More loinc work

example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsServerExample.java

@@ -5,9 +5,9 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
-import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.rp.dstu3.ActivityDefinitionResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.MeasureResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.PlanDefinitionResourceProvider;
@@ -149,7 +149,7 @@ public class CdsServerExample extends RestfulServer {
 		 * so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
 		 * with this feature.
 		 */
-		registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
+		registerProvider(myAppCtx.getBean(TerminologyUploaderProvider.class));
 	}
 
 	public IResourceProvider getProvider(String name) {

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -8,7 +8,6 @@ import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
-import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
 import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@@ -79,7 +78,7 @@ public class JpaServerDemo extends RestfulServer {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
 		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
-			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
+			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
 		} else if (fhirVersion == FhirVersionEnum.R4) {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class));
 			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -188,7 +188,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 			if (isNotBlank(next.getCode())) {
 				TermConcept termConcept = new TermConcept();
 				termConcept.setCode(next.getCode());
-				termConcept.setCodeSystem(theCodeSystemVersion);
+				termConcept.setCodeSystemVersion(theCodeSystemVersion);
 				termConcept.setDisplay(next.getDisplay());
 				termConcept.addChildren(toPersistedConcepts(next.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);
 				retVal.add(termConcept);

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

@@ -161,7 +161,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 			if (isNotBlank(next.getCode())) {
 				TermConcept termConcept = new TermConcept();
 				termConcept.setCode(next.getCode());
-				termConcept.setCodeSystem(theCodeSystemVersion);
+				termConcept.setCodeSystemVersion(theCodeSystemVersion);
 				termConcept.setDisplay(next.getDisplay());
 				termConcept.addChildren(toPersistedConcepts(next.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);
 				retVal.add(termConcept);

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

@@ -20,28 +20,15 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.util.CoverageIgnore;
+
+import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ForeignKey;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
-
-import ca.uhn.fhir.util.CoverageIgnore;
-
 //@formatter:off
-@Table(name="TRM_CODESYSTEM_VER"
+@Table(name = "TRM_CODESYSTEM_VER"
 	// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
 )
 @Entity()
@@ -54,17 +41,23 @@ public class TermCodeSystemVersion implements Serializable {
 
 	@Id()
 	@SequenceGenerator(name = "SEQ_CODESYSTEMVER_PID", sequenceName = "SEQ_CODESYSTEMVER_PID")
-	@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CODESYSTEMVER_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEMVER_PID")
 	@Column(name = "PID")
 	private Long myId;
 
 	@OneToOne()
-	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey=@ForeignKey(name="FK_CODESYSVER_RES_ID"))
+	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
 	private ResourceTable myResource;
 
 	@Column(name = "CS_VERSION_ID", nullable = true, updatable = false)
 	private String myCodeSystemVersionId;
-
+	/**
+	 * This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
+	 * issued. It should be made non-nullable at some point.
+	 */
+	@ManyToOne
+	@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true)
+	private TermCodeSystem myCodeSystem;
 	@SuppressWarnings("unused")
 	@OneToOne(mappedBy = "myCurrentVersion", optional = true)
 	private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
@@ -76,26 +69,6 @@ public class TermCodeSystemVersion implements Serializable {
 		super();
 	}
 
-	public Collection<TermConcept> getConcepts() {
-		if (myConcepts == null) {
-			myConcepts = new ArrayList<>();
-		}
-		return myConcepts;
-	}
-
-	public Long getPid() {
-		return myId;
-	}
-
-	@Override
-	public int hashCode() {
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + ((myResource.getId() == null) ? 0 : myResource.getId().hashCode());
-		result = prime * result + ((myCodeSystemVersionId == null) ? 0 : myCodeSystemVersionId.hashCode());
-		return result;
-	}
-
 	@CoverageIgnore
 	@Override
 	public boolean equals(Object obj) {
@@ -125,20 +98,48 @@ public class TermCodeSystemVersion implements Serializable {
 		return true;
 	}
 
-	public ResourceTable getResource() {
+	public TermCodeSystem getCodeSystem() {
-		return myResource;
+		return myCodeSystem;
+	}
+
+	public void setCodeSystem(TermCodeSystem theCodeSystem) {
+		myCodeSystem = theCodeSystem;
 	}
 
 	public String getCodeSystemVersionId() {
 		return myCodeSystemVersionId;
 	}
 
-	public void setResource(ResourceTable theResource) {
-		myResource = theResource;
-	}
-
 	public void setCodeSystemVersionId(String theCodeSystemVersionId) {
 		myCodeSystemVersionId = theCodeSystemVersionId;
 	}
 
+	public Collection<TermConcept> getConcepts() {
+		if (myConcepts == null) {
+			myConcepts = new ArrayList<>();
+		}
+		return myConcepts;
+	}
+
+	public Long getPid() {
+		return myId;
+	}
+
+	public ResourceTable getResource() {
+		return myResource;
+	}
+
+	public void setResource(ResourceTable theResource) {
+		myResource = theResource;
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((myResource.getId() == null) ? 0 : myResource.getId().hashCode());
+		result = prime * result + ((myCodeSystemVersionId == null) ? 0 : myCodeSystemVersionId.hashCode());
+		return result;
+	}
+
 }

