Protocol Validation Pipeline & XNAT 1.8.7

[Alex]

Hi,

We had the Protocol Validation pipeline installed and working on XNAT 1.8.4. After the upgrade to 1.8.7.1, when I attempt to run the pipeline I get the attached error and the following exception in the log:

*********************************

java.lang.ClassNotFoundException:
        Requested Screen not found: Default
        Turbine looked in the following modules.packages path:
        [org.apache.turbine.app.xnat.modules, org.nrg.xnat.turbine.modules, org.nrg.xdat.turbine.modules, org.apache.turbine.app.xnat17.modules, org.apache.turbine.modules]
        at org.apache.turbine.modules.ScreenLoader.getInstance(ScreenLoader.java:196)
        at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:142)
        at org.apache.turbine.modules.Page.build(Page.java:56)

*********************************

It could be that the error and the upgrade is a coincidence, but I can't think of any other changes made to the instance. 

Any pointers on troubleshooting this issue?

Somewhat related: since the pipeline engine will not be supported in XNAT 1.9, are there any plans for a Protocol Validation container that can be launched via the Container Service?

Thank you, 

Alex

[Charlie Moore]

Hi Alex,

Does upgrading to 1.8.8 of both XNAT and the pipeline engine resolve the issue for you?

Thanks,

Charlie Moore

[Alex Kogan]

Hi Charlie,

I upgraded to the latest pipeline engine and XNAT 1.8.8, but the problem persists. Now I suspect that it's not related to the XNAT version as I discovered that I ended up with two versions of the same Protocol Validation pipeline in different projects. In one project the pipeline works and in the other project it doesn't. I queried /pipelines/project/{projectId} to see what the difference is and here are the results from both projects:

The working pipeline:

{
  "ResultSet": {
    "Result": [
      {
        "Path": "/var/lib/nunda/pipeline/catalog/validation_tools/Validate.xml",
        "Generates": "",
        "Description": "This pipeline will check the experiment for acquisition parameters. This pipeline is Schematron based and generates a ProtocolValidation assessor. ",
        "StepId": "AUTO_ARCHIVE_PROTOCOLCHECK",
        "Applies To": "All Datatypes",
        "Descendant": "All Datatypes",
        "Name": "ProtocolCheck",
        "Datatype": "All Datatypes"
      }
    ]
  }
}


The broken pipeline:

{
  "ResultSet": {
    "Result": [
      {
        "Path": "/var/lib/nunda/pipeline/catalog/validation_tools/Validate.xml",
        "Generates": "",
        "Description": "This pipeline will check the experiment for acquisition parameters. This pipeline is Schematron based and generates a ProtocolValidation assessor. ",
        "StepId": "Validate",
        "Applies To": "All Datatypes",
        "Descendant": "All Datatypes",
        "Name": "Validate",
        "Datatype": "All Datatypes"
      }
    ]
  }
}

I tried deleting and re-adding the pipeline to the project where it doesn't work - it made no difference. Both pipelines seem to refer to the same xml file. Any idea what is going on here?

Thank you,

Alex

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[Alex]

Just to provide a conclusion, I figured out how to fix this problem. Instead of trying to figure out why the pipeline worked in some projects and not in others, I removed the pipeline from the instance completely, made sure the pipeline engine updated to the latest version, restarted the application server, and then re-added the pipeline to the instance and then to the relevant projects. Everything was working as expected after that. 

[Ajay Kurani]

Hi XNAT Experts,

   When updating XNAT to v1.8.8 there was also an update to the pipeline engine.  As I was under the impression pipeline engine will be phased out in v1.9, I wanted to better understand if there are plans to keep pipeline engine/schematron functionality moving forward.  Alternatively, if the pipeline engine is still being phased out, are there plans to build a container to replace schematron functionality?  This info would help us to plan if we need to start developing containers internally or focus on other pipelines as to not duplicate efforts by the XNAT team.  Any insights would be greatly appreciated!

Sincerely,

Ajay

[Kate Alpert]

Hi, Ajay,

While the pipeline engine is deprecated, we are aware that the community still uses it (in particular, to run HPC jobs). As such, we have continued to make small patches when necessary. We do plan to EOL the pipeline engine and recommend using container service wherever possible.

To your specific question, protocol validation via container is on our radar, but it isn't at the top of the priority list right now. We'd love a community contribution in this vein!

Best,

Kate