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Onto-Med / top-deployment

Deployment instructions and resources for the TOP Framework
https://onto-med.github.io/top-deployment/
MIT License
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Resource has invalid reference: #Patient/CT001, Unable to load resource: /org/hl7/fhir/r4/model/profile/profiles-resources.xml #61

Open KonradHoeffner opened 8 months ago

KonradHoeffner commented 8 months ago

When using the default data source (Hapi Adapter) from the configs directory and executing a query for BMI, I get the following warnings in the Docker Compose logs and no query result:

backend-1   | 2024-02-14 11:11:46.971  WARN 1 --- [pool-3-thread-6] ca.uhn.fhir.parser.LenientErrorHandler   : Resource has invalid reference: #Patient/CT001
backend-1   | 2024-02-14 11:12:04.200  INFO 1 --- [pool-3-thread-7] c.s.t.b.service.PhenotypeQueryService    : Running PhenotypeQueryService query 'c387bd6e-7519-46f1-94ff-1dbec8dce539' for repository 'testrepo'...
backend-1   | 2024-02-14 11:12:04.234  INFO 1 --- [pool-3-thread-7] ca.uhn.fhir.context.FhirContext          : Creating new FHIR context for FHIR version [R4]
backend-1   | 2024-02-14 11:12:04.235  INFO 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-resources.xml
backend-1   | 2024-02-14 11:12:04.235  WARN 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Unable to load resource: /org/hl7/fhir/r4/model/profile/profiles-resources.xml
backend-1   | 2024-02-14 11:12:04.235  INFO 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-types.xml
backend-1   | 2024-02-14 11:12:04.236  WARN 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Unable to load resource: /org/hl7/fhir/r4/model/profile/profiles-types.xml
backend-1   | 2024-02-14 11:12:04.236  INFO 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-others.xml
backend-1   | 2024-02-14 11:12:04.236  WARN 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Unable to load resource: /org/hl7/fhir/r4/model/profile/profiles-others.xml
backend-1   | 2024-02-14 11:12:04.236  INFO 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Loading structure definitions from classpath: /org/hl7/fhir/r4/model/extension/extension-definitions.xml
backend-1   | 2024-02-14 11:12:04.236  WARN 1 --- [pool-3-thread-7] .u.f.c.s.DefaultProfileValidationSupport : Unable to load resource: /org/hl7/fhir/r4/model/extension/extension-definitions.xml
ChristophB commented 8 months ago

Resource has invalid reference: #Patient/CT001 refers to invalid patient IDs in the public HAPI server.

As for the other warnings: maybe @AlexU75 can explain this.