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Fixes for the translation of parameter issues as part of the output f…
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…or $validate-code operation. (#6438)

* Move the validation providers to the test utilities package such that they can be reused.

* Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues.

* New tests for issue translation. Move test class to a different package so that we can add another test class.

* Some simplification in the issue API to simplify building of issues.

* Fix compilation errors.

* Update providers to allow multiple responses and add  support for the fetchCodeSystem call through method find.

* Setup the first test for resource validation with remote terminology providers.

* Fix NullPointerException

* avoid calling validateCode for CodeSystem where system is null

* Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies.

* Revert local change to debug for duplicate errors.

* Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious.

* Simplify test setup.

* Add some more javadoc

* Add javadoc for the new test class

* Add more tests

* Address code review comments in IValidationSupport.

* Add changelog
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@codeforgreen
codeforgreen authored Nov 5, 2024
1 parent 34359b2 commit 3f042fd
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303 changes: 262 additions & 41 deletions hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
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7 changes: 7 additions & 0 deletions ...main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6422-fixes-remote-terminology-issues.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
---
type: fix
issue: 6422
title: "Previously, since 7.4.4 the validation issue detail codes were not translated correctly for Remote Terminology
validateCode calls. The detail code used was `invalid-code` for all use-cases which resulted in profile binding strength
not being applied to the issue severity as expected when validating resources against a profile.
This has been fixed and issue detail codes are translated correctly."
5 changes: 3 additions & 2 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1044,7 +1044,8 @@ private void expandValueSetHandleIncludeOrExclude(
if (theExpansionOptions != null
&& !theExpansionOptions.isFailOnMissingCodeSystem()
// Code system is unknown, therefore NOT_FOUND
&& e.getCodeValidationIssue().getCoding() == CodeValidationIssueCoding.NOT_FOUND) {
&& e.getCodeValidationIssue()
.hasIssueDetailCode(CodeValidationIssueCoding.NOT_FOUND.getCode())) {
return;
}
throw new InternalErrorException(Msg.code(888) + e);
Expand Down Expand Up @@ -2190,7 +2191,7 @@ private CodeValidationResult createFailureCodeValidationResult(
.setSeverity(IssueSeverity.ERROR)
.setCodeSystemVersion(theCodeSystemVersion)
.setMessage(theMessage)
.addCodeValidationIssue(new CodeValidationIssue(
.addIssue(new CodeValidationIssue(
theMessage,
IssueSeverity.ERROR,
CodeValidationIssueCode.CODE_INVALID,
Expand Down
167 changes: 52 additions & 115 deletions ...OperationWithRemoteTerminologyR4Test.java → ...idateCodeWithRemoteTerminologyR4Test.java
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Original file line number Diff line number Diff line change
@@ -1,29 +1,21 @@
package ca.uhn.fhir.jpa.provider.r4;
package ca.uhn.fhir.jpa.validation;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import jakarta.servlet.http.HttpServletRequest;
import ca.uhn.fhir.test.utilities.validation.IValidationProviders;
import ca.uhn.fhir.test.utilities.validation.IValidationProvidersR4;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
Expand All @@ -33,25 +25,23 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;

import java.util.ArrayList;
import java.util.List;

import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_VALIDATE_CODE;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.AssertionsForClassTypes.assertThatExceptionOfType;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;

/*
/**
* This set of integration tests that instantiates and injects an instance of
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport}
* into the ValidationSupportChain, which tests the logic of dynamically selecting the correct Remote Terminology
* implementation. It also exercises the code found in
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport#invokeRemoteValidateCode}
* implementation. It also exercises the validateCode output translation code found in
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport}
*/
public class ValidateCodeOperationWithRemoteTerminologyR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateCodeOperationWithRemoteTerminologyR4Test.class);
public class ValidateCodeWithRemoteTerminologyR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateCodeWithRemoteTerminologyR4Test.class);
private static final String DISPLAY = "DISPLAY";
private static final String DISPLAY_BODY_MASS_INDEX = "Body mass index (BMI) [Ratio]";
private static final String CODE_BODY_MASS_INDEX = "39156-5";
Expand All @@ -64,8 +54,8 @@ public class ValidateCodeOperationWithRemoteTerminologyR4Test extends BaseResour
protected static RestfulServerExtension ourRestfulServerExtension = new RestfulServerExtension(ourCtx);

private RemoteTerminologyServiceValidationSupport mySvc;
private MyCodeSystemProvider myCodeSystemProvider;
private MyValueSetProvider myValueSetProvider;
private IValidationProviders.MyValidationProvider<CodeSystem> myCodeSystemProvider;
private IValidationProviders.MyValidationProvider<ValueSet> myValueSetProvider;

