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:
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c89d12232f
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92e9859272
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@ -7,18 +7,22 @@ import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.util.BundleUtil;
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import ca.uhn.fhir.util.JsonUtil;
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import ca.uhn.fhir.util.ParametersUtil;
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import org.apache.commons.lang3.Validate;
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import org.checkerframework.framework.qual.InvisibleQualifier;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.annotation.Nonnull;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@ -30,6 +34,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
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* operation in order to validate codes.
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*/
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public class RemoteTerminologyServiceValidationSupport extends BaseValidationSupport implements IValidationSupport {
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private static final Logger ourLog = LoggerFactory.getLogger(RemoteTerminologyServiceValidationSupport.class);
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private String myBaseUrl;
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private List<Object> myClientInterceptors = new ArrayList<>();
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@ -57,10 +62,7 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
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// so let's try to get it from the VS if is is not present
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String codeSystem = theCodeSystem;
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if (isNotBlank(theCode) && isBlank(codeSystem)) {
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ValueSet vs = (ValueSet) theValueSet;
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if ( vs.getCompose() != null && vs.getCompose().getInclude() != null && vs.getCompose().getInclude().size() > 0) {
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codeSystem = vs.getCompose().getInclude().iterator().next().getSystem();
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}
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codeSystem = extractCodeSystemForCode((ValueSet) theValueSet, theCode);
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}
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// Remote terminology services shouldn't be used to validate codes with an implied system
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@ -75,6 +77,54 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
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return invokeRemoteValidateCode(codeSystem, theCode, theDisplay, valueSetUrl, valueSet);
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}
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/**
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* Try to obtain the codeSystem of the received code from the received ValueSet
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*/
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private String extractCodeSystemForCode(ValueSet theValueSet, String theCode) {
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if (theValueSet.getCompose() == null || theValueSet.getCompose().getInclude() == null
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|| theValueSet.getCompose().getInclude().isEmpty()) {
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return null;
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}
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if (theValueSet.getCompose().getInclude().size() == 1) {
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ValueSet.ConceptSetComponent include = theValueSet.getCompose().getInclude().iterator().next();
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return getVersionedCodeSystem(include);
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}
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// when component has more than one include, their codeSystem(s) could be different, so we need to make sure
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// that we are picking up the system for the include to which the code corresponds
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for (ValueSet.ConceptSetComponent include: theValueSet.getCompose().getInclude()) {
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if (include.hasSystem()) {
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for (ValueSet.ConceptReferenceComponent concept : include.getConcept()) {
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if (concept.hasCodeElement() && concept.getCode().equals(theCode)) {
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return getVersionedCodeSystem(include);
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}
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}
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}
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}
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// at this point codeSystem couldn't be extracted for a multi-include ValueSet. Just on case it was
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// because the format was not well handled, let's allow to watch the VS by an easy logging change
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try {
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ourLog.trace("CodeSystem couldn't be extracted for code: {} for ValueSet: {}",
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theCode, JsonUtil.serialize(theValueSet));
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} catch (IOException theE) {
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ourLog.error("IOException trying to serialize ValueSet to json: " + theE);
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}
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return null;
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}
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private String getVersionedCodeSystem(ValueSet.ConceptSetComponent theComponent) {
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String codeSystem = theComponent.getSystem();
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if ( ! codeSystem.contains("|") && theComponent.hasVersion()) {
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codeSystem += "|" + theComponent.getVersion();
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}
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return codeSystem;
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}
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@Override
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public IBaseResource fetchCodeSystem(String theSystem) {
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IGenericClient client = provideClient();
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@ -136,37 +186,13 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
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IGenericClient client = provideClient();
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IBaseParameters input = ParametersUtil.newInstance(getFhirContext());
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IBaseParameters input = buildValidateCodeInputParameters(theCodeSystem, theCode, theDisplay, theValueSetUrl, theValueSet);
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String resourceType = "ValueSet";
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if (theValueSet == null && theValueSetUrl == null) {
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resourceType = "CodeSystem";
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ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "url", theCodeSystem);
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ParametersUtil.addParameterToParametersString(getFhirContext(), input, "code", theCode);
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if (isNotBlank(theDisplay)) {
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ParametersUtil.addParameterToParametersString(getFhirContext(), input, "display", theDisplay);
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}
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} else {
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if (isNotBlank(theValueSetUrl)) {
