Is it possible to have a timer functionality which will keep checking the database after every 2 minutes for status in DB and once DB shows flag as complete then end the call?
SIP setup AAEP 7.1, OD 7.1

In the config for the connection pool there is a validation query that validates connections. So unless access is completely lost to the database I would not see a need for the timer you suggest. Also you can surround the DB operation with a try/catch and exit the application.

<Resource auth="Container" dataSourceName="java:/comp/env/jdbc/conferenceCPDS" defaultMaxActive="10" defaultMaxIdle="5" defaultMaxWait="10000" factory="org.apache.tomcat.dbcp.dbcp.datasources.PerUserPoolDataSourceFactory" logAbandoned="true" name="jdbc/conference" removeAbandoned="true" removeAbandonedTimeout="300" testOnBorrow="false" type="org.apache.tomcat.dbcp.dbcp.datasources.PerUserPoolDataSource" validationQuery="select 1 from AnyTable"/>

I will rephrase the query, what I meant is :
when customer calls in and routed to AAEP based IVR call flow, in the call flow I need to keep check the state of the agent by quering the DB every 2 minutes.
If agent is free then transfer the call to agent else again after 2 minutes query the database and check the state of the agent in the DB.
So how only when state is set to available transfer the call and thus need to query every 2 minutes.
How can I do this?

You could do something like that using CCXML and a speech app and sending events between VXML and CCXML (added in OD 7.0).

The Speech (VXML) app could send an event to CCXML to start the query process and then CCXML would send an event back when the agent was available.

Using this method the customer call will remain on AAEP and keep hearing the music or the flow?
will this only be event passing or the call would be passed between the CCXML and VXML application ?
In this way ccxml will query the db and return the state of agent in db to vxml app and customer call be on application ?

This is a very advanced approach. But yes the call remains on AAEP and the Speech application run. Not in all speech applications there is a ccxml and vxml component. By default the EP provides a dfault ccxml application that handles the call and starts the configured dialog.

I am thinking for your needs you may just want to Play a prompt, then check the database and repeat (a slow poll). Much simpler.