Hello
I tried to import Existing CPAS Analysis Results from an other server.
Unfortunately I am always running into a null pointer exception (see below).
I tried to import a pep file and I have both, the pep and prot file available in the import folder.
The source server is a windows, the server where I try the import is a linux, don't know if this is relevant.
Additional question: How can I get rid of the jobs in the data pipeline section, which actually failed, but are now in waiting state?
Any ideas?
Best regards, Christian
java.lang.NullPointerException
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:160)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
at org.labkey.pipeline.analysis.FileAnalysisJob.findFile(FileAnalysisJob.java:134)
at org.labkey.pipeline.analysis.FileAnalysisJob.findInputFile(FileAnalysisJob.java:81)
at org.labkey.pipeline.api.AbstractWorkDirectory.getDir(AbstractWorkDirectory.java:157)
at org.labkey.pipeline.api.AbstractWorkDirectory.newFile(AbstractWorkDirectory.java:180)
at org.labkey.pipeline.analysis.CommandTaskImpl.newWorkFile(CommandTaskImpl.java:306)
at org.labkey.pipeline.analysis.CommandTaskImpl.getWorkFiles(CommandTaskImpl.java:295)
at org.labkey.pipeline.analysis.CommandTaskImpl.getProcessPaths(CommandTaskImpl.java:277)
at org.labkey.api.pipeline.cmd.TaskPathToCommandArgs.getPaths(TaskPathToCommandArgs.java:57)
at org.labkey.api.pipeline.cmd.PathToCommandArgs.toArgsInner(PathToCommandArgs.java:28)
at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
at org.labkey.api.pipeline.cmd.ListToCommandArgs.toArgsInner(ListToCommandArgs.java:70)
at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
at org.labkey.api.pipeline.cmd.EnumToCommandArgs.toArgsInner(EnumToCommandArgs.java:67)
at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
at org.labkey.pipeline.analysis.CommandTaskImpl$Factory.isParticipant(CommandTaskImpl.java:189)
at org.labkey.api.pipeline.PipelineJob.findRunnableTask(PipelineJob.java:716)
at org.labkey.api.pipeline.PipelineJob.runStateMachine(PipelineJob.java:659)
at org.labkey.api.pipeline.PipelineJob.setQueue(PipelineJob.java:473)
at org.labkey.pipeline.api.PipelineQueueImpl.addJob(PipelineQueueImpl.java:83)
at org.labkey.pipeline.api.PipelineServiceImpl.queueJob(PipelineServiceImpl.java:290)
at org.labkey.pipeline.analysis.AnalysisController$StartAnalysisAction.execute(AnalysisController.java:211)
at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:271)
at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:251)
at org.labkey.api.action.ApiAction.handlePost(ApiAction.java:144)
at org.labkey.api.action.ApiAction.handleRequest(ApiAction.java:95)
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:803)
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:210)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
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:151)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)
at java.lang.Thread.run(Thread.java:619) |
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| christian.pfaff responded: |
2011-04-06 06:52 |
Besides: get rid of broken jobs via Admin Console -> Pipeline |
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| jeckels responded: |
2011-04-07 09:43 |
Hi Christian,
What sequence did you follow to try to import the results? From the error that you posted, it looks like the server is attempting to do a search, not just load existing results. If you haven't already, try going to the Data Pipeline, click on Process and Import Data, browse to the .prot.xml file, select it, click the Import Data button, and choose Import ProteinProphet in the dialog box.
If you have jobs that are stuck but not in the COMPLETE or ERROR state, you can get rid of them by first selecting them from the list, clicking on the Complete button to mark them as COMPLETE, and then selecting them again and clicking on the Delete button.
Thanks,
Josh |
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| christian.pfaff responded: |
2011-04-07 23:30 |
Importing the .prot.xml file fixed the issue.
A new problem was, that the fasta file was not available on the target server (see stack trace below).
What I did to cure this was to upload the fasta file onto the server and adjust the search_database tag local_path attribute in both xml files. et voila, it worked.
Thank you very much, for your help.
Best regards, Christian
08 Apr 2011 08:15:48,784 INFO : Starting to load ProteinProphet file /CHBS/apps/itox/s_itoxadm/labkey/CPASDemo/testimport/2011_03_03_LS16_11-301608_PBMCs_2E7_nitroBet_24h.prot.xml
08 Apr 2011 08:15:48,794 INFO : Resolved referenced PepXML file to /CHBS/apps/itox/s_itoxadm/labkey/CPASDemo/testimport/2011_03_03_LS16_11-301608_PBMCs_2E7_nitroBet_24h.pep.xml
08 Apr 2011 08:15:48,813 INFO : Starting to clear out any previously imported data for 2011_03_03_LS16_11-301608_PBMCs_2E7_nitroBet_24h.pep.xml
08 Apr 2011 08:15:48,945 INFO : 0.13 seconds to clear out any previously imported data for 2011_03_03_LS16_11-301608_PBMCs_2E7_nitroBet_24h.pep.xml
08 Apr 2011 08:15:48,945 INFO : Starting to import FASTA file //phchbs-s3751/CPAS$/NBxShare/fasta/ipi.HUMAN.v3.70_updated_2011_02_22.fasta
08 Apr 2011 08:15:48,947 ERROR: MS2 import failed due to a missing file.
java.io.FileNotFoundException: //phchbs-s3751/CPAS$/NBxShare/fasta/ipi.HUMAN.v3.70_updated_2011_02_22.fasta
at org.labkey.ms2.protein.FastaDbLoader.loadAnnotations(FastaDbLoader.java:771)
at org.labkey.ms2.PepXmlImporter.writeRunInfo(PepXmlImporter.java:206)
at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:92)
at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:199)
at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:585)
at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:570)
at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:349)
at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:78)
at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
08 Apr 2011 08:15:48,953 ERROR: ProteinProphet load failed
java.io.FileNotFoundException: //phchbs-s3751/CPAS$/NBxShare/fasta/ipi.HUMAN.v3.70_updated_2011_02_22.fasta
at org.labkey.ms2.protein.FastaDbLoader.loadAnnotations(FastaDbLoader.java:771)
at org.labkey.ms2.PepXmlImporter.writeRunInfo(PepXmlImporter.java:206)
at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:92)
at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:199)
at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:585)
at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:570)
at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:349)
at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:78)
at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619) |
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