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ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "url", theValueSetUrl);
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}
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ParametersUtil.addParameterToParametersString(getFhirContext(), input, "code", theCode);
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if (isNotBlank(theCodeSystem)) {
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ParametersUtil.addParameterToParametersUri(getFhirContext(), input, "system", theCodeSystem);
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}
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if (isNotBlank(theDisplay)) {
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ParametersUtil.addParameterToParametersString(getFhirContext(), input, "display", theDisplay);
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}
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if (theValueSet != null) {
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ParametersUtil.addParameterToParameters(getFhirContext(), input, "valueSet", theValueSet);
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}
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}
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IBaseParameters output = client
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.operation()
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.onType(resourceType)
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@ -203,6 +229,35 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
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return retVal;
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}
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protected IBaseParameters buildValidateCodeInputParameters(String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl, IBaseResource theValueSet) {
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IBaseParameters params = ParametersUtil.newInstance(getFhirContext());
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if (theValueSet == null && theValueSetUrl == null) {
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ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "url", theCodeSystem);
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ParametersUtil.addParameterToParametersString(getFhirContext(), params, "code", theCode);
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if (isNotBlank(theDisplay)) {
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ParametersUtil.addParameterToParametersString(getFhirContext(), params, "display", theDisplay);
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}
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return params;
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}
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if (isNotBlank(theValueSetUrl)) {
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ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "url", theValueSetUrl);
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}
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ParametersUtil.addParameterToParametersString(getFhirContext(), params, "code", theCode);
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if (isNotBlank(theCodeSystem)) {
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ParametersUtil.addParameterToParametersUri(getFhirContext(), params, "system", theCodeSystem);
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}
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if (isNotBlank(theDisplay)) {
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ParametersUtil.addParameterToParametersString(getFhirContext(), params, "display", theDisplay);
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}
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if (theValueSet != null) {
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ParametersUtil.addParameterToParameters(getFhirContext(), params, "valueSet", theValueSet);
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}
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return params;
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}
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/**
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* Sets the FHIR Terminology Server base URL
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*
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@ -3,15 +3,21 @@ package org.hl7.fhir.common.hapi.validation.support;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.ConceptValidationOptions;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.parser.IJsonLikeParser;
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import ca.uhn.fhir.rest.annotation.IdParam;
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import ca.uhn.fhir.rest.annotation.Operation;
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import ca.uhn.fhir.rest.annotation.OperationParam;
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import ca.uhn.fhir.rest.annotation.RequiredParam;
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import ca.uhn.fhir.rest.annotation.Search;
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import ca.uhn.fhir.rest.client.api.IClientInterceptor;
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import ca.uhn.fhir.rest.client.api.IHttpRequest;
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import ca.uhn.fhir.rest.client.api.IHttpResponse;
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import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.server.IResourceProvider;
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import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
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import ca.uhn.fhir.util.ParametersUtil;
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import com.google.common.collect.Lists;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.CodeSystem;
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@ -23,10 +29,12 @@ import org.hl7.fhir.r4.model.UriType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.RegisterExtension;
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import javax.servlet.http.HttpServletRequest;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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@ -35,6 +43,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.lessThan;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertNull;
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public class RemoteTerminologyServiceValidationSupportTest {
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mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx);
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mySvc.setBaseUrl(baseUrl);
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mySvc.addClientInterceptor(new LoggingInterceptor(false));
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mySvc.addClientInterceptor(new LoggingInterceptor(true));
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}
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@AfterEach
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* Remote terminology services shouldn't be used to validate codes with an implied system
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*/
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@Test
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public void testValidateCodeInValueSet_InferSystem_codeSystemNotPresent() {
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public void testValidateCodeInValueSet_InferSystem() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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ValueSet valueSet = new ValueSet();
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@ -166,23 +175,159 @@ public class RemoteTerminologyServiceValidationSupportTest {
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* Remote terminology services can be used to validate codes when code system is present,
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* even when inferSystem is true
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*/
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@Test
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public void testValidateCodeInValueSet_InferSystem_codeSystemIsPresent() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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@Nested
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public class ExtractCodeSystemFromValueSet {
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Collections.singletonList(new ValueSet.ConceptSetComponent().setSystem(systemUrl)) ));
