Make sure a loinc CodeSystem always has a ForcedId

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java

@@ -51,7 +51,6 @@ import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.patch.FhirPatch;
 import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@@ -169,7 +168,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired
 	private IRequestPartitionHelperSvc myRequestPartitionHelperService;
 	@Autowired
-	private HapiTransactionService myTransactionService;
+	protected HapiTransactionService myTransactionService;
 	@Autowired
 	private MatchUrlService myMatchUrlService;
 	@Autowired
@@ -221,7 +220,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	/**
 	 * Called for FHIR create (POST) operations
 	 */
-	private DaoMethodOutcome doCreateForPost(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
+	protected DaoMethodOutcome doCreateForPost(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
 		if (theResource == null) {
 			String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "missingBody");
 			throw new InvalidRequestException(msg);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java

@@ -109,8 +109,10 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 	public IBaseResource fetchCodeSystem(String theSystem) {
 		if (myTermReadSvc.isLoincNotGenericUnversionedCodeSystem(theSystem)) {
 			Optional<IBaseResource> currentCSOpt = getCodeSystemCurrentVersion(new UriType(theSystem));
-			return currentCSOpt.orElseThrow(() -> new ResourceNotFoundException(
+			if (! currentCSOpt.isPresent()) {
-				"Couldn't find current version CodeSystem for url: " + theSystem));
+				ourLog.info("Couldn't find current version of CodeSystem: " + theSystem);
+			}
+			return currentCSOpt.orElse(null);
 		}
 
 		return fetchResource(myCodeSystemType, theSystem);
@@ -125,7 +127,16 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 
 		IFhirResourceDao<? extends IBaseResource> valueSetResourceDao = myDaoRegistry.getResourceDao(myCodeSystemType);
 		String forcedId = "loinc";
-		IBaseResource codeSystem = valueSetResourceDao.read(new IdDt("CodeSystem", forcedId));
+
+		// try/catch ignores exception because we need code to fall back to other options
+		IBaseResource codeSystem;
+		try {
+			codeSystem = valueSetResourceDao.read(new IdDt("CodeSystem", forcedId));
+
+		} catch (Exception theE) {
+			return Optional.empty();
+		}
+
 		return Optional.ofNullable(codeSystem);
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -46,12 +47,14 @@ import org.hl7.fhir.r4.model.Coding;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
+import java.security.InvalidParameterException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.Set;
 
 import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@@ -173,4 +176,17 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 
 	}
 
+
+	@Override
+	public DaoMethodOutcome create(CodeSystem theResource, String theIfNoneExist, boolean thePerformIndexing,
+											 @Nonnull TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
+		// loinc CodeSystem must have an ID
+		if (isNotBlank(theResource.getUrl()) && theResource.getUrl().contains("loinc")
+			&& isBlank(theResource.getIdElement().getIdPart())) {
+			throw new InvalidParameterException("'loinc' CodeSystem must have an ID");
+		}
+		return myTransactionService.execute(theRequestDetails, theTransactionDetails,
+			tx -> doCreateForPost(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails));
+	}
+
 }

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

@@ -86,6 +86,7 @@ import java.util.UUID;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@@ -139,6 +140,9 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			CodeSystem codeSystemResource = new CodeSystem();
 			codeSystemResource.setUrl(theSystem);
 			codeSystemResource.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+			if (isBlank(codeSystemResource.getIdElement().getIdPart()) && theSystem.contains("loinc")) {
+				codeSystemResource.setId("loinc");
+			}
 			myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(codeSystemResource);
 
 			cs = myCodeSystemDao.findByCodeSystemUri(theSystem);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java

@@ -33,6 +33,8 @@ import org.springframework.context.ApplicationContext;
 import org.springframework.context.event.ContextRefreshedEvent;
 import org.springframework.context.event.EventListener;
 
+import java.security.InvalidParameterException;
+
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
@@ -63,6 +65,9 @@ public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl imple
 	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
 		validateCodeSystemForStorage(theCodeSystemResource);
 		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
+			if (theCodeSystemResource.getUrl().contains("loinc")) {
+				throw new InvalidParameterException("LOINC CodeSystem must have an 'ID' element");
+			}
 			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
 			return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl, theRequestDetails).getId();
 		} else {

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

@@ -501,7 +501,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
 		cs.setUrl("http://loinc.org");
 		cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
-		myCodeSystemDao.create(cs);
+		cs.setId("loinc");
+		myCodeSystemDao.update(cs);
 
 		Group group = new Group();
 		group.setId("ABC");
@@ -567,8 +568,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		CodeSystem cs = new CodeSystem();
 		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
 		cs.setUrl("http://loinc.org");
-		cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
+		cs.addConcept().setCode("123-4").setDisplay("Code 123 4").setId("loinc");
-		myCodeSystemDao.create(cs);
+		myCodeSystemDao.update(cs);
 
 		Group group = new Group();
 		group.setId("ABC");
@@ -628,14 +629,15 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		ValueSet vs = new ValueSet();
 		vs.setUrl("http://example.com/fhir/ValueSet/observation-vitalsignresult");
-		vs.getCompose().addInclude().setSystem("http://loinc.org");
+		vs.getCompose().addInclude().setSystem("http://loinc.org").setId("loinc");
 		myValueSetDao.create(vs);
 
 		CodeSystem cs = new CodeSystem();
 		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
 		cs.setUrl("http://loinc.org");
 		cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
-		myCodeSystemDao.create(cs);
+		cs.setId("loinc");
+		myCodeSystemDao.update(cs);
 
 		Group group = new Group();
 		group.setId("ABC");
@@ -936,6 +938,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			// Valid code
 			obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 			obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("CODE3").setDisplay("Display 3");
+			obs.getCode().getCodingFirstRep().setId("loinc");
 			oo = validateAndReturnOutcome(obs);
 			assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encode(oo));