Hello Nicklas,
it was reason 2: there was a rawdatatype definition missing inside the
new raw-data-type.xml
thus the display problem.
Again thanks alot for your help!
Best regards,
Reha
Nicklas Nordborg wrote:
The error happens because we get 'null' for the RawDataType for (at
least) one raw bioassay. The page displays correctly some times because
the 'bad' raw bioassay is not on it. The RawDataType is a required
property and it should never be null. I can think of two reasons for it
to happen:
1. There is a problem with the upgrade between 2.4 --> 2.5. The upgrade
changed the way Affymetrix data is handled. We are not aware of any
problems, but since we are not Affymetrix users ourselves we have only
been able to do tests with a few data sets. To check this you need to
find out which raw bioassay that is causing the problem and then
manually check in the database the value of the 'rawdatatype' column.
The hard part may be to find which raw bioassay is causing it. If you
hide the 'Raw data type' column the page should be able to display
correctly.
2. A raw data type definition has been removed from the
raw-data-types.xml file. If you have made modifications to this file,
check that you did'nt accidentaly overwite it during the upgrade.
In any case, we'll try to fix the BASE code to handle this error better.
/Nicklas
Reha Yildirimman wrote:
Didn't realize that I didn't copy the complete error message:
ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception
java.lang.NullPointerException
at
org.apache.jsp.views.rawbioassays.list_005frawbioassays_jsp._jspService(list_005frawbioassays_jsp.java:1295)
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:332)
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:72)
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:595)
Thanks in advance
Reha
Nicklas Nordborg wrote:
Reha Yildirimman wrote:
Hello,
I recently updated our BASE system from 2.2 > 2.5.0 > 2.5.1 and now
have the following problem.
When I try to view rawbioassays (we currently have ~2000,
view-setting is 99 assays per page) and I click on any page number
the page wont be completely displayed , i.e. just until item 12 (the
number is always different).
When I reset the view by selecting a saved profile (showing name, raw
data type, array design, has data) the current page is displayed
properly.
Checking the log file (catalina.out) I get the following message:
ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception
java.lang.NullPointerException
Can you send the complete stacktrace? It is hard to do anything
without knowing were in the code the error happens. Since the error
doesn't happen every time, I guess there is some special case that is
not handled properly in the BASE code.
/Nicklas
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