Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/services/service.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) 2006,2007 Mitch Garnaat http://garnaat.org/
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2 #
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3 # Permission is hereby granted, free of charge, to any person obtaining a
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4 # copy of this software and associated documentation files (the
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5 # "Software"), to deal in the Software without restriction, including
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6 # without limitation the rights to use, copy, modify, merge, publish, dis-
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7 # tribute, sublicense, and/or sell copies of the Software, and to permit
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8 # persons to whom the Software is furnished to do so, subject to the fol-
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9 # lowing conditions:
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10 #
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11 # The above copyright notice and this permission notice shall be included
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12 # in all copies or substantial portions of the Software.
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13 #
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14 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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15 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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16 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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17 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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18 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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19 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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20 # IN THE SOFTWARE.
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21
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22 import boto
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23 from boto.services.message import ServiceMessage
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24 from boto.services.servicedef import ServiceDef
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25 from boto.pyami.scriptbase import ScriptBase
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26 from boto.utils import get_ts
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27 import time
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28 import os
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29 import mimetypes
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30
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31
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32 class Service(ScriptBase):
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33
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34 # Time required to process a transaction
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35 ProcessingTime = 60
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36
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37 def __init__(self, config_file=None, mimetype_files=None):
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38 super(Service, self).__init__(config_file)
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39 self.name = self.__class__.__name__
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40 self.working_dir = boto.config.get('Pyami', 'working_dir')
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41 self.sd = ServiceDef(config_file)
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42 self.retry_count = self.sd.getint('retry_count', 5)
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43 self.loop_delay = self.sd.getint('loop_delay', 30)
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44 self.processing_time = self.sd.getint('processing_time', 60)
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45 self.input_queue = self.sd.get_obj('input_queue')
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46 self.output_queue = self.sd.get_obj('output_queue')
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47 self.output_domain = self.sd.get_obj('output_domain')
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48 if mimetype_files:
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49 mimetypes.init(mimetype_files)
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50
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51 def split_key(key):
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52 if key.find(';') < 0:
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53 t = (key, '')
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54 else:
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55 key, type = key.split(';')
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56 label, mtype = type.split('=')
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57 t = (key, mtype)
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58 return t
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59
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60 def read_message(self):
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61 boto.log.info('read_message')
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62 message = self.input_queue.read(self.processing_time)
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63 if message:
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64 boto.log.info(message.get_body())
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65 key = 'Service-Read'
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66 message[key] = get_ts()
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67 return message
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68
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69 # retrieve the source file from S3
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70 def get_file(self, message):
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71 bucket_name = message['Bucket']
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72 key_name = message['InputKey']
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73 file_name = os.path.join(self.working_dir, message.get('OriginalFileName', 'in_file'))
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74 boto.log.info('get_file: %s/%s to %s' % (bucket_name, key_name, file_name))
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75 bucket = boto.lookup('s3', bucket_name)
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76 key = bucket.new_key(key_name)
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77 key.get_contents_to_filename(os.path.join(self.working_dir, file_name))
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78 return file_name
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79
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80 # process source file, return list of output files
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81 def process_file(self, in_file_name, msg):
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82 return []
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83
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84 # store result file in S3
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85 def put_file(self, bucket_name, file_path, key_name=None):
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86 boto.log.info('putting file %s as %s.%s' % (file_path, bucket_name, key_name))
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87 bucket = boto.lookup('s3', bucket_name)
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88 key = bucket.new_key(key_name)
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89 key.set_contents_from_filename(file_path)
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90 return key
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91
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92 def save_results(self, results, input_message, output_message):
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93 output_keys = []
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94 for file, type in results:
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95 if 'OutputBucket' in input_message:
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96 output_bucket = input_message['OutputBucket']
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97 else:
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98 output_bucket = input_message['Bucket']
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99 key_name = os.path.split(file)[1]
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100 key = self.put_file(output_bucket, file, key_name)
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101 output_keys.append('%s;type=%s' % (key.name, type))
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102 output_message['OutputKey'] = ','.join(output_keys)
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103
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104 # write message to each output queue
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105 def write_message(self, message):
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106 message['Service-Write'] = get_ts()
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107 message['Server'] = self.name
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108 if 'HOSTNAME' in os.environ:
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109 message['Host'] = os.environ['HOSTNAME']
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110 else:
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111 message['Host'] = 'unknown'
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112 message['Instance-ID'] = self.instance_id
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113 if self.output_queue:
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114 boto.log.info('Writing message to SQS queue: %s' % self.output_queue.id)
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115 self.output_queue.write(message)
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116 if self.output_domain:
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117 boto.log.info('Writing message to SDB domain: %s' % self.output_domain.name)
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118 item_name = '/'.join([message['Service-Write'], message['Bucket'], message['InputKey']])
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119 self.output_domain.put_attributes(item_name, message)
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120
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121 # delete message from input queue
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122 def delete_message(self, message):
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123 boto.log.info('deleting message from %s' % self.input_queue.id)
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124 self.input_queue.delete_message(message)
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125
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126 # to clean up any files, etc. after each iteration
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127 def cleanup(self):
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128 pass
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129
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130 def shutdown(self):
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131 on_completion = self.sd.get('on_completion', 'shutdown')
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132 if on_completion == 'shutdown':
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133 if self.instance_id:
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134 time.sleep(60)
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135 c = boto.connect_ec2()
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136 c.terminate_instances([self.instance_id])
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137
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138 def main(self, notify=False):
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139 self.notify('Service: %s Starting' % self.name)
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140 empty_reads = 0
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141 while self.retry_count < 0 or empty_reads < self.retry_count:
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142 try:
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143 input_message = self.read_message()
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144 if input_message:
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145 empty_reads = 0
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146 output_message = ServiceMessage(None, input_message.get_body())
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147 input_file = self.get_file(input_message)
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148 results = self.process_file(input_file, output_message)
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149 self.save_results(results, input_message, output_message)
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150 self.write_message(output_message)
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151 self.delete_message(input_message)
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152 self.cleanup()
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153 else:
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154 empty_reads += 1
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155 time.sleep(self.loop_delay)
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156 except Exception:
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157 boto.log.exception('Service Failed')
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158 empty_reads += 1
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159 self.notify('Service: %s Shutting Down' % self.name)
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160 self.shutdown()
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161