Data Not Archiving - 1.4rc2
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dalter
Jun 4, 2009, 2:45:39 PM6/4/09
to xnat_discussion
All,
I'm having the same issues first posted in the "Unable to archive the
data ( stay as queued )" thread : (http://groups.google.com/group/
xnat_discussion/browse_thread/thread/98e45a3580653a3e/f32e36f6796d1640?
lnk=gst&q=archive#f32e36f6796d1640)
The author of that thread noted the issue in v. 1.3.3, we're seeing it
with 1.4rc2.
We upload data via the webpage / DICOM Browser / DICOM Uploader
(doesn't matter which), then move it from prearchive to the specific
subject. Data shows as "Archiving", but never moves to archive. I've
verified this by looking in both the archive and prearchive
subdirectories on the XNAT server; data / images are in the
prearchive, nothing in archive. Permissions in the XNAT directory (/
data/xnat) are all set to the proper user / group.
What was the specific issue that was causing this in 1.3.3, and was a
fix incorporated in later code? If not, how do we correct this on our
server?
Thanks,
Duane
I'm having the same issues first posted in the "Unable to archive the
data ( stay as queued )" thread : (http://groups.google.com/group/
xnat_discussion/browse_thread/thread/98e45a3580653a3e/f32e36f6796d1640?
lnk=gst&q=archive#f32e36f6796d1640)
The author of that thread noted the issue in v. 1.3.3, we're seeing it
with 1.4rc2.
We upload data via the webpage / DICOM Browser / DICOM Uploader
(doesn't matter which), then move it from prearchive to the specific
subject. Data shows as "Archiving", but never moves to archive. I've
verified this by looking in both the archive and prearchive
subdirectories on the XNAT server; data / images are in the
prearchive, nothing in archive. Permissions in the XNAT directory (/
data/xnat) are all set to the proper user / group.
What was the specific issue that was causing this in 1.3.3, and was a
fix incorporated in later code? If not, how do we correct this on our
server?
Thanks,
Duane
Timothy Olsen
Jun 4, 2009, 3:31:57 PM6/4/09
to xnat_di...@googlegroups.com
Duane,
I don't remember what the exact issue was. The 1.3.3 architecture for Transferring data from the prearchive to the archive was entirely different then in POST-1.3 versions. It used to be handled within XNAT's java code. Now it is managed by the pipeline manager. Alexis was an early adopter of 1.4 and hasn't reported the same issue continuing. I'm guessing this is a different issue. A lot has changed in the last two years.
Have you reviewed your TOMCAT/webapps/PROJECT/logs/xdat.log||application.log? Are there any pertinent exceptions at the time of the failed archive (besides the annoying ‘Display Field not Found’ and ‘relation "xdat_meta_element_meta_data" does not exist’ exceptions… I really need to make XNAT conceal those, they’re non-impactful)? Also check the XNAT_HOME/pipeline/logs directory.
It may also be informative to check if auto-archiving is working. Have you tried configuring your project to auto-archive (using the Manage tab on the Project page)? If not, set it to skip the prearchive, then resend the files to the DICOM Server (using DICOM Browser or DICOM Uploader). FYI, you may need to restart the DICOM Server to allow the re-storage of any duplicate UIDs. If the upload process uses the auto-archive feature via the DICOM server, then it skips the Pipeline's transfer code for the physical transfer (the files are actually directly uploaded into the archive folder).
Furthermore, I just setup a vanilla RC2 from CVS. I logged in as admin. Created a project called TEST. Uploaded the sample1.zip dataset via the Upload Images dialog. Archived it (including creating a new subject via the archive page link). The subsequent MR report page said the process was queued (as is expected initially after an archive). I refreshed the page after 30 seconds and the files were there (with snapshots). The Image Viewer successfully displayed the images. When I return to the prearchive for my TEST project, there is nothing there.
If you (Max & Duane) could attempt to repeat the test I performed (using the sample1.zip), that may prove informative.
