Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/emr/step.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 # Copyright (c) 2010 Spotify AB
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2 # Copyright (c) 2010-2011 Yelp
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3 #
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4 # Permission is hereby granted, free of charge, to any person obtaining a
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5 # copy of this software and associated documentation files (the
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6 # "Software"), to deal in the Software without restriction, including
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7 # without limitation the rights to use, copy, modify, merge, publish, dis-
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8 # tribute, sublicense, and/or sell copies of the Software, and to permit
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9 # persons to whom the Software is furnished to do so, subject to the fol-
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10 # lowing conditions:
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11 #
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12 # The above copyright notice and this permission notice shall be included
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13 # in all copies or substantial portions of the Software.
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14 #
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15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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21 # IN THE SOFTWARE.
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22
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23 from boto.compat import six
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24
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25
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26 class Step(object):
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27 """
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28 Jobflow Step base class
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29 """
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30 def jar(self):
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31 """
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32 :rtype: str
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33 :return: URI to the jar
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34 """
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35 raise NotImplemented()
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36
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37 def args(self):
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38 """
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39 :rtype: list(str)
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40 :return: List of arguments for the step
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41 """
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42 raise NotImplemented()
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43
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44 def main_class(self):
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45 """
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46 :rtype: str
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47 :return: The main class name
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48 """
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49 raise NotImplemented()
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50
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51
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52 class JarStep(Step):
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53 """
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54 Custom jar step
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55 """
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56 def __init__(self, name, jar, main_class=None,
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57 action_on_failure='TERMINATE_JOB_FLOW', step_args=None):
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58 """
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59 A elastic mapreduce step that executes a jar
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60
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61 :type name: str
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62 :param name: The name of the step
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63 :type jar: str
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64 :param jar: S3 URI to the Jar file
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65 :type main_class: str
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66 :param main_class: The class to execute in the jar
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67 :type action_on_failure: str
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68 :param action_on_failure: An action, defined in the EMR docs to
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69 take on failure.
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70 :type step_args: list(str)
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71 :param step_args: A list of arguments to pass to the step
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72 """
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73 self.name = name
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74 self._jar = jar
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75 self._main_class = main_class
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76 self.action_on_failure = action_on_failure
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77
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78 if isinstance(step_args, six.string_types):
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79 step_args = [step_args]
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80
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81 self.step_args = step_args
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82
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83 def jar(self):
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84 return self._jar
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85
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86 def args(self):
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87 args = []
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88
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89 if self.step_args:
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90 args.extend(self.step_args)
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91
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92 return args
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93
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94 def main_class(self):
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95 return self._main_class
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96
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97
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98 class StreamingStep(Step):
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99 """
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100 Hadoop streaming step
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101 """
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102 def __init__(self, name, mapper, reducer=None, combiner=None,
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103 action_on_failure='TERMINATE_JOB_FLOW',
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104 cache_files=None, cache_archives=None,
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105 step_args=None, input=None, output=None,
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106 jar='/home/hadoop/contrib/streaming/hadoop-streaming.jar'):
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107 """
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108 A hadoop streaming elastic mapreduce step
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109
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110 :type name: str
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111 :param name: The name of the step
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112 :type mapper: str
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113 :param mapper: The mapper URI
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114 :type reducer: str
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115 :param reducer: The reducer URI
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116 :type combiner: str
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117 :param combiner: The combiner URI. Only works for Hadoop 0.20
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118 and later!
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119 :type action_on_failure: str
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120 :param action_on_failure: An action, defined in the EMR docs to
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121 take on failure.
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122 :type cache_files: list(str)
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123 :param cache_files: A list of cache files to be bundled with the job
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124 :type cache_archives: list(str)
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125 :param cache_archives: A list of jar archives to be bundled with
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126 the job
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127 :type step_args: list(str)
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128 :param step_args: A list of arguments to pass to the step
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129 :type input: str or a list of str
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130 :param input: The input uri
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131 :type output: str
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132 :param output: The output uri
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133 :type jar: str
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134 :param jar: The hadoop streaming jar. This can be either a local
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135 path on the master node, or an s3:// URI.
