HTTP Status 500 – Internal Server Error


Type Exception Report

Message org.apache.ibatis.exceptions.PersistenceException:

Description The server encountered an unexpected condition that prevented it from fulfilling the request.

Exception

javax.servlet.ServletException: org.apache.ibatis.exceptions.PersistenceException: 
### Error querying database.  Cause: org.apache.ibatis.type.TypeException: Could not set parameters for mapping: ParameterMapping{property='geneId', mode=IN, javaType=class java.lang.String, jdbcType=INTEGER, numericScale=null, resultMapId='null', jdbcTypeName='null', expression='null'}. Cause: org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
### The error may exist in org/xenbase/gene/dto/gene-mapping.xml
### The error may involve org.xenbase.gene.dao.GeneDao.getXenopusChildGeneFeatures-Inline
### The error occurred while setting parameters
### SQL: SELECT f.*, fp.type_id as proptype_id, o.abbreviation organism_name     FROM feature f          JOIN feature_relationship fr ON fr.subject_id = f.feature_id          JOIN organism o ON o.organism_id = f.organism_id       LEFT JOIN featureprop fp ON fp.feature_id = f.feature_id AND fp.type_id IN (68, 69)    WHERE fr.object_id = CAST(? AS INTEGER)      AND fr.type_id = 500      AND f.type_id = 1214      AND f.organism_id IN (SELECT organism_id FROM supported_organism_current_v)    ORDER BY f.SORTABLE_NAME, organism_id
### Cause: org.apache.ibatis.type.TypeException: Could not set parameters for mapping: ParameterMapping{property='geneId', mode=IN, javaType=class java.lang.String, jdbcType=INTEGER, numericScale=null, resultMapId='null', jdbcTypeName='null', expression='null'}. Cause: org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
	org.apache.struts.action.RequestProcessor.processException(RequestProcessor.java:508)
	org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:415)
	org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:225)
	org.apache.struts.action.ActionServlet.process(ActionServlet.java:1950)
	org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:469)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:655)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	org.xenbase.utility.filters.XSSFilter.doFilter(XSSFilter.java:18)
	org.xenbase.utility.filters.UmbrellaGeneFilter.doFilter(UmbrellaGeneFilter.java:38)
	org.xenbase.utility.filters.HTTPStoHTTP.doFilter(HTTPStoHTTP.java:171)
	org.xenbase.utility.filters.RetrieveUserFilter.doFilter(RetrieveUserFilter.java:96)

Root Cause

org.apache.ibatis.exceptions.PersistenceException: 
### Error querying database.  Cause: org.apache.ibatis.type.TypeException: Could not set parameters for mapping: ParameterMapping{property='geneId', mode=IN, javaType=class java.lang.String, jdbcType=INTEGER, numericScale=null, resultMapId='null', jdbcTypeName='null', expression='null'}. Cause: org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
### The error may exist in org/xenbase/gene/dto/gene-mapping.xml
### The error may involve org.xenbase.gene.dao.GeneDao.getXenopusChildGeneFeatures-Inline
### The error occurred while setting parameters
### SQL: SELECT f.*, fp.type_id as proptype_id, o.abbreviation organism_name     FROM feature f          JOIN feature_relationship fr ON fr.subject_id = f.feature_id          JOIN organism o ON o.organism_id = f.organism_id       LEFT JOIN featureprop fp ON fp.feature_id = f.feature_id AND fp.type_id IN (68, 69)    WHERE fr.object_id = CAST(? AS INTEGER)      AND fr.type_id = 500      AND f.type_id = 1214      AND f.organism_id IN (SELECT organism_id FROM supported_organism_current_v)    ORDER BY f.SORTABLE_NAME, organism_id
### Cause: org.apache.ibatis.type.TypeException: Could not set parameters for mapping: ParameterMapping{property='geneId', mode=IN, javaType=class java.lang.String, jdbcType=INTEGER, numericScale=null, resultMapId='null', jdbcTypeName='null', expression='null'}. Cause: org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
	org.apache.ibatis.exceptions.ExceptionFactory.wrapException(ExceptionFactory.java:30)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:156)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
	org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
	org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
	org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:141)
	org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
	jdk.proxy6/jdk.proxy6.$Proxy216.getXenopusChildGeneFeatures(Unknown Source)
	org.xenbase.gene.dao.XGeneData.getXenopusChildGeneFeatures(XGeneData.java:1051)
	org.xenbase.gene.actions.GoTermAction.display(GoTermAction.java:35)
	jdk.internal.reflect.GeneratedMethodAccessor10138.invoke(Unknown Source)
	java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	java.base/java.lang.reflect.Method.invoke(Method.java:568)
	org.apache.struts.extras.actions.DispatchAction.dispatchMethod(DispatchAction.java:273)
	org.apache.struts.extras.actions.DispatchAction.execute(DispatchAction.java:173)
	org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:413)
	org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:225)
	org.apache.struts.action.ActionServlet.process(ActionServlet.java:1950)
	org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:469)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:655)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	org.xenbase.utility.filters.XSSFilter.doFilter(XSSFilter.java:18)
	org.xenbase.utility.filters.UmbrellaGeneFilter.doFilter(UmbrellaGeneFilter.java:38)
	org.xenbase.utility.filters.HTTPStoHTTP.doFilter(HTTPStoHTTP.java:171)
	org.xenbase.utility.filters.RetrieveUserFilter.doFilter(RetrieveUserFilter.java:96)

