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

• Click on Pipelines tab.
• Click on Add More Pipelines
• Click on Add (for Validate.xml pipeline)
• Select Is this pipeline to be launched automatically while archiving?
• Set the value of Experiment Type to xnat:mrSessionData
• Set the value of Content attribute set within the validation catalog to v1.0
• Click on Submit

 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