Make sure the validator can get at codes defined in notpresent

codesystems

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/OperationOutcomeUtil.java

@@ -108,9 +108,13 @@ public class OperationOutcomeUtil {
 		if (theOutcome == null) {
 			return false;
 		}
+		return getIssueCount(theCtx, theOutcome) > 0;
+	}
+
+	public static int getIssueCount(FhirContext theCtx, IBaseOperationOutcome theOutcome) {
 		RuntimeResourceDefinition ooDef = theCtx.getResourceDefinition(theOutcome);
 		BaseRuntimeChildDefinition issueChild = ooDef.getChildByName("issue");
-		return issueChild.getAccessor().getValues(theOutcome).size() > 0;
+		return issueChild.getAccessor().getValues(theOutcome).size();
 	}
 
 	public static IBaseOperationOutcome newInstance(FhirContext theCtx) {
@@ -152,5 +156,4 @@ public class OperationOutcomeUtil {
 			locationChild.getMutator().addValue(theIssue, locationElem);
 		}
 	}
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java

@@ -173,4 +173,11 @@ public class TermCodeSystemVersion implements Serializable {
 			"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemDisplayName));
 		myCodeSystemDisplayName = theCodeSystemDisplayName;
 	}
+
+	public TermConcept addConcept() {
+		TermConcept concept = new TermConcept();
+		concept.setCodeSystemVersion(this);
+		getConcepts().add(concept);
+		return concept;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java

@@ -5,10 +5,6 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.UrlUtil;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
@@ -174,13 +170,6 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 	@CoverageIgnore
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
-		SearchParameterMap map = new SearchParameterMap();
-		map.add(CodeSystem.SP_URL, new UriParam(theSystem));
-		map.setLoadSynchronousUpTo(1);
-		IBundleProvider outcome = myCodeSystemResourceDao.search(map);
-		if (outcome.size() > 0) {
-			return (CodeSystem) outcome.getResources(0, 1).get(0);
-		}
 		return null;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java

@@ -5,10 +5,6 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.util.ValidateUtil;
@@ -185,13 +181,6 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
 	@CoverageIgnore
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
-		SearchParameterMap map = new SearchParameterMap();
-		map.add(org.hl7.fhir.r5.model.CodeSystem.SP_URL, new UriParam(theSystem));
-		map.setLoadSynchronousUpTo(1);
-		IBundleProvider outcome = myCodeSystemResourceDao.search(map);
-		if (outcome.size() > 0) {
-			return (org.hl7.fhir.r5.model.CodeSystem) outcome.getResources(0, 1).get(0);
-		}
 		return null;
 	}
 
@@ -281,7 +270,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
 	public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-		return txTemplate.execute(t-> {
+		return txTemplate.execute(t -> {
 			Optional<TermConcept> codeOpt = findCode(theCodeSystem, theCode);
 			if (codeOpt.isPresent()) {
 				TermConcept code = codeOpt.get();

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

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
@@ -8,10 +10,12 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
@@ -28,16 +32,18 @@ import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.util.Collections;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertThat;
+import static org.junit.Assert.*;
-import static org.junit.Assert.fail;
 
 public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
 	@Autowired
 	private IValidatorModule myValidatorModule;
+	@Autowired
+	private IHapiTerminologySvc myTerminologySvc;
 
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
@@ -106,6 +112,43 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		assertThat(ooString, containsString("Element '/f:Observation.device': minimum required = 1, but only found 0"));
 	}
 
+	@Test
+	public void testValidateUsingExternallyDefinedCode() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl("http://foo");
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		IIdType csId = myCodeSystemDao.create(codeSystem).getId();
+
+		TermCodeSystemVersion csv = new TermCodeSystemVersion();
+		csv.addConcept().setCode("bar").setDisplay("Bar Code");
+		myTerminologySvc.storeNewCodeSystemVersion(codeSystem, csv, mySrd, Collections.emptyList(), Collections.emptyList());
+
+		// Validate a resource containing this codesystem in a field with an extendable binding
+		Patient patient = new Patient();
+		patient.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>hello</div>");
+		patient
+			.addIdentifier()
+			.setSystem("http://example.com")
+			.setValue("12345")
+			.getType()
+			.addCoding()
+			.setSystem("http://foo")
+			.setCode("bar");
+		MethodOutcome outcome = myPatientDao.validate(patient, null, encode(patient), EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
+		IBaseOperationOutcome oo = outcome.getOperationOutcome();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+
+		// It would be ok for this to produce 0 issues, or just an information message too
+		assertEquals(1, OperationOutcomeUtil.getIssueCount(myFhirCtx, oo));
+		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
+
+	}
+
+	private String encode(Patient thePatient) {
+		return myFhirCtx.newJsonParser().encodeResourceToString(thePatient);
+	}
+
+
 	private OperationOutcome doTestValidateResourceContainingProfileDeclaration(String methodName, EncodingEnum enc) throws IOException {
 		Bundle vss = loadResourceFromClasspath(Bundle.class, "/org/hl7/fhir/r4/model/valueset/valuesets.xml");
 		myValueSetDao.update((ValueSet) findResourceByIdInBundle(vss, "observation-status"), mySrd);

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/ValidationSupportChain.java

@@ -98,11 +98,9 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
+			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
-				CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
+			if (retVal != null) {
-				if (retVal != null) {
+				return retVal;
-					return retVal;
-				}
 			}
 		}
 		return null;

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/ValidationSupportChain.java

@@ -77,11 +77,9 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
+			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
-				CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
+			if (retVal != null) {
-				if (retVal != null) {
+				return retVal;
-					return retVal;
-				}
 			}
 		}
 		return null;

hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/ValidationSupportChain.java

@@ -75,11 +75,9 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
+			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
-				CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
+			if (retVal != null) {
-				if (retVal != null) {
+				return retVal;
-					return retVal;
-				}
 			}
 		}
 		return null;

src/changes/changes.xml

@@ -218,6 +218,10 @@
 				handled by method implementations that did not have any <![CDATA[<code>@IncludeParam</code>]]> defined. This
 				is now corrected. Thanks to Tuomo Ala-Vannesluoma for reporting and providing a test case!
 			</action>
+			<action type="fix">
+				The JPA server failed to find codes defined in not-present codesystems in some cases, and reported
+				that the CodeSystem did not exist. This has been corrected.
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">