Tim
dalter
Jun 4, 2009, 5:15:42 PM6/4/09
to xnat_discussion
Tim,
Ran test as you outlined. Had data both prearchive / move to archive
after subject creation, and auto-archive via the 'Manage' tab. Same
results as before: status shows as "Transferring" if prearchived, or
as 'Queued' if viewing the "Work Flow Status" from the archive subject
page. Did get some log traces:
xnat.log:
2009-06-04 15:59:14,142 [http-8080-1] ERROR
org.nrg.xdat.search.DisplaySearch -
org.nrg.xdat.collections.DisplayFieldCollection
$DisplayFieldNotFoundException: Display Field not found: 'LABEL'
at
org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWException
(DisplayFieldCollection.java:50)
at org.nrg.xdat.schema.SchemaElement.getDisplayField
(SchemaElement.java:81)
at org.nrg.xdat.search.DisplaySearch.addDisplayField
(DisplaySearch.java:1561)
at
org.nrg.xnat.restlet.resources.ProjectSubjectList.getRepresentation
(ProjectSubjectList.java:217)
at org.restlet.resource.Resource.handleGet(Resource.java:463)
at org.restlet.Finder.handle(Finder.java:351)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:
130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at com.noelios.restlet.application.ApplicationHelper.handle
(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:342)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at org.restlet.Component.handle(Component.java:888)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:
68)
at com.noelios.restlet.http.HttpServerHelper.handle
(HttpServerHelper.java:147)
at com.noelios.restlet.ext.servlet.ServerServlet.service
(ServerServlet.java:790)
at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service
(XNATRestletServlet.java:24)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:433)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:286)
at org.apache.coyote.http11.Http11Processor.process
(Http11Processor.java:845)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run
(JIoEndpoint.java:447)
at java.lang.Thread.run(Unknown Source)
2009-06-04 15:59:51,853 [http-8080-1] ERROR
org.nrg.xdat.search.DisplaySearch -
org.nrg.xdat.collections.DisplayFieldCollection
$DisplayFieldNotFoundException: Display Field not found: 'LABEL'
at
org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWException
(DisplayFieldCollection.java:50)
at org.nrg.xdat.schema.SchemaElement.getDisplayField
(SchemaElement.java:81)
at org.nrg.xdat.search.DisplaySearch.addDisplayField
(DisplaySearch.java:1561)
at
org.nrg.xnat.restlet.resources.ProjectSubjectList.getRepresentation
(ProjectSubjectList.java:217)
at org.restlet.resource.Resource.handleGet(Resource.java:463)
at org.restlet.Finder.handle(Finder.java:351)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:
130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at com.noelios.restlet.application.ApplicationHelper.handle
(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:342)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at org.restlet.Component.handle(Component.java:888)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:
68)
at com.noelios.restlet.http.HttpServerHelper.handle
(HttpServerHelper.java:147)
at com.noelios.restlet.ext.servlet.ServerServlet.service
(ServerServlet.java:790)
at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service
(XNATRestletServlet.java:24)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:433)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:286)
at org.apache.coyote.http11.Http11Processor.process
(Http11Processor.java:845)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run
(JIoEndpoint.java:447)
at java.lang.Thread.run(Unknown Source)
application.log:
2009-06-04 16:00:26,925 [Thread-34] ERROR
org.nrg.pipeline.ProcessLauncher - Couldnt launch /data/xnat/
pipeline/bin/XnatPipelineLauncher -pipeline xnat_tools/Transfer.xml -
id XNAT2_E00004 -label SampleID -host http://dhcp80ff55cc.dynamic.uiowa.edu:8080/xnat/
-supressNotification -u admin -dataType xnat:mrSessionData -project
"TEST_666" -notify duane...@uiowa.edu -notify duane...@uiowa.edu
-parameter tbpath='/data/xnat/cache/TEST_666/Thumbnail/' -parameter
cachepath='/data/xnat/cache/TEST_666/transfer_bk/20090604_155837/
Sample_ID_1_MR' -parameter xnat_project='TEST_666' -parameter
userfullname='A.Admin' -parameter cpath='/data/xnat/cache/TEST_666/'
-parameter useremail='duane...@uiowa.edu' -parameter
mailhost='localhost' -parameter session='XNAT2_E00004' -parameter
sourceDir='/data/xnat/prearchive/TEST_666/20090604_155837/
Sample_ID_1_MR' -parameter xnatserver='XNAT2' -parameter
destinationDir='/data/xnat/archive/TEST_666/arc001/SampleID/' -
parameter createQc='1' -parameter sessionType='xnat:mrSessionData' -
parameter adminemail='duane...@uiowa.edu' -parameter
sessionLabel='SampleID' -pwd 'cfokl'
pipeline_2009_06_04_16_00_23.log:
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -log
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/log4j.properties
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -config
