Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/StressTestR4Test.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
@@ -31,10 +32,8 @@ import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
-import org.junit.After;
+import org.hl7.fhir.r4.model.codesystems.HttpVerb;
-import org.junit.AfterClass;
+import org.junit.*;
-import org.junit.Before;
-import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.util.AopTestUtils;
@@ -337,6 +336,45 @@ public class StressTestR4Test extends BaseResourceProviderR4Test {
 		assertEquals(1202, resultsAndIncludes.size());
 	}
 
+	@Ignore
+	@Test
+	public void testUpdateListWithLargeNumberOfEntries() {
+		int numPatients = 3000;
+
+		ListResource lr = new ListResource();
+		lr.setId(IdType.newRandomUuid());
+
+		{
+			Bundle bundle = new Bundle();
+			for (int i = 0; i < numPatients; ++i) {
+				Patient patient = new Patient();
+				patient.setId(IdType.newRandomUuid());
+				bundle.addEntry().setFullUrl(patient.getId()).setResource(patient).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
+				lr.addEntry().setItem(new Reference(patient.getId()));
+			}
+			bundle.addEntry().setFullUrl(lr.getId()).setResource(lr).getRequest().setMethod(HTTPVerb.POST).setUrl("List");
+
+			StopWatch sw = new StopWatch();
+			ourLog.info("Saving list with {} entries", lr.getEntry().size());
+			mySystemDao.transaction(null, bundle);
+			ourLog.info("Saved {} resources in {}", bundle.getEntry().size(), sw);
+		}
+
+		{
+			Bundle bundle = new Bundle();
+
+			Patient newPatient = new Patient();
+			newPatient.setId(IdType.newRandomUuid());
+			bundle.addEntry().setFullUrl(newPatient.getId()).setResource(newPatient).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
+			lr.addEntry().setItem(new Reference(newPatient.getId()));
+			bundle.addEntry().setFullUrl(lr.getId()).setResource(lr).getRequest().setMethod(HTTPVerb.PUT).setUrl(lr.getIdElement().toUnqualifiedVersionless().getValue());
+
+			StopWatch sw = new StopWatch();
+			ourLog.info("Updating list with {} entries", lr.getEntry().size());
+			mySystemDao.transaction(null, bundle);
+			ourLog.info("Updated {} resources in {}", bundle.getEntry().size(), sw);
+		}
+	}
 
 	@Test
 	public void testMultithreadedSearch() throws Exception {

hapi-fhir-jpaserver-model/pom.xml

@@ -46,6 +46,11 @@
 			<artifactId>hapi-fhir-structures-r4</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-r5</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/any/AnyListResource.java

@@ -43,6 +43,8 @@ public class AnyListResource {
 				return new AnyListResource(new org.hl7.fhir.dstu3.model.ListResource());
 			case R4:
 				return new AnyListResource(new org.hl7.fhir.r4.model.ListResource());
+			case R5:
+				return new AnyListResource(new org.hl7.fhir.r5.model.ListResource());
 			default:
 				throw new UnsupportedOperationException(version + " not supported");
 		}
@@ -63,6 +65,11 @@ public class AnyListResource {
 		myListResource = theListResourceR4;
 	}
 
+	public AnyListResource(org.hl7.fhir.r5.model.ListResource theListResourceR5) {
+		myFhirVersion = FhirVersionEnum.R5;
+		myListResource = theListResourceR5;
+	}
+
 	public static AnyListResource fromResource(IBaseResource theListResource) {
 		if (theListResource instanceof ca.uhn.fhir.model.dstu2.resource.ListResource) {
 			return new AnyListResource((ca.uhn.fhir.model.dstu2.resource.ListResource) theListResource);
@@ -70,6 +77,8 @@ public class AnyListResource {
 			return new AnyListResource((org.hl7.fhir.dstu3.model.ListResource) theListResource);
 		} else if (theListResource instanceof org.hl7.fhir.r4.model.ListResource) {
 			return new AnyListResource((org.hl7.fhir.r4.model.ListResource) theListResource);
+		} else if (theListResource instanceof org.hl7.fhir.r5.model.ListResource) {
+			return new AnyListResource((org.hl7.fhir.r5.model.ListResource) theListResource);
 		} else {
 			throw new UnsupportedOperationException("Cannot convert " + theListResource.getClass().getName() + " to AnyList");
 		}
@@ -94,6 +103,11 @@ public class AnyListResource {
 		return (org.hl7.fhir.r4.model.ListResource) get();
 	}
 
