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error message while uploading Flow Cytometry data

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error message while uploading Flow Cytometry data gang_zhang  2011-01-13 10:56
Status: Closed
 
Getting an error message while uploading a package of .fcs files and flowjo workspace file.
' an error occured trying to load: java.lang.nullpointerexception (java.lang.nullpointerexception'.

From the logs, the stack trace is:

java.lang.NullPointerException
    at org.labkey.pipeline.api.PipeRootImpl.findRootPath(PipeRootImpl.java:144)
    at org.labkey.pipeline.api.PipeRootImpl.relativePath(PipeRootImpl.java:195)
    at org.labkey.flow.script.FlowPipelineProvider.updateFileProperties(FlowPipelineProvider.java:113)
    at org.labkey.pipeline.PipelineController$ActionsAction.execute(PipelineController.java:506)
    at org.labkey.pipeline.PipelineController$ActionsAction.execute(PipelineController.java:468)
    at org.labkey.api.action.ApiAction.handlePost(ApiAction.java:144)
    at org.labkey.api.action.ApiAction.handleGet(ApiAction.java:103)
    at org.labkey.api.action.ApiAction.handleRequest(ApiAction.java:97)
    at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:167)
    at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
    at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:349)
    at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:756)
    at org.labkey.api.view.ViewServlet.service(ViewServlet.java:166)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:603)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:138)
    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:172)
    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.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837)
    at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640)
    at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1287)
    at java.lang.Thread.run(Unknown Source)
 
 
Matthew Bellew responded:  2011-01-13 11:24
I see where a NULL check can be added. I'm curious that I haven't seen this before. Is this reproducible? I'm wondering if it was a timing problem, like where someone was importing a run and uploading files at the same time.

If it's blocking, I think a simple fix will avoid this.