Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/sql/test/Test_DbSQLite.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 from commons.core.sql.DbSQLite import DbSQLite
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35
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36 class Test_DbSQLite(unittest.TestCase):
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37
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38 def setUp( self ):
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39 self._iDb = DbSQLite("test.db")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 self._uniqId = "%s" % time.strftime("%Y%m%d%H%M%S")
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41
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42 def tearDown( self ):
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43 if self._iDb.open():
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44 self._iDb.close()
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45 self._iDb.delete()
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46 self._iDb = None
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47
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48 def test_open_True(self):
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49 self._iDb.close()
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50 self.assertTrue( self._iDb.open(1) )
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51
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52 def test_open_False(self):
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53 self._iDb.close()
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54 self._iDb.host = "/toto/toto.db"
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55 self.assertFalse( self._iDb.open(1) )
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56 self._iDb.host = "test.db"
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57
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58 def test_updateInfoTable(self):
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59 tableName = "dummyTable" + self._uniqId
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60 info = "Table_for_test"
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61
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62 self._iDb.updateInfoTable(tableName, info)
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63
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64 sqlCmd = 'SELECT file FROM info_tables WHERE name = "%s"' % ( tableName )
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65 self._iDb.execute( sqlCmd )
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66 results = self._iDb.fetchall()
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67 obsResult = False
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68 if (info,) in results:
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69 obsResult = True
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70 sqlCmd = 'DELETE FROM info_tables WHERE name = "%s"' % ( tableName )
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71 self._iDb.execute( sqlCmd )
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72
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73 self.assertTrue( obsResult )
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74
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75 def test_doesTableExist_True(self):
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76 tableName = "dummyTable" + self._uniqId
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77 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % ( tableName )
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78 self._iDb.execute( sqlCmd )
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79 self.assertTrue( self._iDb.doesTableExist(tableName) )
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80
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81 def test_dropTable(self):
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82 tableName = "dummyTable" + self._uniqId
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83 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % tableName
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84 self._iDb.execute( sqlCmd )
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85 sqlCmd = "CREATE TABLE info_tables ( name varchar(255), file varchar(255) )"
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86 self._iDb.execute( sqlCmd )
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87 sqlCmd = 'INSERT INTO info_tables VALUES ("%s","")' % tableName
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88 self._iDb.execute( sqlCmd )
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89
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90 self._iDb.dropTable(tableName)
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91 self.assertFalse( self._iDb.doesTableExist(tableName) )
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92
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93 def test_doesTableExist_False(self):
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94 tableName = "dummyTable" + self._uniqId
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95 self.assertFalse( self._iDb.doesTableExist(tableName) )
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96
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97 def test_createJobTable_is_table_created(self):
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98 self._iDb.createTable("dummyJobTable", "jobs")
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99 isTableCreated = self._iDb.doesTableExist("dummyJobTable")
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100 self.assertTrue(isTableCreated)
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101
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102 def test_createJobTable_field_list(self):
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103 self._iDb.createTable("dummyJobTable", "jobs")
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104 obsLFiled = self._iDb.getFieldList("dummyJobTable")
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105 expLField = ["jobid", "jobname", "groupid", "command", "launcher", "queue", "status", "time", "node"]
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106 self.assertEquals(expLField, obsLFiled)
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107
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108 def test_createTable(self):
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109 tableName = "dummyJobTable" + self._uniqId
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110 self._iDb.createTable(tableName, "job")
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111 obsLFiled = self._iDb.getFieldList(tableName)
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112 expLField = ["jobid", "jobname", "groupid", "command", "launcher", "queue", "status", "time", "node"]
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113 self.assertEquals(expLField, obsLFiled)
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114
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115 def test_createTable_with_overwrite_Job(self):
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116 tableName = "dummyJobTable" + self._uniqId
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117 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % tableName
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118 self._iDb.execute( sqlCmd )
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119 sqlCmd = "CREATE TABLE info_tables ( name varchar(255), file varchar(255) )"
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120 self._iDb.execute( sqlCmd )
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121 sqlCmd = 'INSERT INTO info_tables VALUES ("%s","")' % tableName
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122 self._iDb.execute( sqlCmd )
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123
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124 self._iDb.createTable(tableName, "job", True)
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125 obsLFiled = self._iDb.getFieldList(tableName)
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126 expLField = ["jobid", "jobname", "groupid", "command", "launcher", "queue", "status", "time", "node"]
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127 self.assertEquals(expLField, obsLFiled)
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128
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129 def test_getSize_empty_table(self):
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130 tableName = "dummyJobTable" + self._uniqId
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131 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % ( tableName )
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132 self._iDb.execute( sqlCmd )
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133 expSize = 0
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134 obsSize = self._iDb.getSize(tableName)
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135 self.assertEquals( expSize, obsSize )
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136
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137 def test_getSize_one_rows(self):
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138 tableName = "dummyJobTable" + self._uniqId
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139 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % ( tableName )
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140 self._iDb.execute( sqlCmd )
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141 sqlCmd = "INSERT INTO %s (dummyColumn) VALUES ('toto')" % tableName
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142 self._iDb.execute( sqlCmd )
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143 expSize = 1
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144 obsSize = self._iDb.getSize(tableName)
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145 self.assertEquals( expSize, obsSize )
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146
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147 def test_isEmpty_True(self):
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148 tableName = "dummyTable" + self._uniqId
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149 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % ( tableName )
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150 self._iDb.execute( sqlCmd )
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151 self.assertTrue(self._iDb.isEmpty(tableName))
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152
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153 def test_isEmpty_False(self):
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154 tableName = "dummyTable" + self._uniqId
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155 sqlCmd = "CREATE TABLE %s ( dummyColumn varchar(255) )" % (tableName)
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156 self._iDb.execute(sqlCmd)
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157 sqlCmd = "INSERT INTO %s (dummyColumn) VALUES ('toto')" % tableName
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158 self._iDb.execute(sqlCmd)
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159 self.assertFalse(self._iDb.isEmpty(tableName))
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160
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161 if __name__ == "__main__":
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162 unittest.main()