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/pipeline.config
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -catalogPath
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/catalog
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -pipeline
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - xnat_tools/
Transfer.xml
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -id
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - XNAT2_E00004
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -label
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - SampleID
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -host
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
http://dhcp80ff55cc.dynamic.uiowa.edu:8080/xnat/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -
supressNotification
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -u
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - admin
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -dataType
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnat:mrSessionData
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -project
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - TEST_666
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -notify
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - duane-
al...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -notify
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - duane-
al...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - tbpath=/data/
xnat/cache/TEST_666/Thumbnail/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - cachepath=/
data/xnat/cache/TEST_666/transfer_bk/20090604_155837/Sample_ID_1_MR
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnat_project=TEST_666
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
userfullname=A.Admin
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - cpath=/data/
xnat/cache/TEST_666/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
useremail=duane...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
mailhost=localhost
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
session=XNAT2_E00004
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - sourceDir=/
data/xnat/prearchive/TEST_666/20090604_155837/Sample_ID_1_MR
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnatserver=XNAT2
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
destinationDir=/data/xnat/archive/TEST_666/arc001/SampleID/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - createQc=1
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
sessionType=xnat:mrSessionData
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
adminemail=duane...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
sessionLabel=SampleID
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -pwd*******
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
====================================
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldnt
search for queued workflows
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}
Server.userException
faultSubcode:
faultString: java.lang.RuntimeException: No compiler found in your
classpath! (you may need to add 'tools.jar')
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}hostname:dhcp80ff55cc.dynamic.uiowa.edu
java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add 'tools.jar')
at org.apache.axis.message.SOAPFaultBuilder.createFault
(SOAPFaultBuilder.java:222)
at org.apache.axis.message.SOAPFaultBuilder.endElement
(SOAPFaultBuilder.java:129)
at org.apache.axis.encoding.DeserializationContext.endElement
(DeserializationContext.java:1087)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement
(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:395)
at org.apache.axis.encoding.DeserializationContext.parse
(DeserializationContext.java:227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke
(MustUnderstandChecker.java:62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at org.nrg.xnattools.xml.AbsService.createServiceSession
(AbsService.java:100)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:97)
at
org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold
(XNATPipelineLauncher.java:119)
at org.nrg.pipeline.client.XNATPipelineLauncher.launch
(XNATPipelineLauncher.java:44)
at org.nrg.pipeline.client.XNATPipelineLauncher.main
(XNATPipelineLauncher.java:253)
INFO main org.nrg.pipeline.utils.PipelineUtils - Loop Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Parameter Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Output resolved
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ExecutionManager - Launching step 0
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher -
java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add 'tools.jar')
The 'tools.jar' bothers me; it is on the server, and in the classpath
(I'm assuming $JAVA_HOME). I'm not sure what else I should be looking
at here, any help you can give is appreciated.
Duane.
On Jun 4, 3:31 pm, Timothy Olsen <t...@npg.wustl.edu> wrote:
> Duane,
>
> I don't remember what the exact issue was. The 1.3.3 architecture for Transferring data from the prearchive to the archive was entirely different then in POST-1.3 versions. It used to be handled within XNAT's java code. Now it is managed by the pipeline manager. Alexis was an early adopter of 1.4 and hasn't reported the same issue continuing. I'm guessing this is a different issue. A lot has changed in the last two years.
>
> Have you reviewed your TOMCAT/webapps/PROJECT/logs/xdat.log||application.log? Are there any pertinent exceptions at the time of the failed archive (besides the annoying 'Display Field not Found' and 'relation "xdat_meta_element_meta_data" does not exist' exceptions... I really need to make XNAT conceal those, they're non-impactful)? Also check the XNAT_HOME/pipeline/logs directory.
Ran test as you outlined. Had data both prearchive / move to archive
after subject creation, and auto-archive via the 'Manage' tab. Same
results as before: status shows as "Transferring" if prearchived, or
as 'Queued' if viewing the "Work Flow Status" from the archive subject
page. Did get some log traces:
xnat.log:
2009-06-04 15:59:14,142 [http-8080-1] ERROR
org.nrg.xdat.search.DisplaySearch -
org.nrg.xdat.collections.DisplayFieldCollection
$DisplayFieldNotFoundException: Display Field not found: 'LABEL'
at
org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWException
(DisplayFieldCollection.java:50)
at org.nrg.xdat.schema.SchemaElement.getDisplayField
(SchemaElement.java:81)
at org.nrg.xdat.search.DisplaySearch.addDisplayField
(DisplaySearch.java:1561)
at
org.nrg.xnat.restlet.resources.ProjectSubjectList.getRepresentation
(ProjectSubjectList.java:217)
at org.restlet.resource.Resource.handleGet(Resource.java:463)
at org.restlet.Finder.handle(Finder.java:351)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:
130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at com.noelios.restlet.application.ApplicationHelper.handle
(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:342)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at org.restlet.Component.handle(Component.java:888)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:
68)
at com.noelios.restlet.http.HttpServerHelper.handle
(HttpServerHelper.java:147)
at com.noelios.restlet.ext.servlet.ServerServlet.service
(ServerServlet.java:790)
at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service
(XNATRestletServlet.java:24)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:433)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:286)
at org.apache.coyote.http11.Http11Processor.process
(Http11Processor.java:845)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run
(JIoEndpoint.java:447)
at java.lang.Thread.run(Unknown Source)
2009-06-04 15:59:51,853 [http-8080-1] ERROR
org.nrg.xdat.search.DisplaySearch -
org.nrg.xdat.collections.DisplayFieldCollection
$DisplayFieldNotFoundException: Display Field not found: 'LABEL'
at
org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWException
(DisplayFieldCollection.java:50)
at org.nrg.xdat.schema.SchemaElement.getDisplayField
(SchemaElement.java:81)
at org.nrg.xdat.search.DisplaySearch.addDisplayField
(DisplaySearch.java:1561)
at
org.nrg.xnat.restlet.resources.ProjectSubjectList.getRepresentation
(ProjectSubjectList.java:217)
at org.restlet.resource.Resource.handleGet(Resource.java:463)
at org.restlet.Finder.handle(Finder.java:351)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:
130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at com.noelios.restlet.application.ApplicationHelper.handle
(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:342)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:
124)
at org.restlet.Component.handle(Component.java:888)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:
68)
at com.noelios.restlet.http.HttpServerHelper.handle
(HttpServerHelper.java:147)
at com.noelios.restlet.ext.servlet.ServerServlet.service
(ServerServlet.java:790)
at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service
(XNATRestletServlet.java:24)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:433)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:286)
at org.apache.coyote.http11.Http11Processor.process
(Http11Processor.java:845)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run
(JIoEndpoint.java:447)
at java.lang.Thread.run(Unknown Source)
application.log:
2009-06-04 16:00:26,925 [Thread-34] ERROR
org.nrg.pipeline.ProcessLauncher - Couldnt launch /data/xnat/
pipeline/bin/XnatPipelineLauncher -pipeline xnat_tools/Transfer.xml -
id XNAT2_E00004 -label SampleID -host http://dhcp80ff55cc.dynamic.uiowa.edu:8080/xnat/
-supressNotification -u admin -dataType xnat:mrSessionData -project
"TEST_666" -notify duane...@uiowa.edu -notify duane...@uiowa.edu
-parameter tbpath='/data/xnat/cache/TEST_666/Thumbnail/' -parameter
cachepath='/data/xnat/cache/TEST_666/transfer_bk/20090604_155837/
Sample_ID_1_MR' -parameter xnat_project='TEST_666' -parameter
userfullname='A.Admin' -parameter cpath='/data/xnat/cache/TEST_666/'
-parameter useremail='duane...@uiowa.edu' -parameter
mailhost='localhost' -parameter session='XNAT2_E00004' -parameter
sourceDir='/data/xnat/prearchive/TEST_666/20090604_155837/
Sample_ID_1_MR' -parameter xnatserver='XNAT2' -parameter
destinationDir='/data/xnat/archive/TEST_666/arc001/SampleID/' -
parameter createQc='1' -parameter sessionType='xnat:mrSessionData' -
parameter adminemail='duane...@uiowa.edu' -parameter
sessionLabel='SampleID' -pwd 'cfokl'
pipeline_2009_06_04_16_00_23.log:
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -log
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/log4j.properties
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -config
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/pipeline.config
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -catalogPath
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - /home/xnat/
pipeline/catalog
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -pipeline
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - xnat_tools/
Transfer.xml
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -id
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - XNAT2_E00004
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -label
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - SampleID
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -host
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
http://dhcp80ff55cc.dynamic.uiowa.edu:8080/xnat/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -
supressNotification
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -u
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - admin
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -dataType
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnat:mrSessionData
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -project
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - TEST_666
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -notify
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - duane-
al...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -notify
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - duane-
al...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - tbpath=/data/
xnat/cache/TEST_666/Thumbnail/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - cachepath=/
data/xnat/cache/TEST_666/transfer_bk/20090604_155837/Sample_ID_1_MR
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnat_project=TEST_666
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
userfullname=A.Admin
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - cpath=/data/
xnat/cache/TEST_666/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
useremail=duane...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
mailhost=localhost
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
session=XNAT2_E00004
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - sourceDir=/
data/xnat/prearchive/TEST_666/20090604_155837/Sample_ID_1_MR
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
xnatserver=XNAT2
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
destinationDir=/data/xnat/archive/TEST_666/arc001/SampleID/
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - createQc=1
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
sessionType=xnat:mrSessionData
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
adminemail=duane...@uiowa.edu
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -parameter
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
sessionLabel=SampleID
INFO main org.nrg.pipeline.client.XNATPipelineLauncher - -pwd*******
INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
====================================
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldnt
search for queued workflows
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}
Server.userException
faultSubcode:
faultString: java.lang.RuntimeException: No compiler found in your
classpath! (you may need to add 'tools.jar')
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}hostname:dhcp80ff55cc.dynamic.uiowa.edu
java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add 'tools.jar')
at org.apache.axis.message.SOAPFaultBuilder.createFault
(SOAPFaultBuilder.java:222)
at org.apache.axis.message.SOAPFaultBuilder.endElement
(SOAPFaultBuilder.java:129)
at org.apache.axis.encoding.DeserializationContext.endElement
(DeserializationContext.java:1087)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement
(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:395)
at org.apache.axis.encoding.DeserializationContext.parse
(DeserializationContext.java:227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke
(MustUnderstandChecker.java:62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at org.nrg.xnattools.xml.AbsService.createServiceSession
(AbsService.java:100)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:97)
at
org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold
(XNATPipelineLauncher.java:119)
at org.nrg.pipeline.client.XNATPipelineLauncher.launch
(XNATPipelineLauncher.java:44)
at org.nrg.pipeline.client.XNATPipelineLauncher.main
(XNATPipelineLauncher.java:253)
INFO main org.nrg.pipeline.utils.PipelineUtils - Loop Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Parameter Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Output resolved
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /home/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ExecutionManager - Launching step 0
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher -
java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add 'tools.jar')
The 'tools.jar' bothers me; it is on the server, and in the classpath
(I'm assuming $JAVA_HOME). I'm not sure what else I should be looking
at here, any help you can give is appreciated.
Duane.
On Jun 4, 3:31 pm, Timothy Olsen <t...@npg.wustl.edu> wrote:
> Duane,
>
> I don't remember what the exact issue was. The 1.3.3 architecture for Transferring data from the prearchive to the archive was entirely different then in POST-1.3 versions. It used to be handled within XNAT's java code. Now it is managed by the pipeline manager. Alexis was an early adopter of 1.4 and hasn't reported the same issue continuing. I'm guessing this is a different issue. A lot has changed in the last two years.
>
>
> It may also be informative to check if auto-archiving is working. Have you tried configuring your project to auto-archive (using the Manage tab on the Project page)? If not, set it to skip the prearchive, then resend the files to the DICOM Server (using DICOM Browser or DICOM Uploader). FYI, you may need to restart the DICOM Server to allow the re-storage of any duplicate UIDs. If the upload process uses the auto-archive feature via the DICOM server, then it skips the Pipeline's transfer code for the physical transfer (the files are actually directly uploaded into the archive folder).
>
> Furthermore, I just setup a vanilla RC2 from CVS. I logged in as admin. Created a project called TEST. Uploaded the sample1.zip<http://nrg.wustl.edu/1.4/sample1.zip> dataset via the Upload Images dialog. Archived it (including creating a new subject via the archive page link). The subsequent MR report page said the process was queued (as is expected initially after an archive). I refreshed the page after 30 seconds and the files were there (with snapshots). The Image Viewer successfully displayed the images. When I return to the prearchive for my TEST project, there is nothing there.
> It may also be informative to check if auto-archiving is working. Have you tried configuring your project to auto-archive (using the Manage tab on the Project page)? If not, set it to skip the prearchive, then resend the files to the DICOM Server (using DICOM Browser or DICOM Uploader). FYI, you may need to restart the DICOM Server to allow the re-storage of any duplicate UIDs. If the upload process uses the auto-archive feature via the DICOM server, then it skips the Pipeline's transfer code for the physical transfer (the files are actually directly uploaded into the archive folder).
>
Timothy Olsen
Jun 4, 2009, 5:54:48 PM6/4/09
to xnat_di...@googlegroups.com
Is your JAVA_HOME pointing at a JDK installation or just a JRE? I think that we saw this issue before when there was a JRE being used. XNAT requires a full JDK.
What operating system are you on? What is your java version?
What operating system are you on? What is your java version?
dalter
Jun 4, 2009, 11:21:38 PM6/4/09
to xnat_discussion
OS is RHEL 5.3
JAVA_HOME is pointing at Sun JDK 1.6.0_14; also have JRE_HOME defined
and referencing Sun JRE 1.6.0_13. $JAVA_HOME and $JRE_HOME are
pointing to '/opt/jdk1.6.0_14' and '/usr/java/jre1.6.0_13',
respectively. Also have the Red Hat JDK (java-1.6.0-sun-
devel-1.6.0.13-1jpp.1.el5) and JRE (java-1.6.0-sun-1.6.0.13-1jpp.
1.el5) RPMs installed on the system. XNAT was compiled against the
Sun downloaded packages; we weren't sure if the original issues we
were seeing were due to problems with the Red Hat packages, so pulled
the JDK / JRE from Sun and compiled / exported those.
