Emre unknown sys validation clean

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java

@@ -255,6 +255,22 @@ default boolean isCodeSystemSupported(ValidationSupportContext theValidationSupp
 		return false;
 	}
 
+	/**
+	 * For most validation support modules, this method should return the same value as {@link IValidationSupport#isCodeSystemSupported(ValidationSupportContext, String)} and
+	 * no specific implementation is required other than the default implementation provided here.
+	 * A validation support module should override this only if it wants to generate a validation result even for an unsupported CodeSystem.
+	 * For example, {@link org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport} overrides this method to generate issues for unknown CodeSystems.
+	 *
+	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
+	 *                                    other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
+	 * @param theSystem                   The URI for the code system, e.g. <code>"http://loinc.org"</code>
+	 * @return Returns <code>true</code> if a validation result can be generated by this validation support module even when the code system is not supported.
+	 */
+	default boolean canGenerateValidationResultForCodeSystem(
+			ValidationSupportContext theValidationSupportContext, String theSystem) {
+		return isCodeSystemSupported(theValidationSupportContext, theSystem);
+	}
+
 	/**
 	 * Returns <code>true</code> if a Remote Terminology Service is currently configured
 	 *

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

@@ -890,8 +890,11 @@ public ResourceLoaderImpl jpaResourceLoader() {
 
 	@Bean
 	public UnknownCodeSystemWarningValidationSupport unknownCodeSystemWarningValidationSupport(
-			FhirContext theFhirContext) {
-		return new UnknownCodeSystemWarningValidationSupport(theFhirContext);
+			FhirContext theFhirContext, JpaStorageSettings theStorageSettings) {
+		UnknownCodeSystemWarningValidationSupport support =
+				new UnknownCodeSystemWarningValidationSupport(theFhirContext);
+		support.setNonExistentCodeSystemSeverity(theStorageSettings.getIssueSeverityForUnknownCodeSystem());
+		return support;
 	}
 
 	@Bean

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

@@ -60,6 +60,7 @@ public InMemoryTerminologyServerValidationSupport inMemoryTerminologyServerValid
 		InMemoryTerminologyServerValidationSupport retVal =
 				new InMemoryTerminologyServerValidationSupport(theFhirContext);
 		retVal.setIssueSeverityForCodeDisplayMismatch(theStorageSettings.getIssueSeverityForCodeDisplayMismatch());
+		retVal.setIssueSeverityForUnknownCodeSystem(theStorageSettings.getIssueSeverityForUnknownCodeSystem());
 		return retVal;
 	}
 

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java

@@ -368,7 +368,7 @@ public void testValidateCodeOperation() {
 			.map(t -> ((IPrimitiveType<String>) t.getValue()).getValue())
 			.findFirst()
 			.orElseThrow(IllegalArgumentException::new);
-		assertThat(message).contains("Terminology service was unable to provide validation for https://url#1");
+		assertThat(message).contains("CodeSystem is unknown and can't be validated: https://url for 'https://url#1'");
 	}
 
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -725,11 +725,11 @@ public void testValidate() {
 			fail(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
 		}
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(11, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+		assertEquals(12, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
-		assertEquals(9, myCaptureQueriesListener.countCommits());
+		assertEquals(10, myCaptureQueriesListener.countCommits());
 
 		// Validate again (should rely only on caches)
 		myCaptureQueriesListener.clear();

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/interceptor/RemoteTerminologyServiceJpaR4Test.java

@@ -309,12 +309,13 @@ public void testValidateMultipleCodings() {
 			"None of the codings provided are in the value set 'IdentifierType'");
 
 		// Verify 1
-		Assertions.assertEquals(2, myCaptureQueriesListener.countGetConnections());
+		Assertions.assertEquals(3, myCaptureQueriesListener.countGetConnections());
 		assertThat(ourValueSetProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
 			"http://hl7.org/fhir/ValueSet/identifier-type",
 			"http://hl7.org/fhir/ValueSet/identifier-type"
 		);
 		assertThat(ourCodeSystemProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
+			"http://terminology.hl7.org/CodeSystem/v2-0203",
 			"http://terminology.hl7.org/CodeSystem/v2-0203",
 			"http://terminology.hl7.org/CodeSystem/v2-0203"
 		);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/validation/performance/ValidationCanonicalizationTest.java

@@ -148,22 +148,27 @@ public void testCanonicalization() {
 
 		private void assertHasInvalidCodeError(OperationOutcome theOperationOutcome) {
 			List<OperationOutcomeIssueComponent> issues = theOperationOutcome.getIssue();
-			assertEquals(3, issues.size());
+			assertEquals(4, issues.size());
 
-			OperationOutcomeIssueComponent issue1 = issues.get(0);
+			OperationOutcomeIssueComponent issue0 = issues.get(0);
+			assertEquals(IssueSeverity.ERROR, issue0.getSeverity());
+			String expectedMessage0 = "CodeSystem is unknown and can't be validated: http://acme.org/invalid for 'http://acme.org/invalid#invalid'";
+			assertEquals(expectedMessage0, issue0.getDiagnostics());
+
+			OperationOutcomeIssueComponent issue1 = issues.get(1);
 			assertEquals(IssueSeverity.ERROR, issue1.getSeverity());
 			assertEquals("Parameters.parameter[0].resource/*Procedure/null*/.code", issue1.getLocation().get(0).getValue());
 			Map<String, String> formatValues = Map.of("conceptNumber", String.valueOf(NUM_CONCEPTS));
 			String expectedMessage1 = "None of the codings provided are in the value set 'Value Set Combined' (http://acme.org/ValueSet/valueset-combined|1), and a coding from this value set is required) (codes = http://acme.org/CodeSystem/codesystem-1#codesystem-1-concept-${conceptNumber}, http://acme.org/CodeSystem/codesystem-2#codesystem-2-concept-${conceptNumber}, http://acme.org/invalid#invalid)";
 			assertEquals(formatMessage(expectedMessage1, formatValues), issue1.getDiagnostics());
 
-			OperationOutcomeIssueComponent issue2 = issues.get(1);
+			OperationOutcomeIssueComponent issue2 = issues.get(2);
 			assertEquals(IssueSeverity.INFORMATION, issue2.getSeverity());
 			assertEquals("Parameters.parameter[0].resource/*Procedure/null*/.code.coding[2]", issue2.getLocation().get(0).getValue());
 			String expectedMessage2 = "This element does not match any known slice defined in the profile http://example.org/fhir/StructureDefinition/TestProcedure|1.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) - Does not match slice 'slice1' (discriminator: ($this memberOf 'http://acme.org/ValueSet/valueset-1'))";
 			assertEquals(expectedMessage2, issue2.getDiagnostics());
 
-			OperationOutcomeIssueComponent issue3 = issues.get(2);
+			OperationOutcomeIssueComponent issue3 = issues.get(3);
 			assertEquals(IssueSeverity.INFORMATION, issue3.getSeverity());
 			assertEquals("Parameters.parameter[0].resource/*Procedure/null*/.code.coding[2]", issue3.getLocation().get(0).getValue());
 			String expectedMessage3 = "This element does not match any known slice defined in the profile http://example.org/fhir/StructureDefinition/TestProcedure|1.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) - Does not match slice 'slice2' (discriminator: ($this memberOf 'http://acme.org/ValueSet/valueset-2'))";

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/validation/ValidateCodeWithRemoteTerminologyR4Test.java

@@ -140,8 +140,7 @@ public void validateCodeOperationOnCodeSystem_byCodingAndUrlWhereCodeSystemIsUnk
 		ourLog.info(resp);
 
 		assertFalse(((BooleanType) respParam.getParameterValue("result")).booleanValue());
-		assertThat(respParam.getParameterValue("message").toString()).isEqualTo("Terminology service was unable to provide validation for " + INVALID_CODE_SYSTEM_URI +
-			"#P");
+		assertThat(respParam.getParameterValue("message").toString()).isEqualTo("CodeSystem is unknown and can't be validated: %s for '%s%s'", INVALID_CODE_SYSTEM_URI, INVALID_CODE_SYSTEM_URI, "#P");
 	}
 
