FHIR Chat · NPE only in CI build

Stream: IG creation

Topic: NPE only in CI build

Rick Geimer (Mar 18 2019 at 05:30):

I received the following in the CI build for davinci-pdex (davinci-epdx github):

Validating Resources (38.0271sec)
java.lang.NullPointerException (38.0296sec)
Publishing Content Failed: null (38.0297sec)
(38.0297sec)
Use -? to get command line help (38.0297sec)
(38.0297sec)
Stack Dump (for debugging): (38.0297sec)
java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.ValidationServices.fetch(ValidationServices.java:60)
at org.hl7.fhir.r5.validation.InstanceValidator.checkReference(InstanceValidator.java:1753)

Rick Geimer (Mar 18 2019 at 05:32):

This was after adding a miminal Patient resource example to the IG.

The build runs fine locally using the latest publisher pulled from build.fhir.org after receiving the NPE. The patient example is also valid according to HAPI validation.

Rick Geimer (Mar 18 2019 at 05:33):

Will comment out the example in the build for now, which will result in a single build error in this IG until the NPE is looked into.

Rick Geimer (Mar 18 2019 at 05:39):

@Grahame Grieve The latest content is in github if you want to try running a local build yourself, but with the offending ImplementationGuide.definition.resource element commented out.

Grahame Grieve (Mar 18 2019 at 12:06):

I can't reproduce this

Rick Geimer (Mar 18 2019 at 14:02):

That's my point. The only place it occurs is on the CI Build. I just uncommented that patient and committed the IG resource to github. The build failed again with that NPE:

http://build.fhir.org/ig/HL7/davinci-epdx/build.log

Rick Geimer (Mar 18 2019 at 14:03):

Validating Resources (34.0030sec)
java.lang.NullPointerException (34.0066sec)
Publishing Content Failed: null (34.0067sec)
(34.0067sec)
Use -? to get command line help (34.0068sec)
(34.0068sec)
Stack Dump (for debugging): (34.0068sec)
java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.ValidationServices.fetch(ValidationServices.java:60)
at org.hl7.fhir.r5.validation.InstanceValidator.checkReference(InstanceValidator.java:1753)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3773)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3783)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3783)
at org.hl7.fhir.r5.validation.InstanceValidator.start(InstanceValidator.java:2716)
at org.hl7.fhir.r5.validation.InstanceValidator.validateResource(InstanceValidator.java:4089)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:738)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:698)
at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:2877)
at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:2854)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:619)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:554)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5103)
Exception in thread "main" java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5113)

Bryn Rhodes (Mar 18 2019 at 15:58):

I'm seeing what looks like the same issue in the DEQM build now; it builds locally for me, but gets that error in the CI build.

Eric Haas (Mar 18 2019 at 16:56):

here is the branch that has the NPE error :

https://github.com/HL7/davinci-deqm/tree/20190318_NPE_Error

The trace is vitrually the same as Rick's. The first resource that is validated locally is devicerequest-deqm and like Rick this validates fine using UHN $validate. I'll check the rest in a minute

Eric Haas (Mar 18 2019 at 18:24):

I did an independent validation of all the generated DEQM resources using UHN $validate and here is what I found:

Eric Haas (Mar 18 2019 at 18:25):

1. ...validating file "CapabilityStatement-receiver-server.json" as CapabilityStatement
CapabilityStatements: Generated Output ERROR [CapabilityStatement]
Profile http://hl7.org/fhir/StructureDefinition/CapabilityStatement, Element 'CapabilityStatement.acceptUnknown': minimum required = 1, but only found 0

Even though the source file do indeed contain this element is absent in all the capabilityStatements

2. ...validating file "StructureDefinition-practitioner-deqm.json" as StructureDefinition
Validation output

ERROR [StructureDefinition.snapshot.element[16].example.valueUri]
URI values cannot have whitespace
ERROR [StructureDefinition.snapshot.element[25].example.valueUri]
URI values cannot have whitespace

one these elements is "id": "Practitioner.identifier.system" and the offending bit...

"example": [
  {
    "label": "General",
    "valueUri": "http://www.acme.com/identifiers/patient or urn:ietf:rfc:3986 if the Identifier.value itself is a full uri"
  }
],
...

This element traces all the way back to US Core and I can't find it in my copy or the repo copy of the US Core source spreadsheet. It show ups in the output files however. I don't recollect ever having adding this to US Core ( although I may certainly have at some point) This error occurs for StructureDefinition-organization-deqm.json and StructureDefinition-pracititioner-deqm.json

3. lots of errors in the expansions.json Bundle but I did not investigate that.

Nagesh Bashyam (Mar 18 2019 at 18:56):

Any update on the issue, I am seeing the same thing in CRN build.
http://build.fhir.org/ig/HL7/coordinated-registry-network/build.log

Eric Haas (Mar 18 2019 at 18:59):

Is everybody profiling off of US Core?

Eric Haas (Mar 18 2019 at 18:59):

is that the common thread?

Grahame Grieve (Mar 18 2019 at 19:19):

I'll do a new release. The error makes no sense to me

Eric Haas (Mar 18 2019 at 22:28):

still happening and here my trace

Validating Resources                                                             (41.0376sec)
 .. validate /scratch/ig-build-temp-9TFFOE/repo/source/resources/ig              (41.0376sec)
 .. /scratch/ig-build-temp-9TFFOE/repo/source/resources/ig                       (41.0376sec)
     validating Data Exchange For Quality Measures                               (41.0376sec)
java.lang.NullPointerException                                                   (41.0379sec)
Publishing Content Failed: null                                                  (41.0380sec)
                                                                                 (41.0380sec)
Use -? to get command line help                                                  (41.0380sec)
                                                                                 (41.0380sec)
Stack Dump (for debugging):                                                      (41.0380sec)
java.lang.NullPointerException
    at org.hl7.fhir.igtools.publisher.ValidationServices.fetch(ValidationServices.java:62)
    at org.hl7.fhir.r5.validation.InstanceValidator.checkReference(InstanceValidator.java:1753)
    at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3773)
    at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3783)
    at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3783)
    at org.hl7.fhir.r5.validation.InstanceValidator.start(InstanceValidator.java:2716)
    at org.hl7.fhir.r5.validation.InstanceValidator.validateResource(InstanceValidator.java:4089)
    at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:738)
    at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:698)
    at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:2877)
    at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:2854)
    at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:619)
    at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:554)
    at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5103)
Exception in thread "main" java.lang.NullPointerException
    at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5113)