Cannot run pipeline on 1.7-snapshot
Bogdan Mitrea
/xnat/pipeline/xnat-tools/XnatDataClient -r "http://xnat.url/xnat//data/experiments/XNAT_E00001/scans/6/resources/DICOM/files" -m GET -b -a -s D2577B5E3DDD383B9DA3EB662E57CFDE
and this is the error message:
--------------------------------------------------------------------------------------
Exception in thread "main" java.lang.NoClassDefFoundError: com/fasterxml/jackson/databind/ObjectMapper
at org.nrg.xnat.client.data.XnatDataClient.handleBatchTransfer(XnatDataClient.java:319)
at org.nrg.xnat.client.data.XnatDataClient.handleEntity(XnatDataClient.java:300)
at org.nrg.xnat.client.data.XnatDataClient.launch(XnatDataClient.java:165)
at org.nrg.xnat.client.data.XnatDataClient.main(XnatDataClient.java:90)
Caused by: java.lang.ClassNotFoundException: com.fasterxml.jackson.databind.ObjectMapper
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 4 more
I noticed the additional '/' in the URI but I don't know how it got there and if it triggers the exception.
Any help is appreciated.
Thank you.
Bogdan
Herrick, Rick
Hi Bogdan,
That’s a bug in the pipeline configuration. There’s a missing dependency in the XnatDataClient script. I updated the download bundle, which you can get from https://bitbucket.org/xnatdev/xnat-pipeline/downloads. Try replacing your pipeline source folder with the contents of that zip file and try again.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
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Bogdan Mitrea
Exception in thread "main" java.lang.NoClassDefFoundError: org/springframework/util/MultiValueMap
at org.nrg.pipeline.utils.MailUtils.setMailService(MailUtils.java:150)
at org.nrg.pipeline.client.CommandLineArguments.<init>(CommandLineArguments.java:246)
at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:258)
Caused by: java.lang.ClassNotFoundException: org.springframework.util.MultiValueMap
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 3 more
Spiro Pantazatos
Bogdan Mitrea
Spiro Pantazatos
Thank you for your suggestion Spiro, but it doesn't work for me.
I went back to square one and used the xnat-dev vagrant box( from bitbucket repo). I checked out the latest version from the repositories for both the pipeline engine and xnat-web. I installed the pipeline engine using ./gradlew (and custom gradle.settings file) and deployed xnat-web using ./gradlew war deployToTomcat.
I get the same error for both the autorun pipeline and the DicomToNifiti pipeline from the catalog (pipeline.log attached).If I run the command in the terminal, I get:
Param Value Pair id=XNAT_E00001Param Value Pair host=http://10.11.5.80/Param Value Pair u=d9eed5d8-e0d5-4fd8-b889-5432638e875dParam Value Pair pwd=********Param Value Pair label=90002Param Value Pair project=brainPipeParam Value Pair mailhost=localhostParam Value Pair userfullname=A.AdminParam Value Pair builddir=/data/xnat/build/brainPipe/20160823_194201Param Value Pair xnatserver=XNATParam Value Pair adminemail=y...@yoursite.org
Param Value Pair useremail=administrator@xnat.org
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Bogdan Mitrea
Hi Bogdan,
I don't remember running the ./gradew command when installing XNAT 1.7. Did you follow the installation instructions from the 2016 workshop? Maybe the differences are in using gradle to install (vs. not)?
On Tue, Aug 23, 2016 at 4:09 PM, Bogdan Mitrea <bogdan...@gmail.com> wrote:
Thank you for your suggestion Spiro, but it doesn't work for me.
I went back to square one and used the xnat-dev vagrant box( from bitbucket repo). I checked out the latest version from the repositories for both the pipeline engine and xnat-web. I installed the pipeline engine using ./gradlew (and custom gradle.settings file) and deployed xnat-web using ./gradlew war deployToTomcat.
I get the same error for both the autorun pipeline and the DicomToNifiti pipeline from the catalog (pipeline.log attached).If I run the command in the terminal, I get:
Param Value Pair id=XNAT_E00001Param Value Pair host=http://10.11.5.80/Param Value Pair u=d9eed5d8-e0d5-4fd8-b889-5432638e875dParam Value Pair pwd=********Param Value Pair label=90002Param Value Pair project=brainPipeParam Value Pair mailhost=localhostParam Value Pair userfullname=A.AdminParam Value Pair builddir=/data/xnat/build/brainPipe/20160823_194201Param Value Pair xnatserver=XNATParam Value Pair adminemail=y...@yoursite.org
Param Value Pair useremail=admini...@xnat.org
To unsubscribe from this group and all its topics, send an email to xnat_discussi...@googlegroups.com.
Herrick, Rick
The problem you’re seeing is due to the script templates being out of sync with the versions of jars in the pipeline’s lib folder. The NoClassDefFoundError is for a class that’s in the spring-core jar, but the jar isn’t getting included because the reference is invalid. I just spent a while working through these dependencies to make sure everything resolves to something that actually exists and pushed up a new version of the pipeline installer:
https://bitbucket.org/xnatdev/xnat-pipeline/downloads/xnat-pipeline-1.7.0-SNAPSHOT.zip
Like Bogdan said, you probably wouldn’t have called ./gradlew directly, but instead called setup.sh or had setup.sh called for you by the Vagrant provisioning scripts. To fix this manually, just download and extract the zip file above. By default, I think the pipeline installer is placed in /data/xnat/src/pipeline, although you can put it wherever you want.
After that, you should delete everything from within the pipeline destination folder:
rm -rf /data/xnat/pipeline/*
You can rebuild your pipeline engine with either setup.sh or gradlew (as mentioned before, setup.sh invokes gradlew). First, change into the directory where you extracted the pipeline installer from the zip file. Running setup.sh looks like this:
./setup.sh ad...@wherever.edu mail.wherever.edu http://your.xnat.url SiteName /data/xnat/pipeline
To build with gradlew directly, you can run with everything on the command line like so:
./gradlew -PxnatUrl=http://yourxnat.url \
-PsiteName=SiteName \
-PadminEmail=ad...@wherever.edu \
-PsmtpServer=mail.wherever.edu \
-Pdestination=/data/xnat/pipeline
Or you can put all of those properties into a file named gradle.properties in the same folder with gradlew:
xnatUrl=http://yourxnat.url
siteName=SiteName
adminEmail=ad...@wherever.edu
smtpServer=mail.wherever.edu
destination=/data/xnat/pipeline
Then run gradlew on the command line:
./gradlew
This definitely fixes the issues with the default autorun pipeline.