Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Test_TableBinSetAdaptator.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os |
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3 import time |
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4 from commons.core.sql.TableBinSetAdaptator import TableBinSetAdaptator |
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5 from commons.core.coord.Set import Set |
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6 from commons.core.sql.DbFactory import DbFactory |
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7 |
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8 class Test_TableBinSetAdaptator(unittest.TestCase): |
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9 |
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10 def setUp(self): |
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11 self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S") , os.getpid()) |
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12 self._iDb = DbFactory.createInstance() |
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13 radicalTableName = "dummySetTable" |
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14 self._tableName = "%s_%s" % (radicalTableName, self._uniqId) |
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15 self._tableName_bin = "%s_idx" % self._tableName |
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16 self._setFileName = "dummySetFile_%s" % self._uniqId |
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17 setF = open( self._setFileName, "w" ) |
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18 setF.write("1\tseq1\tchr1\t1900\t3900\n") |
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19 setF.write("2\tseq2\tchr1\t2\t9\n") |
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20 setF.write("3\tseq3\tchr1\t8\t13\n") |
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21 setF.close() |
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22 self._iDb.createTable(self._tableName, "set", self._setFileName) |
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23 self._iTableBinSetAdaptator = TableBinSetAdaptator(self._iDb, self._tableName) |
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24 |
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25 def tearDown(self): |
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26 self._iDb.dropTable( self._tableName ) |
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27 self._iDb.dropTable( self._tableName_bin ) |
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28 self._iDb.close() |
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29 if os.path.exists(self._setFileName): |
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30 os.remove(self._setFileName) |
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31 |
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32 def test_insASetInSetAndBinTable(self): |
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33 iSet = Set(1, "set1", "seq1", 2, 1) |
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34 self._iDb.createBinSetTable(self._tableName, True) |
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35 self._iTableBinSetAdaptator.insASetInSetAndBinTable(iSet) |
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36 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L), (1L, 1000.0, 'seq1', 1L, 2L, 0L)) |
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37 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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38 self._iDb.execute( sqlCmd ) |
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39 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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40 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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41 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L), (1L, 'set1', 'seq1', 2L, 1L)) |
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42 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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43 self._iDb.execute( sqlCmd ) |
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44 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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45 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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46 |
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47 def test_insASetInSetAndBinTable_delayedCase(self): |
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48 iSet = Set(1, "set1", "seq1", 2, 1) |
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49 self._iDb.createBinSetTable(self._tableName, True) |
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50 self._iTableBinSetAdaptator.insASetInSetAndBinTable(iSet, True) |
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51 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L), (1L, 1000.0, 'seq1', 1L, 2L, 0L)) |
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52 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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53 self._iDb.execute( sqlCmd ) |
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54 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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55 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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56 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L), (1L, 'set1', 'seq1', 2L, 1L)) |
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57 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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58 self._iDb.execute( sqlCmd ) |
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59 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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60 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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61 |
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62 def test_deleteFromIdFromSetAndBinTable(self): |
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63 self._iDb.createBinSetTable(self._tableName, True) |
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64 self._iTableBinSetAdaptator.deleteFromIdFromSetAndBinTable(2) |
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65 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L)) |
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66 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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67 self._iDb.execute( sqlCmd ) |
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68 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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69 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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70 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (3L, 'seq3', 'chr1', 8L, 13L)) |
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71 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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72 self._iDb.execute( sqlCmd ) |
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73 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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74 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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75 |
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76 def test_deleteFromListIdFromSetAndBinTable(self): |
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77 lSetToRemove = [1,2] |
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78 self._iDb.createBinSetTable(self._tableName, True) |
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79 self._iTableBinSetAdaptator.deleteFromListIdFromSetAndBinTable(lSetToRemove) |
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80 expTupleInBinTable = ((3L, 1000.0, 'chr1', 8L, 13L, 1L),) |
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81 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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82 self._iDb.execute( sqlCmd ) |
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83 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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84 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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85 expTupleInSetTable = ((3L, 'seq3', 'chr1', 8L, 13L),) |
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86 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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87 self._iDb.execute( sqlCmd ) |
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88 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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89 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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90 os.remove(self._setFileName) |
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91 |
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92 def test_joinTwoSetsFromSetAndBinTable(self): |
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93 id1 = 1 |
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94 id2 = 2 |
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95 self._iDb.createBinSetTable(self._tableName, True) |
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96 obsNewId = self._iTableBinSetAdaptator.joinTwoSetsFromSetAndBinTable(id1, id2) |
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97 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (1L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L)) |
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98 expNewId = 1 |
