FHIRShExTest

Test script for running ShEx validation against FHIR Example instances

Requirements

• python 3 -- this has been tested with python 3.5.0
• node.js -- JavaScript engine for shex.js
• shex.js -- ShEx validation REST server

Running FHIRShExTest

1. Download the FHIR STU3 Distribution:

   There are a number of ways to accomplish this including:

   • Use the hcls-fhir-rdf download_fhir_spec utility -- > download_fhir_spec -u http://hl7.org/fhir/2016Sep/
   • Download and unzip the FHIR specification
   • Build a local image using the FHIR Build Process. Once the publish.sh or publish.bat script has been run, the final specification will be in the "publish" directory

2. Start the shex.js server as a separate thread:

   > git clone https://github.com/caCDE-QA/shex.js
   > cd shex.js
   > npm update -g shex-test
   > node --no-deprecation ./bin/validate -S http://localhost:4290/validate --regex-module nfax-val-1err --duplicate-shape ignore
     Visit http://localhost:4290/ in browser.
   
     Test with a supplied schema and data:
       curl -i http://localhost:4290/validate -F "schema=@test/cli/1dotOr2dot.shex" -F "shape=http://a.example/S1" -F "data=@test/cli/p2p3.ttl" -F "node=x"
     or preload the schema and just supply the data:
       bin/validate -x test/cli/1dotOr2dot.shex -s http://a.example/S1 -S  http://localhost:4290/validate
     and pass only the data parameters:
       curl -i http://localhost:4290/validate -F "data=@test/cli/p2p3.ttl" -F "node=x"
     Note that shape and node can be relative or prefixed URLs.
   
     Press CTRL+C to stop...

   The latest version of node issues a deprecation warning about calling an asynchronous function without a callback. This is the reason for the --no-deprecation tag in the invocation above.

3. Clone or download FHIRShExTest and install:

   > https://github.com/caCDE-QA/FHIRShExTest.git
   > cd FHIRShExTest
   > virtualenv venv -p python3
   > . FHIRShExTest/bin/activate
   (venv) > python setup.py

4. Copy the local changes to the ShEx specifications to the publish directory

   (venv) > cp changes/* <FHIR specification directory>

5. Run the FHIRShExTest script:

   (venv) > python src/FHIRShExTest -id <FHIR specification directory>  -od data --nosuccesslog
   /Users/mrf7578/Development/fhirstu3/stu3-ballot/publish/claim-example-vision-glasses.ttl	/Users/mrf7578/Development/fhirstu3/stu3-ballot/publish/claim.shex	MissingProperty	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	JsonObj(property='http://www.w3.org/1999/02/22-rdf-syntax-ns#type', type='MissingProperty', valueExpr=JsonObj(type='NodeConstraint', values=['http://hl7.org/fhir/MedicationOrder']))
   /Users/mrf7578/Development/fhirstu3/stu3-ballot/publish/claimresponse-example.ttl	/Users/mrf7578/Development/fhirstu3/stu3-ballot/publish/claimresponse.shex	MissingProperty	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	JsonObj(property='http://www.w3.org/1999/02/22-rdf-syntax-ns#type', type='MissingProperty', valueExpr=JsonObj(type='NodeConstraint', values=['http://hl7.org/fhir/Claim']))
       ...
   /Users/mrf7578/Development/fhirstu3/stu3-ballot/publish/rim.ttl		Not a FHIR resource instance
   Total=499 Successful=480
   Not a FHIR resource: 57
       Missing ShEx file: 0
       On skip list: 0
       Failed validation: 19
       Invalid RDF: 12
   (venv) >

Notes

The Invalid RDF counts above are due to an rdflib error. We are awaiting an alternative resolution from the rdflib authors -- the solution is targeted for the rdflib 4.2.2 milestone. Once this change has been installed, the output should match:

Total=511 Successful=492
Not a FHIR resource: 57
    Missing ShEx file: 0
    On skip list: 0
    Failed validation: 19
    Invalid RDF: 0