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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import unittest
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33 import time
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34 import os
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35 from commons.core.sql.DbMySql import DbMySql
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36 from commons.core.coord.Match import Match
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37 from commons.core.sql.TableMatchAdaptator import TableMatchAdaptator
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38
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39
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40 class Test_TableMatchAdaptator( unittest.TestCase ):
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41
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42 def setUp( self ):
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43 self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S") , os.getpid())
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44 self._configFileName = "dummyConfigFile_%s" % self._uniqId
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45 self._iDb = DbMySql()
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46 self._table = "dummyMatchTable_%s" % self._uniqId
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47 self._tMatchA = TableMatchAdaptator( self._iDb, self._table )
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48
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49 def tearDown( self ):
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50 self._uniqId = None
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51 self._iDb.dropTable( self._table )
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52 self._iDb.close()
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53 self._table = None
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54 self._tMatchA = None
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55
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56 ##################################################################################
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57 ################## Tests for methods in ITableMatchAdaptator #####################
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58 ##################################################################################
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59 def test_insert(self):
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60 match = Match()
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61
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62 tuple = ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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63
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64 match.setFromTuple(tuple)
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65
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66 self._iDb.createTable( self._table, "match", "" )
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67 self._tMatchA.insert( match, False )
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68
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69 expTMatchTuple = (('QName1', 1L, 5L, 5L, 0.1, 0.2, 'SName1', 5L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 1L),)
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70
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71 sqlCmd = "SELECT * FROM %s" % ( self._table )
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72 self._iDb.execute( sqlCmd )
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73 obsTmatchTuple = self._iDb.cursor.fetchall()
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74
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75 self.assertEquals( expTMatchTuple, obsTmatchTuple )
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76
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77
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78 def test_insert_empty_match(self):
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79 match = Match()
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80
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81 tuple = ("", -1, -1, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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82
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83 match.setFromTuple(tuple)
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84
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85 self._iDb.createTable( self._table, "match", "" )
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86 self._tMatchA.insert( match, False )
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87
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88 expTMatchTuple = ()
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89
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90 sqlCmd = "SELECT * FROM %s" % ( self._table )
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91 self._iDb.execute( sqlCmd )
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92 obsTmatchTuple = self._iDb.cursor.fetchall()
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93
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94 self.assertEquals( expTMatchTuple, obsTmatchTuple )
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95
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96
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97 def test_insertList(self):
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98 match1 = Match()
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99 match2 = Match()
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100
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101 tuple1 = ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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102 tuple2 = ("QName2", 2, 5, 5, 0.1, 0.2, "SName2", 6, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
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103
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104 match1.setFromTuple(tuple1)
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105 match2.setFromTuple(tuple2)
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106
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107 self._iDb.createTable( self._table, "match", "" )
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108 self._tMatchA.insertList( [ match1, match2 ], False )
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109
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110 expTMatchTuple = (('QName1', 1L, 5L, 5L, 0.1, 0.2, 'SName1', 5L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 1L),\
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111 ('QName2', 2L, 5L, 5L, 0.1, 0.2, 'SName2', 6L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 2L))
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112
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113 sqlCmd = "SELECT * FROM %s" % ( self._table )
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114 self._iDb.execute( sqlCmd )
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115 obsTmatchTuple = self._iDb.cursor.fetchall()
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116
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117 self.assertEquals( expTMatchTuple, obsTmatchTuple )
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118
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119
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120 def test_getMatchListFromQuery(self):
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121 self._iDb.createTable( self._table, "match", "" )
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122 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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123 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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124 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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125 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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126 match1 = Match()
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127 match1.setFromTuple( tuple1 )
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128 match2 = Match()
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129 match2.setFromTuple( tuple2 )
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130 match3 = Match()
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131 match3.setFromTuple( tuple3 )
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132 match4 = Match()
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133 match4.setFromTuple( tuple4 )
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134 expListMatch = [ match1, match2, match3, match4 ]
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135 self._tMatchA.insertList(expListMatch)
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136
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137 obsListMatch = self._tMatchA.getMatchListFromQuery("QName")
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138
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139 self.assertEquals(expListMatch, obsListMatch)
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140
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141
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142 def test_getMatchListFromQuery_unexisted_seq_name(self):
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143 self._iDb.createTable( self._table, "match", "" )
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144 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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145 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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146 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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147 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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148 match1 = Match()
