Mercurial > repos > shellac > guppy_basecaller
annotate env/bin/mturk @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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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 2012, 2014 Kodi Arfer |
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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 import argparse # Hence, Python 2.7 is required. |
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23 import sys |
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24 import os.path |
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25 import string |
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26 import inspect |
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27 import datetime, calendar |
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28 import boto.mturk.connection, boto.mturk.price, boto.mturk.question, boto.mturk.qualification |
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29 from boto.compat import json |
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30 |
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31 # -------------------------------------------------- |
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32 # Globals |
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33 # ------------------------------------------------- |
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34 |
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35 interactive = False |
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36 con = None |
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37 mturk_website = None |
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38 |
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39 default_nicknames_path = os.path.expanduser('~/.boto_mturkcli_hit_nicknames') |
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40 nicknames = {} |
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41 nickname_pool = set(string.ascii_lowercase) |
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42 |
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43 get_assignments_page_size = 100 |
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44 |
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45 time_units = dict( |
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46 s = 1, |
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47 min = 60, |
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48 h = 60 * 60, |
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49 d = 24 * 60 * 60) |
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50 |
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51 qual_requirements = dict( |
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52 Adult = '00000000000000000060', |
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53 Locale = '00000000000000000071', |
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54 NumberHITsApproved = '00000000000000000040', |
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55 PercentAssignmentsSubmitted = '00000000000000000000', |
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56 PercentAssignmentsAbandoned = '00000000000000000070', |
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57 PercentAssignmentsReturned = '000000000000000000E0', |
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58 PercentAssignmentsApproved = '000000000000000000L0', |
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59 PercentAssignmentsRejected = '000000000000000000S0') |
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60 |
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61 qual_comparators = {v : k for k, v in dict( |
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62 LessThan = '<', LessThanOrEqualTo = '<=', |
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63 GreaterThan = '>', GreaterThanOrEqualTo = '>=', |
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64 EqualTo = '==', NotEqualTo = '!=', |
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65 Exists = 'exists').items()} |
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66 |
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67 example_config_file = '''Example configuration file: |
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68 |
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69 { |
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70 "title": "Pick your favorite color", |
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71 "description": "In this task, you are asked to pick your favorite color.", |
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72 "reward": 0.50, |
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73 "assignments": 10, |
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74 "duration": "20 min", |
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75 "keywords": ["color", "favorites", "survey"], |
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76 "lifetime": "7 d", |
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77 "approval_delay": "14 d", |
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78 "qualifications": [ |
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79 "PercentAssignmentsApproved > 90", |
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80 "Locale == US", |
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81 "2ARFPLSP75KLA8M8DH1HTEQVJT3SY6 exists" |
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82 ], |
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83 "question_url": "http://example.com/myhit", |
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84 "question_frame_height": 450 |
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85 }''' |
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86 |
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87 # -------------------------------------------------- |
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88 # Subroutines |
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89 # -------------------------------------------------- |
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90 |
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91 def unjson(path): |
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92 with open(path) as o: |
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93 return json.load(o) |
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94 |
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95 def add_argparse_arguments(parser): |
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96 parser.add_argument('-P', '--production', |
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97 dest = 'sandbox', action = 'store_false', default = True, |
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98 help = 'use the production site (default: use the sandbox)') |
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99 parser.add_argument('--nicknames', |
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100 dest = 'nicknames_path', metavar = 'PATH', |
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101 default = default_nicknames_path, |
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102 help = 'where to store HIT nicknames (default: {})'.format( |
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103 default_nicknames_path)) |
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104 |
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105 def init_by_args(args): |
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106 init(args.sandbox, args.nicknames_path) |
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107 |
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108 def init(sandbox = False, nicknames_path = default_nicknames_path): |
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109 global con, mturk_website, nicknames, original_nicknames |
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110 |
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111 mturk_website = 'workersandbox.mturk.com' if sandbox else 'www.mturk.com' |
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112 con = boto.mturk.connection.MTurkConnection( |
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113 host = 'mechanicalturk.sandbox.amazonaws.com' if sandbox else 'mechanicalturk.amazonaws.com') |
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114 |
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115 try: |
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116 nicknames = unjson(nicknames_path) |
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117 except IOError: |
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118 nicknames = {} |
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119 original_nicknames = nicknames.copy() |
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120 |
