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

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

# Copyright INRA (Institut National de la Recherche Agronomique)
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#
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## Abstract class, Ancestor of Table*Adaptator
#
class TableAdaptator( object ):
    
    ## Constructor
    #
    # @param iDb DbMySql instance
    # @param table str table name
    #
    def __init__( self, iDb = None, table = "" ):
        self._iDb = iDb
        self._table = table
        
    ## Set connector to database
    #
    # @param iDb database instance
    #
    def setDbConnector( self, iDb ):
        self._iDb = iDb
        
    ## Set table
    #
    # @param table string table name
    #
    def setTable( self, table ):
        self._table = table
    
    ## Return the table name
    #
    def getTable( self ):
        return self._table
        
    ## Return the number of rows in the table
    #
    def getSize( self ):
        return self._iDb.getSize( self._table )
    
    ## Test if table is empty
    #    
    def isEmpty( self ):
        return self._iDb.isEmpty( self._table )
    
    ## Insert an instance of Map or Set or Match or Path or Seq instances
    #
    # @param obj a Map or Set or Match or Path or Seq instance
    # @param delayed boolean
    #
    def insert(self, obj, delayed = False):
        if obj.isEmpty():
            return
        self._escapeAntislash(obj)
        sql_cmd = self._genSqlCmdForInsert(obj, delayed)
        self._iDb.execute(sql_cmd)
    
    ## Insert a list of Map or Set or Match or Path instances
    #
    # @param l a list of object instances
    # @param delayed boolean
    #
    def insertList(self, l, delayed = False):
        for i in l:
            self.insert(i, delayed)
            
    ## Give the data contained in the table as a list of coord object instances
    #
    # @return lObject list of coord object instances
    #
    def getListOfAllCoordObject( self ):
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        lObjs = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
        return lObjs
    
    ## Generate sql command for GetListOverlappingCoord method 
    #  
    # @param obj Map, Set or Match instance
    # @param delayed boolean
    # @return sqlCmd string generated sql command
    #
    def _genSqlCmdForInsert(self, obj, delayed):
        sqlCmd = 'INSERT '
        if delayed :
            sqlCmd += ' DELAYED '
        type2Insert, attr2Insert = self._getTypeAndAttr2Insert(obj)
        sqlCmd +=  'INTO %s VALUES (' % (self._table) 
        sqlCmd +=  ",".join(type2Insert)
        sqlCmd += ")" 
        sqlCmd = sqlCmd % attr2Insert
        return sqlCmd
   
    def _getTypeAndAttr2Insert(self, obj):
        pass
    
    def _getInstanceToAdapt(self):
        pass
    
    def _escapeAntislash(self, obj):
        pass