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149 match1.setFromTuple( tuple1 )
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150 match2 = Match()
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151 match2.setFromTuple( tuple2 )
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152 match3 = Match()
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153 match3.setFromTuple( tuple3 )
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154 match4 = Match()
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155 match4.setFromTuple( tuple4 )
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156 lMatch = [ match1, match2, match3, match4 ]
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157 self._tMatchA.insertList(lMatch)
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158
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159 expListMatch = []
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160 obsListMatch = self._tMatchA.getMatchListFromQuery("Dummy")
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161
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162 self.assertEquals(expListMatch, obsListMatch)
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163
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164
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165 def test_getMatchListFromId(self):
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166 self._iDb.createTable( self._table, "match", "" )
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167 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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168 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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169 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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170 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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171 match1 = Match()
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172 match1.setFromTuple( tuple1 )
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173 match2 = Match()
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174 match2.setFromTuple( tuple2 )
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175 match3 = Match()
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176 match3.setFromTuple( tuple3 )
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177 match4 = Match()
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178 match4.setFromTuple( tuple4 )
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179 lMatch = [ match1, match2, match3, match4 ]
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180 expListMatch = [ match1 ]
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181 self._tMatchA.insertList(lMatch)
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182
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183 obsListMatch = self._tMatchA.getMatchListFromId(1)
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184
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185 self.assertEquals(expListMatch, obsListMatch)
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186
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187
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188 def test_getMatchListFromIdList_empty_id_list( self ):
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189 self._iDb.createTable( self._table, "match", "" )
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190 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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191 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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192 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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193 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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194 match1 = Match()
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195 match1.setFromTuple( tuple1 )
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196 match2 = Match()
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197 match2.setFromTuple( tuple2 )
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198 match3 = Match()
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199 match3.setFromTuple( tuple3 )
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200 match4 = Match()
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201 match4.setFromTuple( tuple4 )
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202 lMatch = [ match1, match2, match3, match4 ]
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203 self._tMatchA.insertList(lMatch)
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204
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205 expList = []
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206 obsList = self._tMatchA.getMatchListFromIdList([])
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207 self.assertEquals(expList, obsList)
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208
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209
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210 def test_getMatchListFromIdList( self ):
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211 self._iDb.createTable( self._table, "match", "" )
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212 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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213 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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214 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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215 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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216 match1 = Match()
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217 match1.setFromTuple( tuple1 )
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218 match2 = Match()
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219 match2.setFromTuple( tuple2 )
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220 match3 = Match()
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221 match3.setFromTuple( tuple3 )
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222 match4 = Match()
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223 match4.setFromTuple( tuple4 )
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224 lMatch = [ match1, match2, match3, match4 ]
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225 self._tMatchA.insertList(lMatch)
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226
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227 lObs = self._tMatchA.getMatchListFromIdList((1, 2, 3))
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228
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229 lExp = [match1, match2, match3]
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230 self.assertEquals(lExp, lObs)
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231
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232 def test_getListOfAllMatches( self ):
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233 self._iDb.createTable( self._table, "match", "" )
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234 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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235 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
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236 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
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237 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
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238 match1 = Match()
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239 match1.setFromTuple( tuple1 )
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240 match2 = Match()
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241 match2.setFromTuple( tuple2 )
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242 match3 = Match()
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243 match3.setFromTuple( tuple3 )
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244 match4 = Match()
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245 match4.setFromTuple( tuple4 )
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246 lMatch = [ match1, match2, match3, match4 ]
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247 expList = [ match1, match2, match3, match4 ]
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248 self._tMatchA.insertList(lMatch)
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249
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250 obsList = self._tMatchA.getListOfAllMatches()
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251 self.assertEqual( expList, obsList )
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252
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253
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254 def test_getListOfAllMatches_empty_table( self ):
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255 self._iDb.createTable( self._table, "match", "" )
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256 expList = []
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257 obsList = self._tMatchA.getListOfAllMatches()
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258 self.assertEqual( expList, obsList )
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259
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260
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261 test_suite = unittest.TestSuite()
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262 test_suite.addTest( unittest.makeSuite( Test_TableMatchAdaptator ) )
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263 if __name__ == "__main__":
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264 unittest.TextTestRunner(verbosity=2).run( test_suite )
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