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121 def save_nicknames(nicknames_path = default_nicknames_path): |
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122 if nicknames != original_nicknames: |
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123 with open(nicknames_path, 'w') as o: |
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124 json.dump(nicknames, o, sort_keys = True, indent = 4) |
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125 print >>o |
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126 |
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127 def parse_duration(s): |
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128 '''Parses durations like "2 d", "48 h", "2880 min", |
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129 "172800 s", or "172800".''' |
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130 x = s.split() |
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131 return int(x[0]) * time_units['s' if len(x) == 1 else x[1]] |
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132 def display_duration(n): |
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133 for unit, m in sorted(time_units.items(), key = lambda x: -x[1]): |
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134 if n % m == 0: |
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135 return '{} {}'.format(n / m, unit) |
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136 |
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137 def parse_qualification(inp): |
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138 '''Parses qualifications like "PercentAssignmentsApproved > 90", |
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139 "Locale == US", and "2ARFPLSP75KLA8M8DH1HTEQVJT3SY6 exists".''' |
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140 inp = inp.split() |
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141 name, comparator, value = inp.pop(0), inp.pop(0), (inp[0] if len(inp) else None) |
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142 qtid = qual_requirements.get(name) |
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143 if qtid is None: |
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144 # Treat "name" as a Qualification Type ID. |
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145 qtid = name |
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146 if qtid == qual_requirements['Locale']: |
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147 return boto.mturk.qualification.LocaleRequirement( |
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148 qual_comparators[comparator], |
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149 value, |
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150 required_to_preview = False) |
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151 return boto.mturk.qualification.Requirement( |
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152 qtid, |
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153 qual_comparators[comparator], |
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154 value, |
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155 required_to_preview = qtid == qual_requirements['Adult']) |
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156 # Thus required_to_preview is true only for the |
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157 # Worker_Adult requirement. |
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158 |
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159 def preview_url(hit): |
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160 return 'https://{}/mturk/preview?groupId={}'.format( |
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161 mturk_website, hit.HITTypeId) |
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162 |
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163 def parse_timestamp(s): |
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164 '''Takes a timestamp like "2012-11-24T16:34:41Z". |
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165 |
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166 Returns a datetime object in the local time zone.''' |
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167 return datetime.datetime.fromtimestamp( |
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168 calendar.timegm( |
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169 datetime.datetime.strptime(s, '%Y-%m-%dT%H:%M:%SZ').timetuple())) |
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170 |
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171 def get_hitid(nickname_or_hitid): |
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172 return nicknames.get(nickname_or_hitid) or nickname_or_hitid |
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173 |
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174 def get_nickname(hitid): |
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175 for k, v in nicknames.items(): |
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176 if v == hitid: |
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177 return k |
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178 return None |
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179 |
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180 def display_datetime(dt): |
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181 return dt.strftime('%e %b %Y, %l:%M %P') |
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182 |
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183 def display_hit(hit, verbose = False): |
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184 et = parse_timestamp(hit.Expiration) |
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185 return '\n'.join([ |
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186 '{} - {} ({}, {}, {})'.format( |
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187 get_nickname(hit.HITId), |
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188 hit.Title, |
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189 hit.FormattedPrice, |
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190 display_duration(int(hit.AssignmentDurationInSeconds)), |
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191 hit.HITStatus), |
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192 'HIT ID: ' + hit.HITId, |
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193 'Type ID: ' + hit.HITTypeId, |
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194 'Group ID: ' + hit.HITGroupId, |
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195 'Preview: ' + preview_url(hit), |
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196 'Created {} {}'.format( |
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197 display_datetime(parse_timestamp(hit.CreationTime)), |
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198 'Expired' if et <= datetime.datetime.now() else |
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199 'Expires ' + display_datetime(et)), |
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200 'Assignments: {} -- {} avail, {} pending, {} reviewable, {} reviewed'.format( |
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201 hit.MaxAssignments, |
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202 hit.NumberOfAssignmentsAvailable, |
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203 hit.NumberOfAssignmentsPending, |
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204 int(hit.MaxAssignments) - (int(hit.NumberOfAssignmentsAvailable) + int(hit.NumberOfAssignmentsPending) + int(hit.NumberOfAssignmentsCompleted)), |
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205 hit.NumberOfAssignmentsCompleted) |
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206 if hasattr(hit, 'NumberOfAssignmentsAvailable') |
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207 else 'Assignments: {} total'.format(hit.MaxAssignments), |
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208 # For some reason, SearchHITs includes the |
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209 # NumberOfAssignmentsFoobar fields but GetHIT doesn't. |
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210 ] + ([] if not verbose else [ |
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211 '\nDescription: ' + hit.Description, |
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212 '\nKeywords: ' + hit.Keywords |
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213 ])) + '\n' |
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214 |
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215 def digest_assignment(a): |
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216 return dict( |
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217 answers = {str(x.qid): str(x.fields[0]) for x in a.answers[0]}, |
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218 **{k: str(getattr(a, k)) for k in ( |
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219 'AcceptTime', 'SubmitTime', |
