upload problems (conflict, 'archive pending', etc)

[goo...@merctech.com]

For a new project, ~40 cases were sent from our clinical archive to
our XNat instance (1.6.4).

There were 30 cases (29 PET, 1 CT) successfully archived.

However, 8 cases remain in pre-archive after several hours. For these cases:

3 show "Archive Pending" status
5 show "Conflict" status

For 1 of the "Archive Pending" cases, clicking on 'Details' shows:
Invalid attribute 'x' of 'xnat:ctScanData/parameters/voxelRes'
the other 2 "Archive Pending" case just show "An error has occurred".

For the 8 cases with status "Conflict", they all show:

CONFLICT-5: Invalid modification of session UID via archive process.
CONFLICT-10: Session processing may already be in progress: WebBasedQCImageCreator. Concurrent modification is discouraged.

Six of the 8 also show:
CONFLICT-17: Session already contains a scan (2) with the same number, but a different UID. - New scan will be renamed to 2_1.
and one shows:
CONFLICT-17: Session already contains a scan (3) with the same number, but a different UID. - New scan will be renamed to 3_1.



I've looked a bit at the log files, and see lots of errors and warnings, but I'm really not sure what entries are
relevent to these problems. Some examples are:



----------------- prearchive.log ------------------------
2015-03-19 16:15:22,404 [org.springframework.jms.listener.DefaultMessageListenerContainer#0-2] ERROR org.nrg.xnat.helpers.prearchive.SessionXmlRebuilderRequestListener - org.nrg.action.ServerException: java.lang.IllegalStateException: org.xml.sax.SAXException: Invalid attribute 'x' of 'xnat:ctScanData/parameters/voxelRes'
at org.nrg.xnat.archive.FinishImageUpload.call(FinishImageUpload.java:143)
at org.nrg.xnat.helpers.prearchive.SessionXmlRebuilderRequestListener.onSessionXmlRebuilderRequest(SessionXmlRebuilderRequestListener.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:622)
at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273)
at org.springframework.jms.listener.adapter.MessageListenerAdapter.invokeListenerMethod(MessageListenerAdapter.java:463)
at org.springframework.jms.listener.adapter.MessageListenerAdapter.onMessage(MessageListenerAdapter.java:355)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:535)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:495)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1058)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1050)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:947
at java.lang.Thread.run(Thread.java:701)
Caused by: java.lang.IllegalStateException: org.xml.sax.SAXException: Invalid attribute 'x' of 'xnat:ctScanData/parameters/voxelRes'
at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:625)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.archive(PrearcDatabase.java:612)
at org.nrg.xnat.archive.FinishImageUpload.call(FinishImageUpload.java:108)
... 17 more
Caused by: org.xml.sax.SAXException: Invalid attribute 'x' of 'xnat:ctScanData/parameters/voxelRes'
at org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader.startElement(SAXReader.java:436)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:274)
at org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader.parse(SAXReader.java:195)
at org.nrg.xnat.turbine.utils.XNATSessionPopulater.populate(XNATSessionPopulater.java:57)
at org.nrg.xnat.archive.PrearcSessionArchiver.<init>(PrearcSessionArchiver.java:132)
at org.nrg.xnat.restlet.services.Archiver.buildArchiver(Archiver.java:278)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:622)
... 19 more


