Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/sql/test/Test_TableMapAdaptator.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 #
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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 import os
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35 from commons.core.sql.TableMapAdaptator import TableMapAdaptator
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36 from commons.core.sql.DbMySql import DbMySql
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37 from commons.core.coord.Map import Map
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38 from commons.core.coord.Set import Set
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39
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40
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41 class Test_TableMapAdaptator( unittest.TestCase ):
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42
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43 def setUp( self ):
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44 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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45 self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
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46 configF = open(self._configFileName, "w" )
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47 configF.write( "[repet_env]\n" )
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48 configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
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49 configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
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50 configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
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51 configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
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52 configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
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53 configF.close()
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54 self._iDb = DbMySql( cfgFileName=self._configFileName )
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55 self._table = "dummyMapTable_%s" % ( self._uniqId )
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56 self._tMapA = TableMapAdaptator( self._iDb, self._table )
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57
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58
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59 def tearDown( self ):
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60 self._uniqId = None
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61 self._iDb.dropTable( self._table )
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62 self._iDb.close()
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63 self._table = None
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64 self._tMapA = None
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65 os.remove( self._configFileName )
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66 self._configFileName = ""
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67
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68 ##################################################################################
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69 ################## Tests for methods in ITableMapAdaptator #######################
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70 ##################################################################################
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71
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72 def test_getEndFromSeqName(self):
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73 self._iDb.createTable( self._table, "map", "" )
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74 map1 = Map()
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75 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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76 map2 = Map()
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77 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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78 for m in [ map1, map2]:
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79 self._tMapA.insert(m)
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80 expEnd = 20
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81 obsEnd = self._tMapA.getEndFromSeqName("desc2")
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82 self.assertEqual(expEnd, obsEnd)
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83
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84
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85 def test_getMapListFromSeqName( self ):
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86 self._iDb.createTable( self._table, "map", "" )
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87 map1 = Map()
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88 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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89 map2 = Map()
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90 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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91 map3 = Map()
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92 map3.setFromString( "name2\tdesc2\t1\t50\n" )
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93 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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94 lExp = [ map2, map3 ]
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95 lObs = self._tMapA.getMapListFromSeqName("name2")
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96 self.assertEqual( lObs, lExp )
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97
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98 def test_getMapListFromChr( self ):
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99 self._iDb.createTable( self._table, "map", "" )
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100 map1 = Map()
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101 map1.setFromString( "name1\tchr1\t1\t120\n" )
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102 map2 = Map()
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103 map2.setFromString( "name2\tchr2\t1\t20\n" )
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104 map3 = Map()
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105 map3.setFromString( "name2\tchr2\t1\t50\n" )
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106 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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107 lExp = [ map2, map3 ]
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108 lObs = self._tMapA.getMapListFromChr("chr2")
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109 self.assertEqual( lObs, lExp )
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110
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111 def test_getSeqNameList(self):
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112 self._iDb.createTable( self._table, "map", "" )
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113 map1 = Map()
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114 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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115 map2 = Map()
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116 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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117 map3 = Map()
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118 map3.setFromString( "name2\tdesc2\t1\t50\n" )
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119 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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120 lExp = ["desc1", "desc2"]
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121 lObs = self._tMapA.getSeqNameList()
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122 self.assertEqual( lObs, lExp )
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123
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124 def test_insert_one_element( self ):
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125 map2Insert = Map()
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126 map2Insert.name="name1"
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127 map2Insert.seqname="name2"
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128 map2Insert.start=1L
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129 map2Insert.end=50L
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130 self._iDb.createTable( self._table, "map", "" )
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131 self._tMapA.insert( map2Insert )
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132 sqlCmd = "SELECT * FROM %s" % ( self._table )
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133 self._iDb.execute( sqlCmd )
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134 expTmapTuple = (('name1', 'name2', 1L, 50L),)
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135 obsTmapTuples = self._iDb.cursor.fetchall()
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136 self.assertEquals( expTmapTuple, obsTmapTuples )
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137
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138 def test_insert_two_elements( self ):
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139 map1 = Map()
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140 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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141 map2 = Map()
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142 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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143 self._iDb.createTable( self._table, "map", "" )
