Stream: implementers
Topic: validation quirks
Jens Villadsen (Jan 13 2021 at 13:30):
I'm seeing conflicting behavour in the validity of the example resources in my IG. As part of my IG, I have the example of a resource here: https://build.fhir.org/ig/hl7dk/dk-medcom/StructureDefinition-medcom-careCommunication-message-examples.html - the QA site of the IG is listed here: https://build.fhir.org/ig/hl7dk/dk-medcom/qa.html#_scratch_ig-build-temp-CMJHI5_repo_fsh-generated_resources_Bundle-CareCommunicationMessageExample and it reports no errors. Now, If I try manually to validate the example resource as listed on https://build.fhir.org/ig/hl7dk/dk-medcom/StructureDefinition-medcom-careCommunication-message-examples.html using the validator, the example bundle full of errors:
ava -jar validator_cli.jar communication.json -version 4.0 -ig http://build.fhir.org/ig/hl7dk/dk-medcom -profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
FHIR Validation tool Version 5.2.13 (Git# 5f67b5bad03d). Built 2020-12-24T05:16:59.673Z (20 days old)
Java: 15 from /Library/Java/JavaVirtualMachines/adoptopenjdk-15.jdk/Contents/Home on x86_64 (64bit). 4096MB available
Paths: Current = /Users/jvi/dk-medcom, Package Cache = /Users/jvi/.fhir/packages
Params: communication.json -version 4.0 -ig http://build.fhir.org/ig/hl7dk/dk-medcom -profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Loading
Load FHIR v4.0 from hl7.fhir.r4.core#4.0.1 - 4575 resources (00:04.0158)
Load hl7.terminology#2.0.0 - 3749 resources (00:00.0930)
Terminology server http://tx.fhir.org - Version 1.9.369 (00:01.0920)
Load http://build.fhir.org/ig/hl7dk/dk-medcom+ .. load IG from dk.fhir.ig.dk-core#current
- 52 resources (01:19.0521)
Get set... go (00:00.0032)
Validating
Profiles: [http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message]
Validate communication.json 00:00.0717
Done. Times: Loading: 01:26.0787, validation: 00:00.0717
*FAILURE*: 10 errors, 2 warnings, 15 notes
Error @ resource.focus[0] : Bundled or contained reference not found within the bundle/resource Communication/CareCommunicationContent
Error @ resource.target[0] : Bundled or contained reference not found within the bundle/resource MessageHeader/CareCommunicationMessageHeader
Error @ resource.managingOrganization : Bundled or contained reference not found within the bundle/resource Organization/BurnCenter
Error @ resource.destination[0].receiver : Bundled or contained reference not found within the bundle/resource Organization/MessageReceiver
Error @ resource.agent[0].who : Bundled or contained reference not found within the bundle/resource Organization/MessageSender
Error @ Bundle (line 2, col2) : Bundle.entry:citizen: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message)
Error @ Bundle (line 2, col2) : Bundle.entry:messageHeader: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message)
Error @ Bundle.entry[3].resource.ofType(Communication).subject (line 161, col6) : Unable to find matching profile for Patient/EricFlame among choices: http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-patient
Error @ Bundle.entry[3].resource.ofType(Communication).encounter (line 164, col6) : Unable to find matching profile for Encounter/EncounterWithLPR3Identifier among choices: http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-lpr3Encounter
Error @ Bundle.entry[4].resource.ofType(Encounter).subject (line 206, col6) : Unable to find matching profile for Patient/EricFlame among choices: http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-patient
Information @ Bundle.entry[0] (line 13, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[1] (line 61, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[2] (line 110, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[3] (line 134, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[4] (line 185, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[5] (line 217, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[6] (line 236, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[7] (line 263, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[8] (line 290, col5) : This element does not match any known slice defined in the profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
Information @ Bundle.entry[3].resource.ofType(Communication).subject (line 161, col6) : Details for Patient/EricFlame matching against Profilehttp://hl7.org/fhir/StructureDefinition/Patient
Information @ Bundle.entry[3].resource.ofType(Communication).subject (line 161, col6) : Details for Patient/EricFlame matching against Profilehttp://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-patient
Information @ Bundle.entry[3].resource.ofType(Communication).encounter (line 164, col6) : Details for Encounter/EncounterWithLPR3Identifier matching against Profilehttp://hl7.org/fhir/StructureDefinition/Encounter
Information @ Bundle.entry[3].resource.ofType(Communication).encounter (line 164, col6) : Details for Encounter/EncounterWithLPR3Identifier matching against Profilehttp://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-lpr3Encounter
Information @ Bundle.entry[4].resource.ofType(Encounter).subject (line 206, col6) : Details for Patient/EricFlame matching against Profilehttp://hl7.org/fhir/StructureDefinition/Patient
Information @ Bundle.entry[4].resource.ofType(Encounter).subject (line 206, col6) : Details for Patient/EricFlame matching against Profilehttp://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-core-patient
Warning @ Bundle.entry[8].resource.ofType(Provenance).activity (line 312, col16) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/provenance-activity-type (http://hl7.org/fhir/ValueSet/provenance-activity-type), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://medcom.dk/fhir/medcom-core/CodeSystem/medcom-messaging-activityCodes#new-message)
Warning @ resource.activity (line 312, col16) : None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/provenance-activity-type (http://hl7.org/fhir/ValueSet/provenance-activity-type), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://medcom.dk/fhir/medcom-core/CodeSystem/medcom-messaging-activityCodes#new-message)
@Grahame Grieve do you have any idea why the validator when executed during the IGpublisher phase does not find the errors that the validator does afterwards.
