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Installation/Configuration of BioInvindex and DB #29

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btagger opened this issue May 10, 2011 · 6 comments
Closed

Installation/Configuration of BioInvindex and DB #29

btagger opened this issue May 10, 2011 · 6 comments

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@btagger
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btagger commented May 10, 2011

Hello,

I'm having an issue with the installation/configuration of the web application. I have followed the Installation instructions (I think correctly!)

  • I have setup MySQL and have populated the bioinvindex database with the two Harvard stem cell studies from the use cases and I have manually confirmed that they are present in the db.
  • I have configured the bioinvindex web app as per the instructions - configuring the profiles.xml and pom.xml files, making sure that the lucene index location matches in the both the profiles.xml file of the web app and the hibernate.properties file of the BII manager.

When I start the web-app (through JBOSS running on port 9600), there are no studies shown (none to browse). Upon inspecting the JBoss output, there are many Query syntax errors in the SQL (Full output at bottom.)

  • Cannot read a list of AssayTechnologies from the DB: java.lang.IllegalArgumentException: org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is not mapped [SELECT distinct t.name from AssayTechnology t where t.name is not null]

The query described in the error is not a valid query on the MySQL DB (created in the BII manager), which I guess is preventing the web application from displaying the studies. I have tried to install/configure on both my local machine and on a server and I'm getting exactly the same behaviour/error - so, at least I'm consistently missing something!

Any help would be greatly appreciated.

Many thanks,

Ben

-- Local Configuration --
Mac OSX 10.6.7
MySQL 5.5.12
MySQL connector driver - 5.1.8
JDK 1.6
JBOSS 6.0.0

---------- JBOSS Output -----------

14:18:08,115 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot read a list of Organisms from the DB: java.lang.IllegalArgumentException: org.hibernate.hql.ast.QuerySyntaxException: PropertyValue is not mapped [SELECT distinct pv.value FROM PropertyValue pv, Property p WHERE pv.type = p.id and lower(p.value) = 'organism']
at org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601) [:3.6.0.Final]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96) [:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141) [:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at uk.ac.ebi.bioinvindex.services.FiltersProvider.getOrganisms(FiltersProvider.java:123) [:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56) [:2.2.1.Final]
at org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103) [:2.2.1.Final]
at uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getOrganisms(FiltersProvider$$_javassist_seam_9.java)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at javax.el.BeanELResolver.getValue(BeanELResolver.java:302) [:1.0.0.Final]
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:175) [:1.0.0.Final]
at com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:71) [:2.0.3-]
at org.jboss.el.parser.AstPropertySuffix.getValue(AstPropertySuffix.java:53) [:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67) [:1.0_02.CR5]
at org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186) [:1.0_02.CR5]
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71) [:1.1.15.B1]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190) [:2.0.3-]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178) [:2.0.3-]
at javax.faces.component.UISelectItems.getValue(UISelectItems.java:125) [:2.0.3-]
at org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161) [:2.2.1.Final]
at com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198) [:2.0.3-]
at com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592) [:2.2.1.Final]
at org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100) [:3.3.3.Final]
at org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176) [:3.3.3.Final]
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117) [:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135) [:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309) [:2.0.3-]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83) [:2.2.1.Final]
at org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530) [:3.3.3.Final]
at org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158) [:2.2.1.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515) [:3.3.3.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275) [:6.0.0.Final]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181) [:6.0.0.Final]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) [:6.0.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285) [:1.1.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261) [:1.1.0.Final]
at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100) [:6.0.0.Final]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) [:6.0.0.Final]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) [:6.0.0.Final]
at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158) [:6.0.0.Final]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) [:6.0.0.Final]
at org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53) [:6.0.0.Final]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654) [:6.0.0.Final]
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951) [:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: PropertyValue is not mapped [SELECT distinct pv.value FROM PropertyValue pv, Property p WHERE pv.type = p.id and lower(p.value) = 'organism']
at org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181) [:3.6.0.Final]
at org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110) [:3.3.1.GA]
at org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:3.3.1.GA]
at org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80) [:3.6.0.Final]
at org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94) [:3.6.0.Final]
at org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156) [:3.3.1.GA]
at org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135) [:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650) [:3.3.1.GA]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93) [:3.6.0.Final]
... 114 more