Root Cause

org.apache.ibatis.type.TypeException: Could not set parameters for mapping: ParameterMapping{property='geneId', mode=IN, javaType=class java.lang.String, jdbcType=INTEGER, numericScale=null, resultMapId='null', jdbcTypeName='null', expression='null'}. Cause: org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
	org.apache.ibatis.scripting.defaults.DefaultParameterHandler.setParameters(DefaultParameterHandler.java:92)
	org.apache.ibatis.executor.statement.PreparedStatementHandler.parameterize(PreparedStatementHandler.java:97)
	org.apache.ibatis.executor.statement.RoutingStatementHandler.parameterize(RoutingStatementHandler.java:65)
	org.apache.ibatis.executor.SimpleExecutor.prepareStatement(SimpleExecutor.java:91)
	org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:64)
	org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:336)
	org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:158)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:110)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:90)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:154)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
	org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
	org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
	org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:141)
	org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
	jdk.proxy6/jdk.proxy6.$Proxy216.getXenopusChildGeneFeatures(Unknown Source)
	org.xenbase.gene.dao.XGeneData.getXenopusChildGeneFeatures(XGeneData.java:1051)
	org.xenbase.gene.actions.GoTermAction.display(GoTermAction.java:35)
	jdk.internal.reflect.GeneratedMethodAccessor10138.invoke(Unknown Source)
	java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	java.base/java.lang.reflect.Method.invoke(Method.java:568)
	org.apache.struts.extras.actions.DispatchAction.dispatchMethod(DispatchAction.java:273)
	org.apache.struts.extras.actions.DispatchAction.execute(DispatchAction.java:173)
	org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:413)
	org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:225)
	org.apache.struts.action.ActionServlet.process(ActionServlet.java:1950)
	org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:469)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:655)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	org.xenbase.utility.filters.XSSFilter.doFilter(XSSFilter.java:18)
	org.xenbase.utility.filters.UmbrellaGeneFilter.doFilter(UmbrellaGeneFilter.java:38)
	org.xenbase.utility.filters.HTTPStoHTTP.doFilter(HTTPStoHTTP.java:171)
	org.xenbase.utility.filters.RetrieveUserFilter.doFilter(RetrieveUserFilter.java:96)

Root Cause

org.apache.ibatis.type.TypeException: Error setting non null for parameter #1 with JdbcType INTEGER . Try setting a different JdbcType for this parameter or a different configuration property. Cause: com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
	org.apache.ibatis.type.BaseTypeHandler.setParameter(BaseTypeHandler.java:76)
	org.apache.ibatis.scripting.defaults.DefaultParameterHandler.setParameters(DefaultParameterHandler.java:90)
	org.apache.ibatis.executor.statement.PreparedStatementHandler.parameterize(PreparedStatementHandler.java:97)
	org.apache.ibatis.executor.statement.RoutingStatementHandler.parameterize(RoutingStatementHandler.java:65)
	org.apache.ibatis.executor.SimpleExecutor.prepareStatement(SimpleExecutor.java:91)
	org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:64)
	org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:336)
	org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:158)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:110)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:90)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:154)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
	org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
	org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
	org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:141)
	org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
	jdk.proxy6/jdk.proxy6.$Proxy216.getXenopusChildGeneFeatures(Unknown Source)
	org.xenbase.gene.dao.XGeneData.getXenopusChildGeneFeatures(XGeneData.java:1051)
	org.xenbase.gene.actions.GoTermAction.display(GoTermAction.java:35)
	jdk.internal.reflect.GeneratedMethodAccessor10138.invoke(Unknown Source)
	java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	java.base/java.lang.reflect.Method.invoke(Method.java:568)
	org.apache.struts.extras.actions.DispatchAction.dispatchMethod(DispatchAction.java:273)
	org.apache.struts.extras.actions.DispatchAction.execute(DispatchAction.java:173)
	org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:413)
	org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:225)
	org.apache.struts.action.ActionServlet.process(ActionServlet.java:1950)
	org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:469)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:655)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	org.xenbase.utility.filters.XSSFilter.doFilter(XSSFilter.java:18)
	org.xenbase.utility.filters.UmbrellaGeneFilter.doFilter(UmbrellaGeneFilter.java:38)
	org.xenbase.utility.filters.HTTPStoHTTP.doFilter(HTTPStoHTTP.java:171)
	org.xenbase.utility.filters.RetrieveUserFilter.doFilter(RetrieveUserFilter.java:96)