2015-03-19 16:18:19,889 [org.springframework.jms.listener.DefaultMessageListenerContainer#0-3] ERROR org.nrg.xnat.helpers.prearchive.SessionXmlRebui
lderRequestListener - org.nrg.action.ServerException: java.lang.IllegalStateException: org.xml.sax.SAXParseException; systemId: file:///path/to/xnat/prearchive/SBRTLung/20150319_161235944/ANON35406.xml; lineNumber: 11; columnNumber: 47; An invalid XML character (Unicode: 0x4) was found in the element content of the document.
at org.nrg.xnat.archive.FinishImageUpload.call(FinishImageUpload.java:143)
at org.nrg.xnat.helpers.prearchive.SessionXmlRebuilderRequestListener.onSessionXmlRebuilderRequest(SessionXmlRebuilderRequestListener.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:622)
at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273)
at org.springframework.jms.listener.adapter.MessageListenerAdapter.invokeListenerMethod(MessageListenerAdapter.java:463)
at org.springframework.jms.listener.adapter.MessageListenerAdapter.onMessage(MessageListenerAdapter.java:355)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:535)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:495)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java :325)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1058)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1050)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:947)
at java.lang.Thread.run(Thread.java:701)
Caused by: java.lang.IllegalStateException: org.xml.sax.SAXParseException; systemId: file:///path/to/xnat/prearchive/SBRTLung/20150319_161235944/ANON35406.xml; lineNumber: 11; columnNumber: 47; An invalid XML character (Unicode: 0x4) was found in the element content of the document
.
at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:625)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.archive(PrearcDatabase.java:612)
at org.nrg.xnat.archive.FinishImageUpload.call(FinishImageUpload.java:108)
... 17 more
Caused by: org.xml.sax.SAXParseException; systemId: file:///path/to/xnat/prearchive/SBRTLung/20150319_161235944/ANON35406.xml; lineNumber: 11; columnNumber: 47; An invalid XML character (Unicode: 0x4) was found in the element content of the document.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:274)
at org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader.parse(SAXReader.java:195)
at org.nrg.xnat.turbine.utils.XNATSessionPopulater.populate(XNATSessionPopulater.java:57)
at org.nrg.xnat.archive.PrearcSessionArchiver.<init>(PrearcSessionArchiver.java:132)
at org.nrg.xnat.restlet.services.Archiver.buildArchiver(Archiver.java:278)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:622)
... 19 more
-------------------------------------------------------------------------------------------------




----------------------- restlet.log --------------------------------------------------------------
2015-03-19 16:45:13,500 [http-8080-12] WARN org.nrg.xnat.restlet.resources.ConfigResource - Couldn't find config for user jdoe and project SBRTLung on tool [seriesImportFilter] path [config]
2015-03-19 16:45:13,506 [http-8080-4] WARN org.nrg.xnat.restlet.resources.ConfigResource - Couldn't find config for user jdoe and project SBRTLungon tool [applet] path [settings]
2015-03-19 16:45:13,532 [http-8080-4] WARN org.nrg.xnat.restlet.resources.ConfigResource - Couldn't find config for user jdoe and project SBRTLungon tool [tracers] path [tracers]
2015-03-19 16:45:13,744 [http-8080-12] WARN org.nrg.xnat.restlet.resources.ConfigResource - Couldn't find config for user jdoe and project SBRTLung on tool [resource_config] path [script]
-------------------------------------------------------------------------------------------------
(Those messages were repeated many times, seemingly once for each case being uploaded to XNAT.)




----------------- turbine.log -------------------------------------
2015-03-19 16:59:30,248 [http-8080-1] ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.turbine.utils.TurbineUt ils.GetPassedParameter threw Exception java.lang.NullPointerException
2015-03-19 18:22:19,485 [http-8080-10] ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.entities.XDATUserDetai ls.getQueryResultsAsArrayList threw Exception org.postgresql.util.PSQLException: ERROR: column "scanner" does not exist Position: 17
2015-03-19 18:22:21,441 [http-8080-10] ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.schema.SchemaElement.g etDisplayField threw Exception org.nrg.xdat.collections.DisplayFieldCollection$DisplayFieldNotFoundException: Display Field not found: 'GEN_AGE'
at org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWException(DisplayFieldCollection.java:53)
--------------------------------------------------------------------
(There were multiple instances of the last entry.)



The velocity.log shows 262 entries for today, when only ~30 cases were uploaded and XNat was largely idle.
According to the XNat Wiki* from 2012, those entries can be ignored...is that still true?
https://wiki.xnat.org/display/XNAT16/Troubleshooting





------------------ xdat.log ------------------------------
xdat.log:java.lang.IllegalStateException: org.xml.sax.SAXParseException;
systemId:
file:///path/to/xnat/prearchive/SBRTLung/20150319_161235944/ANON35406.xml;
lineNumber: 11; columnNumber: 47; An invalid XML character (Unicode: 0x4) was
found in the element content of the document.
----------------------------------------------------------

That line in the XML file is:
<xnat:series_description>&#254;&#222;&#231;^D</xnat:series_description>
note the [CTRL][D].


Any suggestions for troubleshooting?


Thanks,

Mark