14:18:08,170 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot read a list of EndPoints from the DB: java.lang.IllegalArgumentException: org.hibernate.hql.ast.QuerySyntaxException: Measurement is not mapped [SELECT distinct t.name from Measurement t where lower(t.name) is not null]
at org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601) [:3.6.0.Final]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96) [:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141) [:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at uk.ac.ebi.bioinvindex.services.FiltersProvider.getEndPoints(FiltersProvider.java:111) [:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56) [:2.2.1.Final]
at org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103) [:2.2.1.Final]
at uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getEndPoints(FiltersProvider$$_javassist_seam_9.java) [:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at javax.el.BeanELResolver.getValue(BeanELResolver.java:302) [:1.0.0.Final]
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:175) [:1.0.0.Final]
at com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:71) [:2.0.3-]
at org.jboss.el.parser.AstPropertySuffix.getValue(AstPropertySuffix.java:53) [:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67) [:1.0_02.CR5]
at org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186) [:1.0_02.CR5]
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71) [:1.1.15.B1]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190) [:2.0.3-]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178) [:2.0.3-]
at javax.faces.component.UISelectItems.getValue(UISelectItems.java:125) [:2.0.3-]
at org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161) [:2.2.1.Final]
at com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198) [:2.0.3-]
at com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592) [:2.2.1.Final]
at org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100) [:3.3.3.Final]
at org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176) [:3.3.3.Final]
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117) [:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135) [:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309) [:2.0.3-]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83) [:2.2.1.Final]
at org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530) [:3.3.3.Final]
at org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158) [:2.2.1.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515) [:3.3.3.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275) [:6.0.0.Final]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181) [:6.0.0.Final]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) [:6.0.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285) [:1.1.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261) [:1.1.0.Final]
at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100) [:6.0.0.Final]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) [:6.0.0.Final]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) [:6.0.0.Final]
at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158) [:6.0.0.Final]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) [:6.0.0.Final]
at org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53) [:6.0.0.Final]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654) [:6.0.0.Final]
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951) [:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: Measurement is not mapped [SELECT distinct t.name from Measurement t where lower(t.name) is not null]
at org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181) [:3.6.0.Final]
at org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110) [:3.3.1.GA]
at org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:3.3.1.GA]
at org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80) [:3.6.0.Final]
at org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94) [:3.6.0.Final]
at org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156) [:3.3.1.GA]
at org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135) [:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650) [:3.3.1.GA]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93) [:3.6.0.Final]
... 114 more

14:18:08,184 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot read a list of AssayTechnologies from the DB: java.lang.IllegalArgumentException: org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is not mapped [SELECT distinct t.name from AssayTechnology t where t.name is not null]
at org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601) [:3.6.0.Final]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96) [:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141) [:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75) [:2.2.1.Final]
at org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36) [:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at uk.ac.ebi.bioinvindex.services.FiltersProvider.getAssayTechnologies(FiltersProvider.java:87) [:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56) [:2.2.1.Final]
at org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32) [:2.2.1.Final]
at org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68) [:2.2.1.Final]
at org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185) [:2.2.1.Final]
at org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103) [:2.2.1.Final]
at uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getAssayTechnologies(FiltersProvider$$_javassist_seam_9.java) [:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [:1.6.0_24]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [:1.6.0_24]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:335) [:1.0_02.CR5]
at org.jboss.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:280) [:1.0_02.CR5]
at org.jboss.el.parser.AstMethodSuffix.getValue(AstMethodSuffix.java:59) [:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67) [:1.0_02.CR5]
at org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186) [:1.0_02.CR5]
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71) [:1.1.15.B1]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190) [:2.0.3-]
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178) [:2.0.3-]
at javax.faces.component.UISelectItems.getValue(UISelectItems.java:125) [:2.0.3-]
at org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161) [:2.2.1.Final]
at com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198) [:2.0.3-]
at com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840) [:2.0.3-]
at com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164) [:2.0.3-]
at javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592) [:2.2.1.Final]
at org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100) [:3.3.3.Final]
at org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176) [:3.3.3.Final]
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117) [:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135) [:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309) [:2.0.3-]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83) [:2.2.1.Final]
at org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530) [:3.3.3.Final]
at org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69) [:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158) [:2.2.1.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388) [:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515) [:3.3.3.Final]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274) [:6.0.0.Final]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242) [:6.0.0.Final]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275) [:6.0.0.Final]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181) [:6.0.0.Final]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) [:6.0.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285) [:1.1.0.Final]
at org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261) [:1.1.0.Final]
at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88) [:6.0.0.Final]
at org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100) [:6.0.0.Final]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) [:6.0.0.Final]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) [:6.0.0.Final]
at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158) [:6.0.0.Final]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) [:6.0.0.Final]
at org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53) [:6.0.0.Final]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877) [:6.0.0.Final]
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654) [:6.0.0.Final]
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951) [:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is not mapped [SELECT distinct t.name from AssayTechnology t where t.name is not null]
at org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181) [:3.6.0.Final]
at org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110) [:3.3.1.GA]
at org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:3.3.1.GA]
at org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281) [:3.6.0.Final]
at org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183) [:3.6.0.Final]
at org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101) [:3.6.0.Final]
at org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80) [:3.6.0.Final]
at org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94) [:3.6.0.Final]
at org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156) [:3.3.1.GA]
at org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135) [:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650) [:3.3.1.GA]
at org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93) [:3.6.0.Final]
... 113 more

