Merge branch 'master' into master

.travis.yml

@@ -25,5 +25,5 @@ before_script:
 script:
 #  - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
 #  - mvn -Dci=true -e -B -P ALLMODULES,NOPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
-  - mvn -Dci=true -e -B -P ALLMODULES,REDUCED_JPA_TESTS,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
+  - mvn -Dci=true -e -B -P ALLMODULES,REDUCED_JPA_TESTS,ERRORPRONE_JDK8 clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
 

appveyor.yml

@@ -4,4 +4,4 @@ cache:
   - C:\maven\
   - C:\Users\appveyor\.m2\repository
 build_script:
-   - cmd: mvn -P MINPARALLEL,ALLMODULES install
+   - cmd: mvn -P MINPARALLEL,ALLMODULES clean install

examples/src/main/java/example/Copier.java

@@ -0,0 +1,121 @@
+package example;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.util.ResourceReferenceInfo;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Resource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.*;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+@SuppressWarnings("unused")
+public class Copier {
+	private static final Logger ourLog = LoggerFactory.getLogger(Copier.class);
+
+	public static void main(String[] args) {
+		FhirContext ctx = FhirContext.forDstu3();
+		IGenericClient source = ctx.newRestfulGenericClient("http://localhost:8080/baseDstu3");
+		IGenericClient target = ctx.newRestfulGenericClient("https://try.smilecdr.com:8000");
+
+		List<String> resType = Arrays.asList(
+			"Patient", "Organization", "Encounter", "Procedure",
+			"Observation", "ResearchSubject", "Specimen",
+			"ResearchStudy", "Location", "Practitioner"
+		);
+
+		List<IBaseResource> queued = new ArrayList<>();
+		Set<String> sent = new HashSet<>();
+		for (String next : resType) {
+			copy(ctx, source, target, next, queued, sent);
+		}
+
+		while (queued.size() > 0) {
+			ourLog.info("Have {} queued resources to deliver", queued.size());
+
+			for (IBaseResource nextQueued : new ArrayList<>(queued)) {
+
+				String missingRef = null;
+				for (ResourceReferenceInfo nextRefInfo : ctx.newTerser().getAllResourceReferences(nextQueued)) {
+					String nextRef = nextRefInfo.getResourceReference().getReferenceElement().getValue();
+					if (isNotBlank(nextRef) && !sent.contains(nextRef)) {
+						missingRef = nextRef;
+					}
+				}
+				if (missingRef != null) {
+					ourLog.info("Can't send {} because of missing ref {}", nextQueued.getIdElement().getIdPart(), missingRef);
+					continue;
+				}
+
+				IIdType newId = target
+					.update()
+					.resource(nextQueued)
+					.execute()
+					.getId();
+
+				ourLog.info("Copied resource {} and got ID {}", nextQueued.getIdElement().getValue(), newId);
+				sent.add(nextQueued.getIdElement().toUnqualifiedVersionless().getValue());
+				queued.remove(nextQueued);
+			}
+		}
+
+
+	}
+
+	private static void copy(FhirContext theCtx, IGenericClient theSource, IGenericClient theTarget, String theResType, List<IBaseResource> theQueued, Set<String> theSent) {
+		Bundle received = theSource
+			.search()
+			.forResource(theResType)
+			.returnBundle(Bundle.class)
+			.execute();
+		copy(theCtx, theTarget, theResType, theQueued, theSent, received);
+
+		while (received.getLink("next") != null) {
+			ourLog.info("Fetching next page...");
+			received = theSource.loadPage().next(received).execute();
+			copy(theCtx, theTarget, theResType, theQueued, theSent, received);
+		}
+
+	}
+
+	private static void copy(FhirContext theCtx, IGenericClient theTarget, String theResType, List<IBaseResource> theQueued, Set<String> theSent, Bundle theReceived) {
+		for (Bundle.BundleEntryComponent nextEntry : theReceived.getEntry()) {
+			Resource nextResource = nextEntry.getResource();
+			nextResource.setId(theResType + "/" + "CR-" + nextResource.getIdElement().getIdPart());
+
+			boolean haveUnsentReference = false;
+			for (ResourceReferenceInfo nextRefInfo : theCtx.newTerser().getAllResourceReferences(nextResource)) {
+				IIdType nextRef = nextRefInfo.getResourceReference().getReferenceElement();
+				if (nextRef.hasIdPart()) {
+					String newRef = nextRef.getResourceType() + "/" + "CR-" + nextRef.getIdPart();
+					ourLog.info("Changing reference {} to {}", nextRef.getValue(), newRef);
+					nextRefInfo.getResourceReference().setReference(newRef);
+					if (!theSent.contains(newRef)) {
+						haveUnsentReference = true;
+					}
+				}
+			}
+
+			if (haveUnsentReference) {
+				ourLog.info("Queueing {} for delivery after", nextResource.getId());
+				theQueued.add(nextResource);
+				continue;
+			}
+
+			IIdType newId = theTarget
+				.update()
+				.resource(nextResource)
+				.execute()
+				.getId();
+
+			ourLog.info("Copied resource {} and got ID {}", nextResource.getId(), newId);
+			theSent.add(nextResource.getIdElement().toUnqualifiedVersionless().getValue());
+		}
+	}
+
+}

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

@@ -40,16 +40,14 @@ public enum FhirVersionEnum {
 
 	DSTU2_1("org.hl7.fhir.dstu2016may.hapi.ctx.FhirDstu2_1", null, true, new Version("1.4.0")),
 
-	DSTU3("org.hl7.fhir.dstu3.hapi.ctx.FhirDstu3", null, true, new Dstu3Version()), 
+	DSTU3("org.hl7.fhir.dstu3.hapi.ctx.FhirDstu3", null, true, new Dstu3Version()),
-	
+
-	R4("org.hl7.fhir.r4.hapi.ctx.FhirR4", null, true, new R4Version()),
+	R4("org.hl7.fhir.r4.hapi.ctx.FhirR4", null, true, new R4Version()),;
-	
-	;
 
 	private final FhirVersionEnum myEquivalent;
 	private final boolean myIsRi;
-	private volatile Boolean myPresentOnClasspath;
 	private final String myVersionClass;
+	private volatile Boolean myPresentOnClasspath;
 	private volatile IFhirVersion myVersionImplementation;
 	private String myFhirVersionString;
 
@@ -124,15 +122,50 @@ public enum FhirVersionEnum {
 		return myIsRi;
 	}
 
+	public FhirContext newContext() {
+		switch (this) {
+			case DSTU2:
+				return FhirContext.forDstu2();
+			case DSTU2_HL7ORG:
+				return FhirContext.forDstu2Hl7Org();
+			case DSTU2_1:
+				return FhirContext.forDstu2_1();
+			case DSTU3:
+				return FhirContext.forDstu3();
+			case R4:
+				return FhirContext.forR4();
+		}
+		throw new IllegalStateException("Unknown version: " + this); // should not happen
+	}
+
+	/**
+	 * Returns the {@link FhirVersionEnum} which corresponds to a specific version of
+	 * FHIR. Partial version strings (e.g. "3.0") are acceptable.
+	 *
+	 * @return Returns null if no version exists matching the given string
+	 */
+	public static FhirVersionEnum forVersionString(String theVersionString) {
+		for (FhirVersionEnum next : values()) {
+			if (next.getFhirVersionString().startsWith(theVersionString)) {
+				return next;
+			}
+		}
+		return null;
+	}
+
+	private interface IVersionProvider {
+		String provideVersion();
+	}
+
 	private static class Version implements IVersionProvider {
 
+		private String myVersion;
+
 		public Version(String theVersion) {
 			super();
 			myVersion = theVersion;
 		}
 
-		private String myVersion;
-
 		@Override
 		public String provideVersion() {
 			return myVersion;
@@ -140,18 +173,15 @@ public enum FhirVersionEnum {
 
 	}
 
-	private interface IVersionProvider {
-		String provideVersion();
-	}
-
 	/**
 	 * This class attempts to read the FHIR version from the actual model
 	 * classes in order to supply an accurate version string even over time
-	 *
 	 */
 	private static class Dstu3Version implements IVersionProvider {
 
-		public Dstu3Version() {
+		private String myVersion;
+
+		Dstu3Version() {
 			try {
 				Class<?> c = Class.forName("org.hl7.fhir.dstu3.model.Constants");
 				myVersion = (String) c.getDeclaredField("VERSION").get(null);
@@ -160,8 +190,6 @@ public enum FhirVersionEnum {
 			}
 		}
 
-		private String myVersion;
-
 		@Override
 		public String provideVersion() {
 			return myVersion;
@@ -171,7 +199,9 @@ public enum FhirVersionEnum {
 
 	private static class R4Version implements IVersionProvider {
 
-		public R4Version() {
+		private String myVersion;
+
+		R4Version() {
 			try {
 				Class<?> c = Class.forName("org.hl7.fhir.r4.model.Constants");
 				myVersion = (String) c.getDeclaredField("VERSION").get(null);
@@ -180,8 +210,6 @@ public enum FhirVersionEnum {
 			}
 		}
 
-		private String myVersion;
-
 		@Override
 		public String provideVersion() {
 			return myVersion;

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java

@@ -19,18 +19,6 @@ package ca.uhn.fhir.model.api;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
@@ -39,6 +27,14 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.io.Serializable;
+import java.util.*;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * Keys in this map refer to <b>resource metadata keys</b>, which are keys used to access information about specific resource instances that live outside of the resource body. Typically, these are
@@ -64,8 +60,6 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
  */
 public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
-	private static final long serialVersionUID = 1L;
-
 	/**
 	 * If present and populated with a date/time (as an instance of {@link InstantDt}), this value is an indication that the resource is in the deleted state. This key is only used in a limited number
 	 * of scenarios, such as POSTing transaction bundles to a server, or returning resource history.
@@ -81,23 +75,22 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), DELETED_AT);
 		}
 
-		@Override
-		public void put(IResource theResource, InstantDt theObject) {
-			theResource.getResourceMetadata().put(DELETED_AT, theObject);
-		}
-
 		@SuppressWarnings("unchecked")
 		@Override
 		public IPrimitiveType<Date> get(IAnyResource theResource) {
 			return (IPrimitiveType<Date>) theResource.getUserData(DELETED_AT.name());
 		}
 
+		@Override
+		public void put(IResource theResource, InstantDt theObject) {
+			theResource.getResourceMetadata().put(DELETED_AT, theObject);
+		}
+
 		@Override
 		public void put(IAnyResource theResource, IPrimitiveType<Date> theObject) {
 			theResource.setUserData(DELETED_AT.name(), theObject);
 		}
 	};
-
 	/**
 	 * Denotes the search score which a given resource should match in a transaction. See the FHIR transaction definition for information about this. Corresponds to the value in
 	 * <code>Bundle.entry.score</code> in a Bundle resource.
@@ -121,7 +114,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(ENTRY_SCORE, theObject);
 		}
 	};
-
 	/**
 	 * If present and populated with a {@link BundleEntrySearchModeEnum}, contains the "bundle entry search mode", which is the value of the status field in the Bundle entry containing this resource.
 	 * The value for this key corresponds to field <code>Bundle.entry.search.mode</code>. This value can be set to provide a status value of "include" for included resources being returned by a
@@ -135,27 +127,27 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeySupportingAnyResource<BundleEntrySearchModeEnum, String> ENTRY_SEARCH_MODE = new ResourceMetadataKeySupportingAnyResource<BundleEntrySearchModeEnum, String>("ENTRY_SEARCH_MODE") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public BundleEntrySearchModeEnum get(IResource theResource) {
 			return getEnumFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_SEARCH_MODE, BundleEntrySearchModeEnum.class, BundleEntrySearchModeEnum.VALUESET_BINDER);
 		}
 
-		@Override
-		public void put(IResource theResource, BundleEntrySearchModeEnum theObject) {
-			theResource.getResourceMetadata().put(ENTRY_SEARCH_MODE, theObject);
-		}
-
 		@Override
 		public String get(IAnyResource theResource) {
 			return (String) theResource.getUserData(ENTRY_SEARCH_MODE.name());
 		}
 
+		@Override
+		public void put(IResource theResource, BundleEntrySearchModeEnum theObject) {
+			theResource.getResourceMetadata().put(ENTRY_SEARCH_MODE, theObject);
+		}
+
 		@Override
 		public void put(IAnyResource theResource, String theObject) {
 			theResource.setUserData(ENTRY_SEARCH_MODE.name(), theObject);
 		}
 	};
-
 	/**
 	 * If present and populated with a {@link BundleEntryTransactionMethodEnum}, contains the "bundle entry transaction operation", which is the value of the status field in the Bundle entry
 	 * containing this resource. The value for this key corresponds to field <code>Bundle.entry.transaction.operation</code>. This value can be set in resources being transmitted to a server to
@@ -169,18 +161,13 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 * </p>
 	 */
 	public static final ResourceMetadataKeySupportingAnyResource<BundleEntryTransactionMethodEnum, String> ENTRY_TRANSACTION_METHOD = new ResourceMetadataKeySupportingAnyResource<BundleEntryTransactionMethodEnum, String>(
-			"ENTRY_TRANSACTION_OPERATION") {
+		"ENTRY_TRANSACTION_OPERATION") {
-				private static final long serialVersionUID = 1L;
+		private static final long serialVersionUID = 1L;
 
 		@Override
 		public BundleEntryTransactionMethodEnum get(IResource theResource) {
 			return getEnumFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_TRANSACTION_METHOD, BundleEntryTransactionMethodEnum.class,
-					BundleEntryTransactionMethodEnum.VALUESET_BINDER);
+				BundleEntryTransactionMethodEnum.VALUESET_BINDER);
-		}
-
-		@Override
-		public void put(IResource theResource, BundleEntryTransactionMethodEnum theObject) {
-			theResource.getResourceMetadata().put(ENTRY_TRANSACTION_METHOD, theObject);
 		}
 
 		@Override
@@ -188,13 +175,17 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			return (String) theResource.getUserData(ENTRY_TRANSACTION_METHOD.name());
 		}
 
+		@Override
+		public void put(IResource theResource, BundleEntryTransactionMethodEnum theObject) {
+			theResource.getResourceMetadata().put(ENTRY_TRANSACTION_METHOD, theObject);
+		}
+
 		@Override
 		public void put(IAnyResource theResource, String theObject) {
 			theResource.setUserData(ENTRY_TRANSACTION_METHOD.name(), theObject);
 		}
-		
-	};
 
+	};
 	/**
 	 * If present and populated with a string, provides the "alternate link" (the link element in the bundle entry with <code>rel="alternate"</code>). Server implementations may populate this with a
 	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient/1243") in which case the server will convert this to
@@ -205,6 +196,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeyEnum<String> LINK_ALTERNATE = new ResourceMetadataKeyEnum<String>("LINK_ALTERNATE") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public String get(IResource theResource) {
 			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_ALTERNATE);
@@ -215,7 +207,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(LINK_ALTERNATE, theObject);
 		}
 	};
-
 	/**
 	 * If present and populated with a string, provides the "search link" (the link element in the bundle entry with <code>rel="search"</code>). Server implementations may populate this with a
 	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient?name=tester") in which case the server will convert
@@ -226,6 +217,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeyEnum<String> LINK_SEARCH = new ResourceMetadataKeyEnum<String>("LINK_SEARCH") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public String get(IResource theResource) {
 			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_SEARCH);
@@ -236,7 +228,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(LINK_SEARCH, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key represents a previous ID used to identify this resource. This key is currently only used internally during transaction method processing.
 	 * <p>
@@ -245,6 +236,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeyEnum<IdDt> PREVIOUS_ID = new ResourceMetadataKeyEnum<IdDt>("PREVIOUS_ID") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public IdDt get(IResource theResource) {
 			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PREVIOUS_ID);
@@ -255,16 +247,16 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(PREVIOUS_ID, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key represents a {@link List} of profile IDs that this resource claims to conform to.
-	 * 
+	 * <p>
 	 * <p>
 	 * Values for this key are of type <b>List&lt;IdDt&gt;</b>. Note that the returned list is <i>unmodifiable</i>, so you need to create a new list and call <code>put</code> to change its value.
 	 * </p>
 	 */
 	public static final ResourceMetadataKeyEnum<List<IdDt>> PROFILES = new ResourceMetadataKeyEnum<List<IdDt>>("PROFILES") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public List<IdDt> get(IResource theResource) {
 			return getIdListFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PROFILES);
@@ -275,7 +267,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(PROFILES, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key is the bundle entry <b>Published</b> time. This is defined by FHIR as "Time resource copied into the feed", which is generally best left to the current time.
 	 * <p>
@@ -284,11 +275,12 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 * <p>
 	 * <b>Server Note</b>: In servers, it is generally advisable to leave this value <code>null</code>, in which case the server will substitute the current time automatically.
 	 * </p>
-	 * 
+	 *
 	 * @see InstantDt
 	 */
 	public static final ResourceMetadataKeyEnum<InstantDt> PUBLISHED = new ResourceMetadataKeyEnum<InstantDt>("PUBLISHED") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public InstantDt get(IResource theResource) {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PUBLISHED);
@@ -299,9 +291,9 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(PUBLISHED, theObject);
 		}
 	};
-
 	public static final ResourceMetadataKeyEnum<List<BaseCodingDt>> SECURITY_LABELS = new ResourceMetadataKeyEnum<List<BaseCodingDt>>("SECURITY_LABELS") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public List<BaseCodingDt> get(IResource resource) {
 			Object obj = resource.getResourceMetadata().get(SECURITY_LABELS);
@@ -317,7 +309,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 				return securityLabels;
 			} catch (ClassCastException e) {
 				throw new InternalErrorException("Found an object of type '" + obj.getClass().getCanonicalName() + "' in resource metadata for key SECURITY_LABELS - Expected "
-						+ BaseCodingDt.class.getCanonicalName());
+					+ BaseCodingDt.class.getCanonicalName());
 			}
 