 	@Test
@@ -216,6 +215,7 @@ public void validateCodeOperationOnValueSet_byUrlSystemAndCode() {
 	@Test
 	public void validateCodeOperationOnValueSet_byCodingAndUrlWhereValueSetIsUnknown_returnsFalse() {
 		myValueSetProvider.setShouldThrowExceptionForResourceNotFound(false);
+		myCodeSystemProvider.setShouldThrowExceptionForResourceNotFound(false);
 
 		Parameters respParam = myClient
 			.operation()

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java

@@ -363,6 +363,13 @@ public class JpaStorageSettings extends StorageSettings {
 	private IValidationSupport.IssueSeverity myIssueSeverityForCodeDisplayMismatch =
 			IValidationSupport.IssueSeverity.WARNING;
 
+	/**
+	 * @since 7.0.0
+	 */
+	@Nonnull
+	private IValidationSupport.IssueSeverity myIssueSeverityForUnknownCodeSystem =
+			IValidationSupport.IssueSeverity.ERROR;
+
 	/**
 	 * This setting allows preventing a conditional update to invalidate the match criteria.
 	 * <p/>
@@ -2615,6 +2622,30 @@ public void setIssueSeverityForCodeDisplayMismatch(
 		myIssueSeverityForCodeDisplayMismatch = theIssueSeverityForCodeDisplayMismatch;
 	}
 
+	/**
+	 * This setting controls the validation issue severity to report when a code validation
+	 * encounters an unknown CodeSystem. Defaults to {@link IValidationSupport.IssueSeverity#ERROR}.
+	 *
+	 * @since 8.6.0
+	 */
+	@Nonnull
+	public IValidationSupport.IssueSeverity getIssueSeverityForUnknownCodeSystem() {
+		return myIssueSeverityForUnknownCodeSystem;
+	}
+
+	/**
+	 * This setting controls the validation issue severity to report when a code validation
+	 * encounters an unknown CodeSystem. Defaults to {@link IValidationSupport.IssueSeverity#ERROR}.
+	 *
+	 * @param theIssueSeverityForUnknownCodeSystem The severity. Must not be {@literal null}.
+	 * @since 8.6.0
+	 */
+	public void setIssueSeverityForUnknownCodeSystem(
+			@Nonnull IValidationSupport.IssueSeverity theIssueSeverityForUnknownCodeSystem) {
+		Validate.notNull(theIssueSeverityForUnknownCodeSystem, "theIssueSeverityForUnknownCodeSystem must not be null");
+		myIssueSeverityForUnknownCodeSystem = theIssueSeverityForUnknownCodeSystem;
+	}
+
 	/**
 	 * This method returns whether data will be stored in LOB columns as well as the columns
 	 * introduced to migrate away from LOB.  Writing to LOB columns is set to false by

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

@@ -52,6 +52,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 	private final FhirContext myCtx;
 	private VersionCanonicalizer myVersionCanonicalizer;
 	private IssueSeverity myIssueSeverityForCodeDisplayMismatch = IssueSeverity.WARNING;
+	private IssueSeverity myIssueSeverityForUnknownCodeSystem = IssueSeverity.ERROR;
 
 	/**
 	 * Constructor
@@ -107,6 +108,30 @@ public void setIssueSeverityForCodeDisplayMismatch(@Nonnull IssueSeverity theIss
 		myIssueSeverityForCodeDisplayMismatch = theIssueSeverityForCodeDisplayMismatch;
 	}
 
