view commons/core/sql/test/Test_TableMapAdaptator.py @ 31:0ab839023fe4

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import unittest
import time
import os
from commons.core.sql.TableMapAdaptator import TableMapAdaptator
from commons.core.sql.DbMySql import DbMySql
from commons.core.coord.Map import Map
from commons.core.coord.Set import Set


class Test_TableMapAdaptator( unittest.TestCase ):
    
    def setUp( self ):
        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
        self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
        configF = open(self._configFileName, "w" )
        configF.write( "[repet_env]\n" )
        configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
        configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
        configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
        configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
        configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
        configF.close()
        self._iDb = DbMySql( cfgFileName=self._configFileName )
        self._table = "dummyMapTable_%s" % ( self._uniqId )
        self._tMapA = TableMapAdaptator( self._iDb, self._table )
        
        
    def tearDown( self ):
        self._uniqId = None
        self._iDb.dropTable( self._table )
        self._iDb.close()
        self._table = None
        self._tMapA = None
        os.remove( self._configFileName )
        self._configFileName = ""
        
##################################################################################
################## Tests for methods in ITableMapAdaptator #######################
##################################################################################    

    def test_getEndFromSeqName(self):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        for m in [ map1, map2]:
            self._tMapA.insert(m)
        expEnd = 20
        obsEnd = self._tMapA.getEndFromSeqName("desc2")
        self.assertEqual(expEnd, obsEnd)     
        

    def test_getMapListFromSeqName( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name2\tdesc2\t1\t50\n" )
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        lExp = [ map2, map3 ]
        lObs = self._tMapA.getMapListFromSeqName("name2")
        self.assertEqual( lObs, lExp )     

    def test_getMapListFromChr( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tchr1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tchr2\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name2\tchr2\t1\t50\n" )
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        lExp = [ map2, map3 ]
        lObs = self._tMapA.getMapListFromChr("chr2")
        self.assertEqual( lObs, lExp )

    def test_getSeqNameList(self):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name2\tdesc2\t1\t50\n" )
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        lExp = ["desc1", "desc2"]
        lObs = self._tMapA.getSeqNameList()
        self.assertEqual( lObs, lExp )
        
    def test_insert_one_element( self ):
        map2Insert = Map()
        map2Insert.name="name1"
        map2Insert.seqname="name2"
        map2Insert.start=1L
        map2Insert.end=50L
        self._iDb.createTable( self._table, "map", "" )
        self._tMapA.insert( map2Insert )
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        expTmapTuple = (('name1', 'name2', 1L, 50L),)
        obsTmapTuples = self._iDb.cursor.fetchall()
        self.assertEquals( expTmapTuple, obsTmapTuples )
        
    def test_insert_two_elements( self ):   
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        self._iDb.createTable( self._table, "map", "" )
        for m in [ map1, map2 ]: self._tMapA.insert( m )
        expTmapTuple = ( ('name1', 'desc1', 1L, 120L), ('name2', 'desc2', 1L, 20L) )
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        obsTmapTuples = self._iDb.cursor.fetchall()
        self.assertEquals(expTmapTuple, obsTmapTuples )
        
    def test_insertList( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        lmap = [ map1, map2 ]
        self._tMapA.insertList( lmap )
        lExp = lmap
        lObs = self._tMapA.getListOfAllMaps()
        self.assertEqual( lObs, lExp )
        
    def test_getSetListFromSeqName( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name2\tdesc2\t1\t50\n" )
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        explMap = [Set( 1,"name2", "desc2", 1, 20), Set( 2,"name2", "desc2", 1, 50)]
        obslMap = self._tMapA.getSetListFromSeqName("name2")
        self.assertEqual( explMap, obslMap )
        
    def test_getMapListOverlappingCoord( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t70\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc1\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name3\tdesc1\t1\t50\n" ) 
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        explMap = [Map("name2", "desc1", 1, 20), Map("name3", "desc1", 1, 50)]
        obslMap = self._tMapA.getMapListOverlappingCoord("desc1", 1, 60)
        self.assertEqual( explMap, obslMap )
        
    def test_getSetListOverlappingCoord( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t70\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc1\t1\t20\n" )
        map3 = Map()
        map3.setFromString( "name3\tdesc1\t1\t50\n" ) 
        for m in [ map1, map2, map3 ]: self._tMapA.insert( m )
        explSet = [Set(1, "name2", "desc1", 1, 20), Set(2, "name3", "desc1", 1, 50)]
        obslSet = self._tMapA.getSetListOverlappingCoord("desc1", 1, 60)
        self.assertEqual( explSet, obslSet )
        
##################################################################################
########################### Tests for other methods ##############################
##################################################################################
        
    def test_getListOfAllMaps( self ):
        self._iDb.createTable( self._table, "map", "" )
        map1 = Map()
        map1.setFromString( "name1\tdesc1\t1\t120\n" )
        map2 = Map()
        map2.setFromString( "name2\tdesc2\t1\t20\n" )
        for m in [ map1, map2 ]: self._tMapA.insert( m )
        lExp = [ map1, map2 ]
        lObs = self._tMapA.getListOfAllMaps()
        self.assertEqual( lObs, lExp )
        
    def test_getDictPerNameFromMapFile( self ):
        self._iDb.createTable( self._table, "map", "" )
        iMap1 = Map( "chunk1", "chromosome1", 1, 100 )
        iMap2 = Map( "chunk2", "chromosome1", 91, 190 )
        iMap3 = Map( "chunk3", "chromosome2", 1, 100 )
        iMap4 = Map( "chunk1", "chromosome1", 1, 100 )  # redundant with iMap1
        for iMap in [ iMap1, iMap2, iMap3, iMap4 ]:
            self._tMapA.insert( iMap )
        dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 }
        dObs = self._tMapA.getDictPerName()
        self.assertEquals( dExp, dObs )
        
#TODO: Check getListFromSeqName method: uses name instead of seqname
#    def test_getMapListFromSeqNameList( self ):
#        self._iDb.createTable( self._table, "map", "" )
#        map1 = Map()
#        map1.setFromString( "name1\tdesc1\t1\t120\n" )
#        map2 = Map()
#        map2.setFromString( "name2\tdesc2\t1\t20\n" )
#        map3 = Map()
#        map3.setFromString( "name3\tdesc2\t1\t10\n" )
#        map4 = Map()
#        map4.setFromString( "name4\tdesc3\t10\t200\n" )
#        for m in [map1, map2, map3, map4]: self._tMapA.insert( m )
#        
#        lMapToRetrieve = ["name1", "desc2"]
#        lExp = [map1, map2, map3]
#        lObs = self._tMapA.getMapListFromSeqNameList(lMapToRetrieve)
#        self.assertEqual( lObs, lExp )
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_TableMapAdaptator ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )