Stream: implementers
Topic: FHIR Validator Error: Duplicate Resource
May Terry (Nov 05 2019 at 20:54):
Using FHIR validator tool version 4.0.31-SNAPSHOT, I get the following error when running validation on a FHIR example that worked on an earlier validator tool version back from mid-August. The output is the following:
(base) mayt-PC Tue Nov 05 15:45:40 fhirValidator $ java -jar org.hl7.fhir.validator.jar Patient-example-usr4.json -ig hl7.fhir.us.core
FHIR Validation tool Version 4.0.31-SNAPSHOT - Built 2019-11-05T15:35:39.648+11:00 - Git a0ece162e77c
Detected Java version: 12.0.2 from /Library/Java/JavaVirtualMachines/adoptopenjdk-12.jdk/Contents/Home on x86_64 (64bit). 4096MB available
Arguments: Patient-example-usr4.json -ig hl7.fhir.us.core
Directories: Current = /Users/mayt/mltApps/fhirValidator, Package Cache = /Users/mayt/.fhir/packages
.. connect to tx server @ http://tx.fhir.org
.. definitions from hl7.fhir.core#current
Error loading ImplementationGuide-fhir.json: Duplicate Resource http://hl7.org/fhir/ImplementationGuide/fhir
Exception in thread "main" org.hl7.fhir.exceptions.FHIRException: Error loading ImplementationGuide-fhir.json: Duplicate Resource http://hl7.org/fhir/ImplementationGuide/fhir
at org.hl7.fhir.r5.context.SimpleWorkerContext.fromDefinitions(SimpleWorkerContext.java:203)
at org.hl7.fhir.r5.validation.ValidationEngine.loadDefinitions(ValidationEngine.java:409)
at org.hl7.fhir.r5.validation.ValidationEngine.loadInitialDefinitions(ValidationEngine.java:356)
at org.hl7.fhir.r5.validation.ValidationEngine.<init>(ValidationEngine.java:388)
at org.hl7.fhir.r5.validation.Validator.main(Validator.java:489)
Caused by: org.hl7.fhir.exceptions.DefinitionException: Duplicate Resource http://hl7.org/fhir/ImplementationGuide/fhir
at org.hl7.fhir.r5.context.BaseWorkerContext.cacheResource(BaseWorkerContext.java:188)
at org.hl7.fhir.r5.context.SimpleWorkerContext.loadFromFileJson(SimpleWorkerContext.java:271)
at org.hl7.fhir.r5.context.SimpleWorkerContext.loadDefinitionItem(SimpleWorkerContext.java:212)
at org.hl7.fhir.r5.context.SimpleWorkerContext.fromDefinitions(SimpleWorkerContext.java:200)
... 4 more
Any ideas on what to try?
Grahame Grieve (Nov 05 2019 at 20:59):
it's on my list to resolve
Grahame Grieve (Nov 05 2019 at 21:00):
but you need to specify the version - use the parameter -version 4.0
Reece Adamson (Nov 07 2019 at 13:56):
I was also having a similar issue trying to validate a resource with known issues. I previously was able to get validation results back on it, but with the most recent snapshot I'm getting:
Exception in thread "main" java.lang.Error: Not done yet - resolve http://hl7.org/fhir/StructureDefinition/us-core-race
When trying: java -jar org.hl7.fhir.validator.jar patient.json -ig hl7.fhir.us.core -version 4.0
When I remove the us-core-race extension I get a similar Not done yet error on another extension.
Apologies if you were already aware, but I figured I'd bring it up in case it's helpful.
Lloyd McKenzie (Nov 07 2019 at 15:41):
Are you using the most recent validator - as found here: https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar?
May Terry (Nov 07 2019 at 18:31):
@Lloyd McKenzie - I worked on this issue with @Reece Adamson - upon further troubleshooting, it seems like there is some issue regarding error handling. We worked with a FHIR instance that had some errors in it (e.g.: incorrect representation of a complex extension (e.g.: like the race example above), incorrect URLs to coding systems) and each time, the "Not done yet..." type of unhandled exception followed by stack trace appears. As I fixed each error of that severity, it would kick off the same unhandled exception with the next error...all the way until only informational and warning-level errors remained.
May Terry (Nov 07 2019 at 18:38):
The version of the FHIR validator used: FHIR Validation tool Version 4.0.31-SNAPSHOT - Built 2019-11-05T15:35:39.648+11:00 - Git a0ece162e77c
Lloyd McKenzie (Nov 07 2019 at 21:28):
@Grahame Grieve
Grahame Grieve (Nov 07 2019 at 21:28):
it's on my list
Grahame Grieve (Nov 08 2019 at 03:20):
I can't reproduce this?
Reece Adamson (Nov 08 2019 at 17:18):
patient.json here is the example I used.
Just redownloaded and tried again with the same result.
Validator version: FHIR Validation tool Version 4.0.31-SNAPSHOT - Built 2019-11-05T15:35:39.648+11:00 - Git a0ece162e77c
Reece Adamson (Nov 08 2019 at 17:35):
resource.json @Michael O'Keefe and I made another very simple example here that shows the issue. This resource should be valid as far as I can see though.
"system": "http://hl7.org/fhir/v2/0203" seems to be the culprit in this example as without it the validation proceeded.
Grahame Grieve (Nov 09 2019 at 21:56):
fixed next release. btw, the source of a lot of this is that you are validating on the wrong version - the instance is not an r4 instance (r2?) (no excuse for the validator failing, of course)
Reece Adamson (Nov 12 2019 at 14:37):
Thanks @Grahame Grieve, I'll give it a go with the new release!
May Terry (Nov 13 2019 at 13:17):
Thanks @Grahame Grieve ! Looks like this latest validator release 4.0.36-SNAPSHOT fixed my immediate issue.
Last updated: Apr 12 2022 at 19:14 UTC