 		}
@@ -328,17 +320,17 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 		}
 
 	};
-
 	/**
 	 * The value for this key is the list of tags associated with this resource
 	 * <p>
 	 * Values for this key are of type <b>{@link TagList}</b>
 	 * </p>
-	 * 
+	 *
 	 * @see TagList
 	 */
 	public static final ResourceMetadataKeyEnum<TagList> TAG_LIST = new ResourceMetadataKeyEnum<TagList>("TAG_LIST") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public TagList get(IResource theResource) {
 			Object retValObj = theResource.getResourceMetadata().get(TAG_LIST);
@@ -351,7 +343,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 				return (TagList) retValObj;
 			}
 			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + TAG_LIST.name() + " - Expected "
-					+ TagList.class.getCanonicalName());
+				+ TagList.class.getCanonicalName());
 		}
 
 		@Override
@@ -359,7 +351,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(TAG_LIST, theObject);
 		}
 	};
-
 	/**
 	 * If present and populated with a string (as an instance of {@link String}), this value contains the title for this resource, as supplied in any bundles containing the resource.
 	 * <p>
@@ -368,6 +359,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeyEnum<String> TITLE = new ResourceMetadataKeyEnum<String>("TITLE") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public String get(IResource theResource) {
 			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), TITLE);
@@ -378,18 +370,18 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(TITLE, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key is the bundle entry <b>Updated</b> time. This is defined by FHIR as "Last Updated for resource". This value is also used for populating the "Last-Modified" header in the
 	 * case of methods that return a single resource (read, vread, etc.)
 	 * <p>
 	 * Values for this key are of type <b>{@link InstantDt}</b>
 	 * </p>
-	 * 
+	 *
 	 * @see InstantDt
 	 */
 	public static final ResourceMetadataKeyEnum<InstantDt> UPDATED = new ResourceMetadataKeyEnum<InstantDt>("UPDATED") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public InstantDt get(IResource theResource) {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), UPDATED);
@@ -400,7 +392,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(UPDATED, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key is the version ID of the resource object.
 	 * <p>
@@ -409,6 +400,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 */
 	public static final ResourceMetadataKeyEnum<String> VERSION = new ResourceMetadataKeyEnum<String>("VERSION") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public String get(IResource theResource) {
 			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION);
@@ -419,18 +411,18 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(VERSION, theObject);
 		}
 	};
-
 	/**
 	 * The value for this key is the version ID of the resource object.
 	 * <p>
 	 * Values for this key are of type <b>{@link IdDt}</b>
 	 * </p>
-	 * 
+	 *
 	 * @deprecated The {@link IResource#getId()} resource ID will now be populated with the version ID via the {@link IdDt#getVersionIdPart()} method
 	 */
 	@Deprecated
 	public static final ResourceMetadataKeyEnum<IdDt> VERSION_ID = new ResourceMetadataKeyEnum<IdDt>("VERSION_ID") {
 		private static final long serialVersionUID = 1L;
+
 		@Override
 		public IdDt get(IResource theResource) {
 			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION_ID);
@@ -441,7 +433,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(VERSION_ID, theObject);
 		}
 	};
-
+	private static final long serialVersionUID = 1L;
 	private final String myValue;
 
 	public ResourceMetadataKeyEnum(String theValue) {
@@ -504,12 +496,12 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			return new DecimalDt((Double) retValObj);
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-				+ InstantDt.class.getCanonicalName());
+			+ InstantDt.class.getCanonicalName());
 	}
 
 	@SuppressWarnings("unchecked")
 	private static <T extends Enum<?>> T getEnumFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<T> theKey, Class<T> theEnumType,
-			IValueSetEnumBinder<T> theBinder) {
+																								IValueSetEnumBinder<T> theBinder) {
 		Object retValObj = theResourceMetadata.get(theKey);
 		if (retValObj == null) {
 			return null;
@@ -519,7 +511,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			return theBinder.fromCodeString((String) retValObj);
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-				+ InstantDt.class.getCanonicalName());
+			+ InstantDt.class.getCanonicalName());
 	}
 
 	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
@@ -558,11 +550,11 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 		} else if (retValObj instanceof InstantDt) {
 			if (((InstantDt) retValObj).isEmpty()) {
 				return null;
-			} 
+			}
 			return (InstantDt) retValObj;
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-				+ InstantDt.class.getCanonicalName());
+			+ InstantDt.class.getCanonicalName());
 	}
 
 	private static String getStringFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<String> theKey) {
@@ -572,11 +564,11 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 		} else if (retValObj instanceof String) {
 			if (StringUtils.isBlank(((String) retValObj))) {
 				return null;
-			} 
+			}
 			return (String) retValObj;
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-				+ String.class.getCanonicalName());
+			+ String.class.getCanonicalName());
 	}
 
 	private static IdDt toId(ResourceMetadataKeyEnum<?> theKey, Object retValObj) {
@@ -596,18 +588,17 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			return new IdDt(((Number) retValObj).toString());
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-				+ IdDt.class.getCanonicalName());
+			+ IdDt.class.getCanonicalName());
 	}
 
 	public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
 
+		private static final long serialVersionUID = 1L;
+
 		public ResourceMetadataKeySupportingAnyResource(String theValue) {
 			super(theValue);
 		}
 
-		private static final long serialVersionUID = 1L;
-
-		
 		public abstract T2 get(IAnyResource theResource);
 
 		public abstract void put(IAnyResource theResource, T2 theObject);

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -38,6 +38,7 @@ import java.util.*;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
+@SuppressWarnings("WeakerAccess")
 public abstract class BaseParser implements IParser {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
@@ -156,7 +157,6 @@ public abstract class BaseParser implements IParser {
 	}
 
 	private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, IBaseResource theTarget) {
-		Set<String> allIds = new HashSet<String>();
 		Map<String, IBaseResource> existingIdToContainedResource = null;
 
 		if (theTarget instanceof IResource) {
@@ -167,9 +167,8 @@ public abstract class BaseParser implements IParser {
 					if (!nextId.startsWith("#")) {
 						nextId = '#' + nextId;
 					}
-					allIds.add(nextId);
 					if (existingIdToContainedResource == null) {
-						existingIdToContainedResource = new HashMap<String, IBaseResource>();
+						existingIdToContainedResource = new HashMap<>();
 					}
 					existingIdToContainedResource.put(nextId, next);
 				}
@@ -182,9 +181,8 @@ public abstract class BaseParser implements IParser {
 					if (!nextId.startsWith("#")) {
 						nextId = '#' + nextId;
 					}
-					allIds.add(nextId);
 					if (existingIdToContainedResource == null) {
-						existingIdToContainedResource = new HashMap<String, IBaseResource>();
+						existingIdToContainedResource = new HashMap<>();
 					}
 					existingIdToContainedResource.put(nextId, next);
 				}
@@ -480,7 +478,7 @@ public abstract class BaseParser implements IParser {
 	@Override
 	public void setPreferTypes(List<Class<? extends IBaseResource>> thePreferTypes) {
 		if (thePreferTypes != null) {
-			ArrayList<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
+			ArrayList<Class<? extends IBaseResource>> types = new ArrayList<>();
 			for (Class<? extends IBaseResource> next : thePreferTypes) {
 				if (Modifier.isAbstract(next.getModifiers()) == false) {
 					types.add(next);
@@ -516,8 +514,7 @@ public abstract class BaseParser implements IParser {
 				}
 			}
 
-			List<T> newList = new ArrayList<T>();
+			List<T> newList = new ArrayList<>(theProfiles);
-			newList.addAll(theProfiles);
 
 			BaseRuntimeElementDefinition<?> idElement = myContext.getElementDefinition("id");
 			@SuppressWarnings("unchecked")
@@ -1195,8 +1192,10 @@ public abstract class BaseParser implements IParser {
 		}
 
 		public void addContained(IIdType theId, IBaseResource theResource) {
-			myResourceToId.put(theResource, theId);
+			if (!hasId(theId)) {
-			myResources.add(theResource);
+				myResourceToId.put(theResource, theId);
+				myResources.add(theResource);
+			}
 		}
 
 		public List<IBaseResource> getContainedResources() {
@@ -1207,6 +1206,15 @@ public abstract class BaseParser implements IParser {
 			return myResourceToId.get(theNext);
 		}
 
+		public boolean hasId(IIdType theId) {
+			for (IIdType next : myResourceToId.values()) {
+				if (Objects.equals(next.getValue(), theId.getValue())) {
+					return true;
+				}
+			}
+			return false;
+		}
+
 		public boolean isEmpty() {
 			return myResourceToId.isEmpty();
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/IParserErrorHandler.java

@@ -55,7 +55,7 @@ public interface IParserErrorHandler {
 	void incorrectJsonType(IParseLocation theLocation, String theElementName, ValueType theExpectedValueType, ScalarType theExpectedScalarType, ValueType theFoundValueType, ScalarType theFoundScalarType);
 
 	/**
-	 * The parser detected an atttribute value that was invalid (such as: empty "" values are not permitted)
+	 * The parser detected an attribute value that was invalid (such as: empty "" values are not permitted)
 	 * 
 	 * @param theLocation
 	 *           The location in the document. Note that this may be <code>null</code> as the ParseLocation feature is experimental. Use with caution, as the API may change. 
@@ -70,7 +70,7 @@ public interface IParserErrorHandler {
 	 * 
 	 * @param theLocation
 	 *           The location in the document. Note that this may be <code>null</code> as the ParseLocation feature is experimental. Use with caution, as the API may change. 
-	 * @param theReference The actual invalid reference (e.g. "#3")
+	 * @param theElementName The missing element name
 	 * @since 2.1
 	 */
 	void missingRequiredElement(IParseLocation theLocation, String theElementName);
@@ -123,7 +123,7 @@ public interface IParserErrorHandler {
 	 * type which will currently always be set to null. This interface is included here so that
 	 * locations can be added to the API in a future release without changing the API.
 	 */
-	public interface IParseLocation {
+	interface IParseLocation {
 
 		/**
 		 * Returns the name of the parent element (the element containing the element currently being parsed)

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -615,8 +615,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		write(theEventWriter, "resourceType", resDef.getName());
 		if (theResourceId != null && theResourceId.hasIdPart()) {
 			write(theEventWriter, "id", theResourceId.getIdPart());
-			final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+			final List<HeldExtension> extensions = new ArrayList<>(0);
-			final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+			final List<HeldExtension> modifierExtensions = new ArrayList<>(0);
 			// Undeclared extensions
 			extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
 			boolean haveExtension = false;
@@ -724,14 +724,11 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	/**
 	 * This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
 	 * called _name): resource extensions, and extension extensions
-	 *
-	 * @param theChildElem
-	 * @param theParent
 	 */
 	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
 																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
-		List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+		List<HeldExtension> extensions = new ArrayList<>(0);
-		List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+		List<HeldExtension> modifierExtensions = new ArrayList<>(0);
 
 		// Undeclared extensions
 		extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent);
@@ -1053,7 +1050,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				} else {
 					parentElementName = "extension";
 				}
-				getErrorHandler().missingRequiredElement(new ParseLocation(parentElementName), "url");
+				getErrorHandler().missingRequiredElement(new ParseLocation().setParentElementName(parentElementName), "url");
 				url = null;
 			} else {
 				url = getExtensionUrl(jsonElement.getAsString());

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParseLocation.java

@@ -29,9 +29,8 @@ class ParseLocation implements IParseLocation {
 	/**
 	 * Constructor
 	 */
-	public ParseLocation(String theParentElementName) {
+	public ParseLocation() {
 		super();
-		myParentElementName = theParentElementName;
 	}
 
 	@Override
@@ -39,4 +38,9 @@ class ParseLocation implements IParseLocation {
 		return myParentElementName;
 	}
 
+	public ParseLocation setParentElementName(String theParentElementName) {
+		myParentElementName = theParentElementName;
+		return this;
+	}
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java

@@ -806,7 +806,7 @@ class ParserState<T> {
 				@SuppressWarnings("unchecked")
 				List<IBase> securityLabels = (List<IBase>) myMap.get(ResourceMetadataKeyEnum.SECURITY_LABELS);
 				if (securityLabels == null) {
-					securityLabels = new ArrayList<IBase>();
+					securityLabels = new ArrayList<>();
 					myMap.put(ResourceMetadataKeyEnum.SECURITY_LABELS, securityLabels);
 				}
 				IBase securityLabel = myContext.getVersion().newCodingDt();

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java

@@ -139,7 +139,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 							Attribute urlAttr = elem.getAttributeByName(new QName("url"));
 							String url;
 							if (urlAttr == null || isBlank(urlAttr.getValue())) {
-								getErrorHandler().missingRequiredElement(new ParseLocation("extension"), "url");
+								getErrorHandler().missingRequiredElement(new ParseLocation().setParentElementName("extension"), "url");
 								url = null;
 							} else {
 								url = urlAttr.getValue();
@@ -149,7 +149,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 							Attribute urlAttr = elem.getAttributeByName(new QName("url"));
 							String url;
 							if (urlAttr == null || isBlank(urlAttr.getValue())) {
-								getErrorHandler().missingRequiredElement(new ParseLocation("modifierExtension"), "url");
+								getErrorHandler().missingRequiredElement(new ParseLocation().setParentElementName("modifierExtension"), "url");
 								url = null;
 							} else {
 								url = urlAttr.getValue();

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/EncodingEnum.java

@@ -19,12 +19,14 @@ package ca.uhn.fhir.rest.api;
  * limitations under the License.
  * #L%
  */
-import java.util.*;
-
-import org.apache.commons.lang3.ObjectUtils;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
+import org.apache.commons.lang3.ObjectUtils;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
 
 public enum EncodingEnum {
 
@@ -40,39 +42,40 @@ public enum EncodingEnum {
 		public IParser newParser(FhirContext theContext) {
 			return theContext.newXmlParser();
 		}
-	}
+	};
 
-	;
+	/**
-
+	 * "json"
-	/** "json" */
+	 */
-	public  static final String JSON_PLAIN_STRING = "json";
+	public static final String JSON_PLAIN_STRING = "json";
-	private static Map<String, EncodingEnum> ourContentTypeToEncoding;
+	/**
-	
+	 * "xml"
-	private static Map<String, EncodingEnum> ourContentTypeToEncodingNonLegacy;
+	 */
-	private static Map<String, EncodingEnum> ourContentTypeToEncodingStrict;
-	/** "xml" */
 	public static final String XML_PLAIN_STRING = "xml";
+	private static Map<String, EncodingEnum> ourContentTypeToEncoding;
+	private static Map<String, EncodingEnum> ourContentTypeToEncodingLegacy;
+	private static Map<String, EncodingEnum> ourContentTypeToEncodingStrict;
 
 	static {
-		ourContentTypeToEncoding = new HashMap<String, EncodingEnum>();
+		ourContentTypeToEncoding = new HashMap<>();
-		ourContentTypeToEncodingNonLegacy = new HashMap<String, EncodingEnum>();
+		ourContentTypeToEncodingLegacy = new HashMap<>();
-		
+
 		for (EncodingEnum next : values()) {
 			ourContentTypeToEncoding.put(next.myResourceContentTypeNonLegacy, next);
 			ourContentTypeToEncoding.put(next.myResourceContentTypeLegacy, next);
-			ourContentTypeToEncodingNonLegacy.put(next.myResourceContentTypeNonLegacy, next);
+			ourContentTypeToEncodingLegacy.put(next.myResourceContentTypeLegacy, next);
 
 			/*
 			 * See #346
 			 */
 			ourContentTypeToEncoding.put(next.myResourceContentTypeNonLegacy.replace('+', ' '), next);
 			ourContentTypeToEncoding.put(next.myResourceContentTypeLegacy.replace('+', ' '), next);
-			ourContentTypeToEncodingNonLegacy.put(next.myResourceContentTypeNonLegacy.replace('+', ' '), next);
+			ourContentTypeToEncodingLegacy.put(next.myResourceContentTypeLegacy.replace('+', ' '), next);
 
 		}
 
 		// Add before we add the lenient ones
-		ourContentTypeToEncodingStrict = Collections.unmodifiableMap(new HashMap<String, EncodingEnum>(ourContentTypeToEncoding));
+		ourContentTypeToEncodingStrict = Collections.unmodifiableMap(new HashMap<>(ourContentTypeToEncoding));
 
 		/*
 		 * These are wrong, but we add them just to be tolerant of other
@@ -89,7 +92,7 @@ public enum EncodingEnum {
 		ourContentTypeToEncoding.put(JSON_PLAIN_STRING, JSON);
 		ourContentTypeToEncoding.put(XML_PLAIN_STRING, XML);
 
-		ourContentTypeToEncodingNonLegacy = Collections.unmodifiableMap(ourContentTypeToEncodingNonLegacy);
+		ourContentTypeToEncodingLegacy = Collections.unmodifiableMap(ourContentTypeToEncodingLegacy);
 
 	}
 
@@ -107,10 +110,6 @@ public enum EncodingEnum {
 		return myFormatContentType;
 	}
 
-	public String getRequestContentType() {
-		return myFormatContentType;
-	}
-
 	/**
 	 * Will return application/xml+fhir style
 	 */
@@ -150,7 +149,7 @@ public enum EncodingEnum {
 
 	/**
 	 * Returns the encoding for a given content type, or <code>null</code> if no encoding
-	 * is found. 
+	 * is found.
 	 * <p>
 	 * <b>This method is lenient!</b> Things like "application/xml" will return {@link EncodingEnum#XML}
 	 * even if the "+fhir" part is missing from the expected content type.
@@ -163,19 +162,23 @@ public enum EncodingEnum {
 
 	/**
 	 * Returns the encoding for a given content type, or <code>null</code> if no encoding
-	 * is found. 
+	 * is found.
 	 * <p>
 	 * <b>This method is NOT lenient!</b> Things like "application/xml" will return <code>null</code>
 	 * </p>
+	 *
 	 * @see #forContentType(String)
 	 */
 	public static EncodingEnum forContentTypeStrict(String theContentType) {
 		return ourContentTypeToEncodingStrict.get(theContentType);
 	}
 