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220 'HITId', 'AssignmentId', 'WorkerId', |
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221 'AssignmentStatus')}) |
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222 |
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223 # -------------------------------------------------- |
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224 # Commands |
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225 # -------------------------------------------------- |
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226 |
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227 def get_balance(): |
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228 return con.get_account_balance() |
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229 |
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230 def show_hit(hit): |
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231 return display_hit(con.get_hit(hit)[0], verbose = True) |
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232 |
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233 def list_hits(): |
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234 'Lists your 10 most recently created HITs, with the most recent last.' |
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235 return '\n'.join(reversed(map(display_hit, con.search_hits( |
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236 sort_by = 'CreationTime', |
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237 sort_direction = 'Descending', |
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238 page_size = 10)))) |
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239 |
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240 def make_hit(title, description, keywords, reward, question_url, question_frame_height, duration, assignments, approval_delay, lifetime, qualifications = []): |
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241 r = con.create_hit( |
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242 title = title, |
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243 description = description, |
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244 keywords = con.get_keywords_as_string(keywords), |
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245 reward = con.get_price_as_price(reward), |
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246 question = boto.mturk.question.ExternalQuestion( |
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247 question_url, |
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248 question_frame_height), |
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249 duration = parse_duration(duration), |
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250 qualifications = boto.mturk.qualification.Qualifications( |
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251 map(parse_qualification, qualifications)), |
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252 max_assignments = assignments, |
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253 approval_delay = parse_duration(approval_delay), |
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254 lifetime = parse_duration(lifetime)) |
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255 nick = None |
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256 available_nicks = nickname_pool - set(nicknames.keys()) |
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257 if available_nicks: |
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258 nick = min(available_nicks) |
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259 nicknames[nick] = r[0].HITId |
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260 if interactive: |
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261 print 'Nickname:', nick |
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262 print 'HIT ID:', r[0].HITId |
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263 print 'Preview:', preview_url(r[0]) |
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264 else: |
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265 return r[0] |
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266 |
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267 def extend_hit(hit, assignments_increment = None, expiration_increment = None): |
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268 con.extend_hit(hit, assignments_increment, expiration_increment) |
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269 |
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270 def expire_hit(hit): |
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271 con.expire_hit(hit) |
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272 |
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273 def delete_hit(hit): |
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274 '''Deletes a HIT using DisableHIT. |
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275 |
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276 Unreviewed assignments get automatically approved. Unsubmitted |
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277 assignments get automatically approved upon submission. |
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278 |
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279 The API docs say DisableHIT doesn't work with Reviewable HITs, |
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280 but apparently, it does.''' |
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281 con.disable_hit(hit) |
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282 global nicknames |
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283 nicknames = {k: v for k, v in nicknames.items() if v != hit} |
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284 |
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285 def list_assignments(hit, only_reviewable = False): |
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286 # Accumulate all relevant assignments, one page of results at |
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287 # a time. |
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288 assignments = [] |
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289 page = 1 |
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290 while True: |
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291 rs = con.get_assignments( |
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292 hit_id = hit, |
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293 page_size = get_assignments_page_size, |
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294 page_number = page, |
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295 status = 'Submitted' if only_reviewable else None) |
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296 assignments += map(digest_assignment, rs) |
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297 if len(assignments) >= int(rs.TotalNumResults): |
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298 break |
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299 page += 1 |
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300 if interactive: |
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301 print json.dumps(assignments, sort_keys = True, indent = 4) |
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302 print ' '.join([a['AssignmentId'] for a in assignments]) |
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303 print ' '.join([a['WorkerId'] + ',' + a['AssignmentId'] for a in assignments]) |
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304 else: |
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305 return assignments |
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306 |
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307 def grant_bonus(message, amount, pairs): |
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308 for worker, assignment in pairs: |
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309 con.grant_bonus(worker, assignment, con.get_price_as_price(amount), message) |
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310 if interactive: print 'Bonused', worker |
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311 |
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312 def approve_assignments(message, assignments): |
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313 for a in assignments: |
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314 con.approve_assignment(a, message) |
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315 if interactive: print 'Approved', a |
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316 |
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317 def reject_assignments(message, assignments): |
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318 for a in assignments: |
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319 con.reject_assignment(a, message) |
