Thumbnails not available

[Andrey Fedorov]

I installed XNAT following instructions, and all things seem to be working except I do not have the thumbnail previews of the series.

Any hints what could have gone wrong and how to fix this?

[Herrick, Rick]

Hey Andrey,

If you don't have thumbnails, then most likely something is failing in your autorun pipeline, which by default just generates the thumbnail snapshots. Check whether your scan has a failed workflow associated with it (check the History section on the session page or just look at the top of the session and see if there's a *Failed* message there). 

You can also check the application.log in TOMCAT_HOME/webapps/xnat/logs. Messages regarding failed pipeline execution are usually logged there. That will give you the full command-line invokation that XNAT used to run the pipeline (the password will be ******'ed out, so you'll need to replace that). You can copy the pipeline command line and paste it onto the shell or command prompt to try running the pipeline command, which will give you some visibility into what went wrong.

Lastly, you can also check the pipeline logs in PIPELINE_HOME/logs. Each pipeline run will generate its own log file, which can help you see what failed on pipeline execution. Once you resolve that, you can re-run the pipeline to get your snapshots regenerated (and, if you have a failed workflow associated with your session, clear that failed state).

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

---

From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] on behalf of Andrey Fedorov [andrey....@gmail.com]
Sent: Wednesday, June 27, 2012 8:46 AM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] Thumbnails not available

I installed XNAT following instructions, and all things seem to be working except I do not have the thumbnail previews of the series.

Any hints what could have gone wrong and how to fix this?

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[Anda Pacurar]

Hi

This is what have worked for me:

# edit the location tag in AutoRun.xml  in $XNAT_HOME/pipeline/catalog/xnat_tools/

# drop the jwsClasses in $TOMCAT/webapps/xnat/WEB-INF/jwsClasses/axis

ftp://ftp.rotman-baycrest.on.ca/pub/anda/jwsClasses/axis/

All the classes should be stored under $TOMCAT/webapps/xnat/WEB-INF/jwsClasses/axis/ folder 

# rebuild the installation

#eventually run manually the archive procedure and check if the log files are created in  $XNAT_HOME/pipeline/logs

Anda

On Wed, Jun 27, 2012 at 9:46 AM, Andrey Fedorov <andrey....@gmail.com> wrote:

I installed XNAT following instructions, and all things seem to be working except I do not have the thumbnail previews of the series.

Any hints what could have gone wrong and how to fix this?

--

You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
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Thank you

Anda

[Andrey Fedorov]

On Wednesday, June 27, 2012 10:19:43 AM UTC-4, Rick Herrick wrote:

If you don't have thumbnails, then most likely something is failing in your autorun pipeline, which by default just generates the thumbnail snapshots. Check whether your scan has a failed workflow associated with it (check the History section on the session page or just look at the top of the session and see if there's a *Failed* message there). 

There are no "Failed" messages, the session looks clean (see screenshot attached).

But I have also just discovered that when I try to assign a study from Prearchive to a project, the list of subjects is not populated in the image session creation form, even though the project has subjects (see screenshots 2 and 3). Could I mess up the database with the update scripts, as I was trying to add a new datatype?

 

You can also check the application.log in TOMCAT_HOME/webapps/xnat/logs. Messages regarding failed pipeline execution are usually logged there. That will give you the full command-line invokation that XNAT used to run the pipeline (the password will be ******'ed out, so you'll need to replace that). You can copy the pipeline command line and paste it onto the shell or command prompt to try running the pipeline command, which will give you some visibility into what went wrong.

application.log is empty, here are all the logs I have in that directory.

I am not sure how to interpret this, since the dataset was uploaded on June 17, and there is no log with that modification date.

When I look at the earlier dated logs, I do see errors:

2012-06-13 18:39:20,064 [XNAT_DICOM-4] ERROR org.nrg.dcm.Decompress - No library support for decompressing DICOM images

java.lang.NoClassDefFoundError: com/sun/media/imageio/stream/StreamSegmentMapper

at org.dcm4che2.imageioimpl.plugins.dcm.DicomImageReaderSpi.createReaderInstance(DicomImageReaderSpi.java:146)

and

2012-06-12 23:59:54,497 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-3] ERROR org.quartz.core.JobRunShell - Job prearchive-jobs.session-rebuilder threw an unhandled Exception: 

java.lang.NullPointerException

at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:67)

at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)

at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)

at org.quartz.core.JobRunShell.run(JobRunShell.java:216)

here's the list of log files:

-rw-r--r--.  1 xnat xnat   11264 Jun 27 15:04 access.log

-rw-r--r--.  1 xnat xnat   45679 Jun  8 19:05 access.log.2012-06-08

-rw-r--r--.  1 xnat xnat   18954 Jun 13 18:49 access.log.2012-06-13

-rw-r--r--.  1 xnat xnat     493 Jun 14 19:08 access.log.2012-06-14

-rw-r--r--.  1 xnat xnat   33929 Jun 17 18:11 access.log.2012-06-17

-rw-r--r--.  1 xnat xnat    2133 Jun 25 19:11 access.log.2012-06-25

-rw-r--r--.  1 xnat xnat    3416 Jun 26 19:19 access.log.2012-06-26

-rw-r--r--.  1 xnat xnat       0 Jun 26 19:18 application.log

-rw-r--r--.  1 xnat xnat   43581 Jun  8 18:51 application.log.2012-06-08

-rw-r--r--.  1 xnat xnat 1344678 Jun 12 23:59 application.log.2012-06-12

-rw-r--r--.  1 xnat xnat    1610 Jun 13 18:39 application.log.2012-06-13

-rw-r--r--.  1 xnat xnat       0 Jun 26 19:18 avalon.log

-rw-r--r--.  1 xnat xnat    1101 Jun 26 19:19 axis.log

-rw-r--r--.  1 xnat xnat     184 Jun 13 09:43 axis.log.2012-06-08

-rw-r--r--.  1 xnat xnat     734 Jun 13 18:37 axis.log.2012-06-13

drwxr-xr-x.  2 xnat xnat    4096 Jun 17 18:08 inserts

-rw-r--r--.  1 xnat xnat       0 Jun 26 19:18 scheduler.log

-rw-r--r--.  1 xnat xnat    7248 Jun 26 19:18 sql.log

-rw-r--r--.  1 xnat xnat    1208 Jun  8 18:17 sql.log.2012-06-08

-rw-r--r--.  1 xnat xnat  212048 Jun 12 23:59 sql.log.2012-06-12

-rw-r--r--.  1 xnat xnat  180275 Jun 13 18:47 sql.log.2012-06-13

-rw-r--r--.  1 xnat xnat     484 Jun 17 16:54 sql.log.2012-06-17

-rw-r--r--.  1 xnat xnat   14252 Jun 27 15:04 turbine.log

-rw-r--r--.  1 xnat xnat   19599 Jun 13 18:49 turbine.log.2012-06-13

-rw-r--r--.  1 xnat xnat       0 Jun 26 19:18 turbine.log.2012-06-26

-rw-r--r--.  1 xnat xnat   33051 Jun 27 15:04 velocity.log

-rw-r--r--.  1 xnat xnat   41855 Jun 13 18:49 velocity.log.2012-06-13

-rw-r--r--.  1 xnat xnat     813 Jun 14 19:15 velocity.log.2012-06-14

-rw-r--r--.  1 xnat xnat  160597 Jun 17 19:07 velocity.log.2012-06-17

-rw-r--r--.  1 xnat xnat     999 Jun 26 19:19 velocity.log.2012-06-26

-rw-r--r--.  1 xnat xnat    2729 Jun 26 17:09 xdat.log

-rw-r--r--.  1 xnat xnat  127896 Jun  8 18:55 xdat.log.2012-06-08

-rw-r--r--.  1 xnat xnat 5850790 Jun 12 23:59 xdat.log.2012-06-12

-rw-r--r--.  1 xnat xnat 3749658 Jun 13 18:49 xdat.log.2012-06-13

-rw-r--r--.  1 xnat xnat    5559 Jun 17 18:05 xdat.log.2012-06-17

-rw-r--r--.  1 xnat xnat       0 Jun 26 19:18 xnatfs.log

 

Lastly, you can also check the pipeline logs in PIPELINE_HOME/logs. Each pipeline run will generate its own log file, which can help you see what failed on pipeline execution. Once you resolve that, you can re-run the pipeline to get your snapshots regenerated (and, if you have a failed workflow associated with your session, clear that failed state).