-	public static boolean isNonLegacy(String theFormat) {
+	/**
-		return ourContentTypeToEncodingNonLegacy.containsKey(theFormat);
+	 * Is the given type a FHIR legacy (pre-DSTU3) content type?
+	 */
+	public static boolean isLegacy(String theFormat) {
+		return ourContentTypeToEncodingLegacy.containsKey(theFormat);
 	}
 
-	
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IHttpResponse.java

@@ -20,6 +20,8 @@ package ca.uhn.fhir.rest.client.api;
  * #L%
  */
 
+import ca.uhn.fhir.util.StopWatch;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.Reader;
@@ -57,7 +59,7 @@ public interface IHttpResponse {
 	 * <p>
 	 * Buffering the message entity data allows for multiple invocations of
 	 * {@code readEntity(...)} methods on the response instance.
-	 * 
+	 *
 	 * @since 2.2
 	 */
 	void bufferEntity() throws IOException;
@@ -65,31 +67,40 @@ public interface IHttpResponse {
 	/**
 	 * Close the response
 	 */
-	public void close();
+	void close();
 
 	/**
 	 * Returna reader for the response entity
 	 */
-	public Reader createReader() throws IOException;
+	Reader createReader() throws IOException;
 
 	/**
 	 * Get map of the response headers and corresponding string values.
-	 * 
+	 *
 	 * @return response headers as a map header keys and they values.
 	 */
-	public Map<String, List<String>> getAllHeaders();
+	Map<String, List<String>> getAllHeaders();
 
 	/**
-	 * Return all headers in the response with the given type 
+	 * Return all headers in the response with the given type
 	 */
-	public List<String> getHeaders(String theName);
+	List<String> getHeaders(String theName);
 
 	/**
 	 * Extracts {@code Content-Type} value from the response exactly as
 	 * specified by the {@code Content-Type} header. Returns {@code null}
 	 * if not specified.
 	 */
-	public String getMimeType();
+	String getMimeType();
+
+	/**
+	 * @return Returns a StopWatch that was started right before
+	 * the client request was started. The time returned by this
+	 * client includes any time that was spent within the HTTP
+	 * library (possibly including waiting for a connection, and
+	 * any network activity)
+	 */
+	StopWatch getRequestStopWatch();
 
 	/**
 	 * @return the native response, depending on the client library used
@@ -98,21 +109,20 @@ public interface IHttpResponse {
 
 	/**
 	 * Get the status code associated with the response.
-	 * 
+	 *
 	 * @return the response status code.
 	 */
-	public int getStatus();
+	int getStatus();
 
 	/**
 	 * Get the response status information reason phrase associated with the response.
-	 * 
+	 *
 	 * @return the reason phrase.
 	 */
-	public String getStatusInfo();
+	String getStatusInfo();
 
 	/**
 	 * Read the message entity input stream as an InputStream.
 	 */
-	public InputStream readEntity() throws IOException;
+	InputStream readEntity() throws IOException;
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseAndListParam.java

@@ -20,25 +20,32 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
-import java.util.ArrayList;
-import java.util.List;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public abstract class BaseAndListParam<T extends IQueryParameterOr<?>> implements IQueryParameterAnd<T> {
 
-	private List<T> myValues=new ArrayList<T>(); 
+	private List<T> myValues = new ArrayList<>();
-	
+
+	public abstract BaseAndListParam<T> addAnd(T theValue);
+
 	public BaseAndListParam<T> addValue(T theValue) {
 		myValues.add(theValue);
 		return this;
 	}
-	
+
-	public abstract BaseAndListParam<T> addAnd(T theValue);
+	@Override
+	public List<T> getValuesAsQueryTokens() {
+		return myValues;
+	}
+
+	abstract T newInstance();
 
 	@Override
 	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, List<QualifiedParamList> theParameters) throws InvalidRequestException {
@@ -50,11 +57,9 @@ public abstract class BaseAndListParam<T extends IQueryParameterOr<?>> implement
 		}
 	}
 
-	abstract T newInstance();
-
 	@Override
-	public List<T> getValuesAsQueryTokens() {
+	public String toString() {
-		return myValues;
+		return myValues.toString();
 	}
 
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseOrListParam.java

@@ -20,23 +20,35 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
-import java.util.ArrayList;
-import java.util.List;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 
+import java.util.ArrayList;
+import java.util.List;
+
 abstract class BaseOrListParam<MT extends BaseOrListParam<?, ?>, PT extends IQueryParameterType> implements IQueryParameterOr<PT> {
 
-	private List<PT> myList=new ArrayList<PT>();
+	private List<PT> myList = new ArrayList<>();
+
+	@SuppressWarnings("unchecked")
+	public MT add(PT theParameter) {
+		if (theParameter != null) {
+			myList.add(theParameter);
+		}
+		return (MT) this;
+	}
+
+	public abstract MT addOr(PT theParameter);
+
+	@Override
+	public List<PT> getValuesAsQueryTokens() {
+		return myList;
+	}
+
+	abstract PT newInstance();
 
-//	public void addToken(T theParam) {
-//		Validate.notNull(theParam,"Param can not be null");
-//		myList.add(theParam);
-//	}
-	
 	@Override
 	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, QualifiedParamList theParameters) {
 		myList.clear();
@@ -47,21 +59,9 @@ abstract class BaseOrListParam<MT extends BaseOrListParam<?, ?>, PT extends IQue
 		}
 	}
 
-	abstract PT newInstance();
-
-	public abstract MT addOr(PT theParameter);
-	
-	@SuppressWarnings("unchecked")
-	public MT add(PT theParameter) {
-		if (theParameter != null) {
-			myList.add(theParameter);
-		}
-		return (MT) this;
-	}
-	
 	@Override
-	public List<PT> getValuesAsQueryTokens() {
+	public String toString() {
-		return myList;
+		return myList.toString();
 	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseParamWithPrefix.java

@@ -107,5 +107,4 @@ public abstract class BaseParamWithPrefix<T extends BaseParam> extends BaseParam
 		myPrefix = thePrefix;
 		return (T) this;
 	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateParam.java

@@ -20,21 +20,26 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.context.FhirContext;
-
+import ca.uhn.fhir.model.api.IQueryParameterOr;
-import java.util.*;
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
-
+import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
+import ca.uhn.fhir.model.primitive.DateDt;
+import ca.uhn.fhir.model.primitive.DateTimeDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.api.QualifiedParamList;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.util.Collections;
-import ca.uhn.fhir.model.api.IQueryParameterOr;
+import java.util.Date;
-import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import java.util.List;
-import ca.uhn.fhir.model.primitive.*;
+import java.util.Objects;
-import ca.uhn.fhir.rest.api.QualifiedParamList;
+
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import ca.uhn.fhir.util.ValidateUtil;
 
 public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQueryParameterType , */IQueryParameterOr<DateParam> {
 
@@ -222,6 +227,23 @@ public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQuer
 		
 	}
 
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == this) {
+			return true;
+		}
+		if (!(obj instanceof DateParam)) {
+			return false;
+		}
+		DateParam other = (DateParam) obj;
+		return	Objects.equals(getValue(), other.getValue()) &&
+					Objects.equals(getPrefix(), other.getPrefix());
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(getValue(), getPrefix());
+	}
 
 	@Override
 	public String toString() {
@@ -241,8 +263,5 @@ public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQuer
 		protected boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision) {
 			return true;
 		}
-
 	}
-
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java

@@ -413,6 +413,24 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 
 	}
 
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == this) {
+			return true;
+		}
+		if (!(obj instanceof DateRangeParam)) {
+			return false;
+		}
+		DateRangeParam other = (DateRangeParam) obj;
+		return	Objects.equals(myLowerBound, other.myLowerBound) &&
+					Objects.equals(myUpperBound, other.myUpperBound);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(myLowerBound, myUpperBound);
+	}
+
 	@Override
 	public String toString() {
 		StringBuilder b = new StringBuilder();
@@ -484,7 +502,5 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 				throw new DataFormatException("Upper bound comparator must be < or <=, can not be " + myUpperBound.getPrefix().getValue());
 			}
 		}
-
 	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java

@@ -32,9 +32,9 @@ import java.util.List;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  * http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -192,10 +192,10 @@ public class ParameterUtil {
 	}
 
 	public static Object fromInteger(Class<?> theType, IntegerDt theArgument) {
+		if (theArgument == null) {
+			return null;
+		}
 		if (theType.equals(Integer.class)) {
-			if (theArgument == null) {
-				return null;
-			}
 			return theArgument.getValue();
 		}
 		IPrimitiveType<?> retVal = (IPrimitiveType<?>) ReflectionUtil.newInstance(theType);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java

@@ -104,24 +104,33 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
 	void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
 		String q = theQualifier;
 		String resourceType = null;
+		boolean skipSetValue = false;
 		if (isNotBlank(q)) {
 			if (q.startsWith(":")) {
 				int nextIdx = q.indexOf('.');
 				if (nextIdx != -1) {
 					resourceType = q.substring(1, nextIdx);
 					myChain = q.substring(nextIdx + 1);
+					// type is explicitly defined so use it
+					myId.setParts(null, resourceType, theValue, null);
+					skipSetValue = true;
 				} else {
 					resourceType = q.substring(1);
 				}
 			} else if (q.startsWith(".")) {
 				myChain = q.substring(1);
+				// type not defined but this is a chain, so treat value as opaque
+				myId.setParts(null, null, theValue, null);
+				skipSetValue = true;
 			}
 		}
 
-		setValue(theValue);
+		if (!skipSetValue) {
+			setValue(theValue);
 
-		if (isNotBlank(resourceType) && isBlank(getResourceType())) {
+			if (isNotBlank(resourceType) && isBlank(getResourceType())) {
-			setValue(resourceType + '/' + theValue);
+				setValue(resourceType + '/' + theValue);
+			}
 		}
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/TokenOrListParam.java

@@ -69,14 +69,12 @@ public class TokenOrListParam extends BaseOrListParam<TokenOrListParam, TokenPar
 
 	/**
 	 * Add a new token to this list
-	 * 
+	 *  @param theSystem
-	 * @param theSystem
 	 *            The system to use for the one token to pre-populate in this list
-	 * @param theValue
-	 *            The value to use for the one token to pre-populate in this list
 	 */
-	public void add(String theSystem, String theValue) {
+	public TokenOrListParam add(String theSystem, String theValue) {
 		add(new TokenParam(theSystem, theValue));
+		return this;
 	}
 
 	public List<BaseCodingDt> getListAsCodings() {

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

@@ -36,6 +36,45 @@ import ca.uhn.fhir.rest.api.RequestTypeEnum;
  */
 public class BundleUtil {
 
+	/**
+	 * @return Returns <code>null</code> if the link isn't found or has no value
+	 */
+	public static String getLinkUrlOfType(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation) {
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
+		BaseRuntimeChildDefinition entryChild = def.getChildByName("link");
+		List<IBase> links = entryChild.getAccessor().getValues(theBundle);
+		for (IBase nextLink : links) {
+
+			boolean isRightRel = false;
+			BaseRuntimeElementCompositeDefinition relDef = (BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
+			BaseRuntimeChildDefinition relChild = relDef.getChildByName("relation");
+			List<IBase> relValues = relChild.getAccessor().getValues(nextLink);
+			for (IBase next : relValues) {
+				IPrimitiveType<?> nextValue = (IPrimitiveType<?>)next;
+				if (theLinkRelation.equals(nextValue.getValueAsString())) {
+					isRightRel = true;
+				}
+			}
+
+			if (!isRightRel) {
+				continue;
+			}
+
+			BaseRuntimeElementCompositeDefinition linkDef = (BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
+			BaseRuntimeChildDefinition urlChild = linkDef.getChildByName("url");
+			List<IBase> values = urlChild.getAccessor().getValues(nextLink);
+			for (IBase nextUrl : values) {
+				IPrimitiveType<?> nextValue = (IPrimitiveType<?>)nextUrl;
+				if (isNotBlank(nextValue.getValueAsString())) {
+					return nextValue.getValueAsString();
+				}
+			}
+
+		}
+
+		return null;
+	}
+
 	@SuppressWarnings("unchecked")
 	public static List<Pair<String, IBaseResource>> getBundleEntryUrlsAndResources(FhirContext theContext, IBaseBundle theBundle) {
 		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
@@ -50,7 +89,7 @@ public class BundleUtil {
 		
 		BaseRuntimeChildDefinition urlChild = requestDef.getChildByName("url");
 
-		List<Pair<String, IBaseResource>> retVal = new ArrayList<Pair<String,IBaseResource>>(entries.size());
+		List<Pair<String, IBaseResource>> retVal = new ArrayList<>(entries.size());
 		for (IBase nextEntry : entries) {
 			
 			String url = null;
@@ -88,7 +127,7 @@ public class BundleUtil {
 	 * Extract all of the resources from a given bundle
 	 */
 	public static List<BundleEntryParts> toListOfEntries(FhirContext theContext, IBaseBundle theBundle) {
-		List<BundleEntryParts> retVal = new ArrayList<BundleEntryParts>();
+		List<BundleEntryParts> retVal = new ArrayList<>();
 
 		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
 		BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
@@ -145,7 +184,7 @@ public class BundleUtil {
 	 */
 	@SuppressWarnings("unchecked")
 	public static <T extends IBaseResource> List<T> toListOfResourcesOfType(FhirContext theContext, IBaseBundle theBundle, Class<T> theTypeToInclude) {
-		List<T> retVal = new ArrayList<T>();
+		List<T> retVal = new ArrayList<>();
 
 		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
 		BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
@@ -170,7 +209,7 @@ public class BundleUtil {
 		private final RequestTypeEnum myRequestType;
 		private final IBaseResource myResource;
 		private final String myUrl;
-		public BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource) {
+		BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource) {
 			super();
 			myRequestType = theRequestType;
 			myUrl = theUrl;

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

@@ -20,25 +20,23 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-
-import ca.uhn.fhir.model.primitive.StringDt;
-
 public class DatatypeUtil {
 
 	/**
 	 * Convert a list of FHIR String objects to a set of native java Strings
 	 */
-	public static Set<String> toStringSet(List<StringDt> theStringList) {
+	public static Set<String> toStringSet(List<? extends IPrimitiveType<?>> theStringList) {
-		HashSet<String> retVal = new HashSet<String>();
+		HashSet<String> retVal = new HashSet<>();
 		if (theStringList != null) {
-			for (StringDt string : theStringList) {
+			for (IPrimitiveType<?> string : theStringList) {
 				if (string != null && string.getValue()!=null) {
-					retVal.add(string.getValue());
+					retVal.add(string.getValueAsString());
 				}
 			}
 		}

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

@@ -0,0 +1,52 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class SearchParameterUtil {
+
+	public static List<String> getBaseAsStrings(FhirContext theContext, IBaseResource theResource) {
+		Validate.notNull(theContext, "theContext must not be null");
+		Validate.notNull(theResource, "theResource must not be null");
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theResource);
+
+		BaseRuntimeChildDefinition base = def.getChildByName("base");
+		List<IBase> baseValues = base.getAccessor().getValues(theResource);
+		List<String> retVal = new ArrayList<>();
+		for (IBase next : baseValues) {
+			IPrimitiveType<?> nextPrimitive = (IPrimitiveType<?>) next;
+			retVal.add(nextPrimitive.getValueAsString());
+		}
+
+		return retVal;
+	}
+
+}

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

@@ -0,0 +1,202 @@
+package ca.uhn.fhir.util;
+
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.time.DateUtils;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.Date;
+import java.util.concurrent.TimeUnit;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+/**
+ * @since HAPI FHIR 3.3.0
+ */
+public class StopWatch {
+
+	private static final NumberFormat DAY_FORMAT = new DecimalFormat("0.0");
+	private static final NumberFormat TEN_DAY_FORMAT = new DecimalFormat("0");
+	private static Long ourNowForUnitTest;
+	private long myStarted = now();
+
+	/**
+	 * Constructor
+	 */
+	public StopWatch() {
+		super();
+	}
+
+	/**
+	 * Constructor
+	 *
+	 * @param theStart The time to record as the start for this timer
+	 */
+	public StopWatch(Date theStart) {
+		myStarted = theStart.getTime();
+	}
+
+	public String formatThroughput(int theNumOperations, TimeUnit theUnit) {
+		double throughput = getThroughput(theNumOperations, theUnit);
+		return new DecimalFormat("0.0").format(throughput);
+	}
+
+	/**
+	 * Given an amount of something completed so far, and a total amount, calculates how long it will take for something to complete
+	 *
+	 * @param theCompleteToDate The amount so far
+	 * @param theTotal          The total (must be higher than theCompleteToDate
+	 * @return A formatted amount of time
+	 */
+	public String getEstimatedTimeRemaining(double theCompleteToDate, double theTotal) {
+		double millis = getMillis();
+		long millisRemaining = (long) (((theTotal / theCompleteToDate) * millis) - (millis));
+		return formatMillis(millisRemaining);
+	}
+
+	public long getMillis(Date theNow) {
+		return theNow.getTime() - myStarted;
+	}
+
+	public long getMillis() {
+		long now = now();
+		return now - myStarted;
+	}
+
+	public long getMillisAndRestart() {
+		long now = now();
+		long retVal = now - myStarted;
+		myStarted = now;
+		return retVal;
+	}
+
+	/**
+	 * @param theNumOperations Ok for this to be 0, it will be treated as 1
+	 */
+	public int getMillisPerOperation(int theNumOperations) {
+		return (int) (((double) getMillis()) / Math.max(1.0, theNumOperations));
+	}
+
+	public Date getStartedDate() {
+		return new Date(myStarted);
+	}
+
+	public double getThroughput(int theNumOperations, TimeUnit theUnit) {
+		if (theNumOperations <= 0) {
+			return 0.0f;
+		}
+
+		long millisElapsed = Math.max(1, getMillis());
+		long periodMillis = theUnit.toMillis(1);
+
+		double numerator = theNumOperations;
+		double denominator = ((double) millisElapsed) / ((double) periodMillis);
+
+		return numerator / denominator;
+	}
+
+	public void restart() {
+		myStarted = now();
+	}
+
+	/**
+	 * Formats value in an appropriate format. See {@link #formatMillis(long)}}
+	 * for a description of the format
+	 *
+	 * @see #formatMillis(long)
+	 */
+	@Override
+	public String toString() {
+		return formatMillis(getMillis());
+	}
+
+	/**
+	 * Append a right-aligned and zero-padded numeric value to a `StringBuilder`.
+	 */
+	static private void append(StringBuilder tgt, String pfx, int dgt, long val) {
+		tgt.append(pfx);
+		if (dgt > 1) {
+			int pad = (dgt - 1);
+			for (long xa = val; xa > 9 && pad > 0; xa /= 10) {
+				pad--;
+			}
+			for (int xa = 0; xa < pad; xa++) {
+				tgt.append('0');
+			}
+		}
+		tgt.append(val);
+	}
+
+	/**
+	 * Formats a number of milliseconds for display (e.g.
+	 * in a log file), tailoring the output to how big
+	 * the value actually is.
+	 * <p>
+	 * Example outputs:
+	 * </p>
+	 * <ul>
+	 * <li>133ms</li>
+	 * <li>00:00:10.223</li>
+	 * <li>1.7 days</li>
+	 * <li>64 days</li>
+	 * </ul>
+	 */
+	public static String formatMillis(long val) {
+		StringBuilder buf = new StringBuilder(20);
+		if (val < (10 * DateUtils.MILLIS_PER_SECOND)) {
+			buf.append(val);
+			buf.append("ms");
+		} else if (val >= DateUtils.MILLIS_PER_DAY) {
+			double days = (double) val / DateUtils.MILLIS_PER_DAY;
+			if (days >= 10) {
+				buf.append(TEN_DAY_FORMAT.format(days));
+				buf.append(" days");
+			} else if (days != 1.0f) {
+				buf.append(DAY_FORMAT.format(days));
+				buf.append(" days");
+			} else {
+				buf.append(DAY_FORMAT.format(days));
+				buf.append(" day");
+			}
+		} else {
+			append(buf, "", 2, ((val % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
+			append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
+			append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
+			if (val <= DateUtils.MILLIS_PER_MINUTE) {
+				append(buf, ".", 3, (val % DateUtils.MILLIS_PER_SECOND));
+			}
+		}
+		return buf.toString();
+	}
+
+	private static long now() {
+		if (ourNowForUnitTest != null) {
+			return ourNowForUnitTest;
+		}
+		return System.currentTimeMillis();
+	}
+
+	@VisibleForTesting
+	static void setNowForUnitTestForUnitTest(Long theNowForUnitTest) {
+		ourNowForUnitTest = theNowForUnitTest;
+	}
+
+}

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

@@ -0,0 +1,64 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.thymeleaf.util.Validate;
+
+import java.util.List;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+/**
+ * Utilities for working with the subscription resource
+ */
+public class SubscriptionUtil {
+
+	private static void populatePrimitiveValue(FhirContext theContext, IBaseResource theSubscription, String theChildName, String theValue) {
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theSubscription);
+		Validate.isTrue(def.getName().equals("Subscription"), "theResource is not a subscription");
+		BaseRuntimeChildDefinition statusChild = def.getChildByName(theChildName);
+		List<IBase> entries = statusChild.getAccessor().getValues(theSubscription);
+		IPrimitiveType<?> instance;
+		if (entries.size() == 0) {
+			BaseRuntimeElementDefinition<?> statusElement = statusChild.getChildByName(theChildName);
+			instance = (IPrimitiveType<?>) statusElement.newInstance(statusChild.getInstanceConstructorArguments());
+			statusChild.getMutator().addValue(theSubscription, instance);
+		} else {
+			instance = (IPrimitiveType<?>) entries.get(0);
+		}
+
+		instance.setValueAsString(theValue);
+	}
+
+	public static void setReason(FhirContext theContext, IBaseResource theSubscription, String theMessage) {
+		populatePrimitiveValue(theContext, theSubscription, "reason", theMessage);
+	}
+
+	public static void setStatus(FhirContext theContext, IBaseResource theSubscription, String theStatus) {
+		populatePrimitiveValue(theContext, theSubscription, "status", theStatus);
+	}
+
+}

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseResource.java

@@ -44,12 +44,12 @@ public interface IBaseResource extends IBase, IElement {
 	/**
 	 * Include constant for <code>*</code> (return all includes)
 	 */
-	public static final Include INCLUDE_ALL = new Include("*", false).toLocked();
+	Include INCLUDE_ALL = new Include("*", false).toLocked();
 
 	/**
 	 * Include set containing only {@link #INCLUDE_ALL}
 	 */
-	public static final Set<Include> WILDCARD_ALL_SET = Collections.unmodifiableSet(new HashSet<Include>(Arrays.asList(INCLUDE_ALL)));
+	Set<Include> WILDCARD_ALL_SET = Collections.unmodifiableSet(new HashSet<>(Arrays.asList(INCLUDE_ALL)));
 
 	IIdType getIdElement();
 	

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -49,6 +49,7 @@ ca.uhn.fhir.parser.ParserState.wrongResourceTypeFound=Incorrect resource type fo
 ca.uhn.fhir.rest.server.RestfulServer.getPagesNonHttpGet=Requests for _getpages must use HTTP GET
 ca.uhn.fhir.rest.server.RestfulServer.unknownMethod=Invalid request: The FHIR endpoint on this server does not know how to handle {0} operation[{1}] with parameters [{2}]
 ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR server. Unable to handle this request, as it does not contain a resource type or operation name.
+ca.uhn.fhir.rest.server.RestfulServer.rootRequest.multitenant=This is the base URL of a multitenant FHIR server. Unable to handle this request, as it does not contain a tenant ID.
 ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body? 
 ca.uhn.fhir.validation.FhirValidator.noPhlocWarningOnStartup=Phloc-schematron library not found on classpath, will not attempt to perform schematron validation
 ca.uhn.fhir.validation.FhirValidator.noPhlocError=Phloc-schematron library not found on classpath, can not enable perform schematron validation
@@ -94,4 +95,3 @@ ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.cannotCreateDuplicateCodeSystemUri=C
 ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 
-  

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopWatchTest.java

@@ -0,0 +1,195 @@
+package ca.uhn.fhir.util;
+
+import org.apache.commons.lang3.time.DateUtils;
+import org.hamcrest.Matchers;
+import org.junit.After;
+import org.junit.Test;
+
+import java.util.Date;
+import java.util.concurrent.TimeUnit;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+public class StopWatchTest {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StopWatchTest.class);
+
+	@After
+	public void after() {
+		StopWatch.setNowForUnitTestForUnitTest(null);
+	}
+
+	private double calculateThroughput(int theMinutesElapsed, int theNumOperations) {
+		StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -theMinutesElapsed));
+		double throughput = sw.getThroughput(theNumOperations, TimeUnit.MINUTES);
+		ourLog.info("{} operations in {}ms = {} ops / second", theNumOperations, sw.getMillis(), throughput);
+		return throughput;
+	}
+
+	@Test
+	public void testEstimatedTimeRemainingOutOfOne() {
+		StopWatch.setNowForUnitTestForUnitTest(777777777L);
+		StopWatch sw = new StopWatch();
+
+		// Less than half
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:09:00", sw.getEstimatedTimeRemaining(0.1, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:09:00", sw.getEstimatedTimeRemaining(1, 10));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE + 100);
+		assertEquals("00:09:00", sw.getEstimatedTimeRemaining(0.1, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:19:00", sw.getEstimatedTimeRemaining(0.05, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:39:00", sw.getEstimatedTimeRemaining(0.025, 1.0));
+
+		// More than half
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:01:00.000", sw.getEstimatedTimeRemaining(0.5, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:00:59.760", sw.getEstimatedTimeRemaining(0.501, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("00:00:40.000", sw.getEstimatedTimeRemaining(0.6, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("6666ms", sw.getEstimatedTimeRemaining(0.9, 1.0));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
+		assertEquals("60ms", sw.getEstimatedTimeRemaining(0.999, 1.0));
+
+	}
+
+	@Test
+	public void testEstimatedTimeRemainingOutOfOneHundred() {
+		StopWatch.setNowForUnitTestForUnitTest(777777777L);
+		StopWatch sw = new StopWatch();
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (10 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("01:30:00", sw.getEstimatedTimeRemaining(10, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("00:04:00", sw.getEstimatedTimeRemaining(20, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (30 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("01:10:00", sw.getEstimatedTimeRemaining(30, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (40 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("01:00:00", sw.getEstimatedTimeRemaining(40, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (50 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("00:50:00", sw.getEstimatedTimeRemaining(50, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (60 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("00:40:00", sw.getEstimatedTimeRemaining(60, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (60 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("00:00:36.363", sw.getEstimatedTimeRemaining(99, 100));
+
+		StopWatch.setNowForUnitTestForUnitTest(777777777L + (60 * DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("360ms", sw.getEstimatedTimeRemaining(99.99, 100));
+
+	}
+
+	@Test
+	public void testFormatMillis() {
+		assertEquals("1000ms", StopWatch.formatMillis(DateUtils.MILLIS_PER_SECOND));
+		assertEquals("00:01:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE));
+		assertEquals("00:01:01", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE + DateUtils.MILLIS_PER_SECOND));
+		assertEquals("01:00:00", StopWatch.formatMillis(DateUtils.MILLIS_PER_HOUR));
+		assertEquals("1.0 day", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY));
+		assertEquals("2.0 days", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY * 2));
+		assertEquals("2.0 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + 1));
+		assertEquals("2.4 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + (10 * DateUtils.MILLIS_PER_HOUR)));
+		assertEquals("11 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 11) + (10 * DateUtils.MILLIS_PER_HOUR)));
+	}
+
+	@Test
+	public void testFormatThroughput60Ops4Min() {
+		StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
+		String throughput = sw.formatThroughput(60, TimeUnit.MINUTES);
+		ourLog.info("{} operations in {}ms = {} ops / second", 60, sw.getMillis(), throughput);
+		assertThat(throughput, oneOf("14.9", "15.0", "15.1", "14,9", "15,0", "15,1"));
+	}
+
+	@Test
+	public void testMillisPerOperation() {
+		int minutes = 60;
+		StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -minutes));
+		int numOperations = 60;
+		int millis = sw.getMillisPerOperation(numOperations);
+		ourLog.info("{} operations in {}ms = {}ms / operation", numOperations, minutes * DateUtils.MILLIS_PER_MINUTE, millis);
+
+		assertThat(millis, Matchers.lessThan(62000));
+		assertThat(millis, Matchers.greaterThan(58000));
+	}
+
+	@Test
+	public void testOperationThroughput30Ops1Min() {
+		double throughput = calculateThroughput(1, 30);
+		assertThat(throughput, greaterThan(29.0));
+		assertThat(throughput, lessThan(31.0));
+	}
+
+	@Test
+	public void testOperationThroughput60Ops1Min() {
+		double throughput = calculateThroughput(1, 60);
+		assertThat(throughput, greaterThan(59.0));
+		assertThat(throughput, lessThan(61.0));
+	}
+
+	@Test
+	public void testOperationThroughput60Ops4Min() {
+		double throughput = calculateThroughput(4, 60);
+		assertThat(throughput, greaterThan(14.0));
+		assertThat(throughput, lessThan(16.0));
+	}
+
+	@Test
+	public void testRestart() throws InterruptedException {
+		StopWatch sw = new StopWatch();
+		Thread.sleep(500);
+		sw.restart();
+		assertThat(sw.getMillis(), lessThan(100L));
+	}
+
+	@Test
+	public void testStopwatch() throws Exception {
+		StopWatch sw = new StopWatch();
+
+		Thread.sleep(100);
+
+		assertThat(sw.getMillis(new Date()), greaterThan(10L));
+		assertThat(sw.getMillis(), greaterThan(10L));
+		assertThat(sw.getStartedDate().getTime(), lessThan(System.currentTimeMillis()));
+	}
+
+	@Test
+	public void testStopwatchWithDate() throws Exception {
+		StopWatch sw = new StopWatch(new Date());
+
+		Thread.sleep(100);
+
+		assertThat(sw.getMillis(new Date()), greaterThan(10L));
+		assertThat(sw.getMillis(), greaterThan(10L));
+		assertThat(sw.getStartedDate().getTime(), lessThan(System.currentTimeMillis()));
+	}
+
+	@Test
+	public void testToString() throws Exception {
+		StopWatch sw = new StopWatch();
+
+		Thread.sleep(100);
+
+		String string = sw.toString();
+		ourLog.info(string);
+		assertThat(string, matchesPattern("^[0-9]{3,4}ms$"));
+	}
+
+}

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -191,6 +191,23 @@
 			<artifactId>phloc-commons</artifactId>
 		</dependency>
 
+		<!--
+		These have been added as explicit dependencies
+		as JDK9 no longer includes them by default
+		-->
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.fusesource.jansi</groupId>
 			<artifactId>jansi</artifactId>

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
 import ca.uhn.fhir.model.dstu2.resource.ValueSet;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
@@ -163,7 +164,7 @@ public class ValidationDataUploader extends BaseCommand {
 			ValueSet next = (ValueSet) i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 
 			count++;
@@ -182,7 +183,7 @@ public class ValidationDataUploader extends BaseCommand {
 			ValueSet next = (ValueSet) i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 
 			count++;
@@ -200,7 +201,7 @@ public class ValidationDataUploader extends BaseCommand {
 			ValueSet next = (ValueSet) i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 			count++;
 		}
@@ -225,7 +226,7 @@ public class ValidationDataUploader extends BaseCommand {
 			}
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading StructureDefinition {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading StructureDefinition {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			try {
 				client.update().resource(next).execute();
 			} catch (Exception e) {
@@ -268,12 +269,14 @@ public class ValidationDataUploader extends BaseCommand {
 
 			int bytes = ctx.newXmlParser().encodeResourceToString(next).length();
 
-			ourLog.info("Uploading ValueSet {}/{} : {} ({} bytes}", new Object[]{count, total, next.getIdElement().getValue(), bytes});
+			ourLog.info("Uploading ValueSet {}/{} : {} ({} bytes}", new Object[] {count, total, next.getIdElement().getValue(), bytes});
 			try {
 				IIdType id = client.update().resource(next).execute().getId();
 				ourLog.info("  - Got ID: {}", id.getValue());
 			} catch (UnprocessableEntityException e) {
 				ourLog.warn("UnprocessableEntityException: " + e.toString());
+			} catch (BaseServerResponseException e) {
+				ourLog.warn("Server responded HTTP " + e.getStatusCode() + ": " + e.toString());
 			}
 			count++;
 		}
@@ -293,7 +296,7 @@ public class ValidationDataUploader extends BaseCommand {
 			org.hl7.fhir.dstu3.model.Resource next = i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			try {
 				client.update().resource(next).execute();
 			} catch (Exception e) {
@@ -318,7 +321,7 @@ public class ValidationDataUploader extends BaseCommand {
 			}
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 			count++;
 		}
@@ -364,7 +367,7 @@ public class ValidationDataUploader extends BaseCommand {
 
 			int bytes = theCtx.newXmlParser().encodeResourceToString(next).length();
 
-			ourLog.info("Uploading ValueSet {}/{} : {} ({} bytes}", new Object[]{count, total, next.getIdElement().getValue(), bytes});
+			ourLog.info("Uploading ValueSet {}/{} : {} ({} bytes}", new Object[] {count, total, next.getIdElement().getValue(), bytes});
 			try {
 				IIdType id = client.update().resource(next).execute().getId();
 				ourLog.info("  - Got ID: {}", id.getValue());
@@ -388,7 +391,7 @@ public class ValidationDataUploader extends BaseCommand {
 			org.hl7.fhir.r4.model.Resource next = i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 
 			count++;
@@ -410,7 +413,7 @@ public class ValidationDataUploader extends BaseCommand {
 			}
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
-			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[]{count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[] {count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 			count++;
 		}
@@ -470,7 +473,7 @@ public class ValidationDataUploader extends BaseCommand {
 				continue;
 			}
 
-			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[]{name, count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {name, count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 
 			count++;
@@ -518,8 +521,12 @@ public class ValidationDataUploader extends BaseCommand {
 				continue;
 			}
 
-			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[]{name, count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {name, count, total, next.getIdElement().getValue()});
-			client.update().resource(next).execute();
+			try {
+				client.update().resource(next).execute();
+			} catch (BaseServerResponseException e) {
+				ourLog.warn("Server responded HTTP " + e.getStatusCode() + ": " + e.toString());
+			}
 
 			count++;
 		}

hapi-fhir-client-okhttp/src/main/java/ca/uhn/fhir/okhttp/client/OkHttpRestfulRequest.java

@@ -27,6 +27,7 @@ import java.util.Map;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.client.api.IHttpRequest;
 import ca.uhn.fhir.rest.client.api.IHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
 import okhttp3.Call;
 import okhttp3.Call.Factory;
 import okhttp3.Request;
@@ -65,9 +66,10 @@ public class OkHttpRestfulRequest implements IHttpRequest {
 
     @Override
     public IHttpResponse execute() throws IOException {
-        myRequestBuilder.method(getHttpVerbName(), myRequestBody);
+		 StopWatch responseStopWatch = new StopWatch();
-        Call call = myClient.newCall(myRequestBuilder.build());
+		 myRequestBuilder.method(getHttpVerbName(), myRequestBody);
-        return new OkHttpRestfulResponse(call.execute());
+		 Call call = myClient.newCall(myRequestBuilder.build());
+		 return new OkHttpRestfulResponse(call.execute(), responseStopWatch);
     }
 
     @Override

hapi-fhir-client-okhttp/src/main/java/ca/uhn/fhir/okhttp/client/OkHttpRestfulResponse.java

@@ -4,6 +4,8 @@ import java.io.*;
 import java.util.List;
 import java.util.Map;
 
+import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
 import org.apache.commons.io.IOUtils;
 
 import ca.uhn.fhir.rest.api.Constants;
@@ -38,13 +40,14 @@ import okhttp3.Response;
  *
  * @author Matthew Clarke | matthew.clarke@orionhealth.com | Orion Health
  */
-public class OkHttpRestfulResponse implements IHttpResponse {
+public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResponse {
 
 	private boolean myEntityBuffered = false;
 	private byte[] myEntityBytes;
 	private Response myResponse;
 