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320 if interactive: print 'Rejected', a |
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321 |
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322 def unreject_assignments(message, assignments): |
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323 for a in assignments: |
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324 con.approve_rejected_assignment(a, message) |
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325 if interactive: print 'Unrejected', a |
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326 |
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327 def notify_workers(subject, text, workers): |
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328 con.notify_workers(workers, subject, text) |
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329 |
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330 def give_qualification(qualification, workers, value = 1, notify = True): |
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331 for w in workers: |
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332 con.assign_qualification(qualification, w, value, notify) |
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333 if interactive: print 'Gave to', w |
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334 |
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335 def revoke_qualification(qualification, workers, message = None): |
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336 for w in workers: |
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337 con.revoke_qualification(w, qualification, message) |
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338 if interactive: print 'Revoked from', w |
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339 |
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340 # -------------------------------------------------- |
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341 # Mainline code |
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342 # -------------------------------------------------- |
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343 |
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344 if __name__ == '__main__': |
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345 interactive = True |
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346 |
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347 parser = argparse.ArgumentParser() |
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348 add_argparse_arguments(parser) |
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349 subs = parser.add_subparsers() |
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350 |
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351 sub = subs.add_parser('bal', |
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352 help = 'display your prepaid balance') |
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353 sub.set_defaults(f = get_balance, a = lambda: []) |
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354 |
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355 sub = subs.add_parser('hit', |
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356 help = 'get information about a HIT') |
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357 sub.add_argument('HIT', |
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358 help = 'nickname or ID of the HIT to show') |
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359 sub.set_defaults(f = show_hit, a = lambda: |
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360 [get_hitid(args.HIT)]) |
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361 |
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362 sub = subs.add_parser('hits', |
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363 help = 'list all your HITs') |
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364 sub.set_defaults(f = list_hits, a = lambda: []) |
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365 |
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366 sub = subs.add_parser('new', |
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367 help = 'create a new HIT (external questions only)', |
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368 epilog = example_config_file, |
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369 formatter_class = argparse.RawDescriptionHelpFormatter) |
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370 sub.add_argument('JSON_PATH', |
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371 help = 'path to JSON configuration file for the HIT') |
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372 sub.add_argument('-u', '--question-url', dest = 'question_url', |
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373 metavar = 'URL', |
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374 help = 'URL for the external question') |
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375 sub.add_argument('-a', '--assignments', dest = 'assignments', |
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376 type = int, metavar = 'N', |
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377 help = 'number of assignments') |
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378 sub.add_argument('-r', '--reward', dest = 'reward', |
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379 type = float, metavar = 'PRICE', |
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380 help = 'reward amount, in USD') |
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381 sub.set_defaults(f = make_hit, a = lambda: dict( |
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382 unjson(args.JSON_PATH).items() + [(k, getattr(args, k)) |
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383 for k in ('question_url', 'assignments', 'reward') |
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384 if getattr(args, k) is not None])) |
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385 |
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386 sub = subs.add_parser('extend', |
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387 help = 'add assignments or time to a HIT') |
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388 sub.add_argument('HIT', |
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389 help = 'nickname or ID of the HIT to extend') |
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390 sub.add_argument('-a', '--assignments', dest = 'assignments', |
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391 metavar = 'N', type = int, |
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392 help = 'number of assignments to add') |
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393 sub.add_argument('-t', '--time', dest = 'time', |
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394 metavar = 'T', |
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395 help = 'amount of time to add to the expiration date') |
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396 sub.set_defaults(f = extend_hit, a = lambda: |
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397 [get_hitid(args.HIT), args.assignments, |
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398 args.time and parse_duration(args.time)]) |
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399 |
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400 sub = subs.add_parser('expire', |
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401 help = 'force a HIT to expire without deleting it') |
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402 sub.add_argument('HIT', |
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403 help = 'nickname or ID of the HIT to expire') |
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404 sub.set_defaults(f = expire_hit, a = lambda: |
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405 [get_hitid(args.HIT)]) |
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406 |
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407 sub = subs.add_parser('rm', |
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408 help = 'delete a HIT') |
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409 sub.add_argument('HIT', |
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410 help = 'nickname or ID of the HIT to delete') |
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411 sub.set_defaults(f = delete_hit, a = lambda: |
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412 [get_hitid(args.HIT)]) |
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413 |
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414 sub = subs.add_parser('as', |
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415 help = "list a HIT's submitted assignments") |
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416 sub.add_argument('HIT', |
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417 help = 'nickname or ID of the HIT to get assignments for') |
