Allow unknown code systems during validation (#2523)

* Allow unknown code systems during validation

* Add changelog

* Test fix

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2523-allow-validation-with-unknown-code-system.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 2523
+title: "A new Validation Support Module has been added called UnknownCodeSystemWarningValidationSupport. This module
+  allows validation to produce a warning but not an error if a code being validated references
+  an unknown code system."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/validation_support_modules.md

@@ -134,6 +134,15 @@ This module will invoke the following operations on the remote terminology serve
 * **POST [base]/CodeSystem/$validate-code** – Validate codes in fields where no specific ValueSet is bound 
 * **POST [base]/ValueSet/$validate-code** – Validate codes in fields where a specific ValueSet is bound 
 
+# UnknownCodeSystemWarningValidationSupport
+
+[JavaDoc](/hapi-fhir/apidocs/hapi-fhir-validation/org/hl7/fhir/common/hapi/validation/support/UnknownCodeSystemWarningValidationSupport.html) / [Source](https://github.com/jamesagnew/hapi-fhir/blob/ja_20200218_validation_api_changes/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/UnknownCodeSystemWarningValidationSupport.java)
+
+This validation support module may be placed at the end of a ValidationSupportChain in order to configure the validator to generate a warning if a resource being validated contains an unknown code system.
+
+Note that this module must also be activated by calling [setAllowNonExistentCodeSystem(true)](/hapi-fhir/apidocs/hapi-fhir-validation/org/hl7/fhir/common/hapi/validation/support/UnknownCodeSystemWarningValidationSupport.html#setAllowNonExistentCodeSystem(boolean)) in order to specify that unknown code systems should be allowed.
+
+
 # Recipes
 
 The IValidationSupport instance passed to the FhirInstanceValidator will often resemble the chain shown in the diagram below. In this diagram:

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -130,6 +130,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@@ -227,7 +228,6 @@ public abstract class BaseConfig {
 		this.searchCoordQueueCapacity = searchCoordQueueCapacity;
 	}
 
-
 	@Bean
 	public BatchConfigurer batchConfigurer() {
 		return new NonPersistedBatchConfigurer();
@@ -834,6 +834,11 @@ public abstract class BaseConfig {
 		return new JpaResourceLoader();
 	}
 
+	@Bean
+	public UnknownCodeSystemWarningValidationSupport unknownCodeSystemWarningValidationSupport() {
+		return new UnknownCodeSystemWarningValidationSupport(fhirContext());
+	}
+
 	public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
 		theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
 		theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

@@ -2184,11 +2184,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			retVal = createFailureCodeValidationResult(theCodeSystem, theCode, append);
 		}
 
-		if (retVal == null) {
-			String append = " - Unable to expand ValueSet[" + theValueSetUrl + "]";
-			retVal = createFailureCodeValidationResult(theCodeSystem, theCode, append);
-		}
-
 		return retVal;
 
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChain.java

@@ -26,8 +26,9 @@ import ca.uhn.fhir.jpa.packages.NpmJpaValidationSupport;
 import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
-import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -52,6 +53,8 @@ public class JpaValidationSupportChain extends ValidationSupportChain {
 	private NpmJpaValidationSupport myNpmJpaValidationSupport;
 	@Autowired
 	private ITermConceptMappingSvc myConceptMappingSvc;
+	@Autowired
+	private UnknownCodeSystemWarningValidationSupport myUnknownCodeSystemWarningValidationSupport;
 
 	public JpaValidationSupportChain(FhirContext theFhirContext) {
 		myFhirContext = theFhirContext;
@@ -77,6 +80,7 @@ public class JpaValidationSupportChain extends ValidationSupportChain {
 		addValidationSupport(myNpmJpaValidationSupport);
 		addValidationSupport(new CommonCodeSystemsTerminologyService(myFhirContext));
 		addValidationSupport(myConceptMappingSvc);
+		addValidationSupport(myUnknownCodeSystemWarningValidationSupport);
 	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -9,7 +9,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
-import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
@@ -28,6 +27,7 @@ import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -69,12 +69,10 @@ import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.util.AopTestUtils;
-import org.springframework.transaction.PlatformTransactionManager;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.Collections;
-import java.util.Locale;
 import java.util.stream.Collectors;
 
 import static org.awaitility.Awaitility.await;
@@ -96,18 +94,111 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	@Autowired
 	private ITermReadSvc myTermReadSvc;
 	@Autowired
-	private ITermCodeSystemStorageSvc myTermCodeSystemStorageSvcc;
-	@Autowired
 	private DaoRegistry myDaoRegistry;
 	@Autowired
 	private JpaValidationSupportChain myJpaValidationSupportChain;
 	@Autowired
-	private PlatformTransactionManager myTransactionManager;
-	@Autowired
 	private ValidationSettings myValidationSettings;
+	@Autowired
+	private UnknownCodeSystemWarningValidationSupport myUnknownCodeSystemWarningValidationSupport;
 
