Hi all, We very recently released our web application which uses BASE as the back end. It's serving microarray data to non-microarray specialists in the insect vector community (e.g. mosquito/malaria research):
http://funcgen.vectorbase.org/ExpressionData/ In a nutshell, we have developed a simplified API which deals with just samples, hybs, experiments, arrays and reporters - and the normalised spot intensity data from one bioassayset (annotated in BASE as "final") per experiment. Then we added some on-the-fly statistics (reporter based, or gene-averaged) to the API and built a web application to serve it all. It's working really well except that I'm getting some very intermittent half-rendered pages with stacktraces in the logs like this: 15-Jul-2008 01:32:52 org.apache.catalina.core.ApplicationDispatcher invoke SEVERE: Servlet.service() for servlet jsp threw exception java.lang.IllegalArgumentException: Filter [isRemoved] currently not enabled at org.hibernate.impl.SessionImpl.getFilterParameterValue(SessionImpl.java:1049) at org.hibernate.engine.QueryParameters.processFilters(QueryParameters.java:401) at org.hibernate.loader.Loader.processFilters(Loader.java:1595) at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1517) at org.hibernate.loader.Loader.scroll(Loader.java:2292) at org.hibernate.loader.hql.QueryLoader.scroll(QueryLoader.java:441) at org.hibernate.hql.ast.QueryTranslatorImpl.scroll(QueryTranslatorImpl.java:390) at org.hibernate.engine.query.HQLQueryPlan.performScroll(HQLQueryPlan.java:245) at org.hibernate.impl.SessionImpl.scroll(SessionImpl.java:1206) at org.hibernate.impl.QueryImpl.scroll(QueryImpl.java:67) at net.sf.basedb.core.hibernate.QueryWrapper.scroll(QueryWrapper.java:116) at net.sf.basedb.core.HibernateUtil.loadIterator(HibernateUtil.java:1502) at net.sf.basedb.core.ItemQuery.iterate(ItemQuery.java:126) then one of the following: at org.vectorbase.funcgen.gesol.DB.base2.Base2AnnotationAdaptor.fetchBySample(Base2AnnotationAdaptor.java:153) at org.vectorbase.funcgen.gesol.DB.base2.Base2SampleAdaptor.fetchByHybridisation(Base2SampleAdaptor.java:119) where our fetchByHybridisation method basically does this: 116: Hybridization hyb = Hybridization.getById(dc, hybID); 117: ItemQuery<? extends MeasuredBioMaterial> sourceQ = hyb.getCreationEvent().getSources(); 118: sourceQ.include(Include.SHARED); sourceQ.setDistinct(true); 119: Iterator<? extends MeasuredBioMaterial> it = sourceQ.iterate(dc); and fetchBySample does this: 150: net.sf.basedb.core.Sample baseSample = net.sf.basedb.core.Sample.getById(dc, sample.getDBID()); 151: ItemQuery<AnnotationType> typeIq = AnnotationType.getQuery(Item.SAMPLE); 152: typeIq.include(Include.SHARED); typeIq.setDistinct(true); 153: ItemResultIterator<AnnotationType> typeIt = typeIq.iterate(dc); More rarely (due to the web pages being accessed less often), other ItemQueries cause a similar stacktrace when list() or iterate() is called. Sometimes the problem filter is "ownedByOrSharedTo" instead of "isRemoved". I've trawled our logs and don't see this error ever being caused by the BASE web interface or plugins. So it looks like our use of the BASE API is problematic somehow. It logs in as a guest user, but otherwise isn't doing anything special AFAIK. Note that the errors date back to before the public release (when I was too busy to look at them in detail). It doesn't seem to be related to a BASE or tomcat upgrade. I googled and didn't find any discussion of this phenomenon. I made sure not to use any BASE-specific search terms. You can see our BASE version info and config at http://funcgen.vectorbase.org/base2 any ideas? many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