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144 for m in [ map1, map2 ]: self._tMapA.insert( m )
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145 expTmapTuple = ( ('name1', 'desc1', 1L, 120L), ('name2', 'desc2', 1L, 20L) )
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146 sqlCmd = "SELECT * FROM %s" % ( self._table )
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147 self._iDb.execute( sqlCmd )
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148 obsTmapTuples = self._iDb.cursor.fetchall()
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149 self.assertEquals(expTmapTuple, obsTmapTuples )
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150
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151 def test_insertList( self ):
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152 self._iDb.createTable( self._table, "map", "" )
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153 map1 = Map()
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154 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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155 map2 = Map()
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156 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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157 lmap = [ map1, map2 ]
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158 self._tMapA.insertList( lmap )
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159 lExp = lmap
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160 lObs = self._tMapA.getListOfAllMaps()
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161 self.assertEqual( lObs, lExp )
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162
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163 def test_getSetListFromSeqName( self ):
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164 self._iDb.createTable( self._table, "map", "" )
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165 map1 = Map()
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166 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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167 map2 = Map()
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168 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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169 map3 = Map()
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170 map3.setFromString( "name2\tdesc2\t1\t50\n" )
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171 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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172 explMap = [Set( 1,"name2", "desc2", 1, 20), Set( 2,"name2", "desc2", 1, 50)]
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173 obslMap = self._tMapA.getSetListFromSeqName("name2")
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174 self.assertEqual( explMap, obslMap )
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175
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176 def test_getMapListOverlappingCoord( self ):
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177 self._iDb.createTable( self._table, "map", "" )
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178 map1 = Map()
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179 map1.setFromString( "name1\tdesc1\t70\t120\n" )
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180 map2 = Map()
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181 map2.setFromString( "name2\tdesc1\t1\t20\n" )
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182 map3 = Map()
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183 map3.setFromString( "name3\tdesc1\t1\t50\n" )
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184 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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185 explMap = [Map("name2", "desc1", 1, 20), Map("name3", "desc1", 1, 50)]
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186 obslMap = self._tMapA.getMapListOverlappingCoord("desc1", 1, 60)
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187 self.assertEqual( explMap, obslMap )
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188
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189 def test_getSetListOverlappingCoord( self ):
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190 self._iDb.createTable( self._table, "map", "" )
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191 map1 = Map()
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192 map1.setFromString( "name1\tdesc1\t70\t120\n" )
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193 map2 = Map()
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194 map2.setFromString( "name2\tdesc1\t1\t20\n" )
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195 map3 = Map()
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196 map3.setFromString( "name3\tdesc1\t1\t50\n" )
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197 for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
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198 explSet = [Set(1, "name2", "desc1", 1, 20), Set(2, "name3", "desc1", 1, 50)]
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199 obslSet = self._tMapA.getSetListOverlappingCoord("desc1", 1, 60)
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200 self.assertEqual( explSet, obslSet )
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201
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202 ##################################################################################
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203 ########################### Tests for other methods ##############################
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204 ##################################################################################
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205
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206 def test_getListOfAllMaps( self ):
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207 self._iDb.createTable( self._table, "map", "" )
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208 map1 = Map()
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209 map1.setFromString( "name1\tdesc1\t1\t120\n" )
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210 map2 = Map()
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211 map2.setFromString( "name2\tdesc2\t1\t20\n" )
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212 for m in [ map1, map2 ]: self._tMapA.insert( m )
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213 lExp = [ map1, map2 ]
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214 lObs = self._tMapA.getListOfAllMaps()
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215 self.assertEqual( lObs, lExp )
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216
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217 def test_getDictPerNameFromMapFile( self ):
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218 self._iDb.createTable( self._table, "map", "" )
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219 iMap1 = Map( "chunk1", "chromosome1", 1, 100 )
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220 iMap2 = Map( "chunk2", "chromosome1", 91, 190 )
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221 iMap3 = Map( "chunk3", "chromosome2", 1, 100 )
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222 iMap4 = Map( "chunk1", "chromosome1", 1, 100 ) # redundant with iMap1
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223 for iMap in [ iMap1, iMap2, iMap3, iMap4 ]:
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224 self._tMapA.insert( iMap )
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225 dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 }
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226 dObs = self._tMapA.getDictPerName()
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227 self.assertEquals( dExp, dObs )
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228
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229 #TODO: Check getListFromSeqName method: uses name instead of seqname
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230 # def test_getMapListFromSeqNameList( self ):
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231 # self._iDb.createTable( self._table, "map", "" )
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232 # map1 = Map()
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233 # map1.setFromString( "name1\tdesc1\t1\t120\n" )
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234 # map2 = Map()
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235 # map2.setFromString( "name2\tdesc2\t1\t20\n" )
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236 # map3 = Map()
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237 # map3.setFromString( "name3\tdesc2\t1\t10\n" )
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238 # map4 = Map()
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239 # map4.setFromString( "name4\tdesc3\t10\t200\n" )
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240 # for m in [map1, map2, map3, map4]: self._tMapA.insert( m )
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241 #
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242 # lMapToRetrieve = ["name1", "desc2"]
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243 # lExp = [map1, map2, map3]
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244 # lObs = self._tMapA.getMapListFromSeqNameList(lMapToRetrieve)
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245 # self.assertEqual( lObs, lExp )
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246
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247 test_suite = unittest.TestSuite()
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248 test_suite.addTest( unittest.makeSuite( Test_TableMapAdaptator ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249 if __name__ == "__main__":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250 unittest.TextTestRunner(verbosity=2).run( test_suite )