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@Test
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public void testUniqueComposeInclude() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Collections.singletonList(new ValueSet.ConceptSetComponent().setSystem(systemUrl)) ));
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// validate service doesn't do early return (as when no code system is present)
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assertNotNull(outcome);
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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// validate service doesn't do early return (as when no code system is present)
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assertNotNull(outcome);
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}
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@Nested
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public class MultiComposeIncludeValueSet {
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@Test
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public void SystemNotPresentReturnsNull() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Lists.newArrayList(new ValueSet.ConceptSetComponent(), new ValueSet.ConceptSetComponent()) ));
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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assertNull(outcome);
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}
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@Test
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public void SystemPresentCodeNotPresentReturnsNull() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
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String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Lists.newArrayList(
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new ValueSet.ConceptSetComponent().setSystem(systemUrl),
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new ValueSet.ConceptSetComponent().setSystem(systemUrl2)) ));
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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assertNull(outcome);
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}
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@Test
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public void SystemPresentCodePresentValidatesOKNoVersioned() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
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String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Lists.newArrayList(
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new ValueSet.ConceptSetComponent().setSystem(systemUrl),
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new ValueSet.ConceptSetComponent().setSystem(systemUrl2).setConcept(
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Lists.newArrayList(
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new ValueSet.ConceptReferenceComponent().setCode("not-the-code"),
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new ValueSet.ConceptReferenceComponent().setCode(CODE) )
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)) ));
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TestClientInterceptor requestInterceptor = new TestClientInterceptor();
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mySvc.addClientInterceptor(requestInterceptor);
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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assertNotNull(outcome);
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assertEquals(systemUrl2, requestInterceptor.getCapturedSystemParameter());
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}
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@Test
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public void SystemPresentCodePresentValidatesOKVersioned() {
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createNextValueSetReturnParameters(true, DISPLAY, null);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(VALUE_SET_URL);
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String systemUrl = "http://hl7.org/fhir/ValueSet/administrative-gender";
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String systemVersion = "3.0.2";
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String systemUrl2 = "http://hl7.org/fhir/ValueSet/other-valueset";
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String system2Version = "4.0.1";
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valueSet.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(
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Lists.newArrayList(
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new ValueSet.ConceptSetComponent().setSystem(systemUrl).setVersion(systemVersion),
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new ValueSet.ConceptSetComponent().setSystem(systemUrl2).setVersion(system2Version).setConcept(
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Lists.newArrayList(
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new ValueSet.ConceptReferenceComponent().setCode("not-the-code"),
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new ValueSet.ConceptReferenceComponent().setCode(CODE) )
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)) ));
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TestClientInterceptor requestInterceptor = new TestClientInterceptor();
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mySvc.addClientInterceptor(requestInterceptor);
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IValidationSupport.CodeValidationResult outcome = mySvc.validateCodeInValueSet(null,
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new ConceptValidationOptions().setInferSystem(true), null, CODE, DISPLAY, valueSet);
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assertNotNull(outcome);
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assertEquals(systemUrl2 + "|" + system2Version, requestInterceptor.getCapturedSystemParameter());
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}
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}
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/**
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* Captures the system parameter of the request
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*/
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private class TestClientInterceptor implements IClientInterceptor {
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private String capturedSystemParameter;
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@Override
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public void interceptRequest(IHttpRequest theRequest) {
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try {
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String content = theRequest.getRequestBodyFromStream();
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if (content != null) {
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IJsonLikeParser parser = (IJsonLikeParser) ourCtx.newJsonParser();
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Parameters params = parser.parseResource(Parameters.class, content);
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List<String> systemValues = ParametersUtil.getNamedParameterValuesAsString(
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ourCtx, params, "system");
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assertEquals(1, systemValues.size());
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capturedSystemParameter = systemValues.get(0);
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}
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} catch (IOException theE) {
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theE.printStackTrace();
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}
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}
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@Override
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public void interceptResponse(IHttpResponse theResponse) throws IOException { }
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public String getCapturedSystemParameter() { return capturedSystemParameter; }
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}
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}
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@Test
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public void testIsValueSetSupported_False() {
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myValueSetProvider.myNextReturnValueSets = new ArrayList<>();
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