14:18:08,208 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot read a list of Assay Platform from the DB
14:18:08,225 INFO [uk.ac.ebi.bioinvindex.services.browse.BrowseStudyBeanModel] Getting total assays
@eamonnmag
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Hi there,

Can you try when running on JBoss 5.0/5.1? Testing on JBoss 6.0 has been limited thus far.

Thanks,

Eamonn

@eamonnmag
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Can you copy/paste the contents. of the profiles.xml file as well with your
DB username/password removed :)

Eamonn

On 10 May 2011 14:30, btagger <
reply@reply.github.com>wrote:

Hello,

I having an issue with the installation/configuration of the web
application. I have followed the Installation instructions (I think
correctly!)

  • I have setup MySQL and have populated the bioinvindex database with the
    two Harvard stem cell studies from the use cases and I have manually
    confirmed that they are present in the db.
  • I have configured the bioinvindex web app as per the instructions -
    configuring the profiles.xml and pom.xml files, making sure that the lucene
    index location matches in the both the profiles.xml file of the web app and
    the hibernate.properties file of the BII manager.

When I start the web-app (through JBOSS running on port 9600), there are no
studies shown (none to browse). Upon inspecting the JBoss output, there are
many Query syntax errors in the SQL (Full output at bottom.)

  • e.g Cannot read a list of AssayTechnologies from the DB:
    java.lang.IllegalArgumentException:
    org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is not mapped
    [SELECT distinct t.name from AssayTechnology t where t.name is not null]

The query described in the error is not a valid query on the MySQL DB
(created in the BII manager), which I guess is preventing the web
application from displaying the studies. I have tried to install/configure
on both my local machine and on a server and I'm getting exactly the same
behaviour/error - so, at least I'm consistently missing something!

Any help would be greatly appreciated.

Many thanks,

Ben

-- Local Configuration --
Mac OSX 10.6.7
MySQL 5.5.12
MySQL connector driver - 5.1.8
JDK 1.6
JBOSS 6.0.0

---------- JBOSS Output -----------

14:18:08,115 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot
read a list of Organisms from the DB: java.lang.IllegalArgumentException:
org.hibernate.hql.ast.QuerySyntaxException: PropertyValue is not mapped
[SELECT distinct pv.value FROM PropertyValue pv, Property p WHERE pv.type =
p.id and lower(p.value) = 'organism']
at
org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601)
[:3.6.0.Final]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96)
[:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at
org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141)
[:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at
uk.ac.ebi.bioinvindex.services.FiltersProvider.getOrganisms(FiltersProvider.java:123)
[:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56)
[:2.2.1.Final]
at
org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103)
[:2.2.1.Final]
at
uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getOrganisms(FiltersProvider$$_javassist_seam_9.java)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at javax.el.BeanELResolver.getValue(BeanELResolver.java:302)
[:1.0.0.Final]
at
javax.el.CompositeELResolver.getValue(CompositeELResolver.java:175)
[:1.0.0.Final]
at
com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:71)
[:2.0.3-]
at
org.jboss.el.parser.AstPropertySuffix.getValue(AstPropertySuffix.java:53)
[:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67)
[:1.0_02.CR5]
at
org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
[:1.0_02.CR5]
at
com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
[:1.1.15.B1]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190)
[:2.0.3-]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178)
[:2.0.3-]
at
javax.faces.component.UISelectItems.getValue(UISelectItems.java:125)
[:2.0.3-]
at
org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161)
[:2.2.1.Final]
at
com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198)
[:2.0.3-]
at
com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at
com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592)
[:2.2.1.Final]
at
org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100)
[:3.3.3.Final]
at
org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176)
[:3.3.3.Final]
at
com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117)
[:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at
com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135)
[:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309)
[:2.0.3-]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83)
[:2.2.1.Final]
at
org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530)
[:3.3.3.Final]
at
org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158)
[:2.2.1.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290)
[:3.3.3.Final]
at
org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515)
[:3.3.3.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181)
[:6.0.0.Final]
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
[:6.0.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285)
[:1.1.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261)
[:1.1.0.Final]
at
org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
[:6.0.0.Final]
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53)
[:6.0.0.Final]
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654)
[:6.0.0.Final]
at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951)
[:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: PropertyValue is not
mapped [SELECT distinct pv.value FROM PropertyValue pv, Property p WHERE
pv.type = p.id and lower(p.value) = 'organism']
at
org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181)
[:3.6.0.Final]
at
org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110)
[:3.3.1.GA]
at
org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:
3.3.1.GA]
at
org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80)
[:3.6.0.Final]
at
org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94)
[:3.6.0.Final]
at
org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156)
[:3.3.1.GA]
at
org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135)
[:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650)
[:3.3.1.GA]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93)
[:3.6.0.Final]
... 114 more

