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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 validate_date_string(line_no, date_string, accumulated_msgs):
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34 try:
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35 datetime.datetime.strptime(date_string, '%Y/%m/%d')
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36 return accumulated_msgs
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37 except ValueError:
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38 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (must be YY/MM/DD)." % line_no)
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39
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40
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41 def validate_decimal(line_no, decimal_string, accumulated_msgs):
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42 try:
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43 decimal.Decimal(decimal_string)
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44 return accumulated_msgs
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45 except Exception:
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46 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect decimal value (%s)." % (line_no, decimal_string))
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47
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48
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49 def validate_email(line_no, email, accumulated_msgs):
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50 if not (VALID_EMAIL_RE.match(email)):
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51 return add_error_msg(accumulated_msgs, "Line %d contains an invalid email address (%s). " % (line_no, email))
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52 elif len(email) > EMAIL_MAX_LEN:
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53 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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54 return accumulated_msgs
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55
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56
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57 accumulated_msgs = ""
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58 # Parse the input file, skipping the header, and validating
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59 # that each data line consists of 31 comma-separated items.
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60 with open(args.input, "r") as ih:
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1
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61 for i, line in enumerate(ih):
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0
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62 if i == 0:
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63 # Skip the header.
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64 continue
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65 line = line.rstrip("\r\n")
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66 if i > 97:
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67 accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 96 data lines.")
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68 stop_error(accumulated_msgs)
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69 items = line.split("\t")
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70 if len(items) != 31:
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71 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 31)." % (i, len(items)))
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72 stop_error()
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73 # Required.
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74 sample_id = items[0]
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75 if len(sample_id) == 0:
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76 accumulated_msgs = empty_value(i, "sample_id", accumulated_msgs)
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77 # Required and validated.
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78 date_entered_db = items[1]
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79 accumulated_msgs = validate_date_string(date_entered_db, accumulated_msgs)
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80 # Required.
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81 user_specimen_id = items[2]
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82 if len(user_specimen_id) == 0:
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83 accumulated_msgs = empty_value(i, "user_specimen_id", accumulated_msgs)
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84 # Optional.
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85 duplicate_sample = items[3]
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86 # Optional.
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87 matching_samples = items[4]
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88 # Optional.
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89 field_call = items[5]
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90 # Optional.
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91 bcoral_genet_id = items[6]
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92 # Optional.
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93 bsym_genet_id = items[7]
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94 # Required.
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95 reef = items[8]
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96 if len(reef) == 0:
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97 accumulated_msgs = empty_value(i, "reef", accumulated_msgs)
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98 # Required.
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99 region = items[9]
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100 if len(region) == 0:
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101 accumulated_msgs = empty_value(i, "region", accumulated_msgs)
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102 # Required and validated.
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103 latitude = items[10]
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104 accumulated_msgs = validate_decimal(i, latitude, accumulated_msgs)
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105 # Required and validated.
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106 longitude = items[11]
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107 accumulated_msgs = validate_decimal(i, longitude, accumulated_msgs)
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108 # Optional.
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109 geographic_origin = items[12]
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110 # Optional.
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111 sample_location = items[13]
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112 # Optional.
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113 latitude_outplant = items[14]
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114 # Optional.
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115 longitude_outplant = items[15]
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116 # Optional.
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117 depth = items[16]
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118 # Optional.
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119 dist_shore = items[17]
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120 # Optional.
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121 disease_resist = items[18]
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122 # Optional.
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123 bleach_resist = items[19]
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124 # Optional.
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125 mortality = items[20]
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126 # Optional.
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127 tle = items[21]
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128 # Optional.
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129 spawning = items[22]
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130 # Required.
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131 collector = items[23]
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132 if len(collector) == 0:
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133 accumulated_msgs = empty_value(i, "collector", accumulated_msgs)
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134 # Required.
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135 org = items[24]
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136 if len(org) == 0:
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137 accumulated_msgs = empty_value(i, "org", accumulated_msgs)
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138 # Required and validated.
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139 collection_date = items[25]
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140 accumulated_msgs = validate_date_string(date_entered_db, accumulated_msgs)
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141 # Required and validated.
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142 contact_email = items[26]
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143 accumulated_msgs = validate_email(contact_email, accumulated_msgs)
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144 # Required.
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145 seq_facility = items[27]
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146 if len(seq_facility) == 0:
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147 accumulated_msgs = empty_value(i, "seq_facility", accumulated_msgs)
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148 # Optional.
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149 array_version = items[28]
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150 # Optional.
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151 data_sharing = items[29]
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152 # Optional.
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153 data_hold = items[30]
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154
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155 if len(accumulated_msgs > 0):
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156 stop_error(accumulated_msgs)
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157
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158 shutil.copy_file(args.input, args.output)
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