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136 """
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137 self.name = name
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138 self.mapper = mapper
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139 self.reducer = reducer
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140 self.combiner = combiner
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141 self.action_on_failure = action_on_failure
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142 self.cache_files = cache_files
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143 self.cache_archives = cache_archives
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144 self.input = input
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145 self.output = output
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146 self._jar = jar
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147
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148 if isinstance(step_args, six.string_types):
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149 step_args = [step_args]
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150
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151 self.step_args = step_args
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152
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153 def jar(self):
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154 return self._jar
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155
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156 def main_class(self):
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157 return None
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158
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159 def args(self):
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160 args = []
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161
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162 # put extra args BEFORE -mapper and -reducer so that e.g. -libjar
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163 # will work
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164 if self.step_args:
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165 args.extend(self.step_args)
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166
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167 args.extend(['-mapper', self.mapper])
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168
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169 if self.combiner:
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170 args.extend(['-combiner', self.combiner])
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171
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172 if self.reducer:
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173 args.extend(['-reducer', self.reducer])
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174 else:
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175 args.extend(['-jobconf', 'mapred.reduce.tasks=0'])
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176
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177 if self.input:
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178 if isinstance(self.input, list):
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179 for input in self.input:
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180 args.extend(('-input', input))
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181 else:
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182 args.extend(('-input', self.input))
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183 if self.output:
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184 args.extend(('-output', self.output))
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185
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186 if self.cache_files:
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187 for cache_file in self.cache_files:
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188 args.extend(('-cacheFile', cache_file))
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189
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190 if self.cache_archives:
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191 for cache_archive in self.cache_archives:
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192 args.extend(('-cacheArchive', cache_archive))
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193
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194 return args
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195
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196 def __repr__(self):
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197 return '%s.%s(name=%r, mapper=%r, reducer=%r, action_on_failure=%r, cache_files=%r, cache_archives=%r, step_args=%r, input=%r, output=%r, jar=%r)' % (
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198 self.__class__.__module__, self.__class__.__name__,
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199 self.name, self.mapper, self.reducer, self.action_on_failure,
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200 self.cache_files, self.cache_archives, self.step_args,
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201 self.input, self.output, self._jar)
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202
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203
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204 class ScriptRunnerStep(JarStep):
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205
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206 ScriptRunnerJar = 's3n://us-east-1.elasticmapreduce/libs/script-runner/script-runner.jar'
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207
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208 def __init__(self, name, **kw):
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209 super(ScriptRunnerStep, self).__init__(name, self.ScriptRunnerJar, **kw)
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210
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211
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212 class PigBase(ScriptRunnerStep):
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213
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214 BaseArgs = ['s3n://us-east-1.elasticmapreduce/libs/pig/pig-script',
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215 '--base-path', 's3n://us-east-1.elasticmapreduce/libs/pig/']
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216
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217
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218 class InstallPigStep(PigBase):
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219 """
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220 Install pig on emr step
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221 """
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222
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223 InstallPigName = 'Install Pig'
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224
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225 def __init__(self, pig_versions='latest'):
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226 step_args = []
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227 step_args.extend(self.BaseArgs)
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228 step_args.extend(['--install-pig'])
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229 step_args.extend(['--pig-versions', pig_versions])
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230 super(InstallPigStep, self).__init__(self.InstallPigName, step_args=step_args)
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231
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232
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233 class PigStep(PigBase):
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234 """
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235 Pig script step
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236 """
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237
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238 def __init__(self, name, pig_file, pig_versions='latest', pig_args=[]):
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239 step_args = []
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240 step_args.extend(self.BaseArgs)
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241 step_args.extend(['--pig-versions', pig_versions])
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242 step_args.extend(['--run-pig-script', '--args', '-f', pig_file])
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243 step_args.extend(pig_args)
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244 super(PigStep, self).__init__(name, step_args=step_args)
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245
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246
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247 class HiveBase(ScriptRunnerStep):
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248
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249 BaseArgs = ['s3n://us-east-1.elasticmapreduce/libs/hive/hive-script',
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250 '--base-path', 's3n://us-east-1.elasticmapreduce/libs/hive/']
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251
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252
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253 class InstallHiveStep(HiveBase):
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254 """
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255 Install Hive on EMR step
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256 """
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257 InstallHiveName = 'Install Hive'
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258
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259 def __init__(self, hive_versions='latest', hive_site=None):
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260 step_args = []
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261 step_args.extend(self.BaseArgs)
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262 step_args.extend(['--install-hive'])
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263 step_args.extend(['--hive-versions', hive_versions])
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264 if hive_site is not None:
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265 step_args.extend(['--hive-site=%s' % hive_site])
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266 super(InstallHiveStep, self).__init__(self.InstallHiveName,
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267 step_args=step_args)
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268
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269
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270 class HiveStep(HiveBase):
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271 """
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272 Hive script step
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273 """
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274
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275 def __init__(self, name, hive_file, hive_versions='latest',
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276 hive_args=None):
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277 step_args = []
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278 step_args.extend(self.BaseArgs)
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279 step_args.extend(['--hive-versions', hive_versions])
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280 step_args.extend(['--run-hive-script', '--args', '-f', hive_file])
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281 if hive_args is not None:
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282 step_args.extend(hive_args)
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283 super(HiveStep, self).__init__(name, step_args=step_args)