14:18:08,170 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot
read a list of EndPoints from the DB: java.lang.IllegalArgumentException:
org.hibernate.hql.ast.QuerySyntaxException: Measurement is not mapped
[SELECT distinct t.name from Measurement t where lower(t.name) is not
null]
at
org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601)
[:3.6.0.Final]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96)
[:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at
org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141)
[:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at
uk.ac.ebi.bioinvindex.services.FiltersProvider.getEndPoints(FiltersProvider.java:111)
[:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56)
[:2.2.1.Final]
at
org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103)
[:2.2.1.Final]
at
uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getEndPoints(FiltersProvider$$_javassist_seam_9.java)
[:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at javax.el.BeanELResolver.getValue(BeanELResolver.java:302)
[:1.0.0.Final]
at
javax.el.CompositeELResolver.getValue(CompositeELResolver.java:175)
[:1.0.0.Final]
at
com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:71)
[:2.0.3-]
at
org.jboss.el.parser.AstPropertySuffix.getValue(AstPropertySuffix.java:53)
[:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67)
[:1.0_02.CR5]
at
org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
[:1.0_02.CR5]
at
com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
[:1.1.15.B1]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190)
[:2.0.3-]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178)
[:2.0.3-]
at
javax.faces.component.UISelectItems.getValue(UISelectItems.java:125)
[:2.0.3-]
at
org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161)
[:2.2.1.Final]
at
com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198)
[:2.0.3-]
at
com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at
com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592)
[:2.2.1.Final]
at
org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100)
[:3.3.3.Final]
at
org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176)
[:3.3.3.Final]
at
com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117)
[:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at
com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135)
[:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309)
[:2.0.3-]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83)
[:2.2.1.Final]
at
org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530)
[:3.3.3.Final]
at
org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158)
[:2.2.1.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290)
[:3.3.3.Final]
at
org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515)
[:3.3.3.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181)
[:6.0.0.Final]
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
[:6.0.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285)
[:1.1.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261)
[:1.1.0.Final]
at
org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
[:6.0.0.Final]
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53)
[:6.0.0.Final]
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654)
[:6.0.0.Final]
at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951)
[:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: Measurement is not
mapped [SELECT distinct t.name from Measurement t where lower(t.name) is
not null]
at
org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181)
[:3.6.0.Final]
at
org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110)
[:3.3.1.GA]
at
org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:
3.3.1.GA]
at
org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80)
[:3.6.0.Final]
at
org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94)
[:3.6.0.Final]
at
org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156)
[:3.3.1.GA]
at
org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135)
[:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650)
[:3.3.1.GA]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93)
[:3.6.0.Final]
... 114 more