+	/**
+	 * This setting controls the validation issue severity to report when a code validation
+	 * finds that the CodeSystem being validated is not known.
+	 * Defaults to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#ERROR}.
+	 *
+	 * @since 8.6.0
+	 */
+	public IssueSeverity getIssueSeverityForUnknownCodeSystem() {
+		return myIssueSeverityForUnknownCodeSystem;
+	}
+
+	/**
+	 * This setting controls the validation issue severity to report when a code validation
+	 * finds that the CodeSystem being validated is not known.
+	 * Defaults to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#ERROR}.
+	 *
+	 * @param theIssueSeverityForUnknownCodeSystem The severity. Must not be {@literal null}.
+	 * @since 8.6.0
+	 */
+	public void setIssueSeverityForUnknownCodeSystem(@Nonnull IssueSeverity theIssueSeverityForUnknownCodeSystem) {
+		Validate.notNull(theIssueSeverityForUnknownCodeSystem, "theIssueSeverityForUnknownCodeSystem must not be null");
+		myIssueSeverityForUnknownCodeSystem = theIssueSeverityForUnknownCodeSystem;
+	}
+
 	@Override
 	public FhirContext getFhirContext() {
 		return myCtx;
@@ -166,7 +191,12 @@ public CodeValidationResult validateCodeInValueSet(
 					theValidationSupportContext, theValueSet, theCodeSystemUrlAndVersion, theCode);
 		} catch (ExpansionCouldNotBeCompletedInternallyException e) {
 			CodeValidationResult codeValidationResult = new CodeValidationResult();
-			codeValidationResult.setSeverity(IssueSeverity.ERROR);
+			if (e.getCodeValidationIssue() != null && e.getCodeValidationIssue().getSeverity() != null) {
+				// preserve the severity from the original issue by assigning it to the result
+				codeValidationResult.setSeverity(e.getCodeValidationIssue().getSeverity());
+			} else {
+				codeValidationResult.setSeverity(IssueSeverity.ERROR);
+			}
 
 			String msg = "Failed to expand ValueSet '" + vsUrl + "' (in-memory). Could not validate code "
 					+ theCodeSystemUrlAndVersion + "#" + theCode;
@@ -859,7 +889,7 @@ private boolean expandValueSetR5IncludeOrExclude(
 			}
 
 			boolean ableToHandleCode = false;
-			String failureMessage = null;
+			MessageWithSeverity failureMessage = null;
 
 			boolean isIncludeCodeSystemIgnored = includeOrExcludeSystemResource != null
 					&& includeOrExcludeSystemResource.getContent() == Enumerations.CodeSystemContentMode.NOTPRESENT;
@@ -991,15 +1021,15 @@ private boolean expandValueSetR5IncludeOrExclude(
 						failureMessage = getFailureMessageForMissingOrUnusableCodeSystem(
 								includeOrExcludeSystemResource, loadedCodeSystemUrl);
 					} else {
-						failureMessage = "Unable to expand value set";
+						failureMessage = new MessageWithSeverity("Unable to expand value set", IssueSeverity.ERROR);
 					}
 				}
 
 				throw new ExpansionCouldNotBeCompletedInternallyException(
-						Msg.code(702) + failureMessage,
+						Msg.code(702) + failureMessage.message,
 						new CodeValidationIssue(
-								failureMessage,
-								IssueSeverity.ERROR,
+								failureMessage.message,
+								failureMessage.severity,
 								CodeValidationIssueCode.NOT_FOUND,
 								CodeValidationIssueCoding.NOT_FOUND));
 			}
@@ -1102,18 +1132,22 @@ private Function<String, CodeSystem> newCodeSystemLoader(ValidationSupportContex
 		}
 	}
 
-	private String getFailureMessageForMissingOrUnusableCodeSystem(
+	private record MessageWithSeverity(String message, IssueSeverity severity) {}
+
+	private MessageWithSeverity getFailureMessageForMissingOrUnusableCodeSystem(
 			CodeSystem includeOrExcludeSystemResource, String loadedCodeSystemUrl) {
+		IssueSeverity severity = IssueSeverity.ERROR;
 		String failureMessage;
 		if (includeOrExcludeSystemResource == null) {
 			failureMessage = "Unable to expand ValueSet because CodeSystem could not be found: " + loadedCodeSystemUrl;
+			severity = myIssueSeverityForUnknownCodeSystem;
 		} else {
 			assert includeOrExcludeSystemResource.getContent() == Enumerations.CodeSystemContentMode.NOTPRESENT;
 			failureMessage =
 					"Unable to expand ValueSet because CodeSystem has CodeSystem.content=not-present but contents were not found: "
 							+ loadedCodeSystemUrl;
 		}
-		return failureMessage;
+		return new MessageWithSeverity(failureMessage, severity);
 	}
 
 	private void addCodes(

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

@@ -13,7 +13,7 @@
 
 /**
  * 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
+ * in order to configure the validator to generate a warning or an error if a resource being validated
  * contains an unknown code system.
  *
  * Note that this module must also be activated by calling {@link #setAllowNonExistentCodeSystem(boolean)}
@@ -45,18 +45,13 @@ public boolean isValueSetSupported(ValidationSupportContext theValidationSupport
 
