Details
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Type:
Bug
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Status: Closed
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Priority:
Blocker
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 1.7.1
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Component/s: Anonymization, Prearchive
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Labels:None
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Environment:
xnat-dev05
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Sprint:1.7.1 Release Sprint 1
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Rank:0|ii131j:
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Sprint:1.7.1 Release Sprint 1
Description
This is what's been going wrong in selenium test QA-181. It occurs with the more complicated anon script used there, but I've recreated it consistently using only the one-line anon script:
(0008,1010) := "King's Crossing"
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- Set up site anonymization to use the above script.
- Set up a new project
- Load some DICOM (I used a subset of sample1) in DICOM browser.
- Modify (0008,1030) to use your project ID.
- Send.
- When the data is all there, rebuild the session in the prearchive.
- The session stays in Rebuilding status and you can't do anything with it. In the logs, there's stuff like...
jms.log:
2016-11-17 10:24:16,583 An error occurred processing a request from user admin to perform Rebuild operation on prearchive session at: /prearchive/projects/r/20161117_102405501/Sample_ID
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java.lang.RuntimeException: org.xml.sax.SAXParseException; Premature end of file.
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at org.nrg.xnat.helpers.prearchive.handlers.PrearchiveRebuildHandler.execute(PrearchiveRebuildHandler.java:103)
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at org.nrg.xnat.services.messaging.prearchive.PrearchiveOperationRequestListener.onRequest(PrearchiveOperationRequestListener.java:25)
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at sun.reflect.GeneratedMethodAccessor642.invoke(Unknown Source)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:606)
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at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:269)
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at org.springframework.jms.listener.adapter.MessageListenerAdapter.invokeListenerMethod(MessageListenerAdapter.java:301)
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at org.springframework.jms.listener.adapter.MessageListenerAdapter.onMessage(MessageListenerAdapter.java:230)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:721)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:681)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
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at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
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at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1164)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1156)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1053)
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at java.lang.Thread.run(Thread.java:744)
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Caused by: org.xml.sax.SAXParseException; Premature end of file.
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at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
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at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
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at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
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at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
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at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
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at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
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at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
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at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
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at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
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at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
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at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
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at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
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at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
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at org.nrg.xdat.bean.reader.XDATXMLReader.parse(XDATXMLReader.java:474)
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at org.nrg.xnat.helpers.prearchive.handlers.PrearchiveRebuildHandler.execute(PrearchiveRebuildHandler.java:68)
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... 16 more
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application.log:
2016-11-17 10:24:16,579 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-7] ERROR org.nrg.session.SessionBuilder - /data/xnat/prearchive/r/20161117_102405501/Sample_ID must contain exactly one session
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org.nrg.session.SessionBuilder$NoUniqueSessionException: No session found
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at org.nrg.session.SessionBuilder.writeSession(SessionBuilder.java:210)
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at org.nrg.session.SessionBuilder.run(SessionBuilder.java:249)
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at org.nrg.xnat.archive.XNATSessionBuilder.buildPetSession(XNATSessionBuilder.java:250)
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at org.nrg.xnat.archive.XNATSessionBuilder.call(XNATSessionBuilder.java:209)
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at org.nrg.xnat.helpers.prearchive.PrearcDatabase$13.extSync(PrearcDatabase.java:1059)
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at org.nrg.xnat.helpers.prearchive.PrearcDatabase$13.extSync(PrearcDatabase.java:1029)
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at org.nrg.xnat.helpers.prearchive.PrearcDatabase$LockAndSync.run(PrearcDatabase.java:1619)
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at org.nrg.xnat.helpers.prearchive.PrearcDatabase.buildSession(PrearcDatabase.java:1080)
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at org.nrg.xnat.helpers.prearchive.handlers.PrearchiveRebuildHandler.execute(PrearchiveRebuildHandler.java:50)
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at org.nrg.xnat.services.messaging.prearchive.PrearchiveOperationRequestListener.onRequest(PrearchiveOperationRequestListener.java:25)
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at sun.reflect.GeneratedMethodAccessor642.invoke(Unknown Source)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:606)
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at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:269)
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at org.springframework.jms.listener.adapter.MessageListenerAdapter.invokeListenerMethod(MessageListenerAdapter.java:301)
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at org.springframework.jms.listener.adapter.MessageListenerAdapter.onMessage(MessageListenerAdapter.java:230)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:721)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:681)
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at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
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at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
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at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1164)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1156)
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at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1053)
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at java.lang.Thread.run(Thread.java:744)
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CC: Dave Maffitt
Issue Links
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Upload also failed through the Upload Assistant with this anon script.