Error message when trying to view chromatogram in Panorama

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Error message when trying to view chromatogram in Panorama Azad Eshghi  2019-07-04
 

Dear folks,

I've "successfully" uploaded data to Panorama, however when I try to view chromatograms I receive an error message. I have attached a screenshot of the message. Thanks in advance.

 
 
vsharma responded:  2019-07-04

Hi Azad,

Can you please post a link to the page on PanoramaWeb where you are seeing this error.

Thanks,
Vagisha

 
Azad Eshghi responded:  2019-07-04

Hi Vagisha,

I really appreciate the quick response, thank you. I have not yet made the data public but here is the full error if it helps?

500: Unexpected server error
[SQLITE_NOTADB] File opened that is not a database file (file is encrypted or is not a database)

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java.sql.SQLException: [SQLITE_NOTADB] File opened that is not a database file (file is encrypted or is not a database)
at org.sqlite.DB.newSQLException(DB.java:383)
at org.sqlite.DB.newSQLException(DB.java:387)
at org.sqlite.DB.throwex(DB.java:374)
at org.sqlite.NativeDB.prepare(Native Method)
at org.sqlite.DB.prepare(DB.java:123)
at org.sqlite.Stmt.executeQuery(Stmt.java:121)
at org.labkey.targetedms.parser.blib.BlibSpectrumReader.hasRetentionTimesTable(BlibSpectrumReader.java:286)
at org.labkey.targetedms.parser.blib.BlibSpectrumReader.hasValidRtTable(BlibSpectrumReader.java:298)
at org.labkey.targetedms.parser.blib.BlibSpectrumReader.readSpectrum(BlibSpectrumReader.java:211)
at org.labkey.targetedms.parser.blib.BlibSpectrumReader.getSpectrum(BlibSpectrumReader.java:90)
at org.labkey.targetedms.view.spectrum.LibrarySpectrumMatchGetter.getMatch(LibrarySpectrumMatchGetter.java:162)
at org.labkey.targetedms.view.spectrum.LibrarySpectrumMatchGetter.getMatches(LibrarySpectrumMatchGetter.java:143)
at org.labkey.targetedms.TargetedMSController.addSpectrumViews(TargetedMSController.java:2080)
at org.labkey.targetedms.TargetedMSController$PrecursorAllChromatogramsChartAction.getView(TargetedMSController.java:1265)
at org.labkey.targetedms.TargetedMSController$PrecursorAllChromatogramsChartAction.getView(TargetedMSController.java:1192)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:77)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:176)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:487)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1265)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1220)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:660)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:798)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:835)
request attributes
LABKEY.OriginalURL = http://localhost:8080/targetedms/U Victoria - Genome BC Proteomics Centre/MRM assay development in DBS/precursorAllChromatogramsChart.view?id=8996259
LABKEY.StartTime = 1562276765194
LABKEY.action = precursorAllChromatogramsChart
org.springframework.web.servlet.DispatcherServlet.CONTEXT = TargetedMS WebApplicationContext: startup date [Fri Apr 26 14:37:58 PDT 2019]; parent: Root WebApplicationContext
LABKEY.controller = targetedms
LABKEY.Counter = 0
org.labkey.api.util.ExceptionUtil$exception = java.sql.SQLException: [SQLITE_NOTADB] File opened that is not a database file (file is encrypted or is not a database)
X-LABKEY-CSRF = 2eb3b4295aa65c83b0fd99082bc98467
LABKEY.container = /U Victoria - Genome BC Proteomics Centre/MRM assay development in DBS
LABKEY.RequestURL = /targetedms/U%20Victoria%20-%20Genome%20BC%20Proteomics%20Centre/MRM%20assay%20development%20in%20DBS/precursorAllChromatogramsChart.view?id=8996259
LABKEY.OriginalURLHelper = /targetedms/U%20Victoria%20-%20Genome%20BC%20Proteomics%20Centre/MRM%20assay%20development%20in%20DBS/precursorAllChromatogramsChart.view?id=8996259

core schema database configuration
Server URL jdbc:postgresql://localhost/labkey
Product Name PostgreSQL
Product Version 10.7
Driver Name PostgreSQL JDBC Driver
Driver Version 42.2.5

 
vsharma responded:  2019-07-04

Hi Azad,

You can send me the link over email (vsharma@uw.edu) if that is better. But I think I have found the folder on PanoramaWeb where you are seeing this error. There is a library associated with your document that is not a Bibliospec library and Panorama is failing while trying to read that library. So far Panorama is only able to read spectrum libraries in Bibliospec format, but it should not fail like this if it sees other formats. I will take a look at this tomorrow and get back to you.

Thanks,
Vagisha

 
Azad Eshghi responded:  2019-07-04

Vagisha, your hint solved the problem. And this is how I fixed it in case someone else encounters this in the future:

-Navigated to peptide settings in Skyline-daily and unchecked libraries in the library tab and selected None for background proteome in the digestion tab.
-Re-uploaded to panorama and all is working well.

Thanks again for the solution.