Re: [base] Null pointer exception on deleting affymetrix raw data
Hi Nicklas, I can confirm that this is entirely an affymetrix issue. ¬Dominic Nicklas Nordborg wrote: > Dominic Oyeniran wrote: > >> The workaround works. >> But thats after I removed each raw bioassay and its associated >> experiment first and thereafter remove all the other items by emptying >> the trash. >> Note I have multiple experiments loaded :affy, genepix and agilent from >> Biosource to Experiment items. >> >> I will try deleting all at one go again and let you know > > I have only tested with a single raw bioassay, not connected to any > experiments or other items. If there are problems deleting a hierarchy > of items it is probably unrelated to the Affymetrix issue. > > There will be a fix for the Affymetrix issue in the 2.4.2 release. > > /Nicklas > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Dominic Oyeniran wrote: > > The workaround works. > But thats after I removed each raw bioassay and its associated > experiment first and thereafter remove all the other items by emptying > the trash. > Note I have multiple experiments loaded :affy, genepix and agilent from > Biosource to Experiment items. > > I will try deleting all at one go again and let you know I have only tested with a single raw bioassay, not connected to any experiments or other items. If there are problems deleting a hierarchy of items it is probably unrelated to the Affymetrix issue. There will be a fix for the Affymetrix issue in the 2.4.2 release. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Nicklas Nordborg wrote: > Dominic Oyeniran wrote: >> I am experiencing the problem with deletion of items. See the exception >> below. >> Description: When you start deleting from the trash can either with >> delete permanently or empty trash, the process dialog comes up but never >> finishes and throws the exception below >> >> The db control is also not closed once an excpetion occurs >> >> I have noticed that it only occurs with raw bio assay. >> >> Any clue on how to solve this. It stops me from re-using a file for >> example since I could delete an already linked file, ad same with other >> items. > > I think this problem only happens for Affymetrix data. I am not able to > reproduce it for any other raw data types. I think the source of the > problem is that when deleting a raw bioassay, BASE also tries to delete > the raw data associated with it. Since Affymetrix data isn't stored in > the database this will of course fail. After that I really don't know > what is happening. The NullPointerException is coming from the cleanup > code that is cleaning up after the first error, thus the DbControl fails > to be closed and the "Found unclosed DbControl" is warning is logged. I > will have to investigate more before I know why the error in the cleanup > code happens. > > In any case, there is an easy workaround. Edit the raw bioassay and > select 'none' as the CEL file. Save the changes and then retry deleting > it from the trashcan again. > > /Nicklas The workaround works. But thats after I removed each raw bioassay and its associated experiment first and thereafter remove all the other items by emptying the trash. Note I have multiple experiments loaded :affy, genepix and agilent from Biosource to Experiment items. I will try deleting all at one go again and let you know Cheers, ¬Dominic - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Dominic Oyeniran wrote: > I am experiencing the problem with deletion of items. See the exception > below. > Description: When you start deleting from the trash can either with > delete permanently or empty trash, the process dialog comes up but never > finishes and throws the exception below > > The db control is also not closed once an excpetion occurs > > I have noticed that it only occurs with raw bio assay. > > Any clue on how to solve this. It stops me from re-using a file for > example since I could delete an already linked file, ad same with other > items. I think this problem only happens for Affymetrix data. I am not able to reproduce it for any other raw data types. I think the source of the problem is that when deleting a raw bioassay, BASE also tries to delete the raw data associated with it. Since Affymetrix data isn't stored in the database this will of course fail. After that I really don't know what is happening. The NullPointerException is coming from the cleanup code that is cleaning up after the first error, thus the DbControl fails to be closed and the "Found unclosed DbControl" is warning is logged. I will have to investigate more before I know why the error in the cleanup code happens. In any case, there is an easy workaround. Edit the raw bioassay and select 'none' as the CEL file. Save the changes and then retry deleting it from the trashcan again. /Nicklas > > java.lang.NullPointerException > at > net.sf.basedb.core.RawDataBatcher.onBeforeClose(RawDataBatcher.java:3 > 07) > at > net.sf.basedb.core.AbstractBatcher.close(AbstractBatcher.java:120) > at net.sf.basedb.core.DbControl.rollback(DbControl.java:269) > at net.sf.basedb.core.DbControl.close(DbControl.java:237) > at net.sf.basedb.core.Trashcan.delete(Trashcan.java:233) > at > org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:26 > 9) > 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:328) > at > org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:3 > 15) > 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(Appl > icationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationF > ilterChain.java:188) > at > net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Ch > aracterEncodingFilter.java:72) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appl > icationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationF > ilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperV > alve.java:210) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextV > alve.java:174) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.j > ava:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.j > ava:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineVal > ve.java:108) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.jav > a:151) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java > :870) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.p > rocessConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpo > int.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFol > lowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadP > ool.java:685) > at java.lang.Thread.run(Thread.java:595) > 13:40:36,156 WARN DbControl:1074 - Found unclosed DbControl during > finalize; is > LoggedIn = true; clientId = 4; userId = 3 > java.lang.Throwable: Please check the code to make sure that > DbControl.close() i > s always called. Stacktrace of code that created this DbControl: > at net.sf.basedb.core.DbControl.(DbControl.java:142) > at > net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26 > 1) > at net.sf.basedb.core.Trashcan.delete(Trashcan.java:184) > at > org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:26 > 9) > at > org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) >