@Autowired
@Qualifier(JpaConfig.JPA_VALIDATION_SUPPORT_CHAIN)
Expand All @@ -76,8 +66,8 @@ public void before() throws Exception {
String baseUrl = "http://localhost:" + ourRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx, baseUrl);
myValidationSupportChain.addValidationSupport(0, mySvc);
myCodeSystemProvider = new MyCodeSystemProvider();
myValueSetProvider = new MyValueSetProvider();
myCodeSystemProvider = new IValidationProvidersR4.MyCodeSystemProviderR4();
myValueSetProvider = new IValidationProvidersR4.MyValueSetProviderR4();
ourRestfulServerExtension.registerProvider(myCodeSystemProvider);
ourRestfulServerExtension.registerProvider(myValueSetProvider);
}
Expand All @@ -103,20 +93,20 @@ public void validateCodeOperationOnCodeSystem_byCodingAndUrlWhereSystemIsDiffere

@Test
public void validateCodeOperationOnCodeSystem_byCodingAndUrl_usingBuiltInCodeSystems() {
myCodeSystemProvider.myReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/v2-0247"));
myCodeSystemProvider.myReturnParams = new Parameters();
myCodeSystemProvider.myReturnParams.addParameter("result", true);
myCodeSystemProvider.myReturnParams.addParameter("display", DISPLAY);
final String code = "P";
final String system = CODE_SYSTEM_V2_0247_URI;;

Parameters params = new Parameters().addParameter("result", true).addParameter("display", DISPLAY);
setupCodeSystemValidateCode(system, code, params);

logAllConcepts();

Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "coding", new Coding().setSystem(CODE_SYSTEM_V2_0247_URI).setCode("P"))
.andParameter("url", new UriType(CODE_SYSTEM_V2_0247_URI))
.withParameter(Parameters.class, "coding", new Coding().setSystem(system).setCode(code))
.andParameter("url", new UriType(system))
.execute();

String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
Expand All @@ -128,7 +118,7 @@ public void validateCodeOperationOnCodeSystem_byCodingAndUrl_usingBuiltInCodeSys

@Test
public void validateCodeOperationOnCodeSystem_byCodingAndUrlWhereCodeSystemIsUnknown_returnsFalse() {
myCodeSystemProvider.myReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.setShouldThrowExceptionForResourceNotFound(false);

Parameters respParam = myClient
.operation()
Expand Down Expand Up @@ -166,21 +156,21 @@ public void validateCodeOperationOnValueSet_byCodingAndUrlWhereSystemIsDifferent

@Test
public void validateCodeOperationOnValueSet_byUrlAndSystem_usingBuiltInCodeSystems() {
myCodeSystemProvider.myReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/list-example-use-codes"));
myValueSetProvider.myReturnValueSets = new ArrayList<>();
myValueSetProvider.myReturnValueSets.add((ValueSet) new ValueSet().setId("ValueSet/list-example-codes"));
myValueSetProvider.myReturnParams = new Parameters();
myValueSetProvider.myReturnParams.addParameter("result", true);
myValueSetProvider.myReturnParams.addParameter("display", DISPLAY);
final String code = "alerts";
final String system = "http://terminology.hl7.org/CodeSystem/list-example-use-codes";
final String valueSetUrl = "http://hl7.org/fhir/ValueSet/list-example-codes";

Parameters params = new Parameters().addParameter("result", true).addParameter("display", DISPLAY);
setupValueSetValidateCode(valueSetUrl, system, code, params);
setupCodeSystemValidateCode(system, code, params);

Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "code", new CodeType("alerts"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/list-example-use-codes"))
.andParameter("url", new UriType("http://hl7.org/fhir/ValueSet/list-example-codes"))
.withParameter(Parameters.class, "code", new CodeType(code))
.andParameter("system", new UriType(system))
.andParameter("url", new UriType(valueSetUrl))
.useHttpGet()
.execute();

