| very long and strange stack trace [message #489514] |
Sun, 04 October 2009 11:31  |
 Thomas Evangelidis
Messages: 6
Registered: July 2009 |
Junior Member |
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I get a very long stack trace whenever I run a project which worked normally a month ago. I don't remember to have made any changes to the code, so it's really bizarre.
I tried to limit the use of threads in the code cause the message contains the word "threadpool" several times. There is also a class which connects to a database and downloads files. The error message also states "cannot open connection", "error in SQL query" and these kind of stuff, don't know if this is the case. 
Can anyone make a rough assumption about what's going wrong???
Any advice would be greatly appreciated!!!
2009-10-04 14:26:20,511 WARN [com.mchange.v2.resourcepool.BasicResourcePool] - <com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@3e04f69a -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception: >
com.mysql.jdbc.exceptions.MySQLNonTransientConnectionExcepti on: Server connection failure during transaction. Due to underlying exception: 'java.net.NoRouteToHostException: No route to host'.
** BEGIN NESTED EXCEPTION **
java.net.NoRouteToHostException
MESSAGE: No route to host
STACKTRACE:
java.net.NoRouteToHostException: No route to host
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.ja va:195)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
at java.net.Socket.connect(Socket.java:525)
at java.net.Socket.connect(Socket.java:475)
at java.net.Socket.<init>(Socket.java:372)
at java.net.Socket.<init>(Socket.java:215)
at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketF actory.java:173)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:268)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2894)
at com.mysql.jdbc.Connection.<init>(Connection.java:1553)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDr iver.java:285)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(Dr iverManagerDataSource.java:135)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPoole dConnection(WrapperConnectionPoolDataSource.java:182)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPoole dConnection(WrapperConnectionPoolDataSource.java:171)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledCon nectionResourcePoolManager.acquireResource(C3P0PooledConnect ionPool.java:137)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(Basi cResourcePool.java:1014)
at com.mchange.v2.resourcepool.BasicResourcePool.access$800(Bas icResourcePool.java:32)
at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.ru n(BasicResourcePool.java:1810)
at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread .run(ThreadPoolAsynchronousRunner.java:547)
** END NESTED EXCEPTION **
Attempted reconnect 3 times. Giving up.
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:888 )
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2969)
at com.mysql.jdbc.Connection.<init>(Connection.java:1553)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDr iver.java:285)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(Dr iverManagerDataSource.java:135)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPoole dConnection(WrapperConnectionPoolDataSource.java:182)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPoole dConnection(WrapperConnectionPoolDataSource.java:171)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledCon nectionResourcePoolManager.acquireResource(C3P0PooledConnect ionPool.java:137)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(Basi cResourcePool.java:1014)
at com.mchange.v2.resourcepool.BasicResourcePool.access$800(Bas icResourcePool.java:32)
at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.ru n(BasicResourcePool.java:1810)
at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread .run(ThreadPoolAsynchronousRunner.java:547)
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.setAutoCommit(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. queryEvolProfiles(ResidueUnitBuilder.java:126)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. setEvolProfiles(ResidueUnitBuilder.java:104)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. buildResidueUnits(ResidueUnitBuilder.java:52)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getResidueUnits(ProteinStructUnitBuilder.java:104)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:50)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: Connections could not be acquired from the underlying database!
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:529)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 19 more
Caused by: com.mchange.v2.resourcepool.CannotAcquireResourceException: A ResourcePool could not acquire a resource from its primary factory or source.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1319)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 22 more
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.createStatement(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.intializePdbSchema(Unk nown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. queryEvolProfiles(ResidueUnitBuilder.java:126)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. setEvolProfiles(ResidueUnitBuilder.java:104)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. buildResidueUnits(ResidueUnitBuilder.java:52)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getResidueUnits(ProteinStructUnitBuilder.java:104)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:50)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: An SQLException was provoked by the following failure: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:531)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 20 more
Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1279)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 23 more
-------------------------------- HandleHibernateException --------------------------------
java.lang.NullPointerException
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:767)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. queryEvolProfiles(ResidueUnitBuilder.java:126)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. setEvolProfiles(ResidueUnitBuilder.java:104)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. buildResidueUnits(ResidueUnitBuilder.java:52)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getResidueUnits(ProteinStructUnitBuilder.java:104)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:50)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
------------------------------------------------------------ ------------------------------
java.sql.SQLException: Error in SQL query select residue_evolution_prop.* from residue_evolution_prop inner join ligand_complex_clst_head on residue_evolution_prop.seq_id = ligand_complex_clst_head.protein_id where struct_id = '1MUC' and ligand_complex_clst_head.chain_id in ('A') null
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:797)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. queryEvolProfiles(ResidueUnitBuilder.java:126)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. setEvolProfiles(ResidueUnitBuilder.java:104)
at org.interactome.siteontology.residueunit.ResidueUnitBuilder. buildResidueUnits(ResidueUnitBuilder.java:52)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getResidueUnits(ProteinStructUnitBuilder.java:104)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:50)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.setAutoCommit(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:108)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .buildLigandSiteMotifs(LigandSiteMotifBuilder.java:48)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getLigandSiteMotifs(ProteinStructUnitBuilder.java:114)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:58)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: An SQLException was provoked by the following failure: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:531)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 19 more
Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1279)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 22 more
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.createStatement(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.intializePdbSchema(Unk nown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:108)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .buildLigandSiteMotifs(LigandSiteMotifBuilder.java:48)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getLigandSiteMotifs(ProteinStructUnitBuilder.java:114)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:58)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: An SQLException was provoked by the following failure: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:531)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 20 more
Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1279)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 23 more
-------------------------------- HandleHibernateException --------------------------------
java.lang.NullPointerException
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:767)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:108)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .buildLigandSiteMotifs(LigandSiteMotifBuilder.java:48)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getLigandSiteMotifs(ProteinStructUnitBuilder.java:114)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:58)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
------------------------------------------------------------ ------------------------------
java.sql.SQLException: Error in SQL query select distinct residue_index, ligand_chain_id from ligand_contact_residue where struct_id = '1MUC' and ligand_contact_residue.chain_id in ('A') null
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:797)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:108)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .getSiteResidueMap(LigandSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.LigandSiteMotifBuilder .buildLigandSiteMotifs(LigandSiteMotifBuilder.java:48)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getLigandSiteMotifs(ProteinStructUnitBuilder.java:114)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:58)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.setAutoCommit(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:88)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.bu ildCatSiteMotifs(CatSiteMotifBuilder.java:43)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getCatSiteMotifs(ProteinStructUnitBuilder.java:121)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:59)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: An SQLException was provoked by the following failure: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:531)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 19 more
Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1279)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 22 more
org.hibernate.exception.GenericJDBCException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.handledNonSpecific Exception(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateCo nverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExce ptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(Connectio nManager.java:144)
at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedCo nnectionProxy.java:50)
at $Proxy0.createStatement(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.intializePdbSchema(Unk nown Source)
at org.pdb.ormapping.util.HibernateUtils.checkCatalog(Unknown Source)
at org.pdb.ormapping.util.HibernateUtils.getStatelessSession(Un known Source)
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:759)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:88)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.bu ildCatSiteMotifs(CatSiteMotifBuilder.java:43)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getCatSiteMotifs(ProteinStructUnitBuilder.java:121)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:59)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
Caused by: java.sql.SQLException: An SQLException was provoked by the following failure: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106 )
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:65)
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:62)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:531)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getCon nection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnectio n(C3P0ConnectionProvider.java:56)
at org.hibernate.jdbc.ConnectionManager.openConnection(Connecti onManager.java:423)
... 20 more
Caused by: com.mchange.v2.resourcepool.ResourcePoolException: A ResourcePool cannot acquire a new resource -- the factory or source appears to be down.
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable (BasicResourcePool.java:1279)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckout Resource(BasicResourcePool.java:557)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResour ce(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPo oledConnection(C3P0PooledConnectionPool.java:525)
... 23 more
-------------------------------- HandleHibernateException --------------------------------
java.lang.NullPointerException
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:767)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:88)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.bu ildCatSiteMotifs(CatSiteMotifBuilder.java:43)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getCatSiteMotifs(ProteinStructUnitBuilder.java:121)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:59)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
------------------------------------------------------------ ------------------------------
java.sql.SQLException: Error in SQL query select ifnull(residue_translator.cif_chain_id, catalytic_residue.chain_id), ifnull(residue_translator.cif_seq_id, catalytic_residue.residue_index), catalytic_residue.site_id from catalytic_residue left join residue_translator on catalytic_residue.struct_id = residue_translator.struct_id and catalytic_residue.chain_id = residue_translator.pdb_chain_id and catalytic_residue.residue_index = residue_translator.pdb_seq_id where residue_translator.struct_id = '1MUC' null
at org.pdb.util.db.QueryLookupValues.querySql(QueryLookupValues .java:797)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:98)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.ge tSiteResidueMap(CatSiteMotifBuilder.java:88)
at org.interactome.siteontology.funcunit.CatSiteMotifBuilder.bu ildCatSiteMotifs(CatSiteMotifBuilder.java:43)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.getCatSiteMotifs(ProteinStructUnitBuilder.java:121)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:59)
at org.interactome.siteontology.funcunit.ProteinStructUnitBuild er.buildProteinStructUnit(ProteinStructUnitBuilder.java:36)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.bu ildProteinStructUnit(ProteinStructUnitIO.java:49)
at org.interactome.siteontology.funcunit.ProteinStructUnitIO.ge tProteinStructUnit(ProteinStructUnitIO.java:98)
at charge.CompareCavities.chargeCompare(CompareCavities.java:13 7)
at charge.CompareCavities.ligandChargeCompare(CompareCavities.j ava:115)
at charge.ProgressGUI.InitializeAndLauchUnparallelCalculations( ProgressGUI.java:423)
at charge.ProgressGUI.<init>(ProgressGUI.java:77)
at charge.ProgressGUI.main(ProgressGUI.java:490)
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