-	public OkHttpRestfulResponse(Response theResponse) {
+	public OkHttpRestfulResponse(Response theResponse, StopWatch theResponseStopWatch) {
+		super(theResponseStopWatch);
 		this.myResponse = theResponse;
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpRequest.java

@@ -27,10 +27,12 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
+import ca.uhn.fhir.util.StopWatch;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.Header;
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpEntityEnclosingRequest;
+import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpRequestBase;
 import org.apache.http.entity.ContentType;
@@ -61,7 +63,9 @@ public class ApacheHttpRequest implements IHttpRequest {
 
 	@Override
 	public IHttpResponse execute() throws IOException {
-		return new ApacheHttpResponse(myClient.execute(myRequest));
+		StopWatch responseStopWatch = new StopWatch();
+		HttpResponse httpResponse = myClient.execute(myRequest);
+		return new ApacheHttpResponse(httpResponse, responseStopWatch);
 	}
 
 	@Override

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpResponse.java

@@ -23,6 +23,8 @@ import java.io.*;
 import java.nio.charset.Charset;
 import java.util.*;
 
+import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.*;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -38,7 +40,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
  * 
  * @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
  */
-public class ApacheHttpResponse implements IHttpResponse {
+public class ApacheHttpResponse extends BaseHttpResponse implements IHttpResponse {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ApacheHttpResponse.class);
 
@@ -46,7 +48,8 @@ public class ApacheHttpResponse implements IHttpResponse {
 	private byte[] myEntityBytes;
 	private final HttpResponse myResponse;
 
-	public ApacheHttpResponse(HttpResponse theResponse) {
+	public ApacheHttpResponse(HttpResponse theResponse, StopWatch theResponseStopWatch) {
+		super(theResponseStopWatch);
 		this.myResponse = theResponse;
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/BaseHttpResponse.java

@@ -0,0 +1,37 @@
+package ca.uhn.fhir.rest.client.impl;
+
+/*-
+ * #%L
+ * HAPI FHIR - Client Framework
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.client.api.IHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
+
+public abstract class BaseHttpResponse implements IHttpResponse {
+	private final StopWatch myRequestStopWatch;
+
+	public BaseHttpResponse(StopWatch theRequestStopWatch) {
+		myRequestStopWatch = theRequestStopWatch;
+	}
+
+	@Override
+	public StopWatch getRequestStopWatch() {
+		return myRequestStopWatch;
+	}
+}

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/LoggingInterceptor.java

@@ -115,7 +115,9 @@ public class LoggingInterceptor implements IClientInterceptor {
 				}
 				respLocation = " (" + locationValue + ")";
 			}
-			myLog.info("Client response: {}{}", message, respLocation);
+
+			String timing = " in " + theResponse.getRequestStopWatch().toString();
+			myLog.info("Client response: {}{}{}", message, respLocation, timing);
 		}
 
 		if (myLogResponseHeaders) {

hapi-fhir-converter/pom.xml

@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -11,6 +12,119 @@
 	<artifactId>hapi-fhir-converter</artifactId>
 	<packaging>jar</packaging>
 
+	<dependencies>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+		</dependency>
+
+		<!-- Server -->
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-server</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu3</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-r4</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>3.3.0-SNAPSHOT</version>
+			<optional>true</optional>
+		</dependency>
+
+		<!-- Testing -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-client</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.xmlunit</groupId>
+			<artifactId>xmlunit-core</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlets</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlet</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-server</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-util</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-webapp</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-http</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+	</dependencies>
+
 	<name>HAPI FHIR - Converter</name>
 
 	<build>
@@ -21,48 +135,4 @@
 			</resource>
 		</resources>
 	</build>
-
-	<dependencies>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-base</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-structures-dstu3</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-structures-r4</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-			<dependency>
-					<groupId>ca.uhn.hapi.fhir</groupId>
-					<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-					<version>3.3.0-SNAPSHOT</version>
-					<optional>true</optional>
-			</dependency>
-	</dependencies>
 </project>

hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptor.java

@@ -0,0 +1,138 @@
+package ca.uhn.hapi.converters.server;
+
+/*-
+ * #%L
+ * HAPI FHIR - Converter
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.ResponseDetails;
+import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
+import org.hl7.fhir.convertors.*;
+import org.hl7.fhir.dstu3.model.Resource;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.util.StringTokenizer;
+
+import static org.apache.commons.lang3.StringUtils.*;
+
+/**
+ * <b>This is an experimental interceptor! Use with caution as
+ * behaviour may change or be removed in a future version of
+ * FHIR.</b>
+ * <p>
+ * This interceptor partially implements the proposed
+ * Versioned API features.
+ * </p>
+ */
+public class VersionedApiConverterInterceptor extends InterceptorAdapter {
+	private final FhirContext myCtxDstu2;
+	private final FhirContext myCtxDstu2Hl7Org;
+	private VersionConvertor_30_40 myVersionConvertor_30_40;
+	private VersionConvertor_10_40 myVersionConvertor_10_40;
+	private VersionConvertor_10_30 myVersionConvertor_10_30;
+
+	public VersionedApiConverterInterceptor() {
+		myVersionConvertor_30_40 = new VersionConvertor_30_40();
+		VersionConvertorAdvisor40 advisor40 = new NullVersionConverterAdvisor40();
+		myVersionConvertor_10_40 = new VersionConvertor_10_40(advisor40);
+		VersionConvertorAdvisor30 advisor30 = new NullVersionConverterAdvisor30();
+		myVersionConvertor_10_30 = new VersionConvertor_10_30(advisor30);
+
+		myCtxDstu2 = FhirContext.forDstu2();
+		myCtxDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
+	}
+
+	@Override
+	public boolean outgoingResponse(RequestDetails theRequestDetails, ResponseDetails theResponseDetails, HttpServletRequest theServletRequest, HttpServletResponse theServletResponse) throws AuthenticationException {
+		String[] formatParams = theRequestDetails.getParameters().get(Constants.PARAM_FORMAT);
+		String accept = null;
+		if (formatParams != null && formatParams.length > 0) {
+			accept = formatParams[0];
+		}
+		if (isBlank(accept)) {
+			accept = defaultString(theServletRequest.getHeader(Constants.HEADER_ACCEPT));
+		}
+		StringTokenizer tok = new StringTokenizer(accept, ";");
+		String wantVersionString = null;
+		while (tok.hasMoreTokens()) {
+			String next = tok.nextToken().trim();
+			if (next.startsWith("fhirVersion=")) {
+				wantVersionString = next.substring("fhirVersion=".length()).trim();
+				break;
+			}
+		}
+
+		FhirVersionEnum wantVersion = null;
+		if (isNotBlank(wantVersionString)) {
+			wantVersion = FhirVersionEnum.forVersionString(wantVersionString);
+		}
+
+		IBaseResource responseResource = theResponseDetails.getResponseResource();
+		FhirVersionEnum haveVersion = responseResource.getStructureFhirVersionEnum();
+
+		IBaseResource converted = null;
+		try {
+			if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
+				converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource));
+			} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
+				converted = myVersionConvertor_30_40.convertResource(toR4(responseResource));
+			} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
+				converted = myVersionConvertor_10_40.convertResource(toR4(responseResource));
+			} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {
+				converted = myVersionConvertor_10_40.convertResource(toDstu2(responseResource));
+			} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.DSTU3) {
+				converted = myVersionConvertor_10_30.convertResource(toDstu3(responseResource));
+			} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.DSTU2) {
+				converted = myVersionConvertor_10_30.convertResource(toDstu2(responseResource));
+			}
+		} catch (FHIRException e) {
+			throw new InternalErrorException(e);
+		}
+
+		if (converted != null) {
+			theResponseDetails.setResponseResource(converted);
+		}
+
+		return true;
+	}
+
+	private org.hl7.fhir.instance.model.Resource toDstu2(IBaseResource theResponseResource) {
+		if (theResponseResource instanceof IResource) {
+			return (org.hl7.fhir.instance.model.Resource) myCtxDstu2Hl7Org.newJsonParser().parseResource(myCtxDstu2.newJsonParser().encodeResourceToString(theResponseResource));
+		}
+		return (org.hl7.fhir.instance.model.Resource) theResponseResource;
+	}
+
+	private Resource toDstu3(IBaseResource theResponseResource) {
+		return (Resource) theResponseResource;
+	}
+
+	private org.hl7.fhir.r4.model.Resource toR4(IBaseResource theResponseResource) {
+		return (org.hl7.fhir.r4.model.Resource) theResponseResource;
+	}
+}

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/NullVersionConverterAdvisor40.java

@@ -0,0 +1,56 @@
+package org.hl7.fhir.convertors;
+
+/*
+ * #%L
+ * HAPI FHIR - Converter
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.Resource;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ValueSet;
+
+public class NullVersionConverterAdvisor40 implements VersionConvertorAdvisor40 {
+
+	@Override
+	public Resource convertR2(org.hl7.fhir.r4.model.Resource resource) throws FHIRException {
+		return null;
+	}
+
+	@Override
+	public org.hl7.fhir.dstu3.model.Resource convertR3(org.hl7.fhir.r4.model.Resource resource) throws FHIRException {
+		return null;
+	}
+
+	@Override
+	public CodeSystem getCodeSystem(ValueSet theSrc) {
+		return null;
+	}
+
+	@Override
+	public void handleCodeSystem(CodeSystem theTgtcs, ValueSet theSource) {
+		//nothing
+	}
+
+	@Override
+	public boolean ignoreEntry(BundleEntryComponent theSrc) {
+		return false;
+	}
+
+}

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertorConstants.java

@@ -0,0 +1,28 @@
+package org.hl7.fhir.convertors;
+
+/*-
+ * #%L
+ * HAPI FHIR - Converter
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+public class VersionConvertorConstants {
+
+  public final static String MODIFIER_REASON_EXTENSION = "http://hl7.org/fhir/tooling/StructureDefinition/r4ModifierReason";
+  public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
+}

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_30.java

@@ -26,7 +26,7 @@ import java.util.List;
 import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.instance.model.CodeableConcept;
 import org.hl7.fhir.instance.model.Reference;
-import org.hl7.fhir.dstu2.utils.ToolingExtensions;
+import org.hl7.fhir.instance.utils.ToolingExtensions;
 import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
 import org.hl7.fhir.dstu3.model.Annotation;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.SystemRestfulInteraction;
@@ -10974,7 +10974,7 @@ public class VersionConvertor_10_30 {
       tgt.setBase(t.asStringValue());
     tgt.setType(convertSearchParamType(src.getType()));
     tgt.setDescription(src.getDescription());
-    org.hl7.fhir.dstu2.utils.ToolingExtensions.setStringExtension(tgt, ToolingExtensions.EXT_EXPRESSION, src.getExpression());
+    org.hl7.fhir.instance.utils.ToolingExtensions.setStringExtension(tgt, ToolingExtensions.EXT_EXPRESSION, src.getExpression());
     tgt.setXpath(src.getXpath());
     tgt.setXpathUsage(convertXPathUsageType(src.getXpathUsage()));
     for (org.hl7.fhir.dstu3.model.CodeType t : src.getTarget())

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_40.java

@@ -20,6 +20,7 @@ package org.hl7.fhir.convertors;
  * #L%
  */
 
+
 /*
   Copyright (c) 2011+, HL7, Inc.
   All rights reserved.
@@ -54,19 +55,26 @@ package org.hl7.fhir.convertors;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.hl7.fhir.dstu2016may.model.BooleanType;
 import org.hl7.fhir.dstu2016may.model.CodeSystem.ConceptDefinitionPropertyComponent;
+import org.hl7.fhir.dstu2016may.model.Reference;
 import org.hl7.fhir.dstu2016may.model.CodeableConcept;
 import org.hl7.fhir.r4.conformance.ProfileUtilities;
+import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeSystem.FilterOperator;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
 import org.hl7.fhir.r4.model.ContactDetail;
+import org.hl7.fhir.r4.model.ElementDefinition;
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent;
 import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r4.model.Enumeration;
+import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemOperator;
 import org.hl7.fhir.r4.model.Timing.EventTiming;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.r4.model.UsageContext;
 import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent;
 import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
@@ -1225,7 +1233,7 @@ public class VersionConvertor_14_40 {
     if (src.hasContentReference())
       tgt.setContentReference(src.getContentReference());
     for (org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent t : src.getType())
-      tgt.addType(convertTypeRefComponent(t));
+      convertTypeRefComponent(t, tgt.getType());
     tgt.setDefaultValue(convertType(src.getDefaultValue()));
     if (src.hasMeaningWhenMissing())
       tgt.setMeaningWhenMissing(src.getMeaningWhenMissing());
@@ -1245,6 +1253,12 @@ public class VersionConvertor_14_40 {
       tgt.setMustSupport(src.getMustSupport());
     if (src.hasIsModifier())
       tgt.setIsModifier(src.getIsModifier());
+    if (tgt.getIsModifier()) {
+      String reason = org.hl7.fhir.dstu2016may.utils.ToolingExtensions.readStringExtension(src, VersionConvertorConstants.MODIFIER_REASON_EXTENSION);
+      if (Utilities.noString(reason))
+        reason = VersionConvertorConstants.MODIFIER_REASON_LEGACY;
+      tgt.setIsModifierReason(reason);
+    }
     if (src.hasIsSummary())
       tgt.setIsSummary(src.getIsSummary());
     tgt.setBinding(convertElementDefinitionBindingComponent(src.getBinding()));
@@ -1288,7 +1302,7 @@ public class VersionConvertor_14_40 {
     if (src.hasContentReference())
       tgt.setContentReference(src.getContentReference());
     for (org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent t : src.getType())
-      tgt.addType(convertTypeRefComponent(t));
+      convertTypeRefComponent(t, tgt.getType());
     tgt.setDefaultValue(convertType(src.getDefaultValue()));
     if (src.hasMeaningWhenMissing())
       tgt.setMeaningWhenMissing(src.getMeaningWhenMissing());
@@ -1308,6 +1322,8 @@ public class VersionConvertor_14_40 {
       tgt.setMustSupport(src.getMustSupport());
     if (src.hasIsModifier())
       tgt.setIsModifier(src.getIsModifier());
+    if (src.hasIsModifierReason() && !VersionConvertorConstants.MODIFIER_REASON_LEGACY.equals(src.getIsModifierReason()))
+        org.hl7.fhir.dstu2016may.utils.ToolingExtensions.setStringExtension(tgt, VersionConvertorConstants.MODIFIER_REASON_EXTENSION, src.getIsModifierReason());
     if (src.hasIsSummary())
       tgt.setIsSummary(src.getIsSummary());
     if (src.hasBinding())
@@ -1438,38 +1454,51 @@ public class VersionConvertor_14_40 {
     return tgt;
   }
 
-  public static org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent convertTypeRefComponent(org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent src) throws FHIRException {
+  static void convertTypeRefComponent(org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent src, List<org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent> list) throws FHIRException {
-    if (src == null || src.isEmpty())
+    if (src == null)
-      return null;
+      return ;
-    org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent tgt = new org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent();
+    org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent tgt = null;
-    copyElement(src, tgt);
+    for (org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent t : list)
-    tgt.setCode(src.getCode());
+      if (t.getCode().equals(src.getCode()))
-    for (org.hl7.fhir.dstu2016may.model.UriType t : src.getProfile()) {
+        tgt = t;
-      if (src.getCode().equals("Reference"))
+    if (tgt == null) {
-        tgt.setTargetProfile(t.getValueAsString());
+      tgt = new org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent();
-      else
+      list.add(tgt);
-        tgt.setProfile(t.getValueAsString());
+      copyElement(src, tgt);
+      tgt.setCode(src.getCode());
     }
-    for (org.hl7.fhir.dstu2016may.model.Enumeration<org.hl7.fhir.dstu2016may.model.ElementDefinition.AggregationMode> t : src.getAggregation())
+    if (tgt.hasTarget()) {
-      tgt.addAggregation(convertAggregationMode(t.getValue()));
+      for (org.hl7.fhir.dstu2016may.model.UriType u : src.getProfile())
-    tgt.setVersioning(convertReferenceVersionRules(src.getVersioning()));
+        tgt.addTargetProfile(u.getValue());
-    return tgt;
+    } else {
+      for (org.hl7.fhir.dstu2016may.model.UriType u : src.getProfile())
+        tgt.addProfile(u.getValue());
+    }
+    for (org.hl7.fhir.dstu2016may.model.Enumeration<org.hl7.fhir.dstu2016may.model.ElementDefinition.AggregationMode> t : src.getAggregation()) {
+      org.hl7.fhir.r4.model.ElementDefinition.AggregationMode a = convertAggregationMode(t.getValue());
+      if (!tgt.hasAggregation(a))
+        tgt.addAggregation(a);
+    }
+    if (src.hasVersioning())
+      tgt.setVersioning(convertReferenceVersionRules(src.getVersioning()));
   }
-
+  
-  public static org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent convertTypeRefComponent(org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent src) throws FHIRException {
+  public static void convertTypeRefComponent(org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent src, List<org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent> list) throws FHIRException {
-    if (src == null || src.isEmpty())
+    if (src == null)
-      return null;
+      return;
     org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent tgt = new org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent();
     copyElement(src, tgt);
     tgt.setCode(src.getCode());
-    if (src.hasCode() && "Reference".equals(src.getCode()))
+    list.add(tgt);
-      tgt.addProfile(src.getTargetProfile());
+    if (src.hasTarget()) {
-    else
+      for (org.hl7.fhir.r4.model.UriType u : src.getTargetProfile()) {
-      tgt.addProfile(src.getProfile());
+        tgt.addProfile(u.getValue());
-    for (org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.ElementDefinition.AggregationMode> t : src.getAggregation())
+      }
-      tgt.addAggregation(convertAggregationMode(t.getValue()));
+    } else {
-    tgt.setVersioning(convertReferenceVersionRules(src.getVersioning()));
+      for (org.hl7.fhir.r4.model.UriType u : src.getProfile()) {
-    return tgt;
+        tgt.addProfile(u.getValue());
+      }
+    }
   }
 
   private static org.hl7.fhir.r4.model.ElementDefinition.AggregationMode convertAggregationMode(org.hl7.fhir.dstu2016may.model.ElementDefinition.AggregationMode src) throws FHIRException {
@@ -1576,7 +1605,10 @@ public class VersionConvertor_14_40 {
     tgt.setStrength(convertBindingStrength(src.getStrength()));
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
-    tgt.setValueSet(convertType(src.getValueSet()));
+    if (src.hasValueSet()) {
+      org.hl7.fhir.r4.model.Type vs = convertType(src.getValueSet());
+      tgt.setValueSet(vs instanceof org.hl7.fhir.r4.model.Reference ? new CanonicalType(((org.hl7.fhir.r4.model.Reference) vs).getReference()) : vs);      
+    }
     return tgt;
   }
 
