Pipelines and XNAT 1.10.0

[Ben Wagner]

Hi XNAT,

  Are there any issues with running the classic pipeline engine with the recent 1.10 update?  I've getting pipelines stuck in queue.  Logs are showing this error below.

Thanks,

Ben

DEBUG main org.nrg.pipeline.client.CommandLineArguments - Pipeline executed with command line: -config /XNAT/BIDS/XNAT_HOME/pipeline/pipeline.config -log /XNAT/BIDS/XNAT_HOME/pipeline/log4j.properties -catalogPath /XNAT/BIDS/XNAT_HOME/pipeline/catalog -pipeline /XNAT/BIDS/XNAT_HOME/pipeline/catalog/ansir/AnsirWorkflow_pipeline_20260316.xml -id ANSIRBIDS_E00031 -host https://ansirbids.biohpc.swmed.edu:8443/xnat -u bb8fd544-8428-4e9d-8db1-03cd09f1955c -pwd XXXXXXXXX -dataType xnat:megSessionData -label LONG_0014_20240604_MEG -supressNotification -project LONG -parameterFile /XNAT/BIDS/XNAT_DATA/build/LONG/20260616_121813/LONG_0014_20240604_MEG/LONG_0014_20240604_MEG_params_20260616.xml -parameter mailhost=localhost -parameter userfullname=P.Pipeline -parameter builddir=/XNAT/BIDS/XNAT_DATA/build/LONG/20260616_121813/ -parameter xnatserver=ANSIRBIDS -parameter adminemail=ben.w...@utsouthwestern.edu -parameter useremail=ben.w...@utsouthwestern.edu -workFlowPrimaryKey 7022
DEBUG main org.nrg.pipeline.utils.PipelineProperties - Initializing the pipeline properties from the specified properties object
DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting admin email to: Ben.W...@utsouthwestern.edu
DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting email ID to: Ben.W...@utsouthwestern.edu
DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting SMTP host to: localhost
DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting REST mail host to: https://ansirbids.biohpc.swmed.edu:8443/xnat/data/services/mail/send
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldn't search for queued workflows
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
        at org.nrg.xnattools.SessionManager.setSessionExpirationTime(SessionManager.java:122)
        at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:90)
        at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
        at org.nrg.xnattools.service.WebServiceClient.connect(WebServiceClient.java:84)
        at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:368)
        at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:352)
        at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:61)
        at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:298)
        at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:260)

[Timothy Olsen]

I don't have it handy to test.

Its worth noting, the pipeline engine likely still needs jdk8.  We didn't do anything to upgrade it.  But, @Mohana Ramaratnam may be able to give more prespective when she gets online (she is in India).

Tim

Timothy R Olsen 

Founder, President

 t...@xnatworks.io

 xnatworks.io | Find us on LinkedIn! 

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[Rick Herrick]

Could you try this? On the server where the pipeline engine runs, try the following command:

curl --cookie-jar cookies.txt --cookie cookies.txt <SERVER>

Then do:

cat cookies.txt

You should see something like this:

# Netscape HTTP Cookie File
# https://curl.se/docs/http-cookies.html
# This file was generated by libcurl! Edit at your own risk.

<SERVER>   FALSE   /   TRUE    0   SESSION_EXPIRATION_TIME 1781635983373
#HttpOnly_<SERVER> FALSE   /   TRUE    0   JSESSIONID  7716FD5887A60C7E81D69A9E14E625AC

Somehow it's not getting that SESSION_EXPIRATION_TIME cookie back on the response and that's causing the error. But XNAT sends that cookie along with the JSESSIONID with every response, whether or not you've authenticated or whatever else, so I'm wondering what will be in those captured cookies.

Rick Herrick 

Senior Software Developer

ri...@xnatworks.io

https://xnatworks.io | Find us on LinkedIn! 

On Tue, Jun 16, 2026 at 12:31 PM Ben Wagner <thewa...@gmail.com> wrote:

--

[Ben Wagner]

Hi Rick and Tim,

  I tried running the pipeline call in pipeline.log call that failed under java 1.8 (/XNAT/BIDS/XNAT_HOME/pipeline/bin/schedule /XNAT/BIDS/XNAT_HOME/pipeline/bin/XnatPipelineLauncher...) and got the same error.  Here are the results of several curl requests:

[ansir_bids@ansirbids tmp]$ curl --cookie-jar cookies.txt --cookie cookies.txt https://ansirbids.biohpc.swmed.edu:8443/xnat

[ansir_bids@ansirbids tmp]$ cat cookies.txt

# Netscape HTTP Cookie File
# https://curl.se/docs/http-cookies.html
# This file was generated by libcurl! Edit at your own risk.

[ansir_bids@ansirbids tmp]$ curl --cookie-jar cookies.txt --cookie cookies.txt https://ansirbids.biohpc.swmed.edu:8443/xnat/data/projects
<SNIP>HTTP Status 401 – Unauthorized</SNIP>

[ansir_bids@ansirbids tmp]$ cat cookies.txt

# Netscape HTTP Cookie File
# https://curl.se/docs/http-cookies.html
# This file was generated by libcurl! Edit at your own risk.

ansirbids.biohpc.swmed.edu      FALSE   /xnat/  TRUE    0       SESSION_EXPIRATION_TIME 1781637232283
#HttpOnly_ansirbids.biohpc.swmed.edu    FALSE   /xnat   TRUE    0       JSESSIONID      7179BF2784878B3005563A41987CE769


[ansir_bids@ansirbids tmp]$ curl -u 'UUU:PPP' --cookie-jar cookies.txt --cookie cookies.txt https://ansirbids.biohpc.swmed.edu:8443/xnat/data/projects
{"ResultSet":{"Result":<SNIPPED>, "totalRecords": "2"}}

[ansir_bids@ansirbids tmp]$ cat cookies.txt

# Netscape HTTP Cookie File
# https://curl.se/docs/http-cookies.html
# This file was generated by libcurl! Edit at your own risk.

#HttpOnly_ansirbids.biohpc.swmed.edu    FALSE   /xnat   TRUE    0       JSESSIONID      2322B8E3A7AFE7B6AF54869CFF32CFA3
ansirbids.biohpc.swmed.edu      FALSE   /xnat/  TRUE    0       SESSION_EXPIRATION_TIME 1781637262294

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[George Kowalski]

This started for me with the 1.9.3.5 upgrade. Still working thru at which version it really beaks 1.9.3.0 ... 

[Ben Wagner]

I've created a pull (https://github.com/NrgXnat/pipeline-xnattools/pull/3) with codex help that seems to be working for me.  

Ben

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[Rick Herrick]

Thanks Ben, we'll look into getting an updated build out, but for anyone who needs this now you can pull the code with Ben's commit, build a new jar with Maven and Java, then just replace the jar in your pipeline engine installation with the newly built jar.

Rick Herrick 

Senior Software Developer

ri...@xnatworks.io

https://xnatworks.io | Find us on LinkedIn! 

To view this discussion visit https://groups.google.com/d/msgid/xnat_discussion/CADVL1QzMURMR2d6DwSMGM0Ndjt2_0MhH-TVSJ%2BKEEzpADOrMyQ%40mail.gmail.com.

[Mohana Ramaratnam]

Hi Ben,

Thanks for your contribution. We have a new release of the xnattools jar here:

https://github.com/NrgXnat/pipeline-xnattools/releases/tag/1.9.0

Regards,
Mohana Ramaratnam,

 moh...@xnatworks.io
 xnatworks.io | Find us on LinkedIn! 

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