Expand All @@ -193,21 +183,20 @@ public void validateCodeOperationOnValueSet_byUrlAndSystem_usingBuiltInCodeSyste

@Test
public void validateCodeOperationOnValueSet_byUrlSystemAndCode() {
myCodeSystemProvider.myReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/list-example-use-codes"));
myValueSetProvider.myReturnValueSets = new ArrayList<>();
myValueSetProvider.myReturnValueSets.add((ValueSet) new ValueSet().setId("ValueSet/list-example-codes"));
myValueSetProvider.myReturnParams = new Parameters();
myValueSetProvider.myReturnParams.addParameter("result", true);
myValueSetProvider.myReturnParams.addParameter("display", DISPLAY_BODY_MASS_INDEX);
final String code = CODE_BODY_MASS_INDEX;
final String system = "http://terminology.hl7.org/CodeSystem/list-example-use-codes";
final String valueSetUrl = "http://hl7.org/fhir/ValueSet/list-example-codes";

Parameters params = new Parameters().addParameter("result", true).addParameter("display", DISPLAY_BODY_MASS_INDEX);
setupValueSetValidateCode(valueSetUrl, system, code, params);

Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "code", new CodeType(CODE_BODY_MASS_INDEX))
.andParameter("url", new UriType("https://loinc.org"))
.andParameter("system", new UriType("http://loinc.org"))
.withParameter(Parameters.class, "code", new CodeType(code))
.andParameter("url", new UriType(valueSetUrl))
.andParameter("system", new UriType(system))
.execute();

String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
Expand All @@ -219,7 +208,7 @@ public void validateCodeOperationOnValueSet_byUrlSystemAndCode() {

@Test
public void validateCodeOperationOnValueSet_byCodingAndUrlWhereValueSetIsUnknown_returnsFalse() {
myValueSetProvider.myReturnValueSets = new ArrayList<>();
myValueSetProvider.setShouldThrowExceptionForResourceNotFound(false);

Parameters respParam = myClient
.operation()
Expand All @@ -238,70 +227,18 @@ public void validateCodeOperationOnValueSet_byCodingAndUrlWhereValueSetIsUnknown
" - Unknown or unusable ValueSet[" + UNKNOWN_VALUE_SYSTEM_URI + "]");
}

@SuppressWarnings("unused")
private static class MyCodeSystemProvider implements IResourceProvider {
private List<CodeSystem> myReturnCodeSystems;
private Parameters myReturnParams;

@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theCodeSystemUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay
) {
return myReturnParams;
}

@Search
public List<CodeSystem> find(@RequiredParam(name = "url") UriParam theUrlParam) {
assert myReturnCodeSystems != null;
return myReturnCodeSystems;
}
private void setupValueSetValidateCode(String theUrl, String theSystem, String theCode, IBaseParameters theResponseParams) {
ValueSet valueSet = myValueSetProvider.addTerminologyResource(theUrl);
myValueSetProvider.addTerminologyResource(theSystem);
myValueSetProvider.addTerminologyResponse(OPERATION_VALIDATE_CODE, valueSet.getUrl(), theCode, theResponseParams);

@Override
public Class<? extends IBaseResource> getResourceType() {
return CodeSystem.class;
}
// we currently do this because VersionSpecificWorkerContextWrapper has logic to infer the system when missing
// based on the ValueSet by calling ValidationSupportUtils#extractCodeSystemForCode.
valueSet.getCompose().addInclude().setSystem(theSystem);
}

@SuppressWarnings("unused")
private static class MyValueSetProvider implements IResourceProvider {
private Parameters myReturnParams;
private List<ValueSet> myReturnValueSets;

@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
@OperationParam(name = "valueSet") ValueSet theValueSet
) {
return myReturnParams;
}

@Search
public List<ValueSet> find(@RequiredParam(name = "url") UriParam theUrlParam) {
assert myReturnValueSets != null;
return myReturnValueSets;
}

@Override
public Class<? extends IBaseResource> getResourceType() {
return ValueSet.class;
}

private void setupCodeSystemValidateCode(String theUrl, String theCode, IBaseParameters theResponseParams) {
CodeSystem codeSystem = myCodeSystemProvider.addTerminologyResource(theUrl);
myCodeSystemProvider.addTerminologyResponse(OPERATION_VALIDATE_CODE, codeSystem.getUrl(), theCode, theResponseParams);
}
}
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