 	@Override
 	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
-		return canValidateCodeSystem(theValidationSupportContext, theSystem);
+		return false;
 	}
 
 	@Nullable
 	@Override
 	public LookupCodeResult lookupCode(
 			ValidationSupportContext theValidationSupportContext, @Nonnull LookupCodeRequest theLookupCodeRequest) {
-		// filters out error/fatal
-		if (canValidateCodeSystem(theValidationSupportContext, theLookupCodeRequest.getSystem())) {
-			return new LookupCodeResult().setFound(true);
-		}
-
 		return null;
 	}
 
@@ -68,8 +63,7 @@ public CodeValidationResult validateCode(
 			String theCode,
 			String theDisplay,
 			String theValueSetUrl) {
-		// filters out error/fatal
-		if (!canValidateCodeSystem(theValidationSupportContext, theCodeSystem)) {
+		if (!canGenerateValidationResultForCodeSystem(theValidationSupportContext, theCodeSystem)) {
 			return null;
 		}
 
@@ -80,19 +74,11 @@ public CodeValidationResult validateCode(
 				+ "#" + theCode + "'";
 		result.setMessage(theMessage);
 
-		// For information level, we just strip out the severity+message entirely
-		// so that nothing appears in the validation result
-		if (myNonExistentCodeSystemSeverity == IssueSeverity.INFORMATION) {
-			result.setCode(theCode);
-			result.setSeverity(null);
-			result.setMessage(null);
-		} else {
-			result.addIssue(new CodeValidationIssue(
-					theMessage,
-					myNonExistentCodeSystemSeverity,
-					CodeValidationIssueCode.NOT_FOUND,
-					CodeValidationIssueCoding.NOT_FOUND));
-		}
+		result.addIssue(new CodeValidationIssue(
+				theMessage,
+				myNonExistentCodeSystemSeverity,
+				CodeValidationIssueCode.NOT_FOUND,
+				CodeValidationIssueCoding.NOT_FOUND));
 
 		return result;
 	}
@@ -106,7 +92,7 @@ public CodeValidationResult validateCodeInValueSet(
 			String theCode,
 			String theDisplay,
 			@Nonnull IBaseResource theValueSet) {
-		if (!canValidateCodeSystem(theValidationSupportContext, theCodeSystem)) {
+		if (!canGenerateValidationResultForCodeSystem(theValidationSupportContext, theCodeSystem)) {
 			return null;
 		}
 
@@ -118,35 +104,11 @@ public CodeValidationResult validateCodeInValueSet(
 	}
 
 	/**
-	 * Returns true if non existent code systems will still validate.
-	 * False if they will throw errors.
-	 * @return
-	 */
-	private boolean allowNonExistentCodeSystems() {
-		switch (myNonExistentCodeSystemSeverity) {
-			case ERROR:
-			case FATAL:
-				return false;
-			case WARNING:
-			case INFORMATION:
-				return true;
-			default:
-				ourLog.info("Unknown issue severity " + myNonExistentCodeSystemSeverity.name()
-						+ ". Treating as INFO/WARNING");
-				return true;
-		}
-	}
-
-	/**
-	 * Determines if the code system can (and should) be validated.
-	 * @param theValidationSupportContext
-	 * @param theCodeSystem
-	 * @return
+	 * If a validation support can fetch the code system, returns false. Otherwise, returns true.
 	 */
-	private boolean canValidateCodeSystem(ValidationSupportContext theValidationSupportContext, String theCodeSystem) {
-		if (!allowNonExistentCodeSystems()) {
-			return false;
-		}
+	@Override
+	public boolean canGenerateValidationResultForCodeSystem(
+			ValidationSupportContext theValidationSupportContext, String theCodeSystem) {
 		if (theCodeSystem == null) {
 			return false;
 		}