Here's the full error from the pipeline log

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.net.ConnectException: Connection refused

 faultActor: 

 faultNode: 

 faultDetail: 

{http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: Connection refused

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)

at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)

at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)

at java.net.Socket.connect(Socket.java:579)

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:601)

at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:153)

at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)

at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)

at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)

at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)

at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)

at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)

at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)

at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)

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:120)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:45)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:265)

{http://xml.apache.org/axis/}hostname:localhost.localdomain

java.net.ConnectException: Connection refused

at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)

at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)

at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)

at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)

at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)

at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)

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:120)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:45)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:265)

Caused by: java.net.ConnectException: Connection refused

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)

at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)

at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)

at java.net.Socket.connect(Socket.java:579)

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:601)

at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:153)

at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)

at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)

at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)

at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)

... 14 more

INFO main org.nrg.pipeline.utils.PipelineUtils - Loop Resolved

 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

---

From: xnat_discussion@googlegroups.com [xnat_discussion@googlegroups.com] on behalf of Andrey Fedorov [andrey....@gmail.com]

Sent: Wednesday, June 27, 2012 8:46 AM

To: xnat_discussion@googlegroups.com

Subject: [XNAT Discussion] Thumbnails not available

I installed XNAT following instructions, and all things seem to be working except I do not have the thumbnail previews of the series.

Any hints what could have gone wrong and how to fix this?

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[Andrey Fedorov]

Thanks, Anda. Do you know what is the source of the problem? What are these classes that you have provided?

In any case, looks like my installation is not quite functional at this point, need to resolve the prearchive issue first.

On Wednesday, June 27, 2012 10:23:48 AM UTC-4, anda wrote:

Hi

This is what have worked for me:

# edit the location tag in AutoRun.xml  in $XNAT_HOME/pipeline/catalog/xnat_tools/

# drop the jwsClasses in $TOMCAT/webapps/xnat/WEB-INF/jwsClasses/axis

ftp://ftp.rotman-baycrest.on.ca/pub/anda/jwsClasses/axis/

All the classes should be stored under $TOMCAT/webapps/xnat/WEB-INF/jwsClasses/axis/ folder 

# rebuild the installation

#eventually run manually the archive procedure and check if the log files are created in  $XNAT_HOME/pipeline/logs

Anda

On Wed, Jun 27, 2012 at 9:46 AM, Andrey Fedorov <andrey....@gmail.com> wrote:

I installed XNAT following instructions, and all things seem to be working except I do not have the thumbnail previews of the series.

Any hints what could have gone wrong and how to fix this?

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Thank you

Anda

[Andrey Fedorov]

I resolved the problem with thumbnails. It turned out the issue was due to my attempts to use XNAT via HTTPS with a self-issued SSL key. The first error was 'unable to find valid certification path to requested target', which I resolved following instructions here: http://nodsw.com/blog/leeland/2006/12/06-no-more-unable-find-valid-certification-path-requested-target

Next I had error  "No subject alternative names", and I was not successful to find a resolution, so I resorted to http connection, and now thumbnails are generated correctly.

Are there any instructions how to configure XNAT to work with HTTPS?

[Tim Olsen]

Self-signed certificates are often difficult to get working.  The java cert libraries can be particularly hostile to them.

 

If your pipelines are running on the same machine as your tomcat, you can get around this by having the pipelines connect back to the server over http rather than https, while the rest of your traffic would go over https.  You can do this by adding an –aliasHost variable to your pipeline pointing it to http://localhost:8080/xnat.  This way pipeline uploads don’t even need to go out over the wider network.

 

https://groups.google.com/forum/?fromgroups#!topic/xnat_discussion/2m2CAMq710U

 

Tim

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Thank you

Anda

 

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[Torsten Rohlfing]

Tim:

We've had the same problem here, and I'd like to apply your workaround. Can you give me a quick pointer what file needs to be changed for this to work? (We're running XNAT 1.6).

Thanks!
  Torsten

[Herrick, Rick]

Torsten,

 

Add that to your XnatPipelineLauncher script in the bin folder of your pipeline installation. At the end of that script, you’ll see something like this:

 

java … org.nrg.pipeline.client.XNATPipelineLauncher -config xxx/pipeline.config  -log xxx/log4j.properties -catalogPath xxx/catalog $@

 

After the “-catalogPath xxx/catalog” and before the $@ (or %* on Windows), add:

 

-aliasHost http://localhost:8080/xnat

 

Or whatever the non-SSL path is…

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