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1 __license__ = "MIT"
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2
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3 import unittest
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4 import post_fingerprinter as fp
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5
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6
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7 class SimpleUnitTest(unittest.TestCase):
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8 def setUp(self):
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9 import os
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10
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11 self.kcinput = {"rings": """ENTRY G00015 Glycan
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12 NODE 8
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13 1 Asn 20 0
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14 2 GlcNAc 12 0
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15 3 GlcNAc 3 0
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16 4 Man -5 0
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17 5 Man -12 5
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18 6 Man -12 -5
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19 7 GlcNAc -20 5
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20 8 GlcNAc -20 -5
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21 EDGE 7
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22 1 2:b1 1
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23 2 3:b1 2:4
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24 3 4:b1 3:4
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25 4 5:a1 4:6
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26 5 6:a1 4:3
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27 6 7:b1 5:2
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28 7 8:b1 6:2
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29 ///
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30 ENTRY G00016 Glycan
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31 NODE 9
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32 1 Asn 20 3
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33 2 GlcNAc 12 3
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34 3 LFuc 4 8
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35 4 GlcNAc 3 -2
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36 5 Man -5 -2
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37 6 Man -12 3
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38 7 Man -12 -7
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39 8 GlcNAc -20 3
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40 9 GlcNAc -20 -7
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41 EDGE 8
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42 1 2:b1 1
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43 2 3:a1 2:6
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44 3 4:b1 2:4
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45 4 5:b1 4:4
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46 5 6:a1 5:6
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47 6 7:a1 5:3
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48 7 8:b1 6:2
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49 8 9:b1 7:2
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50 ///
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51 ENTRY G00017 Glycan
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52 NODE 11
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53 1 Asn 24 3
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54 2 GlcNAc 14 3
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55 3 LFuc 7 8
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56 4 GlcNAc 6 -2
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57 5 Man -2 -2
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58 6 Man -8 3
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59 7 Man -8 -7
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60 8 GlcNAc -16 3
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61 9 GlcNAc -16 -7
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62 10 Gal -24 3
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63 11 Gal -24 -7
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64 EDGE 10
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65 1 2:b1 1
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66 2 3:a1 2:6
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67 3 4:b1 2:4
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68 4 5:b1 4:4
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69 5 6:a1 5:6
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70 6 7:a1 5:3
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71 7 8:b1 6:2
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72 8 9:b1 7:2
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73 9 10:b1 8:4
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74 10 11:b1 9:4
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75 ///
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76 ENTRY G00018 Glycan
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77 NODE 13
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78 1 Asn 28 3
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79 2 GlcNAc 18 3
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80 3 LFuc 10 8
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81 4 GlcNAc 9 -2
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82 5 Man 1 -2
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83 6 Man -5 4
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84 7 Man -5 -8
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85 8 GlcNAc -13 4
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86 9 GlcNAc -13 -8
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87 10 Gal -21 4
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88 11 Gal -21 -8
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89 12 Neu5Ac -29 4
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90 13 Neu5Ac -29 -8
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91 EDGE 12
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92 1 2:b1 1
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93 2 3:a1 2:6
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94 3 4:b1 2:4
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95 4 5:b1 4:4
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96 5 6:a1 5:6
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97 6 7:a1 5:3
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98 7 8:b1 6:2
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99 8 9:b1 7:2
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100 9 10:b1 8:4
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101 10 11:b1 9:4
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102 11 12:a2 10:6
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103 12 13:a2 11:6
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104 ///
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105 ENTRY G00019 Glycan
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106 NODE 9
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107 1 Asn 20 0
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108 2 GlcNAc 12 0
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109 3 GlcNAc 3 0
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110 4 Man -5 0
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111 5 Man -12 5
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112 6 Man -12 -5
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113 7 GlcNAc -15 0
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114 8 GlcNAc -20 5
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115 9 GlcNAc -20 -5
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116 EDGE 8
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117 1 2:b1 1
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118 2 3:b1 2:4
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119 3 4:b1 3:4
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120 4 5:a1 4:6
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121 5 6:a1 4:3
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122 6 7:b1 4:4
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123 7 8:b1 5:2
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124 8 9:b1 6:2
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125 ///
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126 ENTRY G00020 Glycan
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127 NODE 9
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128 1 Asn 20 3
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129 2 GlcNAc 11 3
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130 3 GlcNAc 2 3
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131 4 Man -6 3
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132 5 Man -13 9
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133 6 Man -13 -3
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134 7 GlcNAc -21 9
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135 8 GlcNAc -21 2
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136 9 GlcNAc -21 -8
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137 EDGE 8
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138 1 2:b1 1
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139 2 3:b1 2:4
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140 3 4:b1 3:4
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141 4 5:a1 4:6
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142 5 6:a1 4:3
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143 6 7:b1 5:2
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144 7 8:b1 6:4
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145 8 9:b1 6:2
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146 ///
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147 """
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148 }
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149 self.similaritymatrix = {
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150 "rings": """G00015\t 1.000000\t 0.777778\t 0.460526\t 0.304348\t 0.564516\t 0.636364\t \nG00016\t 0.777778\t 1.000000\t 0.592105\t 0.391304\t 0.486111\t 0.538462\t \nG00017\t 0.460526\t 0.592105\t 1.000000\t 0.660870\t 0.339806\t 0.378947\t \nG00018\t 0.304348\t 0.391304\t 0.660870\t 1.000000\t 0.255319\t 0.268657\t \nG00019\t 0.564516\t 0.486111\t 0.339806\t 0.255319\t 1.000000\t 0.444444\t \nG00020\t 0.636364\t 0.538462\t 0.378947\t 0.268657\t 0.444444\t 1.000000\t """
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151 }
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152 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
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153 pass
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154
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155 def tearDown(self):
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156 pass
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157
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158 def test_kcf_input(self):
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159 import StringIO
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160
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161 kchandle = StringIO.StringIO(''.join(self.kcinput["rings"]))
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162 h = fp.post_rings_fingerprinter(kchandle)
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163 # print h
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164 d = fp.extract_dendro_from_fingerprinter_output(h)
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165 # print d
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166 self.assertIn(self.similaritymatrix["rings"], h)
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167 self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", h)
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168 self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", d)
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169
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170 def test_empty_stream(self):
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171 with self.assertRaises(IOError):
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172 fp.post_rings_fingerprinter(None)
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173 with self.assertRaises(IOError):
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174 fp.post_rings_fingerprinter([])
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175 with self.assertRaises(IOError):
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176 fp.post_rings_fingerprinter("")
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177 with self.assertRaises(IOError):
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178 fp.extract_dendro_from_fingerprinter_output(None)
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179 with self.assertRaises(IOError):
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180 fp.extract_dendro_from_fingerprinter_output([])
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181 with self.assertRaises(IOError):
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182 fp.extract_dendro_from_fingerprinter_output("")
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183
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184
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185 def run_tests():
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186 unittest.main()
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187
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188
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189 if __name__ == '__main__':
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190 run_tests()
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