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

@@ -101,7 +101,7 @@ public class TermConcept implements Serializable {
 	}
 
 	public TermConcept(TermCodeSystemVersion theCs, String theCode) {
-		setCodeSystem(theCs);
+		setCodeSystemVersion(theCs);
 		setCode(theCode);
 	}
 
@@ -178,14 +178,14 @@ public class TermConcept implements Serializable {
 		myCode = theCode;
 	}
 
-	public TermCodeSystemVersion getCodeSystem() {
+	public TermCodeSystemVersion getCodeSystemVersion() {
 		return myCodeSystem;
 	}
 
-	public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
+	public void setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
-		myCodeSystem = theCodeSystem;
+		myCodeSystem = theCodeSystemVersion;
-		if (theCodeSystem.getPid() != null) {
+		if (theCodeSystemVersion.getPid() != null) {
-			myCodeSystemVersionPid = theCodeSystem.getPid();
+			myCodeSystemVersionPid = theCodeSystemVersion.getPid();
 		}
 	}
 

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

@@ -408,7 +408,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 			ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
 		}
 
-		theConcept.setCodeSystem(theCodeSystem);
+		theConcept.setCodeSystemVersion(theCodeSystem);
 		theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
 
 		if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
@@ -436,10 +436,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	}
 
 	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
-		if (theNext.getCodeSystem() != null) {
+		if (theNext.getCodeSystemVersion() != null) {
 			return;
 		}
-		theNext.setCodeSystem(theCodeSystemVersion);
+		theNext.setCodeSystemVersion(theCodeSystemVersion);
 		for (TermConceptParentChildLink next : theNext.getChildren()) {
 			populateVersion(next.getChild(), theCodeSystemVersion);
 		}
@@ -667,6 +667,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 				throw new UnprocessableEntityException(msg);
 			}
 		}
+		theCodeSystemVersion.setCodeSystem(codeSystem);
 
 		ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
 
@@ -753,8 +754,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 	private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
 													  IdentityHashMap<TermConcept, Object> theAllConcepts) {
-		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystem() != null, "CodesystemValue is null");
+		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodesystemValue is null");
-		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystem() == theCodeSystem, "CodeSystems are not equal");
+		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code with no code value");
 
 		if (theConceptsStack.contains(theConcept.getCode())) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java

@@ -237,7 +237,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 			def.setDisplay(code.getDisplay());
 			CodeValidationResult retVal = new CodeValidationResult(def);
 			retVal.setProperties(code.toValidationProperties());
-			retVal.setCodeSystemName(code.getCodeSystem().get);
+			retVal.setCodeSystemName(code.getCodeSystemVersion().getCodeSystem().getName());
 			return retVal;
 		}
 

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

@@ -389,7 +389,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		if (concept == null) {
 			concept = new TermConcept();
 			id2concept.put(id, concept);
-			concept.setCodeSystem(codeSystemVersion);
+			concept.setCodeSystemVersion(codeSystemVersion);
 		}
 		return concept;
 	}

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

@@ -39,7 +39,7 @@ public class LoincHierarchyHandler implements IRecordHandler {
       TermConcept retVal = myCode2Concept.get(theCode);
       if (retVal == null) {
          retVal = new TermConcept();
-         retVal.setCodeSystem(myCodeSystemVersion);
+         retVal.setCodeSystemVersion(myCodeSystemVersion);
          retVal.setCode(theCode);
          retVal.setDisplay(theDisplay);
          myCode2Concept.put(theCode, retVal);

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

@@ -5,9 +5,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.convertors.VersionConvertor_30_40;
-import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.ValueSet;
-import org.hl7.fhir.dstu3.model.Parameters;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -16,10 +14,12 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
 public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
@@ -73,6 +73,21 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 		Parameters parameters = VersionConvertor_30_40.convertParameters(parametersR4);
 
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
+
+		assertEquals("SYSTEM", this.<CodeType>getPropertyPart(parameters, "property", "code").get().getValueAsString());
+		assertEquals("Heart", this.<CodeType>getPropertyPart(parameters, "property", "value").get().getValueAsString());
+
+	}
+
+	private <T extends Type> Optional<T> getPropertyPart(Parameters theParameters, String thePropName, String thePart) {
+		return theParameters
+            .getParameter()
+            .stream()
+            .filter(t -> t.getName().equals(thePropName))
+            .flatMap(t -> t.getPart().stream())
+            .filter(t -> t.getName().equals(thePart))
+            .map(t -> (T)t.getValue())
+            .findFirst();
 	}
 
 	private Set<String> toExpandedCodes(ValueSet theExpanded) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -49,12 +49,12 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		cs.setResource(table);
 
 		TermConcept parent = new TermConcept();
-		parent.setCodeSystem(cs);
+		parent.setCodeSystemVersion(cs);
 		parent.setCode("parent");
 		cs.getConcepts().add(parent);
 
 		TermConcept child = new TermConcept();
-		child.setCodeSystem(cs);
+		child.setCodeSystemVersion(cs);
 		child.setCode("child");
 		parent.addChild(child, RelationshipTypeEnum.ISA);
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -8,7 +8,6 @@ import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
-import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
 import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@@ -121,7 +120,7 @@ public class TestRestfulServer extends RestfulServer {
 			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
 			confProvider.setImplementationDescription(implDesc);
 			setServerConformanceProvider(confProvider);
-			plainProviders.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
+			plainProviders.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
 			break;
 		}
 		case "R4": {