phenopackets / hapi-pheno Goto Github PK

In the proocess of posting the variant, I get the following error in the client log:
Caused by: ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException: HTTP 422 Unprocessable Entity: Unable to validate code http://loinc.org#LA6668-3 - Unknown code http://loinc.org#LA6668-3. Code validation occurred using a ValueSet expansion that was pre-calculated at 2022-08-31T16:01:03.170-06:00 (01:09:39 ago)

I can reproduce this from a curl call:
curl -i \ --header "Content-Type: application/fhir+json; charset=UTF-8" \ --header "Accept-Charset: utf-8" \ --header "User-Agent: HAPI-FHIR/5.0.0 (FHIR Client; FHIR 4.0.1/R4; apache)" \ --request GET \ --output codesystem_validate_LA6668-3 \ "$MY_BASE/CodeSystem/loinc/$validate-code?code=LA6668-3&display=test"

Where I get:
"name": "message",
"valueString": "Unable to validate code http://loinc.org#LA6668-3Concept Display "test" does not match expected "Pathogenic" for CodeSystem: http://loinc.org/"

The same concept succeeds on a lookup.

Judging by the first message, I might have a look at valueset expansion that happens when loading loinc.

This is what I fixed by adding the path to core-ig in application.properties, since removed because it's a local path.
If I understood correctly, Peter thought there was an automatic way to do this?

Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'phenopacketDemoRunner': Unsatisfied dependency expressed through field 'hapiUrl';

nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'phenoClientConfiguration': Unsatisfied dependency expressed through field 'applicationProperties';

nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'applicationProperties' defined in file [/Users/roederc/work/git_phenopackets/hapi-pheno-client/target/classes/org/monarchinitiative/hapiphenoclient/configuration/ApplicationProperties.class]: Unexpected exception during bean creation;

nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'ig.path' in value "${ig.path}"

Trying to add a Measurement

List<Measurement> measurementList = bethlem.measurementList();
        for (Measurement measurement : measurementList) {
            IIdType measurementId = postMeasurement(measurement);
            measurement.setId(measurementId);
        }

leads to

HTTP 422 Unprocessable Entity: Observation.subject: max allowed = 0, but found 1

The is strange because the generated structure definition does not seem to have this constraint (we did not specify anything like this in the FSH code)

Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65)
Caused by: java.lang.NoClassDefFoundError: org/slf4j/impl/StaticLoggerBinder

This will allow easy use of the classes in the hapi-pheno-core module to implement the $everything operation

2022-09-01 17:27:46.906 [main] ERROR o.s.boot.SpringApplication [SpringApplication.java:856] Application run failed
java.lang.IllegalStateException: Failed to execute CommandLineRunner
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:807)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:788)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:333)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1309)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1298)
at org.monarchinitiative.hapiphenoclient.PhenoClientConsoleApplication.main(PhenoClientConsoleApplication.java:36)
Caused by: ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException: HTTP 422 Unprocessable Entity: Attachments have data and/or url, or else SHOULD have either contentType and/or language
at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:67)