Opened 16 years ago
Last modified 16 years ago
#975 closed defect
Experimental overview – error/erroneous warning – Duplicate sub-array index — at Initial Version
| Reported by: | Johan Vallon-Christersson | Owned by: | everyone |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | core | Version: | |
| Keywords: | Cc: |
Description
Working in an experiment containing 3 raw bioassays, all from the same hybridization (arrayindex 1, 4, and 5 respectively). For clarification; the hybridization is performed using an Illumina BeadChip that contain a total of 6 arrays (index 1-6).
When displaying the experimental overview a warning was given “Duplicate sub-array index…”
When clicking the hybridization to verify that the warning was incorrectly given (the raw bioassays had separate array indices) the error below occurred (error 1 below).
After, changing the view (by simply going to a new view) and then returning to the experimental overview, the warning about reused array indices was not given.
When first trying to recreate the error (completely new experiment but the same layout) I note that the warning about duplicate sub-array index first appears after I change the validation options to ignore missing protocols.
Warning:
Duplicate sub-array index: 1 (used by HumanWG-6_V2 A)
Change array index on HumanWG-6_V2 A
Change array index on HumanWG-6_V2 A
However, this time an error is not given even if I click to change array index.
I then change the validation options again (change to give warning for missing protocols) and when doing so an error is given (error 2 below)
Once again, after changing the view (by simply going to a new view) and then returning to the experimental overview, the warning about reused array indices is not given.
java.lang.NullPointerException on page /onk/views/experiments/overview/info.jsp Version BASE 2.6.1 (build #4191; schema #52) Web server Apache Tomcat/5.5.26 Database Server MySQL 5.0.51a-log Database Dialect org.hibernate.dialect.MySQLInnoDBDialect JDBC Driver com.mysql.jdbc.Driver (version 5.0) Java runtime Java(TM) SE Runtime Environment (1.6.0_04-b12), Sun Microsystems Inc. Operating system Linux i386 2.6.18-53.1.14.el5PAE Memory Total: 504.4 MB Free: 140.3 MB Max: 976.5 MB Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US; rv:1.8.1.13) Gecko/20080311 Firefox/2.0.0.13 Error message Stack trace
java.lang.NullPointerException ...at org.apache.jsp.views.experiments.overview.info_jsp._jspService(info_jsp.java:162) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) ...at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200) ...at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283) ...at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773) ...at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703) ...at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:895) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) ...at java.lang.Thread.run(Thread.java:619)
17 more...
java.lang.NullPointerException on page /onk/views/experiments/overview/info.jsp Version BASE 2.6.1 (build #4191; schema #52) Web server Apache Tomcat/5.5.26 Database Server MySQL 5.0.51a-log Database Dialect org.hibernate.dialect.MySQLInnoDBDialect JDBC Driver com.mysql.jdbc.Driver (version 5.0) Java runtime Java(TM) SE Runtime Environment (1.6.0_04-b12), Sun Microsystems Inc. Operating system Linux i386 2.6.18-53.1.14.el5PAE Memory Total: 422.1 MB Free: 189.4 MB Max: 976.5 MB Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US; rv:1.8.1.13) Gecko/20080311 Firefox/2.0.0.13 Error message Stack trace
java.lang.NullPointerException ...at org.apache.jsp.views.experiments.overview.info_jsp._jspService(info_jsp.java:162) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) ...at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200) ...at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283) ...at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773) ...at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703) ...at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:895) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) ...at java.lang.Thread.run(Thread.java:619)
17 more...