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99 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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100 self._iDb.execute( sqlCmd ) |
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101 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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102 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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103 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (1L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L)) |
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104 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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105 self._iDb.execute( sqlCmd ) |
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106 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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107 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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108 self.assertEquals(expNewId, obsNewId) |
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109 |
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110 def test_joinTwoSetsFromSetAndBinTable_with_reversed_id(self): |
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111 id1 = 2 |
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112 id2 = 1 |
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113 self._iDb.createBinSetTable(self._tableName, True) |
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114 obsNewId = self._iTableBinSetAdaptator.joinTwoSetsFromSetAndBinTable(id1, id2) |
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115 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (1L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L)) |
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116 expNewId = 1 |
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117 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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118 self._iDb.execute( sqlCmd ) |
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119 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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120 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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121 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (1L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L)) |
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122 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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123 self._iDb.execute( sqlCmd ) |
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124 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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125 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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126 self.assertEquals(expNewId, obsNewId) |
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127 |
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128 def test_getNewId(self): |
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129 self._iDb.createBinSetTable(self._tableName, True) |
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130 obsNewId = self._iTableBinSetAdaptator.getNewId() |
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131 expNewId = 4 |
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132 self.assertEquals(expNewId, obsNewId) |
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133 |
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134 def test_getNewId_empty_table(self): |
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135 self._iDb.dropTable( self._tableName ) |
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136 self._iDb.dropTable( self._tableName_bin ) |
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137 setF = open( self._setFileName, "w" ) |
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138 setF.close() |
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139 self._iDb.createTable( self._tableName, "set", self._setFileName ) |
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140 self._iDb.createBinSetTable(self._tableName, True) |
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141 obsNewId = self._iTableBinSetAdaptator.getNewId() |
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142 expNewId = 1 |
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143 self.assertEquals(expNewId, obsNewId) |
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144 |
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145 def test_getSetListFromQueryCoord(self): |
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146 start = 10 |
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147 end = 4000 |
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148 seqName = 'chr1' |
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149 self._iDb.createBinSetTable(self._tableName, True) |
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150 obsLSet = self._iTableBinSetAdaptator.getSetListFromQueryCoord(seqName, start, end) |
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151 iSet1 = Set(1, "seq1", "chr1", 1900, 3900) |
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152 iSet2 = Set(3, "seq3", "chr1", 8, 13) |
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153 expLSet = [iSet1, iSet2] |
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154 self.assertEquals(expLSet, obsLSet) |
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155 |
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156 def test_getSetListFromQueryCoord_return_empty_list(self): |
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157 start = 4000 |
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158 end = 40000 |
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159 seqName = 'chr1' |
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160 self._iDb.createBinSetTable(self._tableName, True) |
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161 obsLSet = self._iTableBinSetAdaptator.getSetListFromQueryCoord(seqName, start, end) |
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162 expLSet = [] |
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163 self.assertEquals(expLSet, obsLSet) |
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164 |
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165 def test_getSetListStrictlyIncludedInQueryCoord(self): |
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166 start = 10 |
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167 end = 4000 |
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168 seqName = 'chr1' |
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169 self._iDb.createBinSetTable(self._tableName, True) |
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170 obsLSet = self._iTableBinSetAdaptator.getSetListStrictlyIncludedInQueryCoord(seqName, start, end) |
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171 iSet1 = Set(1, "seq1", "chr1", 1900, 3900) |
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172 expLSet = [iSet1] |
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173 self.assertEquals(expLSet, obsLSet) |
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174 |
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175 def test_getSetListStrictlyIncludedInQueryCoord_return_empty_list(self): |
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176 start = 4000 |
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177 end = 40000 |
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178 seqName = 'chr1' |
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179 self._iDb.createBinSetTable(self._tableName, True) |
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180 obsLSet = self._iTableBinSetAdaptator.getSetListStrictlyIncludedInQueryCoord(seqName, start, end) |
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181 expLSet = [] |
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182 self.assertEquals(expLSet, obsLSet) |
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183 |
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184 def test_getIdList(self): |
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185 expLId = [1,2,3] |
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186 self._iDb.createBinSetTable(self._tableName, True) |
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187 obsLId = self._iTableBinSetAdaptator.getIdList() |
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188 self.assertEquals(expLId, obsLId) |
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189 |
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190 def test_getSeqNameList(self): |
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191 self._iDb.dropTable( self._tableName ) |
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192 self._iDb.dropTable( self._tableName_bin ) |
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193 setF = open( self._setFileName, "w" ) |
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194 setF.write("1\tseq1\tchr2\t1900\t3900\n") |
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195 setF.write("2\tseq2\tchr1\t2\t9\n") |
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196 setF.write("3\tseq3\tchr1\t8\t13\n") |
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197 setF.close() |
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198 self._iDb.createTable( self._tableName, "set", self._setFileName ) |
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199 self._iDb.createBinSetTable(self._tableName, True) |
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200 expLSeqName = ["chr1", "chr2"] |