+	@AfterEach
+	public void after() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
+
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setMaximumExpansionSize(DaoConfig.DEFAULT_MAX_EXPANSION_SIZE);
+		myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
+
+		BaseTermReadSvcImpl.setInvokeOnNextCallForUnitTest(null);
+
+		myValidationSettings.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.IGNORE);
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		myUnknownCodeSystemWarningValidationSupport.setAllowNonExistentCodeSystem(UnknownCodeSystemWarningValidationSupport.ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT);
+	}
+
+	/**
+	 * By default an unknown code system should fail vaildation
+	 */
 	@Test
-	public void testValidateCodeInValueSetWithUnknownCodeSystem() {
+	public void testValidateCodeInValueSetWithUnknownCodeSystem_FailValidation() {
+		createStructureDefWithBindingToUnknownCs();
+
+		Observation obs = new Observation();
+		obs.getMeta().addProfile("http://sd");
+		obs.getText().setDivAsString("<div>Hello</div>");
+		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
+		obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
+		obs.getCode().setText("hello");
+		obs.setSubject(new Reference("Patient/123"));
+		obs.addPerformer(new Reference("Practitioner/123"));
+		obs.setEffective(DateTimeType.now());
+		obs.setStatus(ObservationStatus.FINAL);
+
+		OperationOutcome oo;
+
+		// Valid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		String encoded = encode(oo);
+		ourLog.info(encoded);
+		assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encoded);
+
+		// Invalid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		encoded = encode(oo);
+		ourLog.info(encoded);
+		assertEquals(1, oo.getIssue().size(), encoded);
+		assertEquals("The code provided (http://cs#code99) is not in the value set http://vs, and a code from this value set is required: Unknown code system: http://cs", oo.getIssueFirstRep().getDiagnostics(), encoded);
+		assertEquals(OperationOutcome.IssueSeverity.ERROR, oo.getIssueFirstRep().getSeverity(), encoded);
+
+	}
+
+	/**
+	 * By default an unknown code system should fail vaildation
+	 */
+	@Test
+	public void testValidateCodeInValueSetWithUnknownCodeSystem_Warning() {
+		myUnknownCodeSystemWarningValidationSupport.setAllowNonExistentCodeSystem(true);
+
+		createStructureDefWithBindingToUnknownCs();
+
+		Observation obs = new Observation();
+		obs.getMeta().addProfile("http://sd");
+		obs.getText().setDivAsString("<div>Hello</div>");
+		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
+		obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
+		obs.getCode().setText("hello");
+		obs.setSubject(new Reference("Patient/123"));
+		obs.addPerformer(new Reference("Practitioner/123"));
+		obs.setEffective(DateTimeType.now());
+		obs.setStatus(ObservationStatus.FINAL);
+
+		OperationOutcome oo;
+		String encoded;
+
+		// Valid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		encoded = encode(oo);
+		ourLog.info(encoded);
+		assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encoded);
+
+		// Invalid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		encoded = encode(oo);
+		ourLog.info(encoded);
+		assertEquals(1, oo.getIssue().size(), encoded);
+		assertEquals("Error Unknown code system: http://cs validating Coding", oo.getIssueFirstRep().getDiagnostics(), encoded);
+		assertEquals(OperationOutcome.IssueSeverity.WARNING, oo.getIssueFirstRep().getSeverity(), encoded);
+
+	}
+
+	public void createStructureDefWithBindingToUnknownCs() {
 		myValidationSupport.fetchCodeSystem("http://not-exist"); // preload DefaultProfileValidationSupport
 
 		ValueSet vs = new ValueSet();
@@ -132,32 +223,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			.setBinding(new ElementDefinition.ElementDefinitionBindingComponent().setStrength(Enumerations.BindingStrength.REQUIRED).setValueSet("http://vs"))
 			.setId("Observation.value[x]");
 		myStructureDefinitionDao.create(sd);
-
-		Observation obs = new Observation();
-		obs.getMeta().addProfile("http://sd");
-		obs.getText().setDivAsString("<div>Hello</div>");
-		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
-		obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
-		obs.getCode().setText("hello");
-		obs.setSubject(new Reference("Patient/123"));
-		obs.addPerformer(new Reference("Practitioner/123"));
-		obs.setEffective(DateTimeType.now());
-		obs.setStatus(ObservationStatus.FINAL);
-
-		OperationOutcome oo;
-
-		// Valid code
-		obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
-		oo = validateAndReturnOutcome(obs);
-		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
-		assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
-
-		// Invalid code
-		obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
-		oo = validateAndReturnOutcome(obs);
-		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
-		assertEquals("The code provided (http://cs#code99) is not in the value set http://vs, and a code from this value set is required: Unknown code {http://cs}code99 - Unable to expand ValueSet[http://vs]", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
-
 	}
 
