Base1PluginExecuter fails with ConnectionClosedException

[Nicklas Nordborg]

Trying to run a BASE 1 plugin on an experiment which has experimental factors results in an exception. From a bioassay set, select the "Run plugin" button and choose a BASE 1 plugin. In the next step the following exception is thrown:

The connection has been closed.
Stack trace 	

...at DbControl.getItem(DbControl.java:704)
...at ItemResultList.get(ItemResultList.java:214)
...at ItemResultList.access$200(ItemResultList.java:41)
...at ItemResultList$ResultListIterator.next(ItemResultList.java:247)
...at ItemResultList$ResultListIterator.next(ItemResultList.java:223)
...at net.sf.basedb.plugins.Base1PluginExecuter$JobParameter.getPluginParameter(Base1PluginExecuter.java:1775)
...at net.sf.basedb.plugins.Base1PluginExecuter.getJobParametersFromXML(Base1PluginExecuter.java:934)
...at net.sf.basedb.plugins.Base1PluginExecuter.getJobParameters(Base1PluginExecuter.java:1213)

...at net.sf.basedb.plugins.Base1PluginExecuter.getConfigureJobParameters(Base1PluginExecuter.java:1075)
...at net.sf.basedb.plugins.Base1PluginExecuter.getRequestInformation(Base1PluginExecuter.java:335)
...at PluginConfigurationRequest.getRequestInformation(PluginConfigurationRequest.java:137)
...at org.apache.jsp.common.plugin.index_jsp.getJspPage(index_jsp.java:68)
...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:263)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:619)

[Nicklas Nordborg]

(In [3505]) Fixes #632, #622, #643, #644, #645, #646, #647