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1 #!/usr/bin/env python
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2 """
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3 Validate the metadata file associated with Affymetrix 96 well plate data.
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4 """
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5 import argparse
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6 import datetime
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7 import decimal
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8 import re
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9 import shutil
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10 import sys
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11
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12 parser = argparse.ArgumentParser()
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13 parser.add_argument('--input', dest='input', help='Metadata file for Affymetrix 96 well plate data')
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14 parser.add_argument('--output', dest='output', help='Output dataset'),
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15 args = parser.parse_args()
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16
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17 EMAIL_MAX_LEN = 255
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18 VALID_EMAIL_RE = re.compile("[^@]+@[^@]+\.[^@]+")
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19
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20
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21 def add_error_msg(accumulated_msgs, msg):
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22 return "%s\n%s" % (accumulated_msgs, msg)
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23
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24
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25 def empty_value(line_no, label, accumulated_msgs):
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26 return add_error_msg(accumulated_msgs, "The required %s value is missing on line %d." % (label, line_no))
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27
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28
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29 def stop_error(msg):
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30 sys.exit(msg)
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31
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32
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33 def string_as_boolean_string(string):
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34 if str(string).lower() in ['true', 'yes', 'on', '1']:
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35 return 'True'
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36 else:
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37 return 'False'
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38
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39
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40 def validate_date_string(line_no, date_string, column, accumulated_msgs):
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41 if len(date_string) == 0:
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42 return accumulated_msgs
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43 try:
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44 datetime.datetime.strptime(date_string, '%Y-%m-%d')
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45 return accumulated_msgs
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46 except ValueError:
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47 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (%s must be YYYY-MM-DD) for column %s." % (line_no, date_string, column))
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48
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49
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50 def validate_decimal(line_no, decimal_string, column, accumulated_msgs):
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51 try:
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52 decimal.Decimal(decimal_string)
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53 return accumulated_msgs
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54 except Exception:
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55 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect decimal value (%s) for column %s." % (line_no, decimal_string, column))
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56
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57
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58 def validate_email(line_no, email, accumulated_msgs):
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59 if not (VALID_EMAIL_RE.match(email)):
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60 return add_error_msg(accumulated_msgs, "Line %d contains an invalid email address (%s). " % (line_no, email))
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61 elif len(email) > EMAIL_MAX_LEN:
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62 return add_error_msg(accumulated_msgs, "Line %d contains an email address (%) that is longer than the maximum length, %d characters." % (line_no, email))
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63 return accumulated_msgs
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64
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65
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2
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66 def validate_integer(line_no, integer_string, column, accumulated_msgs):
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67 try:
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68 integer_string.isdigit()
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69 return accumulated_msgs
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70 except Exception:
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71 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect integer value (%s) for column %s." % (line_no, integer_string, column))
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72
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73
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0
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74 accumulated_msgs = ""
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75 # Parse the input file, skipping the header, and validating
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76 # that each data line consists of 31 comma-separated items.
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77 with open(args.input, "r") as ih:
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78 for i, line in enumerate(ih):
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79 if i == 0:
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80 # Skip the header.
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81 continue
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82 # Keep 1-based line value for error messages.
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83 line_no = i + 1
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84 line = line.rstrip("\r\n")
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85 items = line.split("\t")
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86 if len(items) != 32:
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87 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 32)." % (line_no, len(items)))
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88 stop_error(accumulated_msgs)
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89 # Required and validated.
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90 # Required.
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91 user_specimen_id = items[0]
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92 if len(user_specimen_id) == 0:
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93 accumulated_msgs = empty_value(line_no, "user_specimen_id", accumulated_msgs)
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94 # Optional.
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95 field_call = items[1]
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96 # Optional.
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97 bcoral_genet_id = items[2]
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98 # Optional.
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99 bsym_genet_id = items[3]
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100 # Required.
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101 reef = items[4]
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102 if len(reef) == 0:
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103 accumulated_msgs = empty_value(line_no, "reef", accumulated_msgs)
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104 # Required.
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105 region = items[5]
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106 if len(region) == 0:
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107 accumulated_msgs = empty_value(line_no, "region", accumulated_msgs)
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108 # Required and validated.
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109 latitude = items[6]
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110 accumulated_msgs = validate_decimal(line_no, latitude, "latitude", accumulated_msgs)
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111 # Required and validated.
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112 longitude = items[7]
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113 accumulated_msgs = validate_decimal(line_no, longitude, "longitude", accumulated_msgs)
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114 # Optional.
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115 geographic_origin = items[8]
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116 # Optional.
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117 colony_location = items[9]
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118 depth = items[10]
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2
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119 # If depth has a value, then it must be integer.
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120 if len(depth) > 0:
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121 accumulated_msgs = validate_integer(line_no, depth, "depth", accumulated_msgs)
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0
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122 # Optional.
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123 disease_resist = items[11]
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124 # Optional.
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125 bleach_resist = items[12]
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126 # Optional.
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127 mortality = items[13]
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128 # Optional.
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129 tle = items[14]
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130 # Optional.
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131 spawning = string_as_boolean_string(items[15])
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132 # Required.
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133 collector_last_name = items[16]
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134 if len(collector_last_name) == 0:
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135 accumulated_msgs = empty_value(line_no, "collector_last_name", accumulated_msgs)
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136 # Required.
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137 collector_first_name = items[17]
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138 if len(collector_first_name) == 0:
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139 accumulated_msgs = empty_value(line_no, "collector_first_name", accumulated_msgs)
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140 # Required.
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141 org = items[18]
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142 if len(org) == 0:
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143 accumulated_msgs = empty_value(line_no, "org", accumulated_msgs)
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144 # Required and validated.
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145 collection_date = items[19]
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146 accumulated_msgs = validate_date_string(line_no, collection_date, "collection_date", accumulated_msgs)
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147 # Required and validated.
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148 contact_email = items[20]
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149 accumulated_msgs = validate_email(line_no, contact_email, accumulated_msgs)
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150 # Required.
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151 seq_facility = items[21]
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152 if len(seq_facility) == 0:
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153 accumulated_msgs = empty_value(line_no, "seq_facility", accumulated_msgs)
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154 # Optional.
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155 array_version = items[22]
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156 # Optional.
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157 public = string_as_boolean_string(items[23])
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158 # Optional.
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159 public_after_date = items[24]
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160 accumulated_msga = validate_date_string(line_no, public_after_date, "public_after_date", accumulated_msgs)
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161 # Required and validated.
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162 sperm_motility = items[25]
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163 accumulated_msgs = validate_decimal(line_no, sperm_motility, "sperm_motility", accumulated_msgs)
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164 # Required and validated.
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165 healing_time = items[26]
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166 accumulated_msgs = validate_decimal(line_no, healing_time, "healing_time", accumulated_msgs)
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167 # Optional.
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168 dna_extraction_method = items[27]
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169 # Optional.
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170 dna_concentration = items[28]
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171 # If dna_concentration has a value, then it must be decimal.
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172 if len(dna_concentration) > 0:
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173 accumulated_msgs = validate_decimal(line_no, dna_concentration, "dna_concentration", accumulated_msgs)
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174 # Optional.
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175 registry_id = items[29]
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176 # Optional.
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177 result_folder_name = items[30]
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178 # Optional.
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179 plate_barcode = items[31]
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180
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181
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182 if len(accumulated_msgs) > 0:
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183 stop_error(accumulated_msgs)
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184
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185 shutil.copyfile(args.input, args.output)
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