miso log

miso.log

2019-10-04 14:15:13 INFO: Checking MISO storage paths...
2019-10-04 14:15:13 INFO: Directory (/storage/miso) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/log) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/temp) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/files) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/files/submission) exists.
2019-10-04 14:15:13 INFO: All storage directories OK
2019-10-04 14:15:13 INFO: Replacing default namingScheme with OicrNamingScheme
2019-10-04 14:15:13 INFO: FrameworkServlet 'miso': initialization started
2019-10-04 14:15:13 INFO: Refreshing WebApplicationContext for namespace 'miso-servlet': startup date
2019-10-04 14:15:13 INFO: Loading XML bean definitions from ServletContext resource [/WEB-INF/miso-ser
2019-10-04 14:15:13 INFO: FrameworkServlet 'miso': initialization completed in 51 ms
2019-10-04 14:15:57 INFO: Found role ROLE_ADMIN for admin
2019-10-04 14:15:57 INFO: Found role ROLE_INTERNAL for admin
2019-10-04 14:15:57 WARN: Resolved exception caused by handler execution: org.springframework.web.Http
2019-10-04 14:16:05 WARN: SQL Error: 1054, SQLState: 42S22
2019-10-04 14:16:05 ERROR: Unknown column 'this_.readLength2' in 'field list'
2019-10-04 14:16:05 ERROR: Returning error page for exception
org.springframework.dao.InvalidDataAccessResourceUsageException: could not extract ResultSet; SQL [n/a
        at org.springframework.orm.hibernate4.SessionFactoryUtils.convertHibernateAccessException(Sess
        at org.springframework.orm.hibernate4.HibernateExceptionTranslator.convertHibernateAccessExcep
        at org.springframework.orm.hibernate4.HibernateExceptionTranslator.translateExceptionIfPossibl
        at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfP
        at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:2
        at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(Persisten
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at uk.ac.bbsrc.tgac.miso.webapp.context.PrometheusInterceptor.invoke(PrometheusInterceptor.jav
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransactio
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterc
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAo
        at uk.ac.bbsrc.tgac.miso.persistence.impl.HibernateSequencingParametersDao$$EnhancerBySpringCG
        at uk.ac.bbsrc.tgac.miso.service.impl.DefaultSequencingParametersService.list(DefaultSequencin
        at uk.ac.bbsrc.tgac.miso.service.impl.DefaultSequencingParametersService$$FastClassBySpringCGL
        at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransactio
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterc
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAo
        at uk.ac.bbsrc.tgac.miso.service.impl.DefaultSequencingParametersService$$EnhancerBySpringCGLI
        at uk.ac.bbsrc.tgac.miso.webapp.controller.MenuController.rebuildConstants(MenuController.java
        at uk.ac.bbsrc.tgac.miso.webapp.controller.MenuController.constantsScript(MenuController.java:
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMeth
        at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHan
        at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeA
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHa
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleIn
        at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHand
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
        at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:635)
...
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2366)
        at org.hibernate.loader.Loader.list(Loader.java:2361)
        at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:124)
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1623)
        at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:374)
        at uk.ac.bbsrc.tgac.miso.persistence.impl.HibernateSequencingParametersDao.list(HibernateSeque
        at uk.ac.bbsrc.tgac.miso.persistence.impl.HibernateSequencingParametersDao$$FastClassBySpringC
        at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvoca
        at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(Persisten
        ... 105 more
Caused by: java.sql.SQLSyntaxErrorException: Unknown column 'this_.readLength2' in 'field list'
        at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:120)
        at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
        at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.j
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:970)
        at com.mysql.cj.jdbc.ClientPreparedStatement.executeQuery(ClientPreparedStatement.java:1020)
        at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedSta
        at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedSta
        at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:79)
        ... 123 more
2019-10-04 14:16:10 INFO: Found role ROLE_ADMIN for admin
2019-10-04 14:16:10 INFO: Found role ROLE_INTERNAL for admin
2019-10-04 14:16:10 WARN: Resolved exception caused by handler execution: org.springframework.web.HttpRequestMethodNotSupportedException: Request method 'POST' not supported