Lloyd McKenzie (Jan 14 2021 at 05:07):
Your fullUrls aren't. I don't know why the IGPublisher isn't rejecting them (@Grahame Grieve ?), but the validator is right to yell. FullURLs must be full uris - either urn:uuid:someguid or http://something/ResourceType/id (maybe plus _history/version). You can't specify a relative reference as a fullUrl.
Jean Duteau (Jan 14 2021 at 06:42):
the IGPublisher hasn't rejected relative URLs ever. I have some old guides that used relative URLs in my examples and they worked. it is only recently that I realized that relative URLs aren't valid there (which should have been obvious from the name of the attribute if not from reading the the definition/comments).
Grahame Grieve (Jan 14 2021 at 07:06):
I don't get those errors. what exact file are you validating?
Jens Villadsen (Jan 14 2021 at 07:44):
The content of https://build.fhir.org/ig/hl7dk/dk-medcom/Bundle-CareCommunicationMessageExample.json.html
Jens Villadsen (Jan 14 2021 at 10:13):
@Lloyd McKenzie right ... I've prefixed all the fullUrls with 'http://example.org/fhir' ... that removed 4 errors ... that leaves 6 errors left, which
really puzzles me.
Error @ resource.focus[0] : Bundled or contained reference not found within the bundle/resource Communication/CareCommunicationContent
Error @ resource.target[0] : Bundled or contained reference not found within the bundle/resource MessageHeader/CareCommunicationMessageHeader
Error @ resource.destination[0].receiver : Bundled or contained reference not found within the bundle/resource Organization/MessageReceiver
Error @ resource.agent[0].who : Bundled or contained reference not found within the bundle/resource Organization/MessageSender
Error @ Bundle (line 1, col2) : Bundle.entry:messageHeader: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message)
Error @ Bundle (line 1, col2) : Bundle.entry:messageHeader: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-messaging-message)
Jens Villadsen (Jan 14 2021 at 10:34):
nop ... my mistake ... I validated against the wrong profile. I still have 10 errors
Oliver Egger (Jan 14 2021 at 11:42):
can you push the file to github in a branch?
Jens Villadsen (Jan 14 2021 at 12:02):
@Oliver Egger 2 sec
Jens Villadsen (Jan 14 2021 at 12:04):
https://gist.github.com/jvitrifork/adef9fb0b5079fb1ed7fb421ec4221a5
Jens Villadsen (Jan 14 2021 at 12:12):
And interestingly enough @Lloyd McKenzie , if I run the validation without the profile - there are no errors or warrnings. Shouldn't that mean that the stated internal references are valid?
Jens Villadsen (Jan 14 2021 at 12:22):
@Oliver Egger let me know if you find something
Oliver Egger (Jan 14 2021 at 13:12):
if I remove all profile references from the bundle i'm down to two errors validating against your bundle profile which are not related to the 'Bundle or container reference message':
java -jar validator_cli.jar "/Users/oliveregger/Desktop/dk/bundle.json" -version 4.0.1 -ig dk.fhir.ig.medcom-core#current -profile http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message
*FAILURE*: 2 errors, 1 warnings, 9 notes
Error @ Bundle (line 1, col2) : Bundle.entry:citizen: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message)
Error @ Bundle (line 1, col2) : Bundle.entry:messageHeader: minimum required = 1, but only found 0 (from http://medcom.dk/fhir/medcom-core/StructureDefinition/medcom-careCommunication-message)
So it looks for me, that either one of the profile definitions is wrong in the bundle and provokes the error or the profile definitions within the bundle triggers another validation where it stumbles over the bundle.entry or hopefully if above two errors are solved all are gone away :-)
Jens Villadsen (Jan 14 2021 at 15:28):
@Oliver Egger I just tried to validate the patient example by itself ... that seems to conform to the patient profile
Jens Villadsen (Jan 14 2021 at 15:29):
so the first error is really funky
Jens Villadsen (Jan 14 2021 at 19:19):
Grahame Grieve said:
I don't get those errors. what exact file are you validating?
https://gist.github.com/jvitrifork/adef9fb0b5079fb1ed7fb421ec4221a5
Jens Villadsen (Jan 17 2021 at 08:32):
Hmmm ... I think I'm on to something ... the last two errors that you see @Oliver Egger looks like they related to the fact that the reference aggregation mode is profiled. Currently it is narrowed down to only allow bundled for the cases managingOrganization for Patient - the same goes for the references on MessageHeader. If I let the aggregation mode instead be referenced, there are no errors. However, the references are in fact part of the bundle and should be part of the bundle. Why this does not pop up as of the IG building process @Grahame Grieve puzzles me.
Jens Villadsen (Jan 17 2021 at 20:08):
It's also present on other IG's - like Davinci (where the error is not present in the QA report):
curl http://build.fhir.org/ig/HL7/davinci-alerts/Bundle-admit-notification-message-bundle-01.json -o davinci.json && java -jar validator_cli.jar davinci.json -version 4.0 -ig http://build.fhir.org/ig/HL7/davinci-alerts -profile http://hl7.org/fhir/us/davinci-alerts/StructureDefinition/notifications-bundle -tx n/a
gives the following errors:
Error @ resource.participant[0].individual : Bundled or contained reference not found within the bundle/resource urn:uuid:0000016f-57cb-cdac-0000-00000000014a
Error @ resource.subject : Bundled or contained reference not found within the bundle/resource urn:uuid:06e1f0dd-5fbe-4480-9bb4-6b54ec02d31b
Error @ resource.location[0].location : Bundled or contained reference not found within the bundle/resource urn:uuid:09188b81-0d1d-453c-b0fa-203ef88c794c
Error @ Bundle.entry[0].resource.ofType(MessageHeader) (line 57, col25) : MessageHeader.focus:admit-notification: minimum required = 1, but only found 0 (from http://hl7.org/fhir/us/davinci-alerts/StructureDefinition/admit-notification-messageheader)
Error @ Bundle.entry[6].resource.ofType(Condition).encounter (line 553, col10) : Unable to find matching profile for urn:uuid:5fe62cd5-bfcf-4d3b-a1e9-80d6f75d6f82 among choices: http://hl7.org/fhir/us/davinci-alerts/StructureDefinition/adt-notification-encounter
Jens Villadsen (Jan 17 2021 at 20:10):
@Lloyd McKenzie I can see you are one of the contributers to the IG. Maybe you can shed some light on these errors?
Jens Villadsen (Jan 18 2021 at 18:30):
The davinci errors that is
Lloyd McKenzie (Jan 18 2021 at 22:59):
I was a contributor, but wasn't involved in the technical work of IG creation. If the validator is complaining (incorrectly) about issues that aren't showing up in publisher QA, that suggests a bug in the validator. @Grahame Grieve ?
Grahame Grieve (Jan 19 2021 at 01:02):
this is on my todo list, but realistically, not until the first week of Feb
Jens Villadsen (Feb 17 2021 at 19:46):
@Grahame Grieve has it become the first week of feb yet down under? I'm sort of confused that the IG does't report the example as an error during the build proces but afterwards if I take the example and parse it to the validator_cli and points it to the freshly generated package then I see a lot of errors.
Grahame Grieve (Feb 24 2021 at 03:35):
still on my todo list
Jens Villadsen (Feb 24 2021 at 14:02):
I'm starting to suspect that you live in a currently undocumented timezone where it's almost always late january ;)
Grahame Grieve (Feb 24 2021 at 22:07):
I really liked late January, since I had a holiday for a week. I'm trying to work only 50-60 hours a week since i'm back, and everyone is noticing
Gino Canessa (Feb 24 2021 at 22:12):
I'm still trying to figure out how March is next week, considering it was just March.
Chris Moesel (Feb 24 2021 at 22:15):
So we still haven't figured out how to clone @Grahame Grieve yet? Darn.
Paul Church (Feb 24 2021 at 22:15):
yeah, it's so strange that it's March 2022 already
Paul Church (Feb 24 2021 at 22:15):
seems like only yesterday it was March 2020
Last updated: Apr 12 2022 at 19:14 UTC
