Stream: conformance
Topic: another validator error
Rob Hausam (Jul 31 2019 at 14:52):
I'm getting this error (which I haven't seen before) with the latest 3.8.15-SNAPSHOT validator when I run it standalone on the IPS example bundle here:
FHIR Validation tool Version 3.8.15-SNAPSHOT - Built 2019-07-31T04:48:42.259Z - Git 654153671a8c
Arguments: /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips
.. connect to tx server @ http://tx.fhir.org
.. definitions from hl7.fhir.core#current
(v4.0.0)
+ .. load IG from hl7.fhir.uv.ips
... Using version 0.3.0
..file: ValueSet-imaging-area-measure-code-uv-ips.json ..file: StructureDefinition-Observation-member-laboratory-uv-ips.json ..file: ValueSet-condition-severity-uv-ips.json ..file: StructureDefinition-abatement-dateTime-uv-ips.json ..file: ValueSet-imaging-numobs-uv-ips.json ..file: StructureDefinition-Organization-laboratory-uv-ips.json ..file: ValueSet-absent-or-unknown-allergies-uv-ips.json ..file: ValueSet-lab-blood-abo-rh-grp-uv-ips.json ..file: ValueSet-procedures-uv-ips.json ..file: StructureDefinition-Quantity-uv-ips.json ..file: ValueSet-target-site-uv-ips.json ..file: StructureDefinition-Specimen-uv-ips.json ..file: ValueSet-whoatc-uv-ips.json ..file: ValueSet-laboratory-and-vital-signs-observations.json ..file: ValueSet-edd-method-uv-ips.json ..file: ValueSet-absent-or-unknown-immunizations-uv-ips.json ..file: ValueSet-allergy-reaction-uv-ips.json ..file: StructureDefinition-Observation-alcoholuse-uv-ips.json ..file: StructureDefinition-Observation-pregnancy-status-uv-ips.json ..file: ValueSet-medicine-active-substances-uv-ips.json ..file: ValueSet-pathology-and-vital-signs-observations.json ..file: ValueSet-imaging-txtobs-code-uv-ips.json ..file: ValueSet-core-problem-list-disorders-uv-ips.json ..file: ValueSet-imaging-volume-measure-code-uv-ips.json ..file: StructureDefinition-Observation-tobaccouse-uv-ips.json ..file: StructureDefinition-Ratio-uv-ips.json ..file: ValueSet-medicine-route-of-administration.json ..file: StructureDefinition-Medication-uv-ips.json ..file: ValueSet-absent-or-unknown-devices-uv-ips.json ..file: StructureDefinition-Observation-pregnancy-edd-uv-ips.json ..file: StructureDefinition-DiagnosticReport-uv-ips.json ..file: ValueSet-absent-or-unknown-procedures-uv-ips.json ..file: ValueSet-vaccines-uv-ips.json ..file: ValueSet-med-uv-ips.json ..file: ValueSet-absent-or-unknown-problems-uv-ips.json ..file: StructureDefinition-MedicationStatement-uv-ips.json ..file: StructureDefinition-AllergyIntolerance-uv-ips.json ..file: ValueSet-medical-devices-uv-ips.json ..file: ValueSet-sub-observation-category-uv-ips.json ..file: ValueSet-specimen-collection-method-uv-ips.json ..file: StructureDefinition-Observation-member-pathology-uv-ips.json ..file: ValueSet-absent-or-unknown-medications-uv-ips.json ..file: StructureDefinition-Procedure-uv-ips.json ..file: ValueSet-allergy-intolerance-substance-condition-uv-ips.json ..file: ValueSet-personal-relationship-uv-ips.json ..file: StructureDefinition-ImagingStudy-uv-ips.json ..file: StructureDefinition-Device-uv-ips.json ..file: ValueSet-imaging-linear-measure-code-uv-ips.json ..file: ValueSet-laboratory-tests-and-panels-uv-ips.json ..file: ValueSet-pregnancy-status-uv-ips.json ..file: StructureDefinition-Condition-uv-ips.json ..file: StructureDefinition-CodeableConcept-uv-ips.json ..file: StructureDefinition-Range-uv-ips.json ..file: StructureDefinition-DeviceUseStatement-uv-ips.json ..file: ValueSet-lab-result-coded-value-uv-ips.json ..file: StructureDefinition-Observation-pregnancy-outcome-uv-ips.json ..file: ValueSet-microorganism-uv-ips.json ..file: ValueSet-observation-codes-uv-ips.json ..file: StructureDefinition-Observation-laboratory-uv-ips.json ..file: StructureDefinition-Organization-observation-uv-ips.json ..file: StructureDefinition-Observation-pathology-uv-ips.json ..file: StructureDefinition-Composition-uv-ips.json ..file: ValueSet-pathology-result-coded-value-uv-ips.json ..file: ImplementationGuide-ig-uv-ips.json ..file: ValueSet-lab-absence-presence-uv-ips.json ..file: ValueSet-medicine-doseform.json ..file: StructureDefinition-Coding-uv-ips.json ..file: ValueSet-imaging-observations-uv-ips.json ..file: CodeSystem-absent-unknown-uv-ips.json ..file: ValueSet-specimen-type-uv-ips.json ..file: ValueSet-current-smoking-status-uv-ips.json ..file: StructureDefinition-Immunization-uv-ips.json ..file: StructureDefinition-Observation-media-uv-ips.json ..file: StructureDefinition-Practitioner-uv-ips.json ..file: StructureDefinition-Observation-uv-ips.json ..file: StructureDefinition-Device-observer-uv-ips.json ..file: StructureDefinition-Patient-uv-ips.json ..file: ValueSet-pregnancies-summary-uv-ips.json ..file: ValueSet-problem-type-uv-ips.json ..file: StructureDefinition-Observation-member-imaging-uv-ips.json ..file: StructureDefinition-Observation-imaging-uv-ips.json ..file: StructureDefinition-participant-uv-ips.json .. validate [/Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml]
Terminology server: Check for supported code systems for http://loinc.org
Exception in thread "main" java.lang.Error: Not done yet - resolve Condition/c64139e7-f02d-409c-bf34-75e8bf23bc80 locally (2)
at org.hl7.fhir.r5.validation.InstanceValidator$ValidatorHostServices.resolveReference(InstanceValidator.java:236)
at org.hl7.fhir.r5.utils.FHIRPathEngine.funcResolve(FHIRPathEngine.java:3291)
at org.hl7.fhir.r5.utils.FHIRPathEngine.evaluateFunction(FHIRPathEngine.java:2721)
at org.hl7.fhir.r5.utils.FHIRPathEngine.execute(FHIRPathEngine.java:1136)
at org.hl7.fhir.r5.utils.FHIRPathEngine.execute(FHIRPathEngine.java:1163)
at org.hl7.fhir.r5.utils.FHIRPathEngine.evaluate(FHIRPathEngine.java:540)
at org.hl7.fhir.r5.utils.FHIRPathEngine.evaluateToBoolean(FHIRPathEngine.java:596)
at org.hl7.fhir.r5.validation.InstanceValidator.evaluateSlicingExpression(InstanceValidator.java:2732)
at org.hl7.fhir.r5.validation.InstanceValidator.sliceMatches(InstanceValidator.java:2724)
at org.hl7.fhir.r5.validation.InstanceValidator.matchSlice(InstanceValidator.java:4226)
at org.hl7.fhir.r5.validation.InstanceValidator.assignChildren(InstanceValidator.java:4140)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3855)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:3990)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3862)
at org.hl7.fhir.r5.validation.InstanceValidator.start(InstanceValidator.java:2895)
at org.hl7.fhir.r5.validation.InstanceValidator.validateResource(InstanceValidator.java:4439)
at org.hl7.fhir.r5.validation.InstanceValidator.validateContains(InstanceValidator.java:3812)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:3985)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3862)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:3990)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:3862)
at org.hl7.fhir.r5.validation.InstanceValidator.start(InstanceValidator.java:2874)
at org.hl7.fhir.r5.validation.InstanceValidator.validateResource(InstanceValidator.java:4439)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:768)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:601)
at org.hl7.fhir.r5.validation.ValidationEngine.validate(ValidationEngine.java:926)
at org.hl7.fhir.r5.validation.ValidationEngine.validate(ValidationEngine.java:840)
at org.hl7.fhir.r5.validation.Validator.main(Validator.java:450)
The interesting thing is (unless I'm somehow mis-reading it) is that it seems to be working in the build (local or other). I'm getting specific validation messages in the QA for that example file.
Grahame Grieve (Jul 31 2019 at 21:57):
how can I reproduce this?
Rob Hausam (Aug 01 2019 at 03:23):
OK, I can give a little more detail. Download the example bundle (link above) and then run the validator against it on the command line. The command I'm using (in my current environment) is java -jar ~/Downloads/org.hl7.fhir.validator.jar ~/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips.
Grahame Grieve (Aug 01 2019 at 06:35):
fixed next release
Rob Hausam (Aug 01 2019 at 22:44):
@Grahame Grieve When do you expect the next release?
Grahame Grieve (Aug 01 2019 at 23:02):
today
Rob Hausam (Aug 03 2019 at 21:11):
With the new validator I've found a serious issue that's preventing me from using it on the command line (for some reason it seems to still be working in the build?). Basically, it seems to no longer be able to recognize StructureDefinitions that are local to the IG (even though the ig package is being specified). The local command I'm using is: java -jar ~/Downloads/org.hl7.fhir.validator.jar ~/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips, and I'm getting:
FHIR Validation tool Version 3.8.19-SNAPSHOT - Built 2019-08-02T12:59:22.146Z - Git fb446cf1e27c
Arguments: /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml -ig hl7.fhir.uv.ips
.. connect to tx server @ http://tx.fhir.org
.. definitions from hl7.fhir.core#current
(v4.0.0)
+ .. load IG from hl7.fhir.uv.ips
... Using version 0.3.0
..file: ImplementationGuide-hl7.fhir.uv.ips.json .. validate [/Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml]
Terminology server: Check for supported code systems for http://loinc.org
*FAILURE* validating /Users/rhausam/git-repo/fhir-ips/examples/IPS-bundle-01.xml: error:1 warn:21 info:2
Error @ Bundle.entry[19].resource.code.coding[0] (line 1066, col14) : Unknown Code System http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips
Information @ Bundle.entry[4].resource.severity (line 441, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6751-7)
Information @ Bundle.entry[10].resource.severity (line 710, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-severity (http://hl7.org/fhir/ValueSet/condition-severity, and a code is recommended to come from this value set) (codes = http://loinc.org#LA6750-9)
Warning @ Bundle.entry[1].resource.contact[0].relationship[0] (line 327, col20) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/patient-contactrelationship (http://hl7.org/fhir/ValueSet/patient-contactrelationship, and a code should come from this value set unless it has no suitable code) (codes = http://terminology.hl7.org/CodeSystem/v3-RoleCode#MTH)
Warning @ Bundle.entry[4].resource.subject.resource.contact[0].relationship[0] (line 327, col20) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/patient-contactrelationship (http://hl7.org/fhir/ValueSet/patient-contactrelationship, and a code should come from this value set unless it has no suitable code) (codes = http://terminology.hl7.org/CodeSystem/v3-RoleCode#MTH)
Warning @ Bundle.entry[4].resource.category[0] (line 434, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-category (http://hl7.org/fhir/ValueSet/condition-category, and a code should come from this value set unless it has no suitable code) (codes = http://loinc.org#75326-9)
Warning @ Bundle.entry[10].resource.category[0] (line 703, col15) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-category (http://hl7.org/fhir/ValueSet/condition-category, and a code should come from this value set unless it has no suitable code) (codes = http://loinc.org#75326-9)
Warning @ Bundle.entry[0].resource.meta.profile[0] (line 16, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Composition-uv-ips" could not be resolved
Warning @ Bundle.entry[1].resource.meta.profile[0] (line 298, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Patient-uv-ips" could not be resolved
Warning @ Bundle.entry[4].resource.meta.profile[0] (line 412, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips" could not be resolved
Warning @ Bundle.entry[5].resource.meta.profile[0] (line 480, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/MedicationStatement-uv-ips" could not be resolved
Warning @ Bundle.entry[6].resource.meta.profile[0] (line 536, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/MedicationStatement-uv-ips" could not be resolved
Warning @ Bundle.entry[7].resource.meta.profile[0] (line 571, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Medication-uv-ips" could not be resolved
Warning @ Bundle.entry[8].resource.meta.profile[0] (line 605, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Medication-uv-ips" could not be resolved
Warning @ Bundle.entry[9].resource.meta.profile[0] (line 639, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/AllergyIntolerance-uv-ips" could not be resolved
Warning @ Bundle.entry[10].resource.meta.profile[0] (line 681, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Condition-uv-ips" could not be resolved
Warning @ Bundle.entry[12].resource.meta.profile[0] (line 766, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-member-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[13].resource.meta.profile[0] (line 803, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-member-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[14].resource.meta.profile[0] (line 840, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-member-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[15].resource.meta.profile[0] (line 877, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-member-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[16].resource.meta.profile[0] (line 914, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[17].resource.meta.profile[0] (line 955, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[18].resource.meta.profile[0] (line 997, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-laboratory-uv-ips" could not be resolved
Warning @ Bundle.entry[19].resource.meta.profile[0] (line 1040, col13) : StructureDefinition reference "http://hl7.org/fhir/uv/ips/StructureDefinition/AllergyIntolerance-uv-ips" could not be resolved
It's also behaving the same way when attempting to validate other instances and in other IGs (specifically livd). The way it is right now it's impossible to obtain any useful information about the validity of a particular instance.
Grahame Grieve (Aug 03 2019 at 21:15):
I'm not sure how the output is linked to the problem?
Rob Hausam (Aug 03 2019 at 21:21):
Not sure that I get your question, but the issue is that the validation output is invalid - the code system that it is giving the error on and the missing StructureDefinitions that it's warning about are all there in the ig package. I think that's true of the missing codes in the value sets, too, but I haven't checked all of them. If it doesn't recognize these items then it can't actually validate anything.
Grahame Grieve (Aug 03 2019 at 21:25):
ok I think that the issue is one Lloyd already reported. I'm going to issue a new IG publisher to fix it, but let's confirm. can you find your package cache (see https://wiki.hl7.org/FHIR_Package_Cache) and find your package?
Rob Hausam (Aug 03 2019 at 21:44):
I didn't see a report from Lloyd on it - if I had I probably would have just +1'ed it. Looking at the package cache is one of the first things that I did, but earlier I hadn't drilled further into the details. And now when I do, it's weird. I haven't made any structural or configuration changes in the ig, but now it appears that all of the generated SD and other files are ending up in the example folder in the package, rather than in the package folder. That seems to be partly true in livd, too (in livd some of them are in package and some in example). I assume this won't be too hard to fix, but at the moment I don't know why it's occurring.
Grahame Grieve (Aug 03 2019 at 21:45):
he didn't report it in Zulip, but you wouldn't have recognised the link
Grahame Grieve (Aug 03 2019 at 21:46):
but it's certainly the same issue. I assumed that the example[x] element in the ig reosurce would only be present it it was true. But that's not always the case.
Rob Hausam (Aug 03 2019 at 22:04):
Packages are looking good now, and validator is working.
Last updated: Apr 12 2022 at 19:14 UTC