@@ -1588,7 +1620,7 @@ public class VersionConvertor_14_40 {
     tgt.setStrength(convertBindingStrength(src.getStrength()));
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
-    tgt.setValueSet(convertType(src.getValueSet()));
+    tgt.setValueSet(src.hasValueSetCanonicalType() ? new org.hl7.fhir.dstu2016may.model.Reference(src.getValueSetCanonicalType().getValue()) : convertType(src.getValueSet()));
     return tgt;
   }
 
@@ -3251,7 +3283,7 @@ public class VersionConvertor_14_40 {
     tgt.setSoftware(convertConformanceSoftwareComponent(src.getSoftware()));
     tgt.setImplementation(convertConformanceImplementationComponent(src.getImplementation()));
     tgt.setFhirVersion(src.getFhirVersion());
-    tgt.setAcceptUnknown(convertUnknownContentCode(src.getAcceptUnknown()));
+//    tgt.setAcceptUnknown(convertUnknownContentCode(src.getAcceptUnknown()));
     for (org.hl7.fhir.dstu2016may.model.CodeType t : src.getFormat())
       tgt.addFormat(t.getValue());
 //    for (org.hl7.fhir.dstu2016may.model.Reference t : src.getProfile())
@@ -3265,6 +3297,18 @@ public class VersionConvertor_14_40 {
     return tgt;
   }
 
+  private static CanonicalType convertReferenceToCanonical(Reference src) throws FHIRException {
+    CanonicalType dst = new CanonicalType(src.getReference());
+    copyElement(src, dst);
+    return dst;
+  }
+
+  private static Reference  convertCanonicalToReference(CanonicalType src) throws FHIRException {
+    Reference dst = new Reference(src.getValue());
+    copyElement(src, dst);
+    return dst;
+  }
+
   public static org.hl7.fhir.dstu2016may.model.Conformance convertConformance(org.hl7.fhir.r4.model.CapabilityStatement src) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
@@ -3300,13 +3344,13 @@ public class VersionConvertor_14_40 {
     tgt.setSoftware(convertConformanceSoftwareComponent(src.getSoftware()));
     tgt.setImplementation(convertConformanceImplementationComponent(src.getImplementation()));
     tgt.setFhirVersion(src.getFhirVersion());
-    tgt.setAcceptUnknown(convertUnknownContentCode(src.getAcceptUnknown()));
+//    tgt.setAcceptUnknown(convertUnknownContentCode(src.getAcceptUnknown()));
     for (org.hl7.fhir.r4.model.CodeType t : src.getFormat())
       tgt.addFormat(t.getValue());
     for (CapabilityStatementRestComponent r : src.getRest())
       for (CapabilityStatementRestResourceComponent rr : r.getResource())
-        for (org.hl7.fhir.r4.model.Reference t : rr.getSupportedProfile())
+        for (org.hl7.fhir.r4.model.CanonicalType t : rr.getSupportedProfile())
-          tgt.addProfile(convertReference(t));
+          tgt.addProfile(convertCanonicalToReference(t));
     for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent t : src.getRest())
       tgt.addRest(convertConformanceRestComponent(t));
     for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementMessagingComponent t : src.getMessaging())
@@ -3337,30 +3381,30 @@ public class VersionConvertor_14_40 {
     default: return org.hl7.fhir.dstu2016may.model.Conformance.ConformanceStatementKind.NULL;
     }
   }
-
+//
-  private static org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode convertUnknownContentCode(org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode src) throws FHIRException {
+//  private static org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode convertUnknownContentCode(org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode src) throws FHIRException {
-    if (src == null)
+//    if (src == null)
-      return null;
+//      return null;
-    switch (src) {
+//    switch (src) {
-    case NO: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.NO;
+//    case NO: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.NO;
-    case EXTENSIONS: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.EXTENSIONS;
+//    case EXTENSIONS: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.EXTENSIONS;
-    case ELEMENTS: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.ELEMENTS;
+//    case ELEMENTS: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.ELEMENTS;
-    case BOTH: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.BOTH;
+//    case BOTH: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.BOTH;
-    default: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.NULL;
+//    default: return org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode.NULL;
-    }
+//    }
-  }
+//  }
-
+//
-  private static org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode convertUnknownContentCode(org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode src) throws FHIRException {
+//  private static org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode convertUnknownContentCode(org.hl7.fhir.r4.model.CapabilityStatement.UnknownContentCode src) throws FHIRException {
-    if (src == null)
+//    if (src == null)
-      return null;
+//      return null;
-    switch (src) {
+//    switch (src) {
-    case NO: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.NO;
+//    case NO: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.NO;
-    case EXTENSIONS: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.EXTENSIONS;
+//    case EXTENSIONS: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.EXTENSIONS;
-    case ELEMENTS: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.ELEMENTS;
+//    case ELEMENTS: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.ELEMENTS;
-    case BOTH: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.BOTH;
+//    case BOTH: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.BOTH;
-    default: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.NULL;
+//    default: return org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode.NULL;
-    }
+//    }
-  }
+//  }
 
   public static org.hl7.fhir.r4.model.ContactDetail convertConformanceContactComponent(org.hl7.fhir.dstu2016may.model.Conformance.ConformanceContactComponent src) throws FHIRException {
     if (src == null || src.isEmpty())
@@ -3509,8 +3553,6 @@ public class VersionConvertor_14_40 {
       tgt.addService(convertCodeableConcept(t));
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
-    for (org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestSecurityCertificateComponent t : src.getCertificate())
-      tgt.addCertificate(convertConformanceRestSecurityCertificateComponent(t));
     return tgt;
   }
 
@@ -3525,32 +3567,6 @@ public class VersionConvertor_14_40 {
       tgt.addService(convertCodeableConcept(t));
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
-    for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestSecurityCertificateComponent t : src.getCertificate())
-      tgt.addCertificate(convertConformanceRestSecurityCertificateComponent(t));
-    return tgt;
-  }
-
-  public static org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestSecurityCertificateComponent convertConformanceRestSecurityCertificateComponent(org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestSecurityCertificateComponent src) throws FHIRException {
-    if (src == null || src.isEmpty())
-      return null;
-    org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestSecurityCertificateComponent tgt = new org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestSecurityCertificateComponent();
-    copyElement(src, tgt);
-    if (src.hasType())
-      tgt.setType(src.getType());
-    if (src.hasBlob())
-      tgt.setBlob(src.getBlob());
-    return tgt;
-  }
-
-  public static org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestSecurityCertificateComponent convertConformanceRestSecurityCertificateComponent(org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestSecurityCertificateComponent src) throws FHIRException {
-    if (src == null || src.isEmpty())
-      return null;
-    org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestSecurityCertificateComponent tgt = new org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestSecurityCertificateComponent();
-    copyElement(src, tgt);
-    if (src.hasType())
-      tgt.setType(src.getType());
-    if (src.hasBlob())
-      tgt.setBlob(src.getBlob());
     return tgt;
   }
 
@@ -3560,7 +3576,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent tgt = new org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent();
     copyElement(src, tgt);
     tgt.setType(src.getType());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfileElement(convertReferenceToCanonical(src.getProfile()));
     for (org.hl7.fhir.dstu2016may.model.Conformance.ResourceInteractionComponent t : src.getInteraction())
       tgt.addInteraction(convertResourceInteractionComponent(t));
     tgt.setVersioning(convertResourceVersionPolicy(src.getVersioning()));
@@ -3588,7 +3604,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestResourceComponent tgt = new org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestResourceComponent();
     copyElement(src, tgt);
     tgt.setType(src.getType());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfile(convertCanonicalToReference(src.getProfileElement()));
     for (org.hl7.fhir.r4.model.CapabilityStatement.ResourceInteractionComponent t : src.getInteraction())
       tgt.addInteraction(convertResourceInteractionComponent(t));
     tgt.setVersioning(convertResourceVersionPolicy(src.getVersioning()));
@@ -3818,7 +3834,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent tgt = new org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent();
     copyElement(src, tgt);
     tgt.setName(src.getName());
-    tgt.setDefinition(convertReference(src.getDefinition()));
+    tgt.setDefinitionElement(convertReferenceToCanonical(src.getDefinition()));
     return tgt;
   }
 
@@ -3828,7 +3844,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestOperationComponent tgt = new org.hl7.fhir.dstu2016may.model.Conformance.ConformanceRestOperationComponent();
     copyElement(src, tgt);
     tgt.setName(src.getName());
-    tgt.setDefinition(convertReference(src.getDefinition()));
+    tgt.setDefinition(convertCanonicalToReference(src.getDefinitionElement()));
     return tgt;
   }
 
@@ -3908,7 +3924,7 @@ public class VersionConvertor_14_40 {
     tgt.setMode(convertDocumentMode(src.getMode()));
     if (src.hasDocumentation())
       tgt.setDocumentation(src.getDocumentation());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfileElement(convertReferenceToCanonical(src.getProfile()));
     return tgt;
   }
 
@@ -3920,7 +3936,7 @@ public class VersionConvertor_14_40 {
     tgt.setMode(convertDocumentMode(src.getMode()));
     if (src.hasDocumentation())
       tgt.setDocumentation(src.getDocumentation());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfile(convertCanonicalToReference(src.getProfileElement()));
     return tgt;
   }
 
@@ -4292,7 +4308,7 @@ public class VersionConvertor_14_40 {
       tgt.setAcronym(src.getAcronym());
     tgt.setSource(convertType(src.getSource()));
     if (src.hasExampleFor())
-      tgt.setExampleFor(convertReference(src.getExampleFor()));
+      tgt.setExampleForElement(convertReferenceToCanonical(src.getExampleFor()));
     return tgt;
   }
 
@@ -4310,7 +4326,7 @@ public class VersionConvertor_14_40 {
       tgt.setAcronym(src.getAcronym());
     tgt.setSource(convertType(src.getSource()));
     if (src.hasExampleFor())
-      tgt.setExampleFor(convertReference(src.getExampleFor()));
+      tgt.setExampleFor(convertCanonicalToReference(src.getExampleForElement()));
     return tgt;
   }
 
@@ -4320,7 +4336,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.ImplementationGuide.ImplementationGuideGlobalComponent tgt = new org.hl7.fhir.r4.model.ImplementationGuide.ImplementationGuideGlobalComponent();
     copyElement(src, tgt);
     tgt.setType(src.getType());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfileElement(convertReferenceToCanonical(src.getProfile()));
     return tgt;
   }
 
@@ -4330,7 +4346,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.dstu2016may.model.ImplementationGuide.ImplementationGuideGlobalComponent tgt = new org.hl7.fhir.dstu2016may.model.ImplementationGuide.ImplementationGuideGlobalComponent();
     copyElement(src, tgt);
     tgt.setType(src.getType());
-    tgt.setProfile(convertReference(src.getProfile()));
+    tgt.setProfile(convertCanonicalToReference(src.getProfileElement()));
     return tgt;
   }
 
@@ -4594,7 +4610,7 @@ public class VersionConvertor_14_40 {
     tgt.setCode(src.getCode());
     if (src.hasComment())
       tgt.setComment(src.getComment());
-    tgt.setBase(convertReference(src.getBase()));
+    tgt.setBaseElement(convertReferenceToCanonical(src.getBase()));
     tgt.setSystem(src.getSystem());
     for (org.hl7.fhir.dstu2016may.model.CodeType t : src.getType())
       tgt.addResource(t.getValue());
@@ -4639,7 +4655,7 @@ public class VersionConvertor_14_40 {
     tgt.setCode(src.getCode());
     if (src.hasComment())
       tgt.setComment(src.getComment());
-    tgt.setBase(convertReference(src.getBase()));
+    tgt.setBase(convertCanonicalToReference(src.getBaseElement()));
     tgt.setSystem(src.getSystem());
     if (src.getType())
       for (org.hl7.fhir.r4.model.CodeType t : src.getResource())
@@ -5054,10 +5070,10 @@ public class VersionConvertor_14_40 {
       tgt.setReadOnly(src.getReadOnly());
     if (src.hasMaxLength())
       tgt.setMaxLength(src.getMaxLength());
-    tgt.setOptions(convertReference(src.getOptions()));
+    tgt.setOptionsElement(convertReferenceToCanonical(src.getOptions()));
     for (org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemOptionComponent t : src.getOption())
       tgt.addOption(convertQuestionnaireItemOptionComponent(t));
-    tgt.setInitial(convertType(src.getInitial()));
+    tgt.addInitial().setValue(convertType(src.getInitial()));
     for (org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemComponent t : src.getItem())
       tgt.addItem(convertQuestionnaireItemComponent(t));
     return tgt;
@@ -5087,10 +5103,11 @@ public class VersionConvertor_14_40 {
       tgt.setReadOnly(src.getReadOnly());
     if (src.hasMaxLength())
       tgt.setMaxLength(src.getMaxLength());
-    tgt.setOptions(convertReference(src.getOptions()));
+    tgt.setOptions(convertCanonicalToReference(src.getOptionsElement()));
     for (org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemOptionComponent t : src.getOption())
       tgt.addOption(convertQuestionnaireItemOptionComponent(t));
-    tgt.setInitial(convertType(src.getInitial()));
+    if (src.hasInitial())
+      tgt.setInitial(convertType(src.getInitialFirstRep().getValue()));
     for (org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent t : src.getItem())
       tgt.addItem(convertQuestionnaireItemComponent(t));
     return tgt;
@@ -5153,8 +5170,10 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemEnableWhenComponent tgt = new org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemEnableWhenComponent();
     copyElement(src, tgt);
     tgt.setQuestion(src.getQuestion());
-    if (src.hasAnswered())
+    if (src.hasAnswered()) {
-      tgt.setHasAnswer(src.getAnswered());
+      tgt.setOperator(QuestionnaireItemOperator.EXISTS);
+      tgt.setAnswer(convertType(src.getAnsweredElement()));
+    }
     tgt.setAnswer(convertType(src.getAnswer()));
     return tgt;
   }
@@ -5165,9 +5184,10 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemEnableWhenComponent tgt = new org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemEnableWhenComponent();
     copyElement(src, tgt);
     tgt.setQuestion(src.getQuestion());
-    if (src.hasHasAnswer())
+    if (src.hasOperator() && src.getOperator() == QuestionnaireItemOperator.EXISTS)
-      tgt.setAnswered(src.getHasAnswer());
+      tgt.setAnswered(src.getAnswerBooleanType().getValue());
-    tgt.setAnswer(convertType(src.getAnswer()));
+    else 
+      tgt.setAnswer(convertType(src.getAnswer()));
     return tgt;
   }
 
@@ -5195,7 +5215,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.QuestionnaireResponse tgt = new org.hl7.fhir.r4.model.QuestionnaireResponse();
     copyDomainResource(src, tgt);
     tgt.setIdentifier(convertIdentifier(src.getIdentifier()));
-    tgt.setQuestionnaire(convertReference(src.getQuestionnaire()));
+    tgt.setQuestionnaireElement(convertReferenceToCanonical(src.getQuestionnaire()));
     tgt.setStatus(convertQuestionnaireResponseStatus(src.getStatus()));
     tgt.setSubject(convertReference(src.getSubject()));
     tgt.setContext(convertReference(src.getEncounter()));
@@ -5214,7 +5234,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.dstu2016may.model.QuestionnaireResponse tgt = new org.hl7.fhir.dstu2016may.model.QuestionnaireResponse();
     copyDomainResource(src, tgt);
     tgt.setIdentifier(convertIdentifier(src.getIdentifier()));
-    tgt.setQuestionnaire(convertReference(src.getQuestionnaire()));
+    tgt.setQuestionnaire(convertCanonicalToReference(src.getQuestionnaireElement()));
     tgt.setStatus(convertQuestionnaireResponseStatus(src.getStatus()));
     tgt.setSubject(convertReference(src.getSubject()));
     tgt.setEncounter(convertReference(src.getContext()));
@@ -5472,9 +5492,11 @@ public class VersionConvertor_14_40 {
       tgt.addMapping(convertStructureDefinitionMappingComponent(t));
     tgt.setKind(convertStructureDefinitionKind(src.getKind()));
     tgt.setAbstract(src.getAbstract());
-    tgt.setContextType(convertExtensionContext(src.getContextType()));
+    for (org.hl7.fhir.dstu2016may.model.StringType t : src.getContext()) {
-    for (org.hl7.fhir.dstu2016may.model.StringType t : src.getContext())
+      org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionContextComponent ec = tgt.addContext();
-      tgt.addContext(t.getValue());
+      ec.setType(convertExtensionContext(src.getContextType()));
+      ec.setExpression(t.getValue());
+    }
     if (src.getDerivation() == org.hl7.fhir.dstu2016may.model.StructureDefinition.TypeDerivationRule.CONSTRAINT)
       tgt.setType(src.getBaseType());
     else
@@ -5490,6 +5512,13 @@ public class VersionConvertor_14_40 {
       tgt.setDifferential(convertStructureDefinitionDifferentialComponent(src.getDifferential()));
       tgt.getDifferential().getElementFirstRep().getType().clear();
     }
+    if (tgt.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
+      for (ElementDefinition ed : tgt.getSnapshot().getElement()) {
+        if (!ed.hasBase()) {
+          ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
+        }
+      }
+    }
     return tgt;
   }
 