14:18:08,184 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot
read a list of AssayTechnologies from the DB:
java.lang.IllegalArgumentException:
org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is not mapped
[SELECT distinct t.name from AssayTechnology t where t.name is not null]
at
org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:601)
[:3.6.0.Final]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:96)
[:3.6.0.Final]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy242.createQuery(Unknown Source) at
org.hibernate.search.jpa.impl.FullTextEntityManagerImpl.createQuery(FullTextEntityManagerImpl.java:141)
[:3.1.1.GA]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.handleCreateQueryWithString(EntityManagerInvocationHandler.java:75)
[:2.2.1.Final]
at
org.jboss.seam.persistence.EntityManagerInvocationHandler.invoke(EntityManagerInvocationHandler.java:36)
[:2.2.1.Final]
at $Proxy243.createQuery(Unknown Source) at
uk.ac.ebi.bioinvindex.services.FiltersProvider.getAssayTechnologies(FiltersProvider.java:87)
[:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at org.jboss.seam.util.Reflections.invoke(Reflections.java:22)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInvocationContext.proceed(RootInvocationContext.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:56)
[:2.2.1.Final]
at
org.jboss.seam.transaction.RollbackInterceptor.aroundInvoke(RollbackInterceptor.java:28)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.BijectionInterceptor.aroundInvoke(BijectionInterceptor.java:77)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.MethodContextInterceptor.aroundInvoke(MethodContextInterceptor.java:44)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.core.SynchronizationInterceptor.aroundInvoke(SynchronizationInterceptor.java:32)
[:2.2.1.Final]
at
org.jboss.seam.intercept.SeamInvocationContext.proceed(SeamInvocationContext.java:68)
[:2.2.1.Final]
at
org.jboss.seam.intercept.RootInterceptor.invoke(RootInterceptor.java:107)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.interceptInvocation(JavaBeanInterceptor.java:185)
[:2.2.1.Final]
at
org.jboss.seam.intercept.JavaBeanInterceptor.invoke(JavaBeanInterceptor.java:103)
[:2.2.1.Final]
at
uk.ac.ebi.bioinvindex.services.FiltersProvider_$$javassist_seam_9.getAssayTechnologies(FiltersProvider$$_javassist_seam_9.java)
[:]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[:1.6.0_24]
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[:1.6.0_24]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:597) [:1.6.0_24]
at
org.jboss.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:335)
[:1.0_02.CR5]
at
org.jboss.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:280)
[:1.0_02.CR5]
at
org.jboss.el.parser.AstMethodSuffix.getValue(AstMethodSuffix.java:59)
[:1.0_02.CR5]
at org.jboss.el.parser.AstValue.getValue(AstValue.java:67)
[:1.0_02.CR5]
at
org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
[:1.0_02.CR5]
at
com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
[:1.1.15.B1]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:190)
[:2.0.3-]
at
javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:178)
[:2.0.3-]
at
javax.faces.component.UISelectItems.getValue(UISelectItems.java:125)
[:2.0.3-]
at
org.jboss.seam.ui.component.UISelectItems.getValue(UISelectItems.java:161)
[:2.2.1.Final]
at
com.sun.faces.renderkit.SelectItemsIterator.initializeItems(SelectItemsIterator.java:198)
[:2.0.3-]
at
com.sun.faces.renderkit.SelectItemsIterator.hasNext(SelectItemsIterator.java:131)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderOptions(MenuRenderer.java:758)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.renderSelect(MenuRenderer.java:840)
[:2.0.3-]
at
com.sun.faces.renderkit.html_basic.MenuRenderer.encodeEnd(MenuRenderer.java:294)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:879)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1650) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at javax.faces.render.Renderer.encodeChildren(Renderer.java:164)
[:2.0.3-]
at
javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:849)
[:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1643) [:2.0.3-]
at
javax.faces.component.UIComponent.encodeAll(UIComponent.java:1646) [:2.0.3-]
at
com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592)
[:2.2.1.Final]
at
org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100)
[:3.3.3.Final]
at
org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176)
[:3.3.3.Final]
at
com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:117)
[:2.0.3-]
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:97) [:2.0.3-]
at
com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:135)
[:2.0.3-]
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:309)
[:2.0.3-]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:324)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83)
[:2.2.1.Final]
at
org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.MultipartFilter.doFilter(MultipartFilter.java:90)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:530)
[:3.3.3.Final]
at
org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:60)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at
org.jboss.seam.web.HotDeployFilter.doFilter(HotDeployFilter.java:53)
[:2.2.1.Final]
at
org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
[:2.2.1.Final]
at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158)
[:2.2.1.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290)
[:3.3.3.Final]
at
org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388)
[:3.3.3.Final]
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515)
[:3.3.3.Final]
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:274)
[:6.0.0.Final]
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:242)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:275)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:181)
[:6.0.0.Final]
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
[:6.0.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.event(CatalinaContext.java:285)
[:1.1.0.Final]
at
org.jboss.modcluster.catalina.CatalinaContext$RequestListenerValve.invoke(CatalinaContext.java:261)
[:1.1.0.Final]
at
org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:88)
[:6.0.0.Final]
at
org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:100)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
[:6.0.0.Final]
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158)
[:6.0.0.Final]
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
[:6.0.0.Final]
at
org.jboss.web.tomcat.service.request.ActiveRequestResponseCacheValve.invoke(ActiveRequestResponseCacheValve.java:53)
[:6.0.0.Final]
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:362)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:877)
[:6.0.0.Final]
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:654)
[:6.0.0.Final]
at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:951)
[:6.0.0.Final]
at java.lang.Thread.run(Thread.java:680) [:1.6.0_24]
Caused by: org.hibernate.hql.ast.QuerySyntaxException: AssayTechnology is
not mapped [SELECT distinct t.name from AssayTechnology t where t.name is
not null]
at
org.hibernate.hql.ast.util.SessionFactoryHelper.requireClassPersister(SessionFactoryHelper.java:181)
[:3.6.0.Final]
at
org.hibernate.hql.ast.tree.FromElementFactory.addFromElement(FromElementFactory.java:110)
[:3.3.1.GA]
at
org.hibernate.hql.ast.tree.FromClause.addFromElement(FromClause.java:93) [:
3.3.1.GA]
at
org.hibernate.hql.ast.HqlSqlWalker.createFromElement(HqlSqlWalker.java:277)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3056)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:2945)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:688)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:544)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:281)
[:3.6.0.Final]
at
org.hibernate.hql.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:229)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:251)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:183)
[:3.6.0.Final]
at
org.hibernate.hql.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:134)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:101)
[:3.6.0.Final]
at
org.hibernate.engine.query.HQLQueryPlan.(HQLQueryPlan.java:80)
[:3.6.0.Final]
at
org.hibernate.engine.query.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:94)
[:3.6.0.Final]
at
org.hibernate.impl.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:156)
[:3.3.1.GA]
at
org.hibernate.impl.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:135)
[:3.3.1.GA]
at org.hibernate.impl.SessionImpl.createQuery(SessionImpl.java:1650)
[:3.3.1.GA]
at
org.hibernate.ejb.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:93)
[:3.6.0.Final]
... 113 more

