Weird errors in prearchive

Simon Doran

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Mar 9, 2020, 1:22:21 PM3/9/20

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Hi All,

Has anyone ever come across either of these two situations before?

1. Blank subject (top and bottom case in screenshot above)

Symptom: Sessions received in XNAT via the DicomReceiver show up with an Error flag in the prearchive. Clicking on Details in the top right pane yields

Digging into the cause a bit more reveals that in the directory corresponding to this scan, there is an XML file (e.g., for the top entry above it is 20100621_120836.xml) that is empty, whereas it should contain the session information. (I'm presuming that the creation of this is one of the things that the session build process does. However, when I remove the file and click on the "Rebuild" button, I just recreate an empty XML file with the same name.)

Most of the logs don't tell me anything that I don't know already:

xdat.log

2020-03-09 16:31:15,180 [http-bio-8080-exec-58] ERROR org.nrg.xdat.turbine.modules.screens.SecureScreen -

org.xml.sax.SAXParseException: Premature end of file.

prearchive.log

2020-03-09 16:59:54,121 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-9] ERROR org.nrg.xnat.helpers.prearchive.PrearcUtils - /home/xnat/data/prearchive/RPYS_RPACS01/20200224_030754479/20100621_120836.xml is empty.

application.log

2020-03-09 16:59:54,105 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-9] ERROR org.nrg.session.SessionBuilder - /home/xnat/data/prearchive/RPYS_RPACS01/20200224_030754479/20100621_120836 must contain exactly one session

org.nrg.session.SessionBuilder$NoUniqueSessionException: No session found

However, dicom.log does provide a bit of clarity:

2020-03-09 16:59:53,991 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-9] ERROR org.nrg.dcm.xnat.DICOMSessionBuilder - Session builder not implemented for SOP class [1.2.840.10008.5.1.4.1.1.11.1] or modality [PR]

Resolution: Not found one yet. What do we do about this? Is XNAT going to reject any session that happens to get sent with a presentation state file in there and throw an error like this? If so, isn't this going to be a big problem going forward?

2. Subject name present (blanked out with purple blob above)

Symptom: Clicking on Details leads to a screen like the following:

Resolution: Easy, just click on Archive in the action box. But the point is that this is a manual intervention and I shouldn't have to do it.

System details: XNAT 1.7.6 build 1694 running under Vagrant.

Any help with either or both of these errors would be much appreciated.

Best wishes,

Simon

Moore, Charlie

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Mar 9, 2020, 2:02:08 PM3/9/20

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Hi Simon,

To clarify, for issue (1), does the session just include presentation states, or is the data that reached the prearchive nothing other than presentation states?

Thanks,

Charlie

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Simon Doran

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Mar 9, 2020, 5:53:13 PM3/9/20

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Hi Charlie,

In the first case, I'm pretty sure that there are normal image data there as well as presentation states, but will have to dig in the cache and prearchive to verify this 100%. For the second case, I'm not sure whether presentation states are there at all, but there are certainly normal images, as you can see in the third screenshot.

Thanks for taking a look.

Best wishes,

Simon,

Moore, Charlie

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Mar 11, 2020, 11:04:16 AM3/11/20

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Hi Simon,

The reason I ask is that the message in the logs implies XNAT (thinks it) only received presentation states. If that’s true, XNAT will fail to create a session from the DICOM, which is documented:

1. Here: https://groups.google.com/d/msg/xnat_discussion/aK8R4rzLRSs/mdL2EEuqAAAJ

2. And here: https://issues.xnat.org/browse/XNAT-4527

Thanks,

Charlie

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> On Behalf Of Simon Doran

Sent: Monday, March 09, 2020 4:53 PM
To: xnat_discussion <xnat_di...@googlegroups.com>

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Simon Doran

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Mar 11, 2020, 12:25:23 PM3/11/20

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Hi Charlie,

I was trying not to splurge too long a stack trace in my message and keep it concise. The full stack trace looks like this and you will see it refers to multiple sessions and no session.

2020-03-09 16:59:53,992 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-9] ERROR org.nrg.session.SessionBuilder - /home/xnat/data/prearchive/RPYS_RPACS01/20200224_030754479/20100621_120836 must contain exactly one session

org.nrg.session.SessionBuilder$NoUniqueSessionException: Multiple sessions found: [no session type identified]

at org.nrg.dcm.xnat.DICOMSessionBuilder.call(DICOMSessionBuilder.java:372)

at org.nrg.dcm.xnat.DICOMSessionBuilder.call(DICOMSessionBuilder.java:44)

at org.nrg.session.SessionBuilder.writeSession(SessionBuilder.java:208)

at org.nrg.session.SessionBuilder.run(SessionBuilder.java:249)

at org.nrg.xnat.archive.XNATSessionBuilder.buildDicomSession(XNATSessionBuilder.java:283)

at org.nrg.xnat.archive.XNATSessionBuilder.call(XNATSessionBuilder.java:203)

at org.nrg.xnat.helpers.prearchive.PrearcDatabase$13.extSync(PrearcDatabase.java:1065)

at org.nrg.xnat.helpers.prearchive.PrearcDatabase$13.extSync(PrearcDatabase.java:1032)

at org.nrg.xnat.helpers.prearchive.PrearcDatabase$LockAndSync.run(PrearcDatabase.java:1633)

at org.nrg.xnat.helpers.prearchive.PrearcDatabase.buildSession(PrearcDatabase.java:1084)

at org.nrg.xnat.helpers.prearchive.handlers.PrearchiveRebuildHandler.execute(PrearchiveRebuildHandler.java:64)

at org.nrg.xnat.services.messaging.prearchive.PrearchiveOperationRequestListener.onRequest(PrearchiveOperationRequestListener.java:27)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:265)

at org.springframework.jms.listener.adapter.MessageListenerAdapter.invokeListenerMethod(MessageListenerAdapter.java:314)

at org.springframework.jms.listener.adapter.MessageListenerAdapter.onMessage(MessageListenerAdapter.java:243)

at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:719)

at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:679)

at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:649)

at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:317)

at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:255)

at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1168)

at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1160)

at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1057)

at java.lang.Thread.run(Thread.java:748)

2020-03-09 16:59:54,105 [org.springframework.jms.listener.DefaultMessageListenerContainer#3-9] ERROR org.nrg.session.SessionBuilder - /home/xnat/data/prearchive/RPYS_RPACS01/20200224_030754479/20100621_120836 must contain exactly one session

org.nrg.session.SessionBuilder$NoUniqueSessionException: No session found

at org.nrg.session.SessionBuilder.writeSession(SessionBuilder.java:210)

at org.nrg.session.SessionBuilder.run(SessionBuilder.java:249)

at org.nrg.xnat.archive.XNATSessionBuilder.buildPetSession(XNATSessionBuilder.java:248)

at org.nrg.xnat.archive.XNATSessionBuilder.call(XNATSessionBuilder.java:207)