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

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


class Test_TableSetAdaptator( 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 = "dummySetTable_%s" % ( self._uniqId )
        self._tSetA = TableSetAdaptator( self._iDb, self._table )
                
    def tearDown( self ):
        self._uniqId = None
        self._iDb.dropTable( self._table )
        self._iDb.close()
        self._table = None
        self._tSetA = None
        os.remove( self._configFileName )
        self._configFileName = ""

    def test_insert(self):
        set2Insert = Set()
        set2Insert.id = 1
        set2Insert.name = "name1"
        set2Insert.seqname = "name2"
        set2Insert.start = 1L
        set2Insert.end = 50L
        self._iDb.createTable( self._table, "set", "" )
        self._tSetA.insert( set2Insert, False )
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        expTsetTuple = ((1, "name1", "name2", 1L, 50L),)
        obsTsetTuples = self._iDb.cursor.fetchall()
        self.assertEquals(expTsetTuple, obsTsetTuples )
    
    def test_insertList ( self ):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        expTsetTuple = ((1, "name1", "desc1", 1, 120), (2, "name2", "desc2", 1, 20))
        obsTsetTuples = self._iDb.cursor.fetchall()
        self.assertEqual( expTsetTuple, obsTsetTuples )

    def test_getIdList(self):
        set2Insert = Set()
        set2Insert.id = 1
        set2Insert.name = "name1"
        set2Insert.seqname = "name2"
        set2Insert.start = 1
        set2Insert.end = 50
        self._iDb.createTable( self._table, "set", "" )
        self._tSetA.insert( set2Insert )
        l = self._tSetA.getIdList()
        self.assertEquals( set2Insert.id, l[0] )
        
    def test_getSeqNameList(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "2\tname2\tdesc2\t1\t50\n" )
        for m in [ set1, set2, set3 ]: self._tSetA.insert( m )
        lExp = ["desc1", "desc2"]
        lObs = self._tSetA.getSeqNameList()
        self.assertEqual( lObs, lExp )
        
    def test_getSetListFromSeqName(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "3\tname2\tdesc2\t1\t50\n" )
        for m in [ set1, set2, set3 ]: self._tSetA.insert( m )
        explSet = [Set( 2,"name2", "desc2", 1, 20), Set( 3,"name2", "desc2", 1, 50)]
        obslSet = self._tSetA.getSetListFromSeqName("desc2")
        self.assertEqual( explSet, obslSet )

    def test_getSetListFromId(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        explSet = [Set( 2,"name2", "desc2", 1, 20)]
        obslSet = self._tSetA.getSetListFromId(2)
        self.assertEqual( explSet, obslSet )
      
    def test_getSetListFromIdList(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        explSet = [Set( 1, "name1", "desc1", 1, 120), Set( 2,"name2", "desc2", 1, 20)]
        lId = [1, 2]
        obslSet = self._tSetA.getSetListFromIdList(lId)
        self.assertEqual( explSet, obslSet )
     
    def test_getSetListFromIdList_emptyList(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        explSet = []
        lId = []
        obslSet = self._tSetA.getSetListFromIdList(lId)
        self.assertEqual( explSet, obslSet )
     
    def test_getSetListOverlappingCoord(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc2\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        explSet = [Set( 1,"name1", "desc2", 1, 120)]
        obslSet = self._tSetA.getSetListOverlappingCoord("desc2", 30, 70)
        self.assertEqual( explSet, obslSet )
      
    def test_deleteFromId(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "3\tname2\tdesc3\t1\t50\n" )
        for m in [ set1, set2, set3 ]: self._tSetA.insert( m )
        self._tSetA.deleteFromId(1)
        expTSetTuples = (( 2,"name2", "desc2", 1, 20), ( 3,"name2", "desc3", 1, 50))
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        obsTsetTuples = self._iDb.cursor.fetchall()
        
        self.assertEqual( expTSetTuples, obsTsetTuples )
  
    def test_deleteFromIdList(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "3\tname2\tdesc3\t1\t50\n" )
        for m in [ set1, set2, set3 ]: self._tSetA.insert( m )
        lId2del = [1, 2]
        self._tSetA.deleteFromIdList(lId2del)
        expTSetTuples = (( 3,"name2", "desc3", 1, 50),)
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        obsTsetTuples = self._iDb.cursor.fetchall()
        