@@ -5535,9 +5564,11 @@ public class VersionConvertor_14_40 {
       tgt.addMapping(convertStructureDefinitionMappingComponent(t));
     tgt.setKind(convertStructureDefinitionKind(src.getKind()));
     tgt.setAbstract(src.getAbstract());
-    tgt.setContextType(convertExtensionContext(src.getContextType()));
+    for (org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionContextComponent  t : src.getContext()) {
-    for (org.hl7.fhir.r4.model.StringType t : src.getContext())
+      if (!tgt.hasContextType())
-      tgt.addContext(t.getValue());
+        tgt.setContextType(convertExtensionContext(t.getType()));
+      tgt.addContext(t.getExpression());
+    }
     if (src.hasBaseDefinition())
       tgt.setBaseDefinition(src.getBaseDefinition());
     if (src.hasType() && src.getDerivation() == org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule.CONSTRAINT)
@@ -5572,23 +5603,23 @@ public class VersionConvertor_14_40 {
     }
   }
 
-  private static org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext convertExtensionContext(org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext src) throws FHIRException {
+  private static org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType convertExtensionContext(org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext src) throws FHIRException {
     if (src == null)
       return null;
     switch (src) {
-    case RESOURCE: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext.RESOURCE;
+    case RESOURCE: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType.FHIRPATH;
-    case DATATYPE: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext.DATATYPE;
+    case DATATYPE: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType.ELEMENT;
-    case EXTENSION: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext.EXTENSION;
+    case EXTENSION: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType.EXTENSION;
-    default: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext.NULL;
+    default: return org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType.NULL;
     }
   }
 
-  private static org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext convertExtensionContext(org.hl7.fhir.r4.model.StructureDefinition.ExtensionContext src) throws FHIRException {
+  private static org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext convertExtensionContext(org.hl7.fhir.r4.model.StructureDefinition.ExtensionContextType src) throws FHIRException {
     if (src == null)
       return null;
     switch (src) {
-    case RESOURCE: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.RESOURCE;
+    case FHIRPATH: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.RESOURCE;
-    case DATATYPE: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.DATATYPE;
+    case ELEMENT: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.DATATYPE;
     case EXTENSION: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.EXTENSION;
     default: return org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext.NULL;
     }
@@ -6186,6 +6217,8 @@ public class VersionConvertor_14_40 {
       tgt.setLabel(src.getLabel());
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
+    tgt.setAccept(convertContentType(src.getAccept()));
+    tgt.setContentType(convertContentType(src.getContentType()));
     if (src.hasDestination())
       tgt.setDestination(src.getDestination());
     if (src.hasEncodeRequestUrl())
@@ -6218,6 +6251,8 @@ public class VersionConvertor_14_40 {
       tgt.setLabel(src.getLabel());
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
+    tgt.setAccept(convertContentType(src.getAccept()));
+    tgt.setContentType(convertContentType(src.getContentType()));
     if (src.hasDestination())
       tgt.setDestination(src.getDestination());
     if (src.hasEncodeRequestUrl())
@@ -6239,6 +6274,24 @@ public class VersionConvertor_14_40 {
     return tgt;
   }
 
+  private static String convertContentType(org.hl7.fhir.dstu2016may.model.TestScript.ContentType src) throws FHIRException {
+    if (src == null)
+      return null;
+    switch (src) {
+    case XML: return "application/fhir+xml";
+    case JSON: return "application/fhir+json";
+    default: return null;
+  }
+}
+
+  private static org.hl7.fhir.dstu2016may.model.TestScript.ContentType convertContentType(String src) throws FHIRException {
+    if (src == null)
+      return null;
+    if (src.contains("xml")) return org.hl7.fhir.dstu2016may.model.TestScript.ContentType.XML;
+    if (src.contains("json")) return org.hl7.fhir.dstu2016may.model.TestScript.ContentType.JSON;
+    return org.hl7.fhir.dstu2016may.model.TestScript.ContentType.NULL;
+  }
+
 
   public static org.hl7.fhir.r4.model.TestScript.SetupActionOperationRequestHeaderComponent convertSetupActionOperationRequestHeaderComponent(org.hl7.fhir.dstu2016may.model.TestScript.SetupActionOperationRequestHeaderComponent src) throws FHIRException {
     if (src == null || src.isEmpty())
@@ -6274,6 +6327,7 @@ public class VersionConvertor_14_40 {
       tgt.setCompareToSourceId(src.getCompareToSourceId());
     if (src.hasCompareToSourcePath())
       tgt.setCompareToSourcePath(src.getCompareToSourcePath());
+    tgt.setContentType(convertContentType(src.getContentType()));
     if (src.hasHeaderField())
       tgt.setHeaderField(src.getHeaderField());
     if (src.hasMinimumId())
@@ -6315,6 +6369,7 @@ public class VersionConvertor_14_40 {
       tgt.setCompareToSourceId(src.getCompareToSourceId());
     if (src.hasCompareToSourcePath())
       tgt.setCompareToSourcePath(src.getCompareToSourcePath());
+    tgt.setContentType(convertContentType(src.getContentType()));
     if (src.hasHeaderField())
       tgt.setHeaderField(src.getHeaderField());
     if (src.hasMinimumId())

hapi-fhir-converter/src/main/java/org/hl7/fhir/dstu2/utils/ToolingExtensions.java

@@ -1,487 +0,0 @@
-package org.hl7.fhir.dstu2.utils;
-
-/*
- * #%L
- * HAPI FHIR - Converter
- * %%
- * Copyright (C) 2014 - 2018 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-import java.net.URISyntaxException;
-
-/*
-Copyright (c) 2011+, HL7, Inc
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, 
-are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice, this 
-   list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice, 
-   this list of conditions and the following disclaimer in the documentation 
-   and/or other materials provided with the distribution.
- * Neither the name of HL7 nor the names of its contributors may be used to 
-   endorse or promote products derived from this software without specific 
-   prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-POSSIBILITY OF SUCH DAMAGE.
-
- */
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import org.hl7.fhir.instance.model.BooleanType;
-import org.hl7.fhir.instance.model.CodeType;
-import org.hl7.fhir.instance.model.CodeableConcept;
-import org.hl7.fhir.instance.model.Coding;
-import org.hl7.fhir.instance.model.DataElement;
-import org.hl7.fhir.instance.model.DomainResource;
-import org.hl7.fhir.instance.model.Element;
-import org.hl7.fhir.instance.model.ElementDefinition;
-import org.hl7.fhir.instance.model.Extension;
-import org.hl7.fhir.instance.model.ExtensionHelper;
-import org.hl7.fhir.instance.model.Factory;
-import org.hl7.fhir.instance.model.Identifier;
-import org.hl7.fhir.instance.model.IntegerType;
-import org.hl7.fhir.instance.model.MarkdownType;
-import org.hl7.fhir.instance.model.PrimitiveType;
-import org.hl7.fhir.instance.model.Questionnaire.GroupComponent;
-import org.hl7.fhir.instance.model.Questionnaire.QuestionComponent;
-import org.hl7.fhir.instance.model.Reference;
-import org.hl7.fhir.instance.model.StringType;
-import org.hl7.fhir.instance.model.Type;
-import org.hl7.fhir.instance.model.UriType;
-import org.hl7.fhir.instance.model.ValueSet;
-import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
-import org.hl7.fhir.instance.model.ValueSet.ValueSetCodeSystemComponent;
-import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
-import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.Utilities;
-
-
-public class ToolingExtensions {
-
-  // validated
-  public static final String EXT_SUBSUMES = "http://hl7.org/fhir/StructureDefinition/valueset-subsumes"; 
-  private static final String EXT_OID = "http://hl7.org/fhir/StructureDefinition/valueset-oid";
-  public static final String EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/valueset-deprecated";
-  public static final String EXT_DEFINITION = "http://hl7.org/fhir/StructureDefinition/valueset-definition";
-  public static final String EXT_COMMENT = "http://hl7.org/fhir/StructureDefinition/valueset-comments";
-  private static final String EXT_IDENTIFIER = "http://hl7.org/fhir/StructureDefinition/identifier";
-  private static final String EXT_TRANSLATION = "http://hl7.org/fhir/StructureDefinition/translation";
-  public static final String EXT_ISSUE_SOURCE = "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-source";
-  public static final String EXT_DISPLAY_HINT = "http://hl7.org/fhir/StructureDefinition/structuredefinition-display-hint"; 
-  public static final String EXT_REPLACED_BY = "http://hl7.org/fhir/StructureDefinition/valueset-replacedby";
-  public static final String EXT_JSON_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type"; 
-  public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type"; 
-  public static final String EXT_REGEX = "http://hl7.org/fhir/StructureDefinition/structuredefinition-regex"; 
-  public static final String EXT_EXPRESSION = "http://hl7.org/fhir/StructureDefinition/structuredefinition-expression";
-  public static final String EXT_SEARCH_EXPRESSION = "http://hl7.org/fhir/StructureDefinition/searchparameter-expression";
-
-  // unregistered?
-
-  public static final String EXT_FLYOVER = "http://hl7.org/fhir/Profile/questionnaire-extensions#flyover";
-  private static final String EXT_QTYPE = "http://www.healthintersections.com.au/fhir/Profile/metadata#type";
-  private static final String EXT_QREF = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
-  private static final String EXTENSION_FILTER_ONLY = "http://www.healthintersections.com.au/fhir/Profile/metadata#expandNeedsFilter";
-  private static final String EXT_TYPE = "http://www.healthintersections.com.au/fhir/Profile/metadata#type";
-  private static final String EXT_REFERENCE = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
-  private static final String EXT_ALLOWABLE_UNITS = "http://hl7.org/fhir/StructureDefinition/elementdefinition-allowedUnits";
-  public static final String EXT_CIMI_REFERENCE = "http://hl7.org/fhir/StructureDefinition/cimi-reference";
-  public static final String EXT_UNCLOSED = "http://hl7.org/fhir/StructureDefinition/valueset-unclosed";
-  public static final String EXT_FMM_LEVEL = "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm";
-
-
-  // specific extension helpers
-
-  public static Extension makeIssueSource(Source source) {
-    Extension ex = new Extension();
-    // todo: write this up and get it published with the pack (and handle the redirect?)
-    ex.setUrl(ToolingExtensions.EXT_ISSUE_SOURCE);
-    CodeType c = new CodeType();
-    c.setValue(source.toString());
-    ex.setValue(c);
-    return ex;
-  }
-
-  public static boolean hasExtension(DomainResource de, String url) {
-    return getExtension(de, url) != null;
-  }
-
-  public static boolean hasExtension(Element e, String url) {
-    return getExtension(e, url) != null;
-  }
-
-  public static void addStringExtension(DomainResource dr, String url, String content) {
-    if (!Utilities.noString(content)) {
-      Extension ex = getExtension(dr, url);
-      if (ex != null)
-        ex.setValue(new StringType(content));
-      else
-        dr.getExtension().add(Factory.newExtension(url, new StringType(content), true));   
-    }
-  }
-
-  public static void addStringExtension(Element e, String url, String content) {
-    if (!Utilities.noString(content)) {
-      Extension ex = getExtension(e, url);
-      if (ex != null)
-        ex.setValue(new StringType(content));
-      else
-        e.getExtension().add(Factory.newExtension(url, new StringType(content), true));   
-    }
-  }
-
-  public static void addIntegerExtension(DomainResource dr, String url, int value) {
-    Extension ex = getExtension(dr, url);
-    if (ex != null)
-      ex.setValue(new IntegerType(value));
-    else
-      dr.getExtension().add(Factory.newExtension(url, new IntegerType(value), true));   
-  }
-
-  public static void addComment(Element nc, String comment) {
-    if (!Utilities.noString(comment))
-      nc.getExtension().add(Factory.newExtension(EXT_COMMENT, Factory.newString_(comment), true));   
-  }
-
-  public static void markDeprecated(Element nc) {
-    setDeprecated(nc);   
-  }
-
-  public static void addSubsumes(ConceptDefinitionComponent nc, String code) {
-    nc.getModifierExtension().add(Factory.newExtension(EXT_SUBSUMES, Factory.newCode(code), true));   
-  }
-
-  public static void addDefinition(Element nc, String definition) {
-    if (!Utilities.noString(definition))
-      nc.getExtension().add(Factory.newExtension(EXT_DEFINITION, Factory.newString_(definition), true));   
-  }
-
-  public static void addDisplayHint(Element def, String hint) {
-    if (!Utilities.noString(hint))
-      def.getExtension().add(Factory.newExtension(EXT_DISPLAY_HINT, Factory.newString_(hint), true));   
-  }
-
-  public static String getDisplayHint(Element def) {
-    return readStringExtension(def, EXT_DISPLAY_HINT);    
-  }
-
-  public static String readStringExtension(Element c, String uri) {
-    Extension ex = ExtensionHelper.getExtension(c, uri);
-    if (ex == null)
-      return null;
-    if (ex.getValue() instanceof UriType)
-      return ((UriType) ex.getValue()).getValue();
-    if (!(ex.getValue() instanceof StringType))
-      return null;
-    return ((StringType) ex.getValue()).getValue();
-  }
-
-  public static String readStringExtension(DomainResource c, String uri) {
-    Extension ex = getExtension(c, uri);
-    if (ex == null)
-      return null;
-    if ((ex.getValue() instanceof StringType))
-      return ((StringType) ex.getValue()).getValue();
-    if ((ex.getValue() instanceof UriType))
-      return ((UriType) ex.getValue()).getValue();
-    if ((ex.getValue() instanceof MarkdownType))
-      return ((MarkdownType) ex.getValue()).getValue();
-    return null;
-  }
-
-  @SuppressWarnings("unchecked")
-  public static PrimitiveType<Type> readPrimitiveExtension(DomainResource c, String uri) {
-    Extension ex = getExtension(c, uri);
-    if (ex == null)
-      return null;
-    return (PrimitiveType<Type>) ex.getValue();
-  }
-
-  public static boolean findStringExtension(Element c, String uri) {
-    Extension ex = ExtensionHelper.getExtension(c, uri);
-    if (ex == null)
-      return false;
-    if (!(ex.getValue() instanceof StringType))
-      return false;
-    return !Utilities.noString(((StringType) ex.getValue()).getValue());
-  }
-
-  public static Boolean readBooleanExtension(Element c, String uri) {
-    Extension ex = ExtensionHelper.getExtension(c, uri);
-    if (ex == null)
-      return null;
-    if (!(ex.getValue() instanceof BooleanType))
-      return null;
-    return ((BooleanType) ex.getValue()).getValue();
-  }
-
-  public static boolean findBooleanExtension(Element c, String uri) {
-    Extension ex = ExtensionHelper.getExtension(c, uri);
-    if (ex == null)
-      return false;
-    if (!(ex.getValue() instanceof BooleanType))
-      return false;
-    return true;
-  }
-
-  public static String getComment(ConceptDefinitionComponent c) {
-    return readStringExtension(c, EXT_COMMENT);    
-  }
-
-  public static Boolean getDeprecated(Element c) {
-    return readBooleanExtension(c, EXT_DEPRECATED);    
-  }
-
-  public static boolean hasComment(ConceptDefinitionComponent c) {
-    return findStringExtension(c, EXT_COMMENT);    
-  }
-
-  public static boolean hasDeprecated(Element c) {
-    return findBooleanExtension(c, EXT_DEPRECATED);    
-  }
-
-  public static List<CodeType> getSubsumes(ConceptDefinitionComponent c) {
-    List<CodeType> res = new ArrayList<CodeType>();
-
-    for (Extension e : c.getExtension()) {
-      if (EXT_SUBSUMES.equals(e.getUrl()))
-        res.add((CodeType) e.getValue());
-    }
-    return res;
-  }
-
-  public static void addFlyOver(GroupComponent group, String text) {
-    if (!Utilities.noString(text))
-      group.getExtension().add(Factory.newExtension(EXT_FLYOVER, Factory.newString_(text), true));   
-
-  }
-
-  public static void setQuestionType(GroupComponent group, String text) {
-    if (!Utilities.noString(text))
-      group.getExtension().add(Factory.newExtension(EXT_QTYPE, Factory.newString_(text), true));   
-  }
-
-  public static void setQuestionReference(GroupComponent group, String text) {
-    if (!Utilities.noString(text))
-      group.getExtension().add(Factory.newExtension(EXT_QREF, Factory.newString_(text), true));   
-  }
-
-  public static void addFlyOver(Element element, String text) {
-    element.getExtension().add(Factory.newExtension(EXT_FLYOVER, Factory.newString_(text), true));       
-  }
-
-  public static void addFilterOnly(Reference element, boolean value) {
-    element.getExtension().add(Factory.newExtension(EXTENSION_FILTER_ONLY, Factory.newBoolean(value), true));       
-  }
-
-  public static void addType(GroupComponent group, String value) {
-    group.getExtension().add(Factory.newExtension(EXT_TYPE, Factory.newString_(value), true));       
-  }
-
-  public static void addReference(QuestionComponent group, String value) {
-    group.getExtension().add(Factory.newExtension(EXT_REFERENCE, Factory.newString_(value), true));       
-  }
-
-  public static void addIdentifier(Element element, Identifier value) {
-    element.getExtension().add(Factory.newExtension(EXT_IDENTIFIER, value, true));       
-  }
-
-  /**
-   * @param name the identity of the extension of interest
-   * @return The extension, if on this element, else null
-   */
-  public static Extension getExtension(DomainResource resource, String name) {
-    if (name == null)
-      return null;
-    if (!resource.hasExtension())
-      return null;
-    for (Extension e : resource.getExtension()) {
-      if (name.equals(e.getUrl()))
-        return e;
-    }
-    return null;
-  }
-
-  public static Extension getExtension(Element el, String name) {
-    if (name == null)
-      return null;
-    if (!el.hasExtension())
-      return null;
-    for (Extension e : el.getExtension()) {
-      if (name.equals(e.getUrl()))
-        return e;
-    }
-    return null;
-  }
-
-  public static void setStringExtension(DomainResource resource, String uri, String value) {
-    Extension ext = getExtension(resource, uri);
-    if (ext != null)
-      ext.setValue(new StringType(value));
-    else
-      resource.getExtension().add(new Extension(new UriType(uri)).setValue(new StringType(value)));
-  }
-
-  public static String getOID(ValueSetCodeSystemComponent define) {
-    return readStringExtension(define, EXT_OID);    
-  }
-
-  public static String getOID(ValueSet vs) {
-    return readStringExtension(vs, EXT_OID);    
-  }
-
-  public static void setOID(ValueSetCodeSystemComponent define, String oid) throws FHIRFormatError, URISyntaxException {
-    if (!oid.startsWith("urn:oid:"))
-      throw new FHIRFormatError("Error in OID format");
-    if (oid.startsWith("urn:oid:urn:oid:"))
-      throw new FHIRFormatError("Error in OID format");
-    define.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
-  }
-  public static void setOID(ValueSet vs, String oid) throws FHIRFormatError, URISyntaxException {
-    if (!oid.startsWith("urn:oid:"))
-      throw new FHIRFormatError("Error in OID format");
-    if (oid.startsWith("urn:oid:urn:oid:"))
-      throw new FHIRFormatError("Error in OID format");
-    vs.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
-  }
-
-  public static boolean hasLanguageTranslation(Element element, String lang) {
-    for (Extension e : element.getExtension()) {
-      if (e.getUrl().equals(EXT_TRANSLATION)) {
-        Extension e1 = ExtensionHelper.getExtension(e, "lang");
-
-        if (e1 != null && e1.getValue() instanceof CodeType && ((CodeType) e.getValue()).getValue().equals(lang))
-          return true;
-      }
-    }
-    return false;
-  }
-
-  public static String getLanguageTranslation(Element element, String lang) {
-    for (Extension e : element.getExtension()) {
-      if (e.getUrl().equals(EXT_TRANSLATION)) {
-        Extension e1 = ExtensionHelper.getExtension(e, "lang");
-
-        if (e1 != null && e1.getValue() instanceof CodeType && ((CodeType) e.getValue()).getValue().equals(lang)) {
-          e1 = ExtensionHelper.getExtension(e, "content");
-          return ((StringType) e.getValue()).getValue();
-        }
-      }
-    }
-    return null;
-  }
-
-  public static void addLanguageTranslation(Element element, String lang, String value) {
-    Extension extension = new Extension().setUrl(EXT_TRANSLATION);
-    extension.addExtension().setUrl("lang").setValue(new StringType(lang));
-    extension.addExtension().setUrl("content").setValue(new StringType(value));
-    element.getExtension().add(extension);
-  }
-
-  public static Type getAllowedUnits(ElementDefinition eld) {
-    for (Extension e : eld.getExtension()) 
-      if (e.getUrl().equals(EXT_ALLOWABLE_UNITS)) 
-        return e.getValue();
-    return null;
-  }
-
-  public static void setAllowableUnits(ElementDefinition eld, CodeableConcept cc) {
-    for (Extension e : eld.getExtension()) 
-      if (e.getUrl().equals(EXT_ALLOWABLE_UNITS)) {
-        e.setValue(cc);
-        return;
-      }
-    eld.getExtension().add(new Extension().setUrl(EXT_ALLOWABLE_UNITS).setValue(cc));
-  }
-
-  public static List<Extension> getExtensions(Element element, String url) {
-    List<Extension> results = new ArrayList<Extension>();
-    for (Extension ex : element.getExtension())
-      if (ex.getUrl().equals(url))
-        results.add(ex);
-    return results;
-  }
-
-  public static List<Extension> getExtensions(DomainResource resource, String url) {
-    List<Extension> results = new ArrayList<Extension>();
-    for (Extension ex : resource.getExtension())
-      if (ex.getUrl().equals(url))
-        results.add(ex);
-    return results;
-  }
-
-  public static void addDEReference(DataElement de, String value) {
-    for (Extension e : de.getExtension()) 
-      if (e.getUrl().equals(EXT_CIMI_REFERENCE)) {
-        e.setValue(new UriType(value));
-        return;
-      }
-    de.getExtension().add(new Extension().setUrl(EXT_CIMI_REFERENCE).setValue(new UriType(value)));
-  }
-
-  public static void setDeprecated(Element nc) {
-    for (Extension e : nc.getExtension()) 
-      if (e.getUrl().equals(EXT_DEPRECATED)) {
-        e.setValue(new BooleanType(true));
-        return;
-      }
-    nc.getExtension().add(new Extension().setUrl(EXT_DEPRECATED).setValue(new BooleanType(true)));    
-  }
-
-  public static void setExtension(Element focus, String url, Coding c) {
-    for (Extension e : focus.getExtension()) 
-      if (e.getUrl().equals(url)) {
-        e.setValue(c);
-        return;
-      }
-    focus.getExtension().add(new Extension().setUrl(url).setValue(c));    
-  }
-
-  public static void removeExtension(DomainResource focus, String url) {
-    Iterator<Extension> i = focus.getExtension().iterator();
-    while (i.hasNext()) {
-      Extension e = i.next(); // must be called before you can call i.remove()
-      if (e.getUrl().equals(url)) {
-        i.remove();
-      }
-    }
-  }
-  
-  public static void removeExtension(Element focus, String url) {
-    Iterator<Extension> i = focus.getExtension().iterator();
-    while (i.hasNext()) {
-      Extension e = i.next(); // must be called before you can call i.remove()
-      if (e.getUrl().equals(url)) {
-        i.remove();
-      }
-    }
-  }
-}

