Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/taskadmin @ 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) 2009 Chris Moyer http://coredumped.org/
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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 # Task/Job Administration utility
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24 #
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25 VERSION="0.1"
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26 __version__ = VERSION
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27 usage = """%prog [options] [command]
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28 Commands:
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29 list|ls List all Tasks in SDB
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30 delete <id> Delete Task with id <id>
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31 get <name> Get Task <name>
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32 create|mk <name> <hour> <command> Create a new Task <name> with command <command> running every <hour>
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33 """
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34
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35 def list():
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36 """List all Tasks in SDB"""
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37 from boto.manage.task import Task
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38 print "%-8s %-40s %s" % ("Hour", "Name", "Command")
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39 print "-"*100
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40 for t in Task.all():
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41 print "%-8s %-40s %s" % (t.hour, t.name, t.command)
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42
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43 def get(name):
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44 """Get a task
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45 :param name: The name of the task to fetch
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46 :type name: str
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47 """
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48 from boto.manage.task import Task
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49 q = Task.find()
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50 q.filter("name like", "%s%%" % name)
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51 for t in q:
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52 print "="*80
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53 print "| ", t.id
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54 print "|%s" % ("-"*79)
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55 print "| Name: ", t.name
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56 print "| Hour: ", t.hour
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57 print "| Command: ", t.command
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58 if t.last_executed:
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59 print "| Last Run: ", t.last_executed.ctime()
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60 print "| Last Status: ", t.last_status
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61 print "| Last Run Log: ", t.last_output
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62 print "="*80
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63
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64 def delete(id):
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65 from boto.manage.task import Task
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66 t = Task.get_by_id(id)
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67 print "Deleting task: %s" % t.name
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68 if raw_input("Are you sure? ").lower() in ["y", "yes"]:
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69 t.delete()
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70 print "Deleted"
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71 else:
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72 print "Canceled"
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73
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74 def create(name, hour, command):
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75 """Create a new task
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76 :param name: Name of the task to create
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77 :type name: str
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78 :param hour: What hour to run it at, "*" for every hour
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79 :type hour: str
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80 :param command: The command to execute
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81 :type command: str
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82 """
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83 from boto.manage.task import Task
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84 t = Task()
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85 t.name = name
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86 t.hour = hour
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87 t.command = command
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88 t.put()
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89 print "Created task: %s" % t.id
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90
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91 if __name__ == "__main__":
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92 try:
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93 import readline
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94 except ImportError:
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95 pass
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96 import boto
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97 import sys
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98 from optparse import OptionParser
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99 from boto.mashups.iobject import IObject
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100 parser = OptionParser(version=__version__, usage=usage)
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101
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102 (options, args) = parser.parse_args()
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103
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104 if len(args) < 1:
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105 parser.print_help()
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106 sys.exit(1)
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107
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108 command = args[0].lower()
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109 if command in ("ls", "list"):
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110 list()
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111 elif command == "get":
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112 get(args[1])
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113 elif command == "create":
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114 create(args[1], args[2], args[3])
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115 elif command == "delete":
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116 delete(args[1])