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418 sub.add_argument('-r', '--reviewable', dest = 'only_reviewable', |
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419 action = 'store_true', |
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420 help = 'show only unreviewed assignments') |
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421 sub.set_defaults(f = list_assignments, a = lambda: |
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422 [get_hitid(args.HIT), args.only_reviewable]) |
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423 |
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424 for command, fun, helpmsg in [ |
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425 ('approve', approve_assignments, 'approve assignments'), |
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426 ('reject', reject_assignments, 'reject assignments'), |
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427 ('unreject', unreject_assignments, 'approve previously rejected assignments')]: |
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428 sub = subs.add_parser(command, help = helpmsg) |
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429 sub.add_argument('ASSIGNMENT', nargs = '+', |
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430 help = 'ID of an assignment') |
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431 sub.add_argument('-m', '--message', dest = 'message', |
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432 metavar = 'TEXT', |
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433 help = 'feedback message shown to workers') |
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434 sub.set_defaults(f = fun, a = lambda: |
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435 [args.message, args.ASSIGNMENT]) |
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436 |
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437 sub = subs.add_parser('bonus', |
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438 help = 'give some workers a bonus') |
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439 sub.add_argument('AMOUNT', type = float, |
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440 help = 'bonus amount, in USD') |
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441 sub.add_argument('MESSAGE', |
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442 help = 'the reason for the bonus (shown to workers in an email sent by MTurk)') |
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443 sub.add_argument('WIDAID', nargs = '+', |
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444 help = 'a WORKER_ID,ASSIGNMENT_ID pair') |
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445 sub.set_defaults(f = grant_bonus, a = lambda: |
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446 [args.MESSAGE, args.AMOUNT, |
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447 [p.split(',') for p in args.WIDAID]]) |
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448 |
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449 sub = subs.add_parser('notify', |
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450 help = 'send a message to some workers') |
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451 sub.add_argument('SUBJECT', |
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452 help = 'subject of the message') |
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453 sub.add_argument('MESSAGE', |
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454 help = 'text of the message') |
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455 sub.add_argument('WORKER', nargs = '+', |
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456 help = 'ID of a worker') |
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457 sub.set_defaults(f = notify_workers, a = lambda: |
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458 [args.SUBJECT, args.MESSAGE, args.WORKER]) |
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459 |
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460 sub = subs.add_parser('give-qual', |
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461 help = 'give a qualification to some workers') |
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462 sub.add_argument('QUAL', |
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463 help = 'ID of the qualification') |
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464 sub.add_argument('WORKER', nargs = '+', |
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465 help = 'ID of a worker') |
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466 sub.add_argument('-v', '--value', dest = 'value', |
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467 metavar = 'N', type = int, default = 1, |
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468 help = 'value of the qualification') |
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469 sub.add_argument('--dontnotify', dest = 'notify', |
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470 action = 'store_false', default = True, |
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471 help = "don't notify workers") |
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472 sub.set_defaults(f = give_qualification, a = lambda: |
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473 [args.QUAL, args.WORKER, args.value, args.notify]) |
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474 |
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475 sub = subs.add_parser('revoke-qual', |
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476 help = 'revoke a qualification from some workers') |
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477 sub.add_argument('QUAL', |
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478 help = 'ID of the qualification') |
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479 sub.add_argument('WORKER', nargs = '+', |
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480 help = 'ID of a worker') |
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481 sub.add_argument('-m', '--message', dest = 'message', |
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482 metavar = 'TEXT', |
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483 help = 'the reason the qualification was revoked (shown to workers in an email sent by MTurk)') |
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484 sub.set_defaults(f = revoke_qualification, a = lambda: |
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485 [args.QUAL, args.WORKER, args.message]) |
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486 |
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487 args = parser.parse_args() |
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488 |
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489 init_by_args(args) |
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490 |
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491 f = args.f |
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492 a = args.a() |
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493 if isinstance(a, dict): |
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494 # We do some introspective gymnastics so we can produce a |
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495 # less incomprehensible error message if some arguments |
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496 # are missing. |
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497 spec = inspect.getargspec(f) |
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498 missing = set(spec.args[: len(spec.args) - len(spec.defaults)]) - set(a.keys()) |
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499 if missing: |
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500 raise ValueError('Missing arguments: ' + ', '.join(missing)) |
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501 doit = lambda: f(**a) |
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502 else: |
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503 doit = lambda: f(*a) |
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504 |
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505 try: |
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506 x = doit() |
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507 except boto.mturk.connection.MTurkRequestError as e: |
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508 print 'MTurk error:', e.error_message |
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509 sys.exit(1) |
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510 |
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511 if x is not None: |
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512 print x |
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513 |
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514 save_nicknames() |