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Issue 3072 using an external terminology server in the fhir server for codes in fhir resources (#3081) 

* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true

* Add test for specific use case added

* Consider ValueSets with multiple component includes

* Fix typo

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto 2021-10-18 15:40:17 -04:00 committed by GitHub
parent c89d12232f
commit 92e9859272
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2 changed files with 244 additions and 44 deletions
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115
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupport.java
View File

@ -7,18 +7,22 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.Validate;
import org.checkerframework.framework.qual.InvisibleQualifier;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -30,6 +34,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* operation in order to validate codes.
*/
public class RemoteTerminologyServiceValidationSupport extends BaseValidationSupport implements IValidationSupport {
private static final Logger ourLog = LoggerFactory.getLogger(RemoteTerminologyServiceValidationSupport.class);
private String myBaseUrl;
private List<Object> myClientInterceptors = new ArrayList<>();
@ -57,10 +62,7 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
// so let's try to get it from the VS if is is not present
String codeSystem = theCodeSystem;
if (isNotBlank(theCode) && isBlank(codeSystem)) {
ValueSet vs = (ValueSet) theValueSet;
if ( vs.getCompose() != null && vs.getCompose().getInclude() != null && vs.getCompose().getInclude().size() > 0) {
codeSystem = vs.getCompose().getInclude().iterator().next().getSystem();
}
codeSystem = extractCodeSystemForCode((ValueSet) theValueSet, theCode);
}
// Remote terminology services shouldn't be used to validate codes with an implied system
@ -75,6 +77,54 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return invokeRemoteValidateCode(codeSystem, theCode, theDisplay, valueSetUrl, valueSet);
}
/**
* Try to obtain the codeSystem of the received code from the received ValueSet
*/
private String extractCodeSystemForCode(ValueSet theValueSet, String theCode) {
if (theValueSet.getCompose() == null || theValueSet.getCompose().getInclude() == null
|| theValueSet.getCompose().getInclude().isEmpty()) {
return null;
}
if (theValueSet.getCompose().getInclude().size() == 1) {
ValueSet.ConceptSetComponent include = theValueSet.getCompose().getInclude().iterator().next();
return getVersionedCodeSystem(include);
}
// when component has more than one include, their codeSystem(s) could be different, so we need to make sure
// that we are picking up the system for the include to which the code corresponds
for (ValueSet.ConceptSetComponent include: theValueSet.getCompose().getInclude()) {
if (include.hasSystem()) {
for (ValueSet.ConceptReferenceComponent concept : include.getConcept()) {
if (concept.hasCodeElement() && concept.getCode().equals(theCode)) {
return getVersionedCodeSystem(include);
}
}
}
}
// at this point codeSystem couldn't be extracted for a multi-include ValueSet. Just on case it was
// because the format was not well handled, let's allow to watch the VS by an easy logging change
try {
ourLog.trace("CodeSystem couldn't be extracted for code: {} for ValueSet: {}",
theCode, JsonUtil.serialize(theValueSet));
} catch (IOException theE) {
ourLog.error("IOException trying to serialize ValueSet to json: " + theE);
}
return null;
}
private String getVersionedCodeSystem(ValueSet.ConceptSetComponent theComponent) {
String codeSystem = theComponent.getSystem();
if ( ! codeSystem.contains("|") && theComponent.hasVersion()) {
codeSystem += "|" + theComponent.getVersion();
}
return codeSystem;
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
IGenericClient client = provideClient();
@ -136,37 +186,13 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
IGenericClient client = provideClient();
IBaseParameters input = ParametersUtil.newInstance(getFhirContext());
IBaseParameters input = buildValidateCodeInputParameters(theCodeSystem, theCode, theDisplay, theValueSetUrl, theValueSet);
String resourceType = "ValueSet";
if (theValueSet == null && theValueSetUrl == null) {
resourceType = "CodeSystem";
ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "url", theCodeSystem);
ParametersUtil.addParameterToParametersString(getFhirContext(), input, "code", theCode);
if (isNotBlank(theDisplay)) {
ParametersUtil.addParameterToParametersString(getFhirContext(), input, "display", theDisplay);
}
} else {
if (isNotBlank(theValueSetUrl)) {
ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "url", theValueSetUrl);
}
ParametersUtil.addParameterToParametersString(getFhirContext(), input, "code", theCode);
if (isNotBlank(theCodeSystem)) {
ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "system", theCodeSystem);
}
if (isNotBlank(theDisplay)) {
ParametersUtil.addParameterToParametersString(getFhirContext(), input, "display", theDisplay);
}
if (theValueSet != null) {
ParametersUtil.addParameterToParameters(getFhirContext(), input, "valueSet", theValueSet);
}
}
IBaseParameters output = client
.operation()
.onType(resourceType)
@ -203,6 +229,35 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return retVal;
}
protected IBaseParameters buildValidateCodeInputParameters(String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl, IBaseResource theValueSet) {
IBaseParameters params = ParametersUtil.newInstance(getFhirContext());
if (theValueSet == null && theValueSetUrl == null) {
ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "url", theCodeSystem);
ParametersUtil.addParameterToParametersString(getFhirContext(), params, "code", theCode);
if (isNotBlank(theDisplay)) {
ParametersUtil.addParameterToParametersString(getFhirContext(), params, "display", theDisplay);
}
return params;
}
if (isNotBlank(theValueSetUrl)) {
ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "url", theValueSetUrl);
}
ParametersUtil.addParameterToParametersString(getFhirContext(), params, "code", theCode);
if (isNotBlank(theCodeSystem)) {
ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "system", theCodeSystem);
}
if (isNotBlank(theDisplay)) {
ParametersUtil.addParameterToParametersString(getFhirContext(), params, "display", theDisplay);
}
if (theValueSet != null) {
ParametersUtil.addParameterToParameters(getFhirContext(), params, "valueSet", theValueSet);
}
return params;
}
/**
* Sets the FHIR Terminology Server base URL
*