+	public org.hl7.fhir.r5.model.ListResource getR5() {
+		Validate.isTrue(myFhirVersion == FhirVersionEnum.R5);
+		return (org.hl7.fhir.r5.model.ListResource) get();
+	}
+
 	public FhirVersionEnum getFhirVersion() {
 		return myFhirVersion;
 	}
@@ -106,6 +120,9 @@ public class AnyListResource {
 			case R4:
 				getR4().getCode().addCoding().setSystem(theSystem).setCode(theCode);
 				break;
+			case R5:
+				getR5().getCode().addCoding().setSystem(theSystem).setCode(theCode);
+				break;
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -119,6 +136,9 @@ public class AnyListResource {
 			case R4:
 				getR4().getIdentifier().add(new org.hl7.fhir.r4.model.Identifier().setSystem(theSystem).setValue(theValue));
 				break;
+			case R5:
+				getR5().getIdentifier().add(new org.hl7.fhir.r5.model.Identifier().setSystem(theSystem).setValue(theValue));
+				break;
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -132,6 +152,9 @@ public class AnyListResource {
 			case R4:
 				getR4().addExtension().setUrl(theUrl).setValue(new org.hl7.fhir.r4.model.StringType(theValue));
 				break;
+			case R5:
+				getR5().addExtension().setUrl(theUrl).setValue(new org.hl7.fhir.r5.model.StringType(theValue));
+				break;
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -143,6 +166,8 @@ public class AnyListResource {
 				return getStringExtensionValueOrNullDstu3(theUrl);
 			case R4:
 				return getStringExtensionValueOrNullR4(theUrl);
+			case R5:
+				return getStringExtensionValueOrNullR5(theUrl);
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -166,6 +191,15 @@ public class AnyListResource {
 		return targetType.getValue();
 	}
 
+	private String getStringExtensionValueOrNullR5(String theUrl) {
+		List<org.hl7.fhir.r5.model.Extension> targetTypes = getR5().getExtensionsByUrl(theUrl);
+		if (targetTypes.size() < 1) {
+			return null;
+		}
+		org.hl7.fhir.r5.model.StringType targetType = (org.hl7.fhir.r5.model.StringType) targetTypes.get(0).getValue();
+		return targetType.getValue();
+	}
+
 	public void addReference(IBaseReference theReference) {
 		switch (myFhirVersion) {
 			case DSTU3:
@@ -174,6 +208,9 @@ public class AnyListResource {
 			case R4:
 				getR4().addEntry().setItem((org.hl7.fhir.r4.model.Reference) theReference);
 				break;
+			case R5:
+				getR5().addEntry().setItem((org.hl7.fhir.r5.model.Reference) theReference);
+				break;
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -187,6 +224,9 @@ public class AnyListResource {
 			case R4:
 				getR4().addEntry().setItem(new org.hl7.fhir.r4.model.Reference(theReferenceId));
 				break;
+			case R5:
+				getR5().addEntry().setItem(new org.hl7.fhir.r5.model.Reference(theReferenceId));
+				break;
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -202,6 +242,10 @@ public class AnyListResource {
 				return getR4().getEntry().stream()
 					.map(entry -> entry.getItem().getReference())
 					.map(reference -> new org.hl7.fhir.r4.model.IdType(reference).toUnqualifiedVersionless().getValue());
+			case R5:
+				return getR5().getEntry().stream()
+					.map(entry -> entry.getItem().getReference())
+					.map(reference -> new org.hl7.fhir.r5.model.IdType(reference).toUnqualifiedVersionless().getValue());
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -213,6 +257,8 @@ public class AnyListResource {
 				return removeItemDstu3(theReferenceId);
 			case R4:
 				return removeItemR4(theReferenceId);
+			case R5:
+				return removeItemR5(theReferenceId);
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
@@ -250,6 +296,22 @@ public class AnyListResource {
 		return removed;
 	}
 
+	private boolean removeItemR5(String theReferenceId) {
+		boolean removed = false;
+		for (org.hl7.fhir.r5.model.ListResource.ListEntryComponent entry : getR5().getEntry()) {
+			if (theReferenceId.equals(entry.getItem().getReference()) && !entry.getDeleted()) {
+				entry.setDeleted(true);
+				removed = true;
+				break;
+			}
+		}
+
+		if (removed) {
+			getR5().getEntry().removeIf(entry -> entry.getDeleted());
+		}
+		return removed;
+	}
+
 	public TokenParam getCodeFirstRep() {
 		switch (myFhirVersion) {
 			case DSTU3:
@@ -258,17 +320,40 @@ public class AnyListResource {
 			case R4:
 				org.hl7.fhir.r4.model.Coding codingR4 = getR4().getCode().getCodingFirstRep();
 				return new TokenParam(codingR4.getSystem(), codingR4.getCode());
+			case R5:
+				org.hl7.fhir.r5.model.Coding codingR5 = getR5().getCode().getCodingFirstRep();
+				return new TokenParam(codingR5.getSystem(), codingR5.getCode());
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}
 	}
 
