Validation.jar failing to handle structuredefinition that is a differential

pecks2 · January 24, 2017, 7:29pm

I am utilizing the validation.jar (org.hl7.fhir.validator.jar) in an attempt to validate against a differential custom structurdefinition… via the following

 java  -jar org.hl7.fhir.validator.jar patient-example.xml -defn validation-min.xml.zip -profile MyPatient.structuredefinition.xml

And I wind up with an IndexOutOfBoundException: Index:0 Size:0, at InstanceValidator.java:2186)

The custom StructureDefinition looks like:

<?xml version="1.0" encoding="utf-8"?>
<StructureDefinition xmlns="http://hl7.org/fhir">
  <meta>
   <lastUpdated value="2017-01-23T14:15:06.425-05:00" />
  </meta>
 <name value="MyPatient" />
 <status value="draft" />
 <date value="2017-01-23T14:12:46.7975804-05:00" />
 <kind value="resource" />
 <constrainedType value="Patient" />
 <abstract value="false" />
  <base value="http://hl7.org/fhir/StructureDefinition/Patient" />
 <differential>
   <element>
     <path value="Patient" />
   </element>
   <element>
     <path value="Patient.gender" />
     <min value="1" />
   </element>
 </differential>
</StructureDefinition>

If I run the program against he default values, it properly runs:

java -jar org.hl7.fhir.validator.jar patient-example.xml -defn validation-min.xml.zip -profile http://hl7.org/fhir/StructureDefinition/daf-patient

If I save a version of my structural definition including a snapshop, and differential and pass that in, the validation works, but only against the snapshot, it completely ignores the differential definition that is in the file… So I can modify the snapshop and get the validation I want, but I don’t get it from the differential.

I don’t understand why the differential only structuredefinition is not working… and throws the error… I assume it is some sort of parsing error, but have no idea what… and I am further confused why when I pass in a full structuredefinition with snapshot and differential, that the differential is completely ignored.

Can someone offer some help? I really would like to utilize differentials, but unless I can figure this out the only option I have is to take snapshots of the base and tweak them to validate what I want to validate which is very bad form to say the least.

lloyd · January 25, 2017, 2:38am

Try using the most recent version of the validator - which can be found here:
http://build.fhir.org/validator.zip

You shouldn’t need to specify -defn anymore.

If the problem still exists, please raise this issue in a change request (link at the bottom of every page in the FHIR spec) and attach your sample instance and profile.

pecks2 · January 25, 2017, 3:33pm

Lloyd,

Looks like there is something wrong with the latest build, looks like it looks for the validator pack at buid.fhir.org which doesn’t exist instead of build.fhir.org

lloyd · January 26, 2017, 4:33am

Yup, that was broken. Fix committed. It should be available in the next 30-60 minutes.

pecks2 · January 26, 2017, 3:29pm

That seems to be better… but I am getting an odd error stating the namespace referenced in the

But I am still having an issue… it seems like its not liking my patient-exmample xml’s XMLNS setting or something as the error is bombing at the end of the first line of my patient-example xml which is :

 <Patient xmlns="http://hl7.org/fhir">

My testdiff.xml structuraldefinition is also set to the “hl7.org/fhir” namespace

<StructureDefinition xmlns="http://hl7.org/fhir">

So, I assume this is some sort of namespace or other setting thing, that is not correct, but I am not sure what.

java -Djava.ext.dirs=. -jar org.hl7.fhir.validator.jar patient-example.xml -profile testdiff.xml
… load FHIR from
… connect to tx server @
(vnull-null)
… validate
Terminology server: Check for supported code systems for http://hl7.org/fhir/patient-contact-relationship
FAILURE validating patient-example.xml: error:1 warn:2 info:0
Error @ Patient (line 1, col38) : StructureDefinition reference “testdiff.xml” could not be resolved

pecks2 · January 26, 2017, 4:30pm

I attempted to change the -profile value to a fully qualified URI since using filename just seemed to throw the same error even if I just fully made up a filename (file that doesn’t exist on the disk…

So changing -profile to be -profile file:///users/myaccount/fhir/validation/mystructdef.xml

and set the URL value inside the structuraldefinition as well… and I wind up with

(vnull-null)

… validate
Exception in thread “main” java.lang.Error: org.hl7.fhir.exceptions.FHIRException: fetching org.hl7.fhir.dstu3.model.StructureDefinition not done yet for URI ‘file:///Users/pecks2/Downloads/validator3/MyPatient.xml’
at org.hl7.fhir.dstu3.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:361)
at org.hl7.fhir.dstu3.validation.InstanceValidator$ResourceProfiles.addProfile(InstanceValidator.java:224)
at org.hl7.fhir.dstu3.validation.InstanceValidator$ResourceProfiles.addProfiles(InstanceValidator.java:220)
at org.hl7.fhir.dstu3.validation.InstanceValidator.validateResource(InstanceValidator.java:3353)
at org.hl7.fhir.dstu3.validation.InstanceValidator.validate(InstanceValidator.java:512)
at org.hl7.fhir.dstu3.validation.InstanceValidator.validate(InstanceValidator.java:362)
at org.hl7.fhir.dstu3.validation.ValidationEngine.validate(ValidationEngine.java:473)
at org.hl7.fhir.dstu3.validation.ValidationEngine.validate(ValidationEngine.java:401)
at org.hl7.fhir.dstu3.validation.Validator.main(Validator.java:248)
Caused by: org.hl7.fhir.exceptions.FHIRException: fetching org.hl7.fhir.dstu3.model.StructureDefinition not done yet for URI ‘file:///Users/pecks2/Downloads/validator3/MyPatient.xml’
at org.hl7.fhir.dstu3.context.SimpleWorkerContext.fetchResourceWithException(SimpleWorkerContext.java:408)
at org.hl7.fhir.dstu3.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:359)
… 8 more

pecks2 · January 26, 2017, 5:05pm

I am beyond perplexed, has anyone ever successfully validated against a custom structure definition that is a differential?

Since defining the file as a full URI (FILE://) seemed to throw all sorts of errors, and the raw file just being passed doesn’t seem to get picked up, I put the file onto an actual web server on my machine… but that too just results in the same error, as if I just passed in the filename:

 $ java -Djava.ext.dirs=. -jar org.hl7.fhir.validator.jar patient-example.xml  -profile http://localhost/MyPatient.xml
  .. load FHIR from http://build.fhir.org/
  .. connect to tx server @ http://fhir3.healthintersections.com.au/open
    (vnull-null)
  .. validate
Terminology server: Check for supported code systems for http://hl7.org/fhir/patient-contact-relationship
*FAILURE* validating patient-example.xml:  error:1 warn:2 info:0
  Error @ Patient (line 1, col38) : StructureDefinition reference "http://localhost/MyPatient.xml" could not be resolved
  Warning @ Patient.contact.relationship (line 121, col19) : None of the codes provided are in the value set     http://hl7.org/fhir/ValueSet/v2-0131 (http://hl7.org/fhir/ValueSet/v2-0131, and a code should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/patient-contact-relationship#partner)
  Warning @ Patient.contact.relationship.coding (line 122, col15) : Unknown Code System http://hl7.org/fhir/patient-contact-relationship

Just passing in the local filename:

$ java -Djava.ext.dirs=. -jar org.hl7.fhir.validator.jar patient-example.xml  -profile MyPatient.xml
  .. load FHIR from http://build.fhir.org/
  .. connect to tx server @ http://fhir3.healthintersections.com.au/open
   (vnull-null)
 .. validate
Terminology server: Check for supported code systems for http://hl7.org/fhir/patient-contact-relationship
*FAILURE* validating patient-example.xml:  error:1 warn:2 info:0
  Error @ Patient (line 1, col38) : StructureDefinition reference "MyPatient.xml" could not be resolved
  Warning @ Patient.contact.relationship (line 121, col19) : None of the codes provided are in the value set    http://hl7.org/fhir/ValueSet/v2-0131 (http://hl7.org/fhir/ValueSet/v2-0131, and a code should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/patient-contact-relationship#partner)
  Warning @ Patient.contact.relationship.coding (line 122, col15) : Unknown Code System http://hl7.org/fhir/patient-contact-relationship

pecks2 · January 30, 2017, 7:34pm

Where is the change request link? I do not see it.

lloyd · January 31, 2017, 1:54am

“Propose a change” - bottom of each page in the spec.