hapi-fhir-converter/src/test/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptorR4Test.java

@@ -0,0 +1,131 @@
+package ca.uhn.hapi.converters.server;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.UrlUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+public class VersionedApiConverterInterceptorR4Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(VersionedApiConverterInterceptorR4Test.class);
+	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static int ourPort;
+
+	private static Server ourServer;
+
+
+	@Test
+	public void testSearchNormal() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"family\": \"FAMILY\""));
+		}
+	}
+
+	@Test
+	public void testSearchConvertToR2() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
+		httpGet.addHeader("Accept", "application/fhir+json; fhirVersion=1.0");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"family\": ["));
+		}
+	}
+
+	@Test
+	public void testSearchConvertToR2ByFormatParam() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=" + UrlUtil.escapeUrlParam("application/fhir+json; fhirVersion=1.0"));
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"family\": ["));
+		}
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
+		servlet.setDefaultPrettyPrint(true);
+		servlet.registerInterceptor(new VersionedApiConverterInterceptor());
+
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Patient.class;
+		}
+
+		@SuppressWarnings("rawtypes")
+		@Search()
+		public List search() {
+			ArrayList<Patient> retVal = new ArrayList<>();
+
+			Patient patient = new Patient();
+			patient.getIdElement().setValue("Patient/A");
+			patient.addName(new HumanName().setFamily("FAMILY"));
+			retVal.add(patient);
+
+			return retVal;
+		}
+
+	}
+
+}

hapi-fhir-converter/src/test/resources/logback-test.xml

@@ -0,0 +1,48 @@
+<configuration>
+
+	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+			<level>INFO</level>
+		</filter>
+		<encoder>
+			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
+		</encoder>
+	</appender>
+
+	<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<logger name="ca.uhn.fhir.jpa.dao.FhirResourceDaoSubscriptionDstu2" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<logger name="org.eclipse.jetty.websocket" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+	
+	<logger name="org.eclipse" additivity="false" level="error">
+	</logger>
+
+	<logger name="ca.uhn.fhir.rest.client" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<logger name="ca.uhn.fhir.jpa.dao" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+	
+	<!-- Set to 'trace' to enable SQL logging -->
+	<logger name="org.hibernate.SQL" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+	<!-- Set to 'trace' to enable SQL Value logging -->
+	<logger name="org.hibernate.type" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<root level="info">
+		<appender-ref ref="STDOUT" />
+	</root>
+
+</configuration>

hapi-fhir-igpacks/src/main/java/ca/uhn/fhir/igpacks/parser/IgPackParserDstu3.java

@@ -23,7 +23,7 @@ package ca.uhn.fhir.igpacks.parser;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.Validate;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsHttpRequest.java

@@ -20,31 +20,31 @@ package ca.uhn.fhir.jaxrs.client;
  * #L%
  */
 
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.client.api.IHttpRequest;
+import ca.uhn.fhir.rest.client.api.IHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
+
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.Invocation;
+import javax.ws.rs.core.Response;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
-import javax.ws.rs.client.Entity;
-import javax.ws.rs.client.Invocation;
-import javax.ws.rs.core.Response;
-
-import ca.uhn.fhir.rest.api.RequestTypeEnum;
-import ca.uhn.fhir.rest.client.api.IHttpRequest;
-import ca.uhn.fhir.rest.client.api.IHttpResponse;
-
 /**
  * A Http Request based on JaxRs. This is an adapter around the class
  * {@link javax.ws.rs.client.Invocation Invocation}
- * 
+ *
  * @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
  */
 public class JaxRsHttpRequest implements IHttpRequest {
 
+	private final Map<String, List<String>> myHeaders = new HashMap<String, List<String>>();
 	private Invocation.Builder myRequest;
 	private RequestTypeEnum myRequestType;
 	private Entity<?> myEntity;
-	private final Map<String, List<String>> myHeaders = new HashMap<String, List<String>>();
 
 	public JaxRsHttpRequest(Invocation.Builder theRequest, RequestTypeEnum theRequestType, Entity<?> theEntity) {
 		this.myRequest = theRequest;
@@ -61,24 +61,22 @@ public class JaxRsHttpRequest implements IHttpRequest {
 		getRequest().header(theName, theValue);
 	}
 
-	/**
+	@Override
-	 * Get the Request
+	public IHttpResponse execute() {
-	 * @return the Request
+		StopWatch responseStopWatch = new StopWatch();
-	 */
+		Invocation invocation = getRequest().build(getRequestType().name(), getEntity());
-	public Invocation.Builder getRequest() {
+		Response response = invocation.invoke();
-		return myRequest;
+		return new JaxRsHttpResponse(response, responseStopWatch);
 	}
 
-	/**
+	@Override
-	 * Get the Request Type
+	public Map<String, List<String>> getAllHeaders() {
-	 * @return the request type
+		return this.myHeaders;
-	 */
-	public RequestTypeEnum getRequestType() {
-		return myRequestType == null ? RequestTypeEnum.GET : myRequestType;
 	}
 
 	/**
 	 * Get the Entity
+	 *
 	 * @return the entity
 	 */
 	public Entity<?> getEntity() {
@@ -86,15 +84,17 @@ public class JaxRsHttpRequest implements IHttpRequest {
 	}
 
 	@Override
-	public IHttpResponse execute() {
+	public String getHttpVerbName() {
-		Invocation invocation = getRequest().build(getRequestType().name(), getEntity());
+		return myRequestType.name();
-		Response response = invocation.invoke();
-		return new JaxRsHttpResponse(response);
 	}
 
-	@Override
+	/**
-	public Map<String, List<String>> getAllHeaders() {
+	 * Get the Request
-		return this.myHeaders;
+	 *
+	 * @return the Request
+	 */
+	public Invocation.Builder getRequest() {
+		return myRequest;
 	}
 
 	@Override
@@ -103,14 +103,18 @@ public class JaxRsHttpRequest implements IHttpRequest {
 		return null;
 	}
 
+	/**
+	 * Get the Request Type
+	 *
+	 * @return the request type
+	 */
+	public RequestTypeEnum getRequestType() {
+		return myRequestType == null ? RequestTypeEnum.GET : myRequestType;
+	}
+
 	@Override
 	public String getUri() {
 		return ""; // TODO: can we get this from somewhere?
 	}
 
-	@Override
-	public String getHttpVerbName() {
-		return myRequestType.name();
-	}
-
 }

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsHttpResponse.java

@@ -25,7 +25,6 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.Reader;
 import java.io.StringReader;
-import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -34,7 +33,8 @@ import java.util.concurrent.ConcurrentHashMap;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
-import org.apache.commons.lang3.ObjectUtils;
+import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
+import ca.uhn.fhir.util.StopWatch;
 
 import ca.uhn.fhir.rest.client.api.IHttpResponse;
 
@@ -42,12 +42,13 @@ import ca.uhn.fhir.rest.client.api.IHttpResponse;
  * A Http Response based on JaxRs. This is an adapter around the class {@link javax.ws.rs.core.Response Response}
  * @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
  */
-public class JaxRsHttpResponse implements IHttpResponse {
+public class JaxRsHttpResponse extends BaseHttpResponse implements IHttpResponse {
 	
 	private boolean myBufferedEntity = false;
 	private final Response myResponse;
 	
-	public JaxRsHttpResponse(Response theResponse) {
+	public JaxRsHttpResponse(Response theResponse, StopWatch theResponseStopWatch) {
+		super(theResponseStopWatch);
 		this.myResponse = theResponse;
 	}
 

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsResponse.java

@@ -91,7 +91,7 @@ public class JaxRsResponse extends RestfulResponse<JaxRsRequest> {
 		StringWriter writer = new StringWriter();
 		if (outcome != null) {
 			FhirContext fhirContext = getRequestDetails().getServer().getFhirContext();
-			IParser parser = RestfulServerUtils.getNewParser(fhirContext, getRequestDetails());
+			IParser parser = RestfulServerUtils.getNewParser(fhirContext, fhirContext.getVersion().getVersion(), getRequestDetails());
 			outcome.execute(parser, writer);
 		}
 		return sendWriterResponse(operationStatus, getParserType(), null, writer);

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/util/JaxRsResponseDstu3Test.java

@@ -114,19 +114,19 @@ public class JaxRsResponseDstu3Test {
 		boolean allowPrefer = true;
 		String resourceName = "Patient";
 		MethodOutcome methodOutcome = new MethodOutcome(theId);
-		response.getRequestDetails().getParameters().put(Constants.PARAM_FORMAT, new String[]{Constants.CT_XML});
+		response.getRequestDetails().addParameter(Constants.PARAM_FORMAT, new String[]{Constants.CT_XML});
 		boolean addContentLocationHeader = true;
 		boolean respondGzip = true;
 		Response result = (Response) RestfulServerUtils.streamResponseAsResource(request.getServer(), createPatient(), theSummaryMode, 200, addContentLocationHeader, respondGzip, this.request);
 		assertEquals(200, result.getStatus());
-		assertEquals("application/xml+fhir; charset=UTF-8", result.getHeaderString(Constants.HEADER_CONTENT_TYPE));
+		assertEquals("application/fhir+xml; charset=UTF-8", result.getHeaderString(Constants.HEADER_CONTENT_TYPE));
 		assertTrue(result.getEntity().toString().contains("<Patient"));
 		assertTrue(result.getEntity().toString().contains("15"));
 	}
 	
 	@Test
 	public void testNoOutcomeXml() throws IOException {
-		response.getRequestDetails().getParameters().put(Constants.PARAM_FORMAT, new String[]{Constants.CT_XML});
+		response.getRequestDetails().addParameter(Constants.PARAM_FORMAT, new String[]{Constants.CT_XML});
 		boolean addContentLocationHeader = true;
 		boolean respondGzip = true;
 		Response result = (Response) RestfulServerUtils.streamResponseAsResource(request.getServer(), null, theSummaryMode, 204, addContentLocationHeader, respondGzip, this.request);

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/util/JaxRsResponseTest.java

@@ -88,7 +88,7 @@ public class JaxRsResponseTest {
 
 	@Test
 	public void testReturnResponseAsXml() throws IOException {
-		response.getRequestDetails().getParameters().put(Constants.PARAM_FORMAT, new String[] { Constants.CT_XML });
+		response.getRequestDetails().addParameter(Constants.PARAM_FORMAT, new String[] { Constants.CT_XML });
 		boolean addContentLocationHeader = true;
 		boolean respondGzip = true;
 		Response result = (Response) RestfulServerUtils.streamResponseAsResource(request.getServer(), createPatient(), theSummaryMode, 200, addContentLocationHeader, respondGzip, this.request);
@@ -100,7 +100,7 @@ public class JaxRsResponseTest {
 
 	@Test
 	public void testNoOutcomeXml() throws IOException {
-		response.getRequestDetails().getParameters().put(Constants.PARAM_FORMAT, new String[] { Constants.CT_XML });
+		response.getRequestDetails().addParameter(Constants.PARAM_FORMAT, new String[] { Constants.CT_XML });
 		boolean addContentLocationHeader = true;
 		boolean respondGzip = true;
 		Response result = (Response) RestfulServerUtils.streamResponseAsResource(request.getServer(), createPatient(), theSummaryMode, 200, addContentLocationHeader, respondGzip, this.request);

hapi-fhir-jpaserver-base/pom.xml

@@ -550,6 +550,27 @@
 						</configuration>
 					</execution>
 				</executions>
+				<dependencies>
+					<!--
+					These have been added as explicit dependencies
+					as JDK9 no longer includes them by default
+					-->
+					<dependency>
+						<groupId>javax.xml.bind</groupId>
+						<artifactId>jaxb-api</artifactId>
+						<version>${jaxb_api_version}</version>
+					</dependency>
+					<dependency>
+						<groupId>com.sun.xml.bind</groupId>
+						<artifactId>jaxb-core</artifactId>
+						<version>${jaxb_core_version}</version>
+					</dependency>
+					<dependency>
+						<groupId>com.sun.xml.bind</groupId>
+						<artifactId>jaxb-impl</artifactId>
+						<version>${jaxb_core_version}</version>
+					</dependency>
+				</dependencies>
 			</plugin>
 			<plugin>
 				<groupId>org.jacoco</groupId>

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

@@ -49,6 +49,8 @@ import javax.annotation.Resource;
 @EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
 public class BaseConfig implements SchedulingConfigurer {
 
+	public static final String TASK_EXECUTOR_NAME = "hapiJpaTaskExecutor";
+
 	@Autