"Add experiment" screen is empty // Deletion manager is empty for MRSessions
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Alina
Feb 8, 2012, 3:41:46 PM2/8/12
to xnat_discussion
Dear all,
I'm running two parallel versions of XNAT 1.5.3 on the same Ubuntu
Lucid Lynx system. In one of them,
(i) the Deletion Manager only shows an empty window on the MRSession
Level,
(ii) the "Add experiment" screen is empty (no experiments visible),
(iii) the "Options"-Box in the tabular view of a project only offers
"Spreadsheet" - all other options are missing.
I know that this sounds fairly disconnected but my gut feeling is,
that it has to be somehow connected - therefore I chose to report it
in one message.
Background: Both XNAT versions were generated from the same tar ball,
but use different databases. One uses our current image data base
(which was taken over from an earlier version) and the test version
uses a newly created database with a few test data sets.
I've added two custom data types, which show up fine in both XNATs.
They are displayed correctly in every view and can be added via
spreadsheet upload in both versions. The "Add experiment"-Link only
works in the test version. In the "official" version it comes back
empty and reports an error ("An error has occurred.").
Also, the deletion manager on MRSession level only displays an empty
screen in the official version. Everything works nicely in the test
version.
I've tried recreating XNAT from scratch several times, but it doesn't
change anything. The only difference I can think of, is that there is
a discarded data type on the official version, which I would like to
get rid of, as I think that it interferes with the new datatypes.
Unfortunately, I'm not very versed with postgres, so I haven't dared
to mess with the official database. I wouldn't know where to begin
anyway! About the only thing I can do is display tables, views and the
likes.
There is also a very weird thing happening in one of the new
datatypes. I don't think it's related to the errors reported above as
it is the same on both versions, but since things tend to be
mysterious with computers, I mention it anyway: I tried to define an
arc like this:
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
<Bridge-Element name="ncrc:lesionsAssessmentData"
field="SESSION_ID"/>
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
That worked nicely for the first customized data type, but it does not
work for this one. It only compiles, if I add the quoted paragraph
with xnat:mrSession instead of my customized name.
In case anyone managed to read until here - it's very much
appreciated. I'm lost and I'd be grateful for any ideas.
Thanks a lot!
I'm running two parallel versions of XNAT 1.5.3 on the same Ubuntu
Lucid Lynx system. In one of them,
(i) the Deletion Manager only shows an empty window on the MRSession
Level,
(ii) the "Add experiment" screen is empty (no experiments visible),
(iii) the "Options"-Box in the tabular view of a project only offers
"Spreadsheet" - all other options are missing.
I know that this sounds fairly disconnected but my gut feeling is,
that it has to be somehow connected - therefore I chose to report it
in one message.
Background: Both XNAT versions were generated from the same tar ball,
but use different databases. One uses our current image data base
(which was taken over from an earlier version) and the test version
uses a newly created database with a few test data sets.
I've added two custom data types, which show up fine in both XNATs.
They are displayed correctly in every view and can be added via
spreadsheet upload in both versions. The "Add experiment"-Link only
works in the test version. In the "official" version it comes back
empty and reports an error ("An error has occurred.").
Also, the deletion manager on MRSession level only displays an empty
screen in the official version. Everything works nicely in the test
version.
I've tried recreating XNAT from scratch several times, but it doesn't
change anything. The only difference I can think of, is that there is
a discarded data type on the official version, which I would like to
get rid of, as I think that it interferes with the new datatypes.
Unfortunately, I'm not very versed with postgres, so I haven't dared
to mess with the official database. I wouldn't know where to begin
anyway! About the only thing I can do is display tables, views and the
likes.
There is also a very weird thing happening in one of the new
datatypes. I don't think it's related to the errors reported above as
it is the same on both versions, but since things tend to be
mysterious with computers, I mention it anyway: I tried to define an
arc like this:
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
<Bridge-Element name="ncrc:lesionsAssessmentData"
field="SESSION_ID"/>
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
That worked nicely for the first customized data type, but it does not
work for this one. It only compiles, if I add the quoted paragraph
with xnat:mrSession instead of my customized name.
In case anyone managed to read until here - it's very much
appreciated. I'm lost and I'd be grateful for any ideas.
Thanks a lot!
Rick Herrick
Feb 8, 2012, 4:41:18 PM2/8/12
to xnat_di...@googlegroups.com
Do you see any errors generated in the log files when you attempt the operations that are failing?
Jordan Woerndle
Feb 8, 2012, 4:16:15 PM2/8/12
to xnat_di...@googlegroups.com
Hi Alina,
Are you getting any messages in any of the log files located in <tomcat>/webapps/xnat(broken)/logs ? If so, can you send them, too?
Are you getting any messages in any of the log files located in <tomcat>/webapps/xnat(broken)/logs ? If so, can you send them, too?
Thanks,
jordan
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deech
Feb 8, 2012, 10:52:18 PM2/8/12
to xnat_di...@googlegroups.com
Hi Alina,
You say you have two parallel XNATs? Are they sitting in the same webapps folder in your Tomcat directory? If so, this has been known to cause problems. You can have at most one XNAT instance in your $TOMCAT_HOME.
-deech
You say you have two parallel XNATs? Are they sitting in the same webapps folder in your Tomcat directory? If so, this has been known to cause problems. You can have at most one XNAT instance in your $TOMCAT_HOME.
-deech
deech
Feb 8, 2012, 10:53:53 PM2/8/12
to xnat_di...@googlegroups.com
Also you do have multiple XNAT's in the same webapps folder the log entries for one have been known to show up in the other's log files.
-deech
-deech
Jörg Stadler
Feb 9, 2012, 3:04:55 AM2/9/12
to xnat_di...@googlegroups.com
> Also you do have multiple XNAT's in the same webapps folder the log
> entries for one have been known to show up in the other's log files.
> entries for one have been known to show up in the other's log files.
Oh. We are running two XNAT's in the same webapps folder. I saw that the
log entries appear only in one log dir and the second one is empty, but
no other errors so far (knock on wood).
What errors can happen by running two XNAT's?
Best,
Joerg
Alina
Feb 9, 2012, 5:07:14 AM2/9/12
to xnat_discussion
Thank you for the hints about two XNATs in the same webapp-folder. I
wanted to include log file entries, but all my logfiles for the
official version were empty - now I know why :).
I've managed to solve the problem (i), (ii) and (iii) by also adding
one of my customized data types under the old name. Somehow there were
apparently remnants of it in the database. Now I have two data types
which are exactly the same, but I think that doesn't pose much of a
problem. The log file problem will solve itself as I'm going to delete
the testversion soon.
However, I'm still left with the "arc"-problem. Without the
xnat:mrSession in the arc, the compiler fails with this helpful
message:
BUILD FAILED
File...... /opt/xnat/xnat_153_release/xnat/maven.xml
Element... java
Line...... 924
Column.... 93
Java returned: 1
Total time: 34 seconds
Finished at: Thu Feb 09 10:39:13 CET 2012
About the only thing, that looks like an error message to me is
this: [java] Exception in thread "main" java.lang.StackOverflowError
And here are the last 250 lines of what I assume to be the
compiler.log:
ERROR org.apache.turbine.services.velocity.TurbineVelocityService -
Class java.util.ArrayList.get threw Exception
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:
104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
at org.apache.turbine.Turbine.doGet(Turbine.java:751)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
243)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
201)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
470)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
163)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
108)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
556)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
401)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
242)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:267)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:245)
at org.apache.tomcat.util.net.JIoEndpoint
$SocketProcessor.run(JIoEndpoint.java:260)
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)
2012-02-09 10:48:23,913 [http-8080-exec-8] ERROR
org.apache.turbine.services.velocity.TurbineVelocityService - Class
java.util.ArrayList.get threw Exception
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:
104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
at
org.nrg.xnat.restlet.representations.TurbineScreenRepresentation.turbineScreen(TurbineScreenRepresentation.java:
60)
at
org.nrg.xnat.restlet.representations.TurbineScreenRepresentation.write(TurbineScreenRepresentation.java:
120)
at
com.noelios.restlet.http.HttpServerCall.writeResponseBody(HttpServerCall.java:
492)
at
com.noelios.restlet.http.HttpServerCall.sendResponse(HttpServerCall.java:
428)
at
com.noelios.restlet.ext.servlet.ServletCall.sendResponse(ServletCall.java:
421)
at
com.noelios.restlet.http.HttpServerConverter.commit(HttpServerConverter.java:
392)
at
com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:
148)
at
com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.java:
881)
at
org.nrg.xnat.restlet.servlet.XNATRestletServlet.service(XNATRestletServlet.java:
99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
243)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
201)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
470)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
163)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
108)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
556)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
401)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
242)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:267)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:245)
at org.apache.tomcat.util.net.JIoEndpoint
$SocketProcessor.run(JIoEndpoint.java:260)
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)
Thanks :),
Alina
wanted to include log file entries, but all my logfiles for the
official version were empty - now I know why :).
I've managed to solve the problem (i), (ii) and (iii) by also adding
one of my customized data types under the old name. Somehow there were
apparently remnants of it in the database. Now I have two data types
which are exactly the same, but I think that doesn't pose much of a
problem. The log file problem will solve itself as I'm going to delete
the testversion soon.
However, I'm still left with the "arc"-problem. Without the
xnat:mrSession in the arc, the compiler fails with this helpful
message:
BUILD FAILED
File...... /opt/xnat/xnat_153_release/xnat/maven.xml
Element... java
Line...... 924
Column.... 93
Java returned: 1
Total time: 34 seconds
Finished at: Thu Feb 09 10:39:13 CET 2012
About the only thing, that looks like an error message to me is
this: [java] Exception in thread "main" java.lang.StackOverflowError
And here are the last 250 lines of what I assume to be the
compiler.log:
ERROR org.apache.turbine.services.velocity.TurbineVelocityService -
Class java.util.ArrayList.get threw Exception
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:
104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
at org.apache.turbine.Turbine.doGet(Turbine.java:751)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
243)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
201)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
470)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
163)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
108)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
556)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
401)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
242)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:267)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:245)
at org.apache.tomcat.util.net.JIoEndpoint
$SocketProcessor.run(JIoEndpoint.java:260)
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)
2012-02-09 10:48:23,913 [http-8080-exec-8] ERROR
org.apache.turbine.services.velocity.TurbineVelocityService - Class
java.util.ArrayList.get threw Exception
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:
104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
at
org.nrg.xnat.restlet.representations.TurbineScreenRepresentation.turbineScreen(TurbineScreenRepresentation.java:
60)
at
org.nrg.xnat.restlet.representations.TurbineScreenRepresentation.write(TurbineScreenRepresentation.java:
120)
at
com.noelios.restlet.http.HttpServerCall.writeResponseBody(HttpServerCall.java:
492)
at
com.noelios.restlet.http.HttpServerCall.sendResponse(HttpServerCall.java:
428)
at
com.noelios.restlet.ext.servlet.ServletCall.sendResponse(ServletCall.java:
421)
at
com.noelios.restlet.http.HttpServerConverter.commit(HttpServerConverter.java:
392)
at
com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:
148)
at
com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.java:
881)
at
org.nrg.xnat.restlet.servlet.XNATRestletServlet.service(XNATRestletServlet.java:
99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
243)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
201)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
470)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
163)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
108)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
556)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
401)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
242)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:267)
at org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:245)
at org.apache.tomcat.util.net.JIoEndpoint
$SocketProcessor.run(JIoEndpoint.java:260)
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)
Thanks :),
Alina
Olsen, Tim
Feb 9, 2012, 10:41:45 AM2/9/12
to xnat_di...@googlegroups.com
I think the only issue here would be the logger issues. Otherwise, it should be fine to have two instances in the same webapp.
TIm
Best,
Joerg
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Olsen, Tim
Feb 9, 2012, 11:00:09 AM2/9/12
to xnat_di...@googlegroups.com
There's a bug in the current version of XNAT with deleting data-types from the Managed Data-types. It would cause the kind of symptoms you were seeing. Until its resolved, you can uncheck the Browseable and Searchable checkboxes in the Data-types section for that data-type and it should essentially disappear from your site.
Regarding your arc problem, I'd like to review what you are trying to do. Can you send your schema and an example display document?
Tim
Thanks :),
Alina
--
Alina
Mar 8, 2012, 10:57:21 AM3/8/12
to xnat_discussion
Hi Tim,
please excuse my long silence, I got hung up with other things
following a longer absence. But now I'm back to XNAT! I unchecked the
relevant boxes and with the old datatype "silently" added the rest
works nicely. All my menus are back to normal.
Here is my schema in the "arc" problem case:
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema targetNamespace="http://nrg.wustl.edu/ncrc"
xmlns:ncrc="http://nrg.wustl.edu/ncrc" xmlns:xdat="http://
nrg.wustl.edu/xdat"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xnat="http://
nrg.wustl.edu/xnat"
elementFormDefault="qualified"
attributeFormDefault="unqualified">
<xs:import namespace="http://nrg.wustl.edu/xnat"
schemaLocation="../lesions/lesions.xsd" />
<xs:element name="Lesions" type="ncrc:lesionsAssessmentData"></
xs:element>
<xs:complexType name="lesionsAssessmentData">
<xs:complexContent>
<xs:extension base="xnat:subjectAssessorData">
<xs:attribute name="T2_count"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T2_volume"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T1_GD_count"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T1_GD_volume"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="comment"
type="xs:string" use="optional"></xs:attribute>
<xs:attribute name="software_used"
type="xs:string" use="optional"></xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:schema>
And here is the the arc-session of the display. Do you really want me
to copy the entire display xml to an email? That would be 231 lines,
so I wanted to make sure before "spamming" the list.
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
<Bridge-Element name="ncrc:lesionsAssessmentData"
field="SESSION_ID"/>
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
<Bridge-Element name="xnat:mrSessionData"
Kind regards,
Alina
please excuse my long silence, I got hung up with other things
following a longer absence. But now I'm back to XNAT! I unchecked the
relevant boxes and with the old datatype "silently" added the rest
works nicely. All my menus are back to normal.
Here is my schema in the "arc" problem case:
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema targetNamespace="http://nrg.wustl.edu/ncrc"
xmlns:ncrc="http://nrg.wustl.edu/ncrc" xmlns:xdat="http://
nrg.wustl.edu/xdat"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xnat="http://
nrg.wustl.edu/xnat"
elementFormDefault="qualified"
attributeFormDefault="unqualified">
<xs:import namespace="http://nrg.wustl.edu/xnat"
schemaLocation="../lesions/lesions.xsd" />
<xs:element name="Lesions" type="ncrc:lesionsAssessmentData"></
xs:element>
<xs:complexType name="lesionsAssessmentData">
<xs:complexContent>
<xs:extension base="xnat:subjectAssessorData">
<xs:attribute name="T2_count"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T2_volume"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T1_GD_count"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="T1_GD_volume"
type="xs:double" use="optional"></xs:attribute>
<xs:attribute name="comment"
type="xs:string" use="optional"></xs:attribute>
<xs:attribute name="software_used"
type="xs:string" use="optional"></xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:schema>
And here is the the arc-session of the display. Do you really want me
to copy the entire display xml to an email? That would be 231 lines,
so I wanted to make sure before "spamming" the list.
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
<Bridge-Element name="ncrc:lesionsAssessmentData"
field="SESSION_ID"/>
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
<Arc-Definition Id="ASSESSOR">
<CommonField id="EXPT_ID" type="STRING"/>
<CommonField id="ASSESSED_EXPT_ID" type="STRING"/>
field="SESSION_ID"/>
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
Thank you for any thoughts.
<Filter field="EXPT_ID" filterType="distinct"/>
<Filter field="ASSESSED_EXPT_ID" filterType="equals"/>
</Arc-Definition>
<Arc name="PARTICIPANT_EXPERIMENT">
<CommonField id="PART_ID" local-field="SUBJECT_ID"/>
<CommonField id="DATE" local-field="DATE"/>
<CommonField id="EXPT_ID" local-field="SESSION_ID"/>
</Arc>
Kind regards,
Alina
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