Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/asadmin @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2 # Copyright (c) 2011 Joel Barciauskas http://joel.barciausk.as/
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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
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22 #
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23 # Auto Scaling Groups Tool
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24 #
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25 VERSION="0.1"
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26 usage = """%prog [options] [command]
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27 Commands:
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28 list|ls List all Auto Scaling Groups
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29 list-lc|ls-lc List all Launch Configurations
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30 delete <name> Delete ASG <name>
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31 delete-lc <name> Delete Launch Configuration <name>
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32 get <name> Get details of ASG <name>
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33 create <name> Create an ASG
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34 create-lc <name> Create a Launch Configuration
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35 update <name> <prop> <value> Update a property of an ASG
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36 update-image <asg-name> <lc-name> Update image ID for ASG by creating a new LC
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37 migrate-instances <name> Shut down current instances one by one and wait for ASG to start up a new instance with the current AMI (useful in conjunction with update-image)
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38
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39 Examples:
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40
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41 1) Create launch configuration
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42 bin/asadmin create-lc my-lc-1 -i ami-1234abcd -t c1.xlarge -k my-key -s web-group -m
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43
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44 2) Create auto scaling group in us-east-1a and us-east-1c with a load balancer and min size of 2 and max size of 6
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45 bin/asadmin create my-asg -z us-east-1a -z us-east-1c -l my-lc-1 -b my-lb -H ELB -p 180 -x 2 -X 6
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46 """
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47
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48 def get_group(autoscale, name):
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49 g = autoscale.get_all_groups(names=[name])
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50 if len(g) < 1:
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51 print "No auto scaling groups by the name of %s found" % name
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52 return sys.exit(1)
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53 return g[0]
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54
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55 def get_lc(autoscale, name):
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56 l = autoscale.get_all_launch_configurations(names=[name])
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57 if len(l) < 1:
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58 print "No launch configurations by the name of %s found" % name
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59 sys.exit(1)
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60 return l[0]
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61
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62 def list(autoscale):
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63 """List all ASGs"""
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64 print "%-20s %s" % ("Name", "LC Name")
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65 print "-"*80
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66 groups = autoscale.get_all_groups()
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67 for g in groups:
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68 print "%-20s %s" % (g.name, g.launch_config_name)
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69
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70 def list_lc(autoscale):
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71 """List all LCs"""
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72 print "%-30s %-20s %s" % ("Name", "Image ID", "Instance Type")
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73 print "-"*80
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74 for l in autoscale.get_all_launch_configurations():
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75 print "%-30s %-20s %s" % (l.name, l.image_id, l.instance_type)
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76
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77 def get(autoscale, name):
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78 """Get details about ASG <name>"""
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79 g = get_group(autoscale, name)
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80 print "="*80
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81 print "%-30s %s" % ('Name:', g.name)
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82 print "%-30s %s" % ('Launch configuration:', g.launch_config_name)
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83 print "%-30s %s" % ('Minimum size:', g.min_size)
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84 print "%-30s %s" % ('Maximum size:', g.max_size)
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85 print "%-30s %s" % ('Desired capacity:', g.desired_capacity)
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86 print "%-30s %s" % ('Load balancers:', ','.join(g.load_balancers))
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87
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88 print
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89
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90 print "Instances"
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91 print "---------"
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92 print "%-20s %-20s %-20s %s" % ("ID", "Status", "Health", "AZ")
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93 for i in g.instances:
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94 print "%-20s %-20s %-20s %s" % \
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95 (i.instance_id, i.lifecycle_state, i.health_status, i.availability_zone)
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96
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97 print
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98
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99 def create(autoscale, name, zones, lc_name, load_balancers, hc_type, hc_period,
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100 min_size, max_size, cooldown, capacity):
