
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783
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784 class SetEnvironmentForInstallAction(BaseAction):
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785 action_type = "set_environment_for_install"
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786
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787 def __init__(self, elem):
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788 pass
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789
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790 def to_bash(self):
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791 # TODO - How could we resolve/check the dependencies?
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792 return ['echo "WARNING: Assuming packages already installed!"'], []
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793
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794
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795 class SetVariable(object):
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796
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797 def __init__(self, elem):
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798 self.action = elem.attrib["action"]
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799 self.name = elem.attrib["name"]
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800 self.raw_value = elem.text
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801
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802
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803 truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
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804 falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
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805
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806
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807 def asbool(obj):
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808 if isinstance(obj, string_types):
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809 obj = obj.strip().lower()
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810 if obj in truthy:
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811 return True
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812 elif obj in falsy:
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813 return False
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814 else:
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815 raise ValueError("String is not true/false: %r" % obj)
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816 return bool(obj)
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817
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818
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819 action_classes = [
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820 DownloadByUrlAction,
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821 DownloadFileAction,
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822 DownloadBinary,
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823 ShellCommandAction,
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824 TemplateShellCommandAction,
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825 MoveFileAction,
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826 MoveDirectoryFilesAction,
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827 SetEnvironmentAction,
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828 ChmodAction,
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829 MakeInstallAction,
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830 AutoconfAction,
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831 ChangeDirectoryAction,
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832 MakeDirectoryAction,
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833 SetupPerlEnvironmentAction,
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834 SetupRubyEnvironmentAction,
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835 SetupPythonEnvironmentAction,
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836 SetupVirtualenvAction,
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837 SetupREnvironmentAction,
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838 SetEnvironmentForInstallAction,
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839 ]
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840
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841 actions_by_type = dict(map(lambda c: (c.action_type, c), action_classes))