 	@Test
@@ -620,8 +685,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	}
 
 
-
-
 	@Test
 	public void testValidateValueSet() {
 		String input = "{\n" +
@@ -692,7 +755,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		assertThat(ooString, containsString("Unknown code in fragment CodeSystem 'http://example.com/codesystem#foo'"));
 
-		assertThat(oo.getIssue().stream().map(t->t.getSeverity().toCode()).collect(Collectors.toList()), contains("warning", "warning"));
+		assertThat(oo.getIssue().stream().map(t -> t.getSeverity().toCode()).collect(Collectors.toList()), contains("warning", "warning"));
 	}
 
 
@@ -1080,8 +1143,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 	}
 
-	private String encode(IBaseResource thePatient) {
+	private String encode(IBaseResource theResource) {
-		return myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(thePatient);
+		return myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theResource);
 	}
 
 
@@ -1245,21 +1308,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		}
 	}
 
-	@AfterEach
-	public void after() {
-		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
-		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
-
-		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
-		myDaoConfig.setMaximumExpansionSize(DaoConfig.DEFAULT_MAX_EXPANSION_SIZE);
-		myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
-
-		BaseTermReadSvcImpl.setInvokeOnNextCallForUnitTest(null);
-
-		myValidationSettings.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.IGNORE);
-		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
-	}
-
 	@Test
 	public void testValidateCapabilityStatement() {
 
@@ -1277,7 +1325,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		cs.getText().setStatus(Narrative.NarrativeStatus.GENERATED).getDiv().setValue("<div>aaaa</div>");
 		CapabilityStatement.CapabilityStatementRestComponent rest = cs.addRest();
 		CapabilityStatement.CapabilityStatementRestResourceComponent patient = rest.addResource();
-		patient		.setType("Patient");
+		patient.setType("Patient");
 		patient.addSearchParam().setName("foo").setType(Enumerations.SearchParamType.DATE).setDefinition("http://example.com/name");
 
 
@@ -1676,5 +1724,4 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	}
 
 
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java

@@ -34,6 +34,7 @@ import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
@@ -245,8 +246,7 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 
 		IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://loinc.org/vs"), null, new StringType("10013-1-9999999999"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
 
-		assertFalse(result.isOk());
+		assertNull(result);
-		assertEquals("Unknown code {http://loinc.org}10013-1-9999999999 - Unable to expand ValueSet[http://loinc.org/vs]", result.getMessage());
 	}
 
 	private Set<String> toExpandedCodes(ValueSet theExpanded) {

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

@@ -0,0 +1,58 @@
+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.ValidationSupportContext;
+import org.hl7.fhir.exceptions.TerminologyServiceException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+/**
+ * This validation support module may be placed at the end of a {@link ValidationSupportChain}
+ * in order to configure the validator to generate a warning if a resource being validated
+ * contains an unknown code system.
+ *
+ * Note that this module must also be activated by calling {@link #setAllowNonExistentCodeSystem(boolean)}
+ * in order to specify that unknown code systems should be allowed.
+ */
+public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSupport {
+	public static final boolean ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT = false;
+
+	private boolean myAllowNonExistentCodeSystem = ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT;
+
+	/**
+	 * Constructor
+	 */
+	public UnknownCodeSystemWarningValidationSupport(FhirContext theFhirContext) {
+		super(theFhirContext);
+	}
+
+	@Override
+	public boolean isValueSetSupported(ValidationSupportContext theValidationSupportContext, String theValueSetUrl) {
+		return true;
+	}
+
+	@Nullable
+	@Override
+	public CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
+		IBaseResource codeSystem = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystem);
+		if (codeSystem != null) {
+			return null;
+		}
+
+		String message = "Unknown code system: " + theCodeSystem;
+		if (!myAllowNonExistentCodeSystem) {
+			return new CodeValidationResult()
+				.setSeverity(IssueSeverity.ERROR)
+				.setMessage(message);
+		}
+
+		throw new TerminologyServiceException(message);
+	}
+
+	public void setAllowNonExistentCodeSystem(boolean theAllowNonExistentCodeSystem) {
+		myAllowNonExistentCodeSystem = theAllowNonExistentCodeSystem;
+	}
+}