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101 """Create an ASG named <name>"""
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102 g = AutoScalingGroup(name=name, launch_config=lc_name,
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103 availability_zones=zones, load_balancers=load_balancers,
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104 default_cooldown=cooldown, health_check_type=hc_type,
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105 health_check_period=hc_period, desired_capacity=capacity,
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106 min_size=min_size, max_size=max_size)
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107 g = autoscale.create_auto_scaling_group(g)
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108 return list(autoscale)
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109
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110 def create_lc(autoscale, name, image_id, instance_type, key_name,
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111 security_groups, instance_monitoring):
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112 l = LaunchConfiguration(name=name, image_id=image_id,
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113 instance_type=instance_type,key_name=key_name,
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114 security_groups=security_groups,
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115 instance_monitoring=instance_monitoring)
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116 l = autoscale.create_launch_configuration(l)
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117 return list_lc(autoscale)
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118
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119 def update(autoscale, name, prop, value):
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120 g = get_group(autoscale, name)
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121 setattr(g, prop, value)
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122 g.update()
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123 return get(autoscale, name)
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124
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125 def delete(autoscale, name, force_delete=False):
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126 """Delete this ASG"""
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127 g = get_group(autoscale, name)
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128 autoscale.delete_auto_scaling_group(g.name, force_delete)
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129 print "Auto scaling group %s deleted" % name
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130 return list(autoscale)
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131
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132 def delete_lc(autoscale, name):
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133 """Delete this LC"""
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134 l = get_lc(autoscale, name)
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135 autoscale.delete_launch_configuration(name)
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136 print "Launch configuration %s deleted" % name
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137 return list_lc(autoscale)
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138
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139 def update_image(autoscale, name, lc_name, image_id, is_migrate_instances=False):
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140 """ Get the current launch config,
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141 Update its name and image id
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142 Re-create it as a new launch config
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143 Update the ASG with the new LC
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144 Delete the old LC """
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145
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146 g = get_group(autoscale, name)
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147 l = get_lc(autoscale, g.launch_config_name)
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148
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149 old_lc_name = l.name
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150 l.name = lc_name
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151 l.image_id = image_id
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152 autoscale.create_launch_configuration(l)
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153 g.launch_config_name = l.name
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154 g.update()
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155
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156 if(is_migrate_instances):
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157 migrate_instances(autoscale, name)
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158 else:
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159 return get(autoscale, name)
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160
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161 def migrate_instances(autoscale, name):
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162 """ Shut down instances of the old image type one by one
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163 and let the ASG start up instances with the new image """
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164 g = get_group(autoscale, name)
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165
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166 old_instances = g.instances
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167 ec2 = boto.connect_ec2()
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168 for old_instance in old_instances:
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169 print "Terminating instance " + old_instance.instance_id
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170 ec2.terminate_instances([old_instance.instance_id])
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171 while True:
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172 g = get_group(autoscale, name)
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173 new_instances = g.instances
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174 for new_instance in new_instances:
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175 hasOldInstance = False
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176 instancesReady = True
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177 if(old_instance.instance_id == new_instance.instance_id):
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178 hasOldInstance = True
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179 print "Waiting for old instance to shut down..."
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180 break
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181 elif(new_instance.lifecycle_state != 'InService'):
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182 instancesReady = False
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183 print "Waiting for instances to be ready...."
