I'm trying to open a scan from an MS2 report. Instead of the scan image I get an image with the text:
Could not find spectra for scan 814 in 219_1-10.mzXML
All of the scans that I tried in this run give the same mmessage. I am able to open this mzXML file through the experiment browser.
The log contains the two exceptions below. Has anyone seen this before?
Thanks,
Bill
ERROR MSXMLParser 2008-05-12 16:09:05,984 http-8080-Processor23 : Error parsing file
org.xml.sax.SAXParseException: The value of attribute "compressedLen" associated with an element type "peaks" must not contain the '<' character.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.systemsbiology.jrap.MSXMLParser.rapHeader(MSXMLParser.java:376)
at org.labkey.ms2.reader.RandomAccessMzxmlIterator.hasNext(RandomAccessMzxmlIterator.java:74)
at org.labkey.ms2.Quantitation.fetchElutionProfiles(Quantitation.java:307)
at org.labkey.ms2.Quantitation.getHeavyElutionProfile(Quantitation.java:204)
at org.labkey.ms2.MS2Controller.showElutionGraph(MS2Controller.java:4027)
at org.labkey.ms2.MS2Controller$ShowHeavyElutionGraphAction.export(MS2Controller.java:4077)
at org.labkey.ms2.MS2Controller$ShowHeavyElutionGraphAction.export(MS2Controller.java:4073)
at org.labkey.api.action.ExportAction.getView(ExportAction.java:23)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:43)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:142)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:285)
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)
ERROR ExceptionUtil 2008-05-12 16:09:06,015 http-8080-Processor25 : Unhandled exception caught in Global.app: 500: Unexpected server error
java.lang.NullPointerException
at org.labkey.ms2.Quantitation.checkScan(Quantitation.java:357)
at org.labkey.ms2.Quantitation.fetchElutionProfiles(Quantitation.java:320)
at org.labkey.ms2.Quantitation.getLightElutionProfile(Quantitation.java:221)
at org.labkey.ms2.MS2Controller.showElutionGraph(MS2Controller.java:4023)
at org.labkey.ms2.MS2Controller$ShowLightElutionGraphAction.export(MS2Controller.java:4067)
at org.labkey.ms2.MS2Controller$ShowLightElutionGraphAction.export(MS2Controller.java:4063)
at org.labkey.api.action.ExportAction.getView(ExportAction.java:23)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:43)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:142)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:285)
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) |