Duane
> id XNAT2_E00004 -label SampleID -hosthttp://dhcp80ff55cc.dynamic.uiowa.edu:8080/xnat/
>
> read more »
JAVA_HOME is pointing at Sun JDK 1.6.0_14; also have JRE_HOME defined
and referencing Sun JRE 1.6.0_13. $JAVA_HOME and $JRE_HOME are
pointing to '/opt/jdk1.6.0_14' and '/usr/java/jre1.6.0_13',
respectively. Also have the Red Hat JDK (java-1.6.0-sun-
devel-1.6.0.13-1jpp.1.el5) and JRE (java-1.6.0-sun-1.6.0.13-1jpp.
1.el5) RPMs installed on the system. XNAT was compiled against the
Sun downloaded packages; we weren't sure if the original issues we
were seeing were due to problems with the Red Hat packages, so pulled
the JDK / JRE from Sun and compiled / exported those.
Duane
> -supressNotification -u admin -dataType xnat:mrSessionData -project
> "TEST_666" -notify duane-al...@uiowa.edu -notify duane-al...@uiowa.edu
> -parameter tbpath='/data/xnat/cache/TEST_666/Thumbnail/' -parameter
> cachepath='/data/xnat/cache/TEST_666/transfer_bk/20090604_155837/
> Sample_ID_1_MR' -parameter xnat_project='TEST_666' -parameter
> userfullname='A.Admin' -parameter cpath='/data/xnat/cache/TEST_666/'
> -parameter useremail='duane-al...@uiowa.edu' -parameter
> cachepath='/data/xnat/cache/TEST_666/transfer_bk/20090604_155837/
> Sample_ID_1_MR' -parameter xnat_project='TEST_666' -parameter
> userfullname='A.Admin' -parameter cpath='/data/xnat/cache/TEST_666/'
> mailhost='localhost' -parameter session='XNAT2_E00004' -parameter
> sourceDir='/data/xnat/prearchive/TEST_666/20090604_155837/
> Sample_ID_1_MR' -parameter xnatserver='XNAT2' -parameter
> destinationDir='/data/xnat/archive/TEST_666/arc001/SampleID/' -
> parameter createQc='1' -parameter sessionType='xnat:mrSessionData' -
> parameter adminemail='duane-al...@uiowa.edu' -parameter
> sourceDir='/data/xnat/prearchive/TEST_666/20090604_155837/
> Sample_ID_1_MR' -parameter xnatserver='XNAT2' -parameter
> destinationDir='/data/xnat/archive/TEST_666/arc001/SampleID/' -
> parameter createQc='1' -parameter sessionType='xnat:mrSessionData' -
> sessionLabel='SampleID' -pwd 'cfokl'
>
> pipeline_2009_06_04_16_00_23.log:
>
> INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
>
> ...
>
> pipeline_2009_06_04_16_00_23.log:
>
> INFO main org.nrg.pipeline.client.XNATPipelineLauncher -
>
>
> read more »
dalter
Jun 8, 2009, 9:14:48 AM6/8/09
to xnat_discussion
bump.
> ...
>
> read more »
>
> read more »
Timothy Olsen
Jun 8, 2009, 10:43:39 AM6/8/09
to xnat_di...@googlegroups.com
Duane,
Can you confirm which java version is being used to start Tomcat? Also, is there a specific java version referenced in XNAT_HOME/pipeline/bin/XNATPipelineLauncher?
Can you confirm which java version is being used to start Tomcat? Also, is there a specific java version referenced in XNAT_HOME/pipeline/bin/XNATPipelineLauncher?
dalter
Jun 8, 2009, 3:34:07 PM6/8/09
to xnat_discussion
Looks like we had a JRE conflict. I'm used to using the RPM-based JDK
and JRE, didn't realize the JRE was bundled in with the Sun-downloaded
JDK. Got rid of the extraneous JRE_HOME we were defining, rebuilt the
app, and all works without a hitch.
> ...
>
> read more »
and JRE, didn't realize the JRE was bundled in with the Sun-downloaded
JDK. Got rid of the extraneous JRE_HOME we were defining, rebuilt the
app, and all works without a hitch.
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