Root Cause

com.ibm.db2.jcc.am.SqlSyntaxErrorException: [jcc][1091][10404][4.25.13] Invalid data conversion: Parameter instance {%=geneId%} is invalid for the requested conversion. ERRORCODE=-4461, SQLSTATE=42815
	com.ibm.db2.jcc.am.b6.a(b6.java:810)
	com.ibm.db2.jcc.am.b6.a(b6.java:66)
	com.ibm.db2.jcc.am.b6.a(b6.java:116)
	com.ibm.db2.jcc.am.bg.a(bg.java:787)
	com.ibm.db2.jcc.am.bg.a(bg.java:693)
	com.ibm.db2.jcc.am.k4.a(k4.java:1687)
	com.ibm.db2.jcc.am.k4.setString(k4.java:1636)
	org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.setString(DelegatingPreparedStatement.java:615)
	org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.setString(DelegatingPreparedStatement.java:615)
	org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.setString(DelegatingPreparedStatement.java:615)
	org.apache.ibatis.type.StringTypeHandler.setNonNullParameter(StringTypeHandler.java:31)
	org.apache.ibatis.type.StringTypeHandler.setNonNullParameter(StringTypeHandler.java:26)
	org.apache.ibatis.type.BaseTypeHandler.setParameter(BaseTypeHandler.java:74)
	org.apache.ibatis.scripting.defaults.DefaultParameterHandler.setParameters(DefaultParameterHandler.java:90)
	org.apache.ibatis.executor.statement.PreparedStatementHandler.parameterize(PreparedStatementHandler.java:97)
	org.apache.ibatis.executor.statement.RoutingStatementHandler.parameterize(RoutingStatementHandler.java:65)
	org.apache.ibatis.executor.SimpleExecutor.prepareStatement(SimpleExecutor.java:91)
	org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:64)
	org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:336)
	org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:158)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:110)
	org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:90)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:154)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
	org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
	org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
	org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
	org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:141)
	org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
	jdk.proxy6/jdk.proxy6.$Proxy216.getXenopusChildGeneFeatures(Unknown Source)
	org.xenbase.gene.dao.XGeneData.getXenopusChildGeneFeatures(XGeneData.java:1051)
	org.xenbase.gene.actions.GoTermAction.display(GoTermAction.java:35)
	jdk.internal.reflect.GeneratedMethodAccessor10138.invoke(Unknown Source)
	java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	java.base/java.lang.reflect.Method.invoke(Method.java:568)
	org.apache.struts.extras.actions.DispatchAction.dispatchMethod(DispatchAction.java:273)
	org.apache.struts.extras.actions.DispatchAction.execute(DispatchAction.java:173)
	org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:413)
	org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:225)
	org.apache.struts.action.ActionServlet.process(ActionServlet.java:1950)
	org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:469)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:655)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	org.xenbase.utility.filters.XSSFilter.doFilter(XSSFilter.java:18)
	org.xenbase.utility.filters.UmbrellaGeneFilter.doFilter(UmbrellaGeneFilter.java:38)
	org.xenbase.utility.filters.HTTPStoHTTP.doFilter(HTTPStoHTTP.java:171)
	org.xenbase.utility.filters.RetrieveUserFilter.doFilter(RetrieveUserFilter.java:96)

Note The full stack trace of the root cause is available in the server logs.


Apache Tomcat/9.0.58 (Ubuntu)