XNAT2012 - Image Session Validation

Video: 

Goal:

At the end of this session, attendees should be able to:

• Create a schematron rule file

• Launch image session validation

Material:

• Participants will need the workshop VM

• Participants would be creating a schematron file to validate the MR Sessions in BOGUS_OUA

• Path to Schematron file /opt/xnat/workshop2012/d2s1-validation

• Online access to the above schematron file: http://hg.xnat.org/workshop2012/src/bae0e4a27fcd/d2s1-validation/mrsession_rules.sch

• /opt/xnat/pipeline_1_6/catalog/validation_tools/Validate.xml is the pipeline which enables validation.

• An assessor, val:ProtocolVal, specified  in <XNAT_HOME>/plugin-resources/project-skeletons/xnat/validation/Validation.xsd, is created which contains the validation results

• https://wiki.xnat.org/display/XNAT/Configuring+the+Protocol+Check+Pipeline

• Talk Powerpoint

Pre-requisites:

• Working knowledge of XML and XPATH

Tasks during the talk:

Step 1: Adding a pipeline to a site

We would add the pipeline /opt/xnat/pipeline_1_6/catalog/validation_tools/Validate.xml to the site

• Login to XNAT as Admin.

• Navigate to Administer -> Pipelines

• Click on Add Pipeline to Repository

• Input:
  

  • Enter Path to Pipeline descriptor xml:   /opt/xnat/pipeline_1_6/catalog/validation_tools/Validate.xml

  • Enter Name of the custom webpage to launch this pipeline: PipelineScreen_protocolcheck.vm

  • Click on Add

  • You will get a message "... was added successfully”

  • If you did everything correct, you will see ProtocolCheck listed in the pipeline repository.

 Step 2: Upload the schematron file as a resource to project BOGUS_OUA

• cd /opt/xnat/workshop2012/d2s1-validation

• /opt/xnat/pipeline_1_6/xnat-tools/XNATRestClient -host

  http://localhost:8080/xnat -u

  admin -p

  admin -m

  PUT -remote

  "/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData"

• /opt/xnat/pipeline_1_6/xnat-tools/XNATRestClient -host http://localhost:8080/xnat -u admin -p admin -m PUT -remote "/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData/files?content=v1.0"

  -local /opt/xnat/workshop2012/d2s1-validation/mrsession_rules.sch
  

• ALTERNATIVELY: curl  -i -u admin:admin -X PUT -T mrsession_rules.sch http://localhost:8080/xnat/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData/files?content=v1.0&inbody=true

 Step 3: Setting up the pipeline for the project BOGUS_OUA

            Navigate to BOGUS_OUA project as project owner

 Step 4: Setup the datatype

• As Admin, click on Administer -> Data types

• Select xnat:mrSessionData

• Under Available Report Actions, enter
  

  • Name:  PipelineScreen_launch_pipeline,

  • Display Name: Build,

  • Popup: always,

  • Secure Access: edit

  • (leave other columns empty)

 Step 5: Launching the pipeline (via Action -> Build)

• Navigate to project BOGUS_OUA

• Select an MRSession

• Click on Action -> Build

• Select ProtocolCheck

• Click on Submit

 Step 6: Launching the pipeline automatically

• Upload a MR Session

• Archive the session