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184 break
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185 if(not hasOldInstance and instancesReady):
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186 break
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187 else:
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188 time.sleep(20)
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189 return get(autoscale, name)
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190
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191 if __name__ == "__main__":
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192 try:
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193 import readline
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194 except ImportError:
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195 pass
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196 import boto
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197 import sys
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198 import time
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199 from optparse import OptionParser
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200 from boto.mashups.iobject import IObject
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201 from boto.ec2.autoscale import AutoScalingGroup
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202 from boto.ec2.autoscale import LaunchConfiguration
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203 parser = OptionParser(version=VERSION, usage=usage)
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204 """ Create launch config options """
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205 parser.add_option("-i", "--image-id",
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206 help="Image (AMI) ID", action="store",
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207 type="string", default=None, dest="image_id")
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208 parser.add_option("-t", "--instance-type",
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209 help="EC2 Instance Type (e.g., m1.large, c1.xlarge), default is m1.large",
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210 action="store", type="string", default="m1.large", dest="instance_type")
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211 parser.add_option("-k", "--key-name",
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212 help="EC2 Key Name",
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213 action="store", type="string", dest="key_name")
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214 parser.add_option("-s", "--security-group",
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215 help="EC2 Security Group",
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216 action="append", default=[], dest="security_groups")
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217 parser.add_option("-m", "--monitoring",
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218 help="Enable instance monitoring",
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219 action="store_true", default=False, dest="instance_monitoring")
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220
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diff changeset
221 """ Create auto scaling group options """
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222 parser.add_option("-z", "--zone", help="Add availability zone", action="append", default=[], dest="zones")
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223 parser.add_option("-l", "--lc-name",
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224 help="Launch configuration name",
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225 action="store", default=None, type="string", dest="lc_name")
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226 parser.add_option("-b", "--load-balancer",
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227 help="Load balancer name",
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228 action="append", default=[], dest="load_balancers")
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229 parser.add_option("-H", "--health-check-type",
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230 help="Health check type (EC2 or ELB)",
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diff changeset
231 action="store", default="EC2", type="string", dest="hc_type")
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232 parser.add_option("-p", "--health-check-period",
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233 help="Health check period in seconds (default 300s)",
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234 action="store", default=300, type="int", dest="hc_period")
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235 parser.add_option("-X", "--max-size",
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236 help="Max size of ASG (default 10)",
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237 action="store", default=10, type="int", dest="max_size")
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238 parser.add_option("-x", "--min-size",
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239 help="Min size of ASG (default 2)",
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240 action="store", default=2, type="int", dest="min_size")
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diff changeset
241 parser.add_option("-c", "--cooldown",
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242 help="Cooldown time after a scaling activity in seconds (default 300s)",
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diff changeset
243 action="store", default=300, type="int", dest="cooldown")
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244 parser.add_option("-C", "--desired-capacity",
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diff changeset
245 help="Desired capacity of the ASG",
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246 action="store", default=None, type="int", dest="capacity")
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247 parser.add_option("-f", "--force",
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248 help="Force delete ASG",
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249 action="store_true", default=False, dest="force")
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250 parser.add_option("-y", "--migrate-instances",
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251 help="Automatically migrate instances to new image when running update-image",
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252 action="store_true", default=False, dest="migrate_instances")
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253
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254 (options, args) = parser.parse_args()
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255
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256 if len(args) < 1:
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257 parser.print_help()
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258 sys.exit(1)
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259
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260 autoscale = boto.connect_autoscale()
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261
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262 print "%s" % (autoscale.region.endpoint)
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263
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264 command = args[0].lower()
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265 if command in ("ls", "list"):
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266 list(autoscale)
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267 elif command in ("ls-lc", "list-lc"):
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268 list_lc(autoscale)
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269 elif command == "get":
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270 get(autoscale, args[1])
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271 elif command == "create":
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272 create(autoscale, args[1], options.zones, options.lc_name,
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273 options.load_balancers, options.hc_type,
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274 options.hc_period, options.min_size, options.max_size,
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275 options.cooldown, options.capacity)
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276 elif command == "create-lc":
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277 create_lc(autoscale, args[1], options.image_id, options.instance_type,
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278 options.key_name, options.security_groups,
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279 options.instance_monitoring)
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280 elif command == "update":
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281 update(autoscale, args[1], args[2], args[3])
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282 elif command == "delete":
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283 delete(autoscale, args[1], options.force)
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284 elif command == "delete-lc":
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285 delete_lc(autoscale, args[1])
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286 elif command == "update-image":
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287 update_image(autoscale, args[1], args[2],
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288 options.image_id, options.migrate_instances)
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289 elif command == "migrate-instances":
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290 migrate_instances(autoscale, args[1])