Fixing ValueSet expansion not supporting canonical url. (#3501)

* 2991 - WIP, starting to implement test to reproduce the issue.

* Adding capability to extract url & version from the valueSet.include.url

* parsing codeSystem canonical URL to extra version if required.

* WIP

* Cleaning up the test.

* Replacing hard code value with variable.

* Removing non required test.

* Modifications following first code review.

* Further modifications following first code review.

* Refining the test for better code coverage.

* Prefixing the change log file name with the hapi-fhir issue number.

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3515-supporting-canonical-system-uri-during-valueset-expansion.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 3515
+jira: SMILE-2991
+title: "Supporting expansion of ValueSet include/exclude system URI expressed in canonical format during validation."

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupport.java

@@ -1,12 +1,12 @@
 package org.hl7.fhir.common.hapi.validation.support;
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.ConceptValidationOptions;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.util.FhirVersionIndependentConcept;
 import org.apache.commons.lang3.Validate;
@@ -36,9 +36,12 @@ import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.contains;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.substringAfter;
+import static org.apache.commons.lang3.StringUtils.substringBefore;
 
 /**
  * This class is a basic in-memory terminology service, designed to expand ValueSets and validate codes
@@ -47,6 +50,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * external term service API)
  */
 public class InMemoryTerminologyServerValidationSupport implements IValidationSupport {
+	private static final String OUR_PIPE_CHARACTER = "|";
+
 	private final FhirContext myCtx;
 
 	public InMemoryTerminologyServerValidationSupport(FhirContext theCtx) {
@@ -539,13 +544,15 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 	}
 
 	/**
-	 * Returns <code>true</code> if at least one code was addded
+	 * Returns <code>true</code> if at least one code was added
 	 */
 	private boolean expandValueSetR5IncludeOrExclude(ValidationSupportContext theValidationSupportContext, Consumer<FhirVersionIndependentConcept> theConsumer, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent theInclude) throws ExpansionCouldNotBeCompletedInternallyException {
+
 		String wantSystemUrl = null;
 		String wantSystemVersion = null;
+
 		if (theWantSystemUrlAndVersion != null) {
-			int versionIndex = theWantSystemUrlAndVersion.indexOf("|");
+			int versionIndex = theWantSystemUrlAndVersion.indexOf(OUR_PIPE_CHARACTER);
 			if (versionIndex > -1) {
 				wantSystemUrl = theWantSystemUrlAndVersion.substring(0, versionIndex);
 				wantSystemVersion = theWantSystemUrlAndVersion.substring(versionIndex + 1);
@@ -554,15 +561,20 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 			}
 		}
 
+		String includeOrExcludeConceptSystemUrl = theInclude.getSystem();
+		String includeOrExcludeConceptSystemVersion = theInclude.getVersion();
+
 		Function<String, CodeSystem> codeSystemLoader = newCodeSystemLoader(theValidationSupportContext);
 		Function<String, org.hl7.fhir.r5.model.ValueSet> valueSetLoader = newValueSetLoader(theValidationSupportContext);
 
 		List<FhirVersionIndependentConcept> nextCodeList = new ArrayList<>();
-		String includeOrExcludeConceptSystemUrl = theInclude.getSystem();
-		String includeOrExcludeConceptSystemVersion = theInclude.getVersion();
 		CodeSystem includeOrExcludeSystemResource = null;
+
 		if (isNotBlank(includeOrExcludeConceptSystemUrl)) {
 
+			includeOrExcludeConceptSystemVersion = optionallyPopulateVersionFromUrl(includeOrExcludeConceptSystemUrl, includeOrExcludeConceptSystemVersion);
+			includeOrExcludeConceptSystemUrl = substringBefore(includeOrExcludeConceptSystemUrl, OUR_PIPE_CHARACTER);
+
 			if (wantSystemUrl != null && !wantSystemUrl.equals(includeOrExcludeConceptSystemUrl)) {
 				return false;
 			}
@@ -573,7 +585,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 
 			String loadedCodeSystemUrl;
 			if (includeOrExcludeConceptSystemVersion != null) {
-				loadedCodeSystemUrl = includeOrExcludeConceptSystemUrl + "|" + includeOrExcludeConceptSystemVersion;
+				loadedCodeSystemUrl = includeOrExcludeConceptSystemUrl + OUR_PIPE_CHARACTER + includeOrExcludeConceptSystemVersion;
 			} else {
 				loadedCodeSystemUrl = includeOrExcludeConceptSystemUrl;
 			}
@@ -810,6 +822,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 		}
 	}
 
+	private String optionallyPopulateVersionFromUrl(String theSystemUrl, String theVersion) {
+		if(contains(theSystemUrl, OUR_PIPE_CHARACTER) && isBlank(theVersion)){
+			theVersion = substringAfter(theSystemUrl, OUR_PIPE_CHARACTER);
+		}
+		return theVersion;
+	}
 
 	public enum FailureType {
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupportTest.java

@@ -14,6 +14,8 @@ import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -423,6 +425,40 @@ public class InMemoryTerminologyServerValidationSupportTest {
 		assertEquals("MODERNA COVID-19 mRNA-1273", valueSet.getExpansion().getContains().get(0).getDisplay());
 	}
 
+    @ParameterizedTest
+	 @ValueSource(strings = {"http://terminology.hl7.org/CodeSystem/v2-0360|2.7","http://terminology.hl7.org/CodeSystem/v2-0360"})
+    void testValidateCodeInValueSet_VsExpandedWithIncludes(String theCodeSystemUri) {
+		 ConceptValidationOptions options = new ConceptValidationOptions();
+		 ValidationSupportContext valCtx = new ValidationSupportContext(myChain);
+		 String codeMD = "MD";
+
+		 CodeSystem cs = new CodeSystem();
+		 cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		 cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		 cs.setUrl(theCodeSystemUri);
+		 cs.addConcept()
+			 .setCode(codeMD)
+			 .setDisplay("Doctor of Medicine");
+		 myPrePopulated.addCodeSystem(cs);
+
+		 ValueSet theValueSet = new ValueSet();
+		 theValueSet.setUrl("http://someValueSetURL");
+		 theValueSet.setVersion("0360");
+		 theValueSet.getCompose().addInclude().setSystem(theCodeSystemUri);
+
+		 String theCodeToValidateCodeSystemUrl = theCodeSystemUri;
+		 String theCodeToValidate = codeMD;
+
+		 IValidationSupport.CodeValidationResult codeValidationResult = mySvc.validateCodeInValueSet(
+			 valCtx,
+			 options,
+			 theCodeToValidateCodeSystemUrl,
+			 theCodeToValidate,
+			 null,
+			 theValueSet);
+
+		 assertTrue(codeValidationResult.isOk());
+	 }
 
     private static class PrePopulatedValidationSupportDstu2 extends PrePopulatedValidationSupport {
 		private final Map<String, IBaseResource> myDstu2ValueSets;