Update to Hibernate 3.3.2

[Nicklas Nordborg]

This update includes the following fix: ​http://opensource.atlassian.com/projects/hibernate/browse/HHH-3528

This issue has prevented us from using proxies with batchable classes. Because of this we have also been forced to FETCH JOIN data that we are not interested in since otherwise the lack of proxies would generate lots of SELECTs for the linked items. There is a short note about this in the documentation ​http://base.thep.lu.se/chrome/site/latest/html/developerdoc/core_ref/core_ref.rules.datalayer.html#core_ref.rules.datalayer.proxies

I am not sure of all places in the code that may benefit from this. One example is in the RawBioAssay.validateFeatures() method. I guess there are a more places in the code, most likely in code that handles raw data, array design features and reporters.

[Nicklas Nordborg]

(In [5025]) References #1350: Update to Hibernate 3.3.2

The new JAR files are in place and seems to work. No queries has been changed yet.

[Nicklas Nordborg]

(In [5026]) References #1350: Update to Hibernate 3.3.2

• Made ArrayDesignBlockData, FeatureData, ReporterData and RawData lazy="true".
• Changed queries to only join information that we need.
• Added test that changes the array design for a raw bioassay

[Nicklas Nordborg]

(In [5027]) Fixes #1350: Update to Hibernate 3.3.2

Updated documentation.

[Nicklas Nordborg]

Discovered a bug in Hibernate that can cause really bad problems in BASE. It is simple to re-create:

1. Log in to BASE
2. Create a new project
3. Select BASE -> Reload permissions from the menu

After that almost every page access results in a very long strack trace with the following root cause near the end of the list:

java.sql.SQLException: Parameter index out of bounds. 11 is not between valid values of 1 and 10
	com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
	com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
	com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
	com.mysql.jdbc.ServerPreparedStatement.getBinding(ServerPreparedStatement.java:930)
	com.mysql.jdbc.ServerPreparedStatement.setInt(ServerPreparedStatement.java:1996)
	com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.setInt(NewProxyPreparedStatement.java:677)
	org.hibernate.type.IntegerType.set(IntegerType.java:64)
	org.hibernate.type.NullableType.nullSafeSet(NullableType.java:154)
	org.hibernate.type.NullableType.nullSafeSet(NullableType.java:136)
	org.hibernate.param.DynamicFilterParameterSpecification.bind(DynamicFilterParameterSpecification.java:78)
	org.hibernate.loader.hql.QueryLoader.bindParameterValues(QueryLoader.java:514)
	org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1593)
	org.hibernate.loader.Loader.doQuery(Loader.java:696)
	org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:259)
	org.hibernate.loader.Loader.doList(Loader.java:2232)
	org.hibernate.loader.Loader.listUsingQueryCache(Loader.java:2161)
	org.hibernate.loader.Loader.list(Loader.java:2121)
	org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:401)
	org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
	org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
	org.hibernate.impl.SessionImpl.list(SessionImpl.java:1149)
	org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
	net.sf.basedb.core.hibernate.QueryWrapper.list(QueryWrapper.java:102)
	net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1574)
	net.sf.basedb.core.ItemQuery.list(ItemQuery.java:92)
	org.apache.jsp.include.menu_jsp._jspService(menu_jsp.java:1271)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:968)
	org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:621)
	net.sf.basedb.clients.web.taglib.Body.doStartTag(Body.java:279)
	org.apache.jsp.my_005fbase.projects.list_005fprojects_jsp._jspService(list_005fprojects_jsp.java:427)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:70)

The only workarounds seems to be to re-start Tomcat.

Similar problems can also appear when doing other things such as changing the active project or modifying the permissions on an item.

The problem is believed to be a bug in Hibernate 3.3.2 and has been reported to the Hibernate developers: ​http://opensource.atlassian.com/projects/hibernate/browse/HHH-4065

[Nicklas Nordborg]

(In [5037]) References #1350: Update to Hibernate 3.3.2

Added a very ugly hack that effectively disables the query plan cache in Hibernate. This forces all queries to be rebuilt from scratch at all times and ensures that the proper number of parameter placeholders are added to the final SQL. The disabling of the cache may result in some performance degradation but this has not yet been investigated.

[Nicklas Nordborg]

Closing this, but we should upgrade Hibernate as soon as HHH-4065 is fixed. See #1364.