+	public TokenParam getIdentifierirstRep() {
+		switch (myFhirVersion) {
+			case DSTU3:
+				org.hl7.fhir.dstu3.model.Identifier identDstu3 = getDstu3().getIdentifierFirstRep();
+				return new TokenParam(identDstu3.getSystem(), identDstu3.getValue());
+			case R4:
+				org.hl7.fhir.r4.model.Identifier identR4 = getR4().getIdentifierFirstRep();
+				return new TokenParam(identR4.getSystem(), identR4.getValue());
+			case R5:
+				org.hl7.fhir.r5.model.Identifier identR5 = getR5().getIdentifierFirstRep();
+				return new TokenParam(identR5.getSystem(), identR5.getValue());
+			default:
+				throw new UnsupportedOperationException(myFhirVersion + " not supported");
+		}
+	}
+
+
+
 	public boolean isEmpty() {
 		switch (myFhirVersion) {
 			case DSTU3:
 				return getDstu3().getEntry().isEmpty();
 			case R4:
 				return getR4().getEntry().isEmpty();
+			case R5:
+				return getR5().getEntry().isEmpty();
 			default:
 				throw new UnsupportedOperationException(myFhirVersion + " not supported");
 		}

hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/any/AnyListResourceTest.java

@@ -0,0 +1,24 @@
+package ca.uhn.fhir.jpa.model.any;
+
+import org.hl7.fhir.r5.model.ListResource;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class AnyListResourceTest {
+	@Test
+	public void getCodeFirstRep() {
+		AnyListResource listResource = AnyListResource.fromResource(new ListResource());
+		listResource.addCode("foo", "bar");
+		assertEquals("foo", listResource.getCodeFirstRep().getSystem());
+		assertEquals("bar", listResource.getCodeFirstRep().getValue());
+	}
+
+	@Test
+	public void getIdentifierFirstRep() {
+		AnyListResource listResource = AnyListResource.fromResource(new ListResource());
+		listResource.addIdentifier("foo", "bar");
+		assertEquals("foo", listResource.getIdentifierirstRep().getSystem());
+		assertEquals("bar", listResource.getIdentifierirstRep().getValue());
+	}
+}

src/changes/changes.xml

@@ -114,6 +114,15 @@
 				could be bypassed if a Content Type was not included.
 			</action>
 		</release>
+		<release version="4.0.1" date="2019-09-03" description="Igloo (Point Release)">
+			<action type="fix">
+				This release contains no new or updated functionality, but addressed a dependency 
+				version that was left incorrectly requiring a SNAPSHOT maven build of the
+				org.hl7.fhir.utilities module. Users who are successfully using HAPI FHIR 4.0.0
+				do not need to upgrade, but any users who were blocked from upgrading due to
+				snapshot dependency issues are advised to upgrade immediately.
+			</action>
+		</release>
 		<release version="4.0.0" date="2019-08-14" description="Igloo">
 			<action type="add">
 				The version of a few dependencies have been bumped to the

src/site/xdoc/index.xml

@@ -67,6 +67,32 @@
 		</section>
 
 		<section name="Announcements">
+			<p>
+				<b>September 3, 2019 - Community Survey and HAPI FHIR 4.0.1</b> -
+				It is time for us to do another HAPI FHIR community survey. The survey is a not-quite-annual 
+				tradition that helps us to set priority for the coming year and get a pulse on how people 
+				are using HAPI FHIR.
+			</p>
+			<p>
+				We would very much appreciate if everyone could take a few minutes to fill it out. The 
+				survey is short (2 pages / 5 mins) so it shouldn't be much of a burden.
+			</p>
+			<p>
+				Access the survey here:
+				<a href="http://bit.ly/33HO4cs">http://bit.ly/33HO4cs</a> (note that this URL was originally posted incorrectly. It is now fixed)
+			</p>
+			<p>
+				In addition, a new HAPI FHIR release (4.0.1) has been uploaded to the
+				Maven Central repos.
+				This release contains no new or updated functionality, but addressed a dependency
+            version that was left incorrectly requiring a SNAPSHOT maven build of the
+            org.hl7.fhir.utilities module. Users who are successfully using HAPI FHIR 4.0.0
+            do not need to upgrade, but any users who were blocked from upgrading due to
+            snapshot dependency issues are advised to upgrade immediately.
+			</p>
+
+
+
 			<p>
 				<b>August 14, 2019 - HAPI FHIR 4.0.0 (Igloo) Released</b> -
 				The next release of HAPI has now been uploaded to the Maven repos and