        self.assertEqual( expTSetTuples, obsTsetTuples )
    
    def test_deleteFromIdListWithEmptyList(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" )
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "3\tname2\tdesc3\t1\t50\n" )
        for m in [ set1, set2, set3 ]: self._tSetA.insert( m )
        lId2del = []
        self._tSetA.deleteFromIdList(lId2del)
        expTSetTuples = ((1L, 'name1', 'desc1', 1L, 120L), (2L, 'name2', 'desc2', 1L, 20L), (3L, 'name2', 'desc3', 1L, 50L))
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        obsTsetTuples = self._iDb.cursor.fetchall()
        
        self.assertEqual( expTSetTuples, obsTsetTuples )
     
    def test_joinTwoSets(self):
        self._iDb.createTable( self._table, "set", "" )
        idSet1 = 5
        set1 = Set()
        set1.setFromString( "5\tname1\tdesc1\t1\t120\n" ) 
        idSet2 = 2
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )
        self._tSetA.joinTwoSets(idSet1, idSet2)
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        
        expTSetTuples = ((2L, "name1", "desc1", 1L, 120L ), (2L, "name2", "desc2", 1L, 20L ))
        obsTSetTuples = self._iDb.cursor.fetchall()
        
        self.assertEqual( expTSetTuples, obsTSetTuples)
        self._iDb.dropTable(self._table)
     
    def test_joinTwoSetsWhereId1InfId2(self):
        self._iDb.createTable( self._table, "set", "" )
        idSet1 = 2
        set1 = Set()
        set1.setFromString( "5\tname1\tdesc1\t1\t120\n" ) 
        
        idSet2 = 5
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        
        lset = [ set1, set2 ]
        self._tSetA.insertList( lset )

        self._tSetA.joinTwoSets(idSet1, idSet2)
        
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._iDb.execute( sqlCmd )
        
        expTSetTuples = ((2L, "name1", "desc1", 1L, 120L ), (2L, "name2", "desc2", 1L, 20L ))
        obsTSetTuples = self._iDb.cursor.fetchall()
        
        self.assertEqual( expTSetTuples, obsTSetTuples)
        self._iDb.dropTable(self._table)
     
    def test_getNewId(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        set1.setFromString( "1\tname1\tdesc1\t1\t120\n" ) 
        set2 = Set()
        set2.setFromString( "2\tname2\tdesc2\t1\t20\n" )
        set3 = Set()
        set3.setFromString( "5\tname1\tdesc1\t1\t120\n" ) 
        set4 = Set()
        set4.setFromString( "8\tname2\tdesc2\t1\t20\n" )
        lset = [ set1, set2, set3, set4 ]
        self._tSetA.insertList( lset )
        expId = 9
        obsId = self._tSetA.getNewId()
        self.assertEqual( expId, obsId)
        self._iDb.dropTable(self._table)
     
    def test_getNewId_set_null(self):
        self._iDb.createTable( self._table, "set", "" )
        set1 = Set()
        lset = [ set1 ]
        self._tSetA.insertList( lset )
        expId = 1
        obsId = self._tSetA.getNewId()
        self.assertEqual( expId, obsId)
        self._iDb.dropTable(self._table)  
        
    def test_getListOfAllSets( self ):
        self._iDb.createTable( self._table, "set" )
        s1 = Set()
        s1.setFromString( "1\tchr1\tTE3\t1\t10\n" )
        s2a = Set()
        s2a.setFromString( "2\tchr1\tTE2\t2\t9\n" )
        s2b = Set()
        s2b.setFromString( "2\tchr1\tTE2\t12\t19\n" )
        lSets = [ s1, s2a, s2b ]
        self._tSetA.insertList( lSets )
        expLSets = [ s1, s2a, s2b ]
        obsLSets = self._tSetA.getListOfAllSets()
        self.assertEqual( expLSets, obsLSets )
        
    def test_getListOfAllSets_empty_table( self ):
        self._iDb.createTable( self._table, "set" )
        expList = []
        obsList = self._tSetA.getListOfAllSets()
        self.assertEqual( expList, obsList )     
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_TableSetAdaptator ) )       
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )