XTamden error aschwin.vanderwoude  2008-05-20 05:01
Status: Closed
 
Hi,

I got the following error when hitting the "X!Tandem peptide search" button.
This is on Labkey/CPAS 8.1 and the xtandem (/tandem_2007-07-01_2) downloaded from the labkey website, and on a Debian Linux box.

Any clues?

-Aschwin

---------
An unexpected error occurred

[Show more details]

java.lang.NullPointerException
       at org.labkey.jsp.compiled.org.labkey.ms2.pipeline.search_jsp._jspService(search_jsp.java:187)
       at org.labkey.api.view.JspView.renderView(JspView.java:103)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:171)
       at org.labkey.api.view.HttpView.render(HttpView.java:131)
       at org.labkey.api.view.HttpView.render(HttpView.java:113)
       at org.labkey.api.view.HttpView.include(HttpView.java:525)
       at org.labkey.jsp.compiled.org.labkey.api.view.template.CommonTemplate_jsp._jspService(CommonTemplate_jsp.java:173)
       at org.labkey.api.view.JspView.renderView(JspView.java:103)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:171)
       at org.labkey.api.view.HttpView.render(HttpView.java:131)
       at org.labkey.api.view.HttpView.render(HttpView.java:113)
       at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:365)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:293)
       at org.labkey.api.view.ViewServlet.dispatchActionController(ViewServlet.java:315)
       at org.labkey.api.view.ViewServlet._dispatchActionURL(ViewServlet.java:152)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:128)
       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 org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:899)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:94)
       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.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:199)
       at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:282)
       at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
       at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697)
       at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
       at java.lang.Thread.run(Thread.java:595)

request attributes
LABKEY.action = searchXTandem
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.springframework.web.context.support.XmlWebApplicationContext@1637d45: display name [MS2 WebApplicationContext]; startup date [Tue May 20 14:56:52 EEST 2008]; parent: org.springframework.web.context.support.XmlWebApplicationContext@32bd65
form = org.labkey.ms2.pipeline.MS2SearchForm@dc135d
org.springframework.validation.BindingResult.form = org.springframework.validation.BeanPropertyBindingResult: 0 errors
LABKEY.container = /Playground
WebPartView.frame = DIV
LABKEY.OriginalURL = http://cpas-proteomics.btk.fi/ms2-pipeline/Playground/searchXTandem.view?
LABKEY.StartTime = 1211284646578
LABKEY.RequestURL = /ms2-pipeline/Playground/searchXTandem.view?
LABKEY.controller = ms2-pipeline

core schema database configuration
Server URL    jdbc:postgresql://localhost/labkey
Product Name    PostgreSQL
Product Version    8.1.11
Driver Name    PostgreSQL Native Driver
Driver Version    PostgreSQL 8.3 JDBC3 with SSL (build 603)
 
 
jeckels responded:  2008-05-20 17:33
It looks like there is something wrong with the FASTA root for your pipeline configuration, though I'm not exactly sure what could cause this problem.

Under the Data Pipeline for that folder, click the Setup button, and then on the Set FASTA Root link. Be sure that it's pointed to a directory that exists and contains FASTA files that the web server has permissions to read.

Thanks,
Josh
 
edwin.lowe responded:  2008-07-02 18:48
I'm having exactly the same problem. Its also happening when i try and submit Sequest Searches.
 
edwin.lowe responded:  2008-07-02 19:28
Also, this was the windows version of the Labkey server. Heres the exact error

java.lang.NullPointerException
       at org.labkey.jsp.compiled.org.labkey.ms2.pipeline.search_jsp._jspService(search_jsp.java:192)
       at org.labkey.api.view.JspView.renderView(JspView.java:103)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:171)
       at org.labkey.api.view.HttpView.render(HttpView.java:131)
       at org.labkey.api.view.HttpView.render(HttpView.java:113)
       at org.labkey.api.view.HttpView.include(HttpView.java:525)
       at org.labkey.jsp.compiled.org.labkey.api.view.template.CommonTemplate_jsp._jspService(CommonTemplate_jsp.java:173)
       at org.labkey.api.view.JspView.renderView(JspView.java:103)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:171)
       at org.labkey.api.view.HttpView.render(HttpView.java:131)
       at org.labkey.api.view.HttpView.render(HttpView.java:113)
       at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:365)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:293)
       at org.labkey.api.view.ViewServlet.dispatchActionController(ViewServlet.java:315)
       at org.labkey.api.view.ViewServlet._dispatchActionURL(ViewServlet.java:152)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:128)
       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 org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:899)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:94)
       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(Unknown Source)

request attributes
LABKEY.action = searchSequest
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.springframework.web.context.support.XmlWebApplicationContext@1aa1db8: display name [MS2 WebApplicationContext]; startup date [Thu Jul 03 11:35:51 EST 2008]; parent: org.springframework.web.context.support.XmlWebApplicationContext@166340c
form = org.labkey.ms2.pipeline.MS2SearchForm@9b1e15
org.springframework.validation.BindingResult.form = org.springframework.validation.BeanPropertyBindingResult: 0 errors
LABKEY.container = /Testing
LABKEY.OriginalURL = http://proteome.csl.utas.edu.au:8080/labkey/ms2-pipeline/Testing/searchSequest.view?
LABKEY.StartTime = 1215049617081
WebPartView.frame = DIV
LABKEY.RequestURL = /labkey/ms2-pipeline/Testing/searchSequest.view?
LABKEY.controller = ms2-pipeline

core schema database configuration
Server URL    jdbc:postgresql://localhost/labkey
Product Name    PostgreSQL
Product Version    8.2.7
Driver Name    PostgreSQL Native Driver
Driver Version    PostgreSQL 8.3 JDBC3 with SSL (build 603)
 
jeckels responded:  2008-07-23 10:22
LabKey Server version 8.2 includes significant improvements and bug fixes for this user interface. Please try again after upgrading.

Thanks,
Josh