14:18:08,208 ERROR [uk.ac.ebi.bioinvindex.services.FiltersProvider] Cannot
read a list of Assay Platform from the DB
14:18:08,225 INFO
[uk.ac.ebi.bioinvindex.services.browse.BrowseStudyBeanModel] Getting total
assays

Reply to this email directly or view it on GitHub:
#29

Eamonn Maguire
Lead Software Engineer - ISA tools http://www.isa-tools.org

University of Oxford Tel: +44(0)1865 610788
Oxford e-Research Center
7 Keble Road, Oxford skype: maguire1986

OX1 3QG, UK

@btagger
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btagger commented May 12, 2011

Hi Eamonn,

Thanks for your reply - I will try with JBoss 5.0/5.1 and get back to you.

Below is the contents of my profiles.xml file. (From the BioInvIndex1.3/ear/ directory):
Am I right in thinking that I need only have changed the MySQL profile (as that is the DB I'm using).

Many thanks,

Ben

    <profile>
        <id>index_local</id>
        <activation>
            <activeByDefault>false</activeByDefault>
        </activation>
        <properties>
            <hibernate.search.default.indexBase>/tmp/bii/luceneindex/</hibernate.search.default.indexBase>
        </properties>
    </profile>

@eamonnmag
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You are correct. It's just the MySQL profile which needs to be edited. We were aware of some issues with JBoss 6, especially with Hibernate. It's possible that you have run into those. I hope that running on JBoss 5.1 sorts your problems out. We haven't seen this error before though.

@btagger
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btagger commented May 13, 2011

Hi Eamonn,

I have rolled-back to JBoss 5.1 and this has solved my problem.

Many thanks for your help.

Ben

@btagger btagger closed this as completed May 13, 2011
@eamonnmag
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No, thank you! :) It's good to know that this sort of error will happen on JBoss 6.0. Let me know if you need any more help.

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