151
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupportTest.java
View File

@ -3,15 +3,21 @@ package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.parser.IJsonLikeParser;
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.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
@ -23,10 +29,12 @@ import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
@ -35,6 +43,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.lessThan;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
public class RemoteTerminologyServiceValidationSupportTest {
@ -64,7 +73,7 @@ public class RemoteTerminologyServiceValidationSupportTest {
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx);
mySvc.setBaseUrl(baseUrl);
mySvc.addClientInterceptor(new LoggingInterceptor(false));
mySvc.addClientInterceptor(new LoggingInterceptor(true));
}
@AfterEach
@ -152,7 +161,7 @@ public class RemoteTerminologyServiceValidationSupportTest {
* Remote terminology services shouldn't be used to validate codes with an implied system
*/
@Test
public void testValidateCodeInValueSet_InferSystem_codeSystemNotPresent() {
public void testValidateCodeInValueSet_InferSystem() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
@ -166,8 +175,11 @@ public class RemoteTerminologyServiceValidationSupportTest {
* Remote terminology services can be used to validate codes when code system is present,
* even when inferSystem is true
*/
@Nested
public class ExtractCodeSystemFromValueSet {
@Test
public void testValidateCodeInValueSet_InferSystem_codeSystemIsPresent() {
public void testUniqueComposeInclude() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
@ -183,6 +195,139 @@ public class RemoteTerminologyServiceValidationSupportTest {
assertNotNull(outcome);
}
@Nested
public class MultiComposeIncludeValueSet {
@Test
public void SystemNotPresentReturnsNull() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(VALUE_SET_URL);
valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
Lists.newArrayList(new ValueSet.ConceptSetComponent(), new ValueSet.ConceptSetComponent()) ));
IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
assertNull(outcome);
}
@Test
public void SystemPresentCodeNotPresentReturnsNull() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(VALUE_SET_URL);
String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
Lists.newArrayList(
new ValueSet.ConceptSetComponent().setSystem(systemUrl),
new ValueSet.ConceptSetComponent().setSystem(systemUrl2)) ));
IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
assertNull(outcome);
}
@Test
public void SystemPresentCodePresentValidatesOKNoVersioned() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(VALUE_SET_URL);
String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
Lists.newArrayList(
new ValueSet.ConceptSetComponent().setSystem(systemUrl),
new ValueSet.ConceptSetComponent().setSystem(systemUrl2).setConcept(
Lists.newArrayList(
new ValueSet.ConceptReferenceComponent().setCode("not-the-code"),
new ValueSet.ConceptReferenceComponent().setCode(CODE) )
)) ));
TestClientInterceptor requestInterceptor = new TestClientInterceptor();
mySvc.addClientInterceptor(requestInterceptor);
IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
assertNotNull(outcome);
assertEquals(systemUrl2, requestInterceptor.getCapturedSystemParameter());
}
@Test
public void SystemPresentCodePresentValidatesOKVersioned() {
createNextValueSetReturnParameters(true, DISPLAY, null);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(VALUE_SET_URL);
String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
String systemVersion = "3.0.2";
String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
String system2Version = "4.0.1";
valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
Lists.newArrayList(
new ValueSet.ConceptSetComponent().setSystem(systemUrl).setVersion(systemVersion),
new ValueSet.ConceptSetComponent().setSystem(systemUrl2).setVersion(system2Version).setConcept(
Lists.newArrayList(
new ValueSet.ConceptReferenceComponent().setCode("not-the-code"),
new ValueSet.ConceptReferenceComponent().setCode(CODE) )
)) ));
TestClientInterceptor requestInterceptor = new TestClientInterceptor();
mySvc.addClientInterceptor(requestInterceptor);
IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
assertNotNull(outcome);
assertEquals(systemUrl2 + "|" + system2Version, requestInterceptor.getCapturedSystemParameter());
}
}
/**
* Captures the system parameter of the request
*/
private class TestClientInterceptor implements IClientInterceptor {
private String capturedSystemParameter;
@Override
public void interceptRequest(IHttpRequest theRequest) {
try {
String content = theRequest.getRequestBodyFromStream();
if (content != null) {
IJsonLikeParser parser = (IJsonLikeParser) ourCtx.newJsonParser();
Parameters params = parser.parseResource(Parameters.class, content);
List<String> systemValues = ParametersUtil.getNamedParameterValuesAsString(
ourCtx, params, "system");
assertEquals(1, systemValues.size());
capturedSystemParameter = systemValues.get(0);
}
} catch (IOException theE) {
theE.printStackTrace();
}
}
@Override
public void interceptResponse(IHttpResponse theResponse) throws IOException { }
public String getCapturedSystemParameter() { return capturedSystemParameter; }
}
}
@Test
public void testIsValueSetSupported_False() {
myValueSetProvider.myNextReturnValueSets = new ArrayList<>();