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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 findKEGG as fk
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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 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
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12 pass
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13
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14 def tearDown(self):
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15 pass
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16
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17 def test_no_db_specified(self):
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18 """should raise error"""
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19 with self.assertRaises(IOError):
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20 m = fk.find_entries_in_KEGG([], " ")
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21 with self.assertRaises(IOError):
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22 m = fk.find_entries_in_KEGG("", " ")
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23 with self.assertRaises(IOError):
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24 m = fk.find_entries_in_KEGG(None, " ")
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25
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26 def test_no_query_specified(self):
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27 """should raise error"""
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28 with self.assertRaises(IOError):
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29 m = fk.find_entries_in_KEGG("glycan", "")
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30 with self.assertRaises(IOError):
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31 m = fk.find_entries_in_KEGG("glycan", [])
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32 with self.assertRaises(IOError):
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33 m = fk.find_entries_in_KEGG("glycan", None)
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34
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35
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36 def test_bad_db(self):
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37 """should raise error"""
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38 import urllib2
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39
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40 with self.assertRaises(urllib2.HTTPError):
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41 m = fk.find_entries_in_KEGG("john", "glucose")
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42
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43 def test_unfindable_entry(self):
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44 """should return an empty string"""
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45 m = fk.find_entries_in_KEGG("glycan", "sally")
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46 emptystring=""
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47 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
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48
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49 def test_find_example(self):
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50 m = fk.find_entries_in_KEGG("glycan", "glucose")
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51 self.assertIsNotNone(m)
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52 self.assertIn("GDP-glucose", m)
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53
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54 def test_query_has_newlines(self):
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55 """
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1
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56 Assume a new line query is an AND query.
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57 """
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58 m = fk.find_entries_in_KEGG("glycan", "glucose\nUDP")
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59 self.assertIsNotNone(m)
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60 print m
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61 self.assertIn("UDP-D-glucose", m)
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62
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63 def test_query_has_newlines_and_a_space(self):
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64 """
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65 glucose\\n UDP. OR's should pass
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66 """
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67 m = fk.find_entries_in_KEGG("glycan", "glucose\n UDP")
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68 self.assertIsNotNone(m)
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69 self.assertIn("UDP-D-glucose", m)
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70
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1
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71 def test_gene_specific_or(self):
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72 """
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73 test "shiga toxin" returns.
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74 /find/genes/"shiga toxin" for keywords "shiga toxin"
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75 """
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76 m = fk.find_entries_in_KEGG("genes","shiga toxin")
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77 self.assertIsNotNone(m)
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78 #. not matching to all entries - that is silly, the db get updated!
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79 self.assertIn("shiga", m)
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80 self.assertIn("toxin", m)
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81 self.assertNotIn("stm:STM0284",m) # should not be found in the OR query
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82
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83 def test_gene_specific_and(self):
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84 """
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85 test "shiga+toxin" returns. it should
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86 /find/genes/shiga+toxin for keywords "shiga" and "toxin"
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87 """
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88 m = fk.find_entries_in_KEGG("genes","shiga+toxin")
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89 self.assertIsNotNone(m)
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90 #. not matching to all entries - that is silly, the db get updated!
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91 self.assertIn("shiga", m)
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92 self.assertIn("toxin", m)
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93 self.assertIn("stm:STM0284",m) # should be found in the AND query
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94
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95 def test_enzyme_specific_1(self):
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96 """
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97 test 2.4.99.1 returns
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98 """
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99 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1")
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100 self.assertIsNotNone(m)
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101 #. not matching to all entries - that is silly, the db get updated!
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102 self.assertIn("2.4.99.1", m)
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103
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104 def test_enzyme_specific_2(self):
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105 """
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106 test 2.4.99.6 returns
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107 """
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108 m = fk.find_entries_in_KEGG("enzyme","2.4.99.6")
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109 self.assertIsNotNone(m)
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110 #. not matching to all entries - that is silly, the db get updated!
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111 self.assertIn("2.4.99.6", m)
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112
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113 def test_enzyme_specific_3(self):
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114 """
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115 test ec: 2.4.99.6 with space (tests stripping space functionality)
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116 """
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117 m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.6")
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118 self.assertIsNotNone(m)
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119 #. not matching to all entries - that is silly, the db get updated!
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120 self.assertIn("2.4.99.6", m)
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121
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122 def test_enzyme_specific_4(self):
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123 """
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124 test ec: 2.4.99. , should return 2.4.99.*
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125 """
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126 m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.")
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127 self.assertIsNotNone(m)
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128 #. not matching to all entries - that is silly, the db get updated!
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129 self.assertIn("2.4.99.1", m)
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130 self.assertIn("2.4.99.6", m)
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131 self.assertIn("2.4.99.11", m)
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132
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133 def test_enzyme_specific_5(self):
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134 """
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135 test ec: 2.4.99.1+2.4.99.6 . AND function, so returns nothing here. Do not expect an enzyme to be doubly classified.
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136 """
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137 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1+2.4.99.6")
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138 self.assertIsNotNone(m)
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139 emptystring=""
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140 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
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141
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142 def test_enzyme_specific_6(self):
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143 """
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144 test ec: 2.4.99.1 2.4.99.6 . OR function, should return something but does not (KEGG FAILURE?).
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145 note that trying this without "" will return the AND function result which is incorrect.
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146 """
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147 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1 2.4.99.6")
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148 self.assertIsNotNone(m)
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149 #self.assertIn("2.4.99.1", m)
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150 emptystring=""
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151 print m
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152 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
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153
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154
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155 def test_enzyme_specific_7(self):
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156 """
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157 test deoxy+1.1.1. . AND function, that should return something
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158 """
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159 m = fk.find_entries_in_KEGG("enzyme","deoxy+1.1.1")
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160 self.assertIsNotNone(m)
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161 print m
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162 self.assertIn("deoxy", m)
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163 self.assertIn("1.1.1", m)
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164
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165 def test_enzyme_specific_8(self):
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166 """
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167 test deoxy 1.1.1. . OR function. should return deoxy or 1.1.1. but does not (KEGG FAILURE?). i
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168 note that trying this without "" will return the AND function result which is incorrect.
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169 """
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170 m = fk.find_entries_in_KEGG("enzyme","deoxy 1.1.1")
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171 self.assertIsNotNone(m)
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172 emptystring=""
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173 print m
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174 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
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175
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