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201 obsLSeqName = self._iTableBinSetAdaptator.getSeqNameList() |
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202 self.assertEquals(expLSeqName, obsLSeqName) |
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203 |
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204 def test_insertListInSetAndBinTable(self): |
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205 iSet1 = Set(1, "seq4", "chr1", 100, 390) |
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206 iSet2 = Set(2, "seq5", "chr1", 1, 13) |
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207 lSet = [iSet1, iSet2] |
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208 self._iDb.createBinSetTable(self._tableName, True) |
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209 self._iTableBinSetAdaptator.insertListInSetAndBinTable(lSet) |
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210 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L), (4L, 1000.0, 'chr1', 100L, 390L, 1L), (4L, 1000.0, 'chr1', 1L, 13L, 1L)) |
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211 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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212 self._iDb.execute( sqlCmd ) |
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213 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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214 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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215 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L), (4L, 'seq4', 'chr1', 100L, 390L), (4L, 'seq5', 'chr1', 1L, 13L)) |
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216 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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217 self._iDb.execute( sqlCmd ) |
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218 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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219 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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220 |
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221 def test_insertListInSetAndBinTableAndMergeAllSets(self): |
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222 iSet1 = Set(1, "seq4", "chr1", 100, 390) |
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223 iSet2 = Set(2, "seq5", "chr1", 1, 13) |
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224 lSet = [iSet1, iSet2] |
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225 self._iDb.createBinSetTable(self._tableName, True) |
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226 self._iTableBinSetAdaptator.insertListInSetAndBinTableAndMergeAllSets(lSet) |
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227 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (5L, 1000.0, 'chr1', 1L, 13L, 1L), (4L, 1000.0, 'chr1', 100L, 390L, 1L)) |
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228 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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229 self._iDb.execute( sqlCmd ) |
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230 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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231 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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232 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (5L, 'seq5', 'chr1', 1L, 13L), (4L, 'seq4', 'chr1', 100L, 390L) ) |
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233 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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234 self._iDb.execute( sqlCmd ) |
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235 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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236 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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237 |
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238 def test_insertListInSetAndBinTableAndRemoveOverlaps(self): |
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239 iSet1 = Set(1, "seq4", "chr1", 100, 390) |
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240 iSet2 = Set(2, "seq5", "chr1", 1, 13) |
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241 lSet = [iSet1, iSet2] |
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242 self._iDb.createBinSetTable(self._tableName, True) |
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243 self._iTableBinSetAdaptator.insertListInSetAndBinTableAndRemoveOverlaps(lSet) |
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244 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L), (4L, 1000.0, 'chr1', 100L, 390L, 1L)) |
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245 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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246 self._iDb.execute( sqlCmd ) |
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247 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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248 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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249 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L), (4L, 'seq4', 'chr1', 100L, 390L)) |
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250 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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251 self._iDb.execute( sqlCmd ) |
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252 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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253 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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254 |
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255 def test_insertListInSetAndBinTableAndRemoveOverlaps_Without_Overlaps(self): |
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256 iSet1 = Set(1, "seq4", "chr1", 100, 390) |
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257 iSet2 = Set(2, "seq5", "chr1", 50, 65) |
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258 lSet = [iSet1, iSet2] |
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259 self._iDb.createBinSetTable(self._tableName, True) |
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260 self._iTableBinSetAdaptator.insertListInSetAndBinTableAndRemoveOverlaps(lSet) |
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261 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L), (4L, 1000.0, 'chr1', 100L, 390L, 1L), (5L, 1000.0, 'chr1', 50L, 65L, 1L)) |
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262 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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263 self._iDb.execute( sqlCmd ) |
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264 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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265 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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266 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L), (4L, 'seq4', 'chr1', 100L, 390L), (5L, 'seq5', 'chr1', 50L, 65L)) |
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267 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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268 self._iDb.execute( sqlCmd ) |
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269 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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270 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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271 |
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272 def test_insertListInSetAndBinTableAndRemoveOverlaps_With_Only_Overlaps(self): |
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273 iSet1 = Set(1, "seq4", "chr1", 1, 5) |
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274 iSet2 = Set(2, "seq5", "chr1", 8, 13) |
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275 lSet = [iSet1, iSet2] |
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276 self._iDb.createBinSetTable(self._tableName, True) |
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277 self._iTableBinSetAdaptator.insertListInSetAndBinTableAndRemoveOverlaps(lSet) |
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278 expTupleInBinTable = ((1L, 10000.0, 'chr1', 1900L, 3900L, 1L), (2L, 1000.0, 'chr1', 2L, 9L, 1L), (3L, 1000.0, 'chr1', 8L, 13L, 1L)) |
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279 sqlCmd = "SELECT * FROM %s" % ( self._tableName_bin ) |
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280 self._iDb.execute( sqlCmd ) |
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281 obsTupleInBinTable = self._iDb.cursor.fetchall() |
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282 self.assertEquals(expTupleInBinTable, obsTupleInBinTable) |
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283 expTupleInSetTable = ((1L, 'seq1', 'chr1', 1900L, 3900L), (2L, 'seq2', 'chr1', 2L, 9L), (3L, 'seq3', 'chr1', 8L, 13L)) |
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284 sqlCmd = "SELECT * FROM %s" % ( self._tableName ) |
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285 self._iDb.execute( sqlCmd ) |
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286 obsTupleInSetTable = self._iDb.cursor.fetchall() |
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287 self.assertEquals(expTupleInSetTable, obsTupleInSetTable) |
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288 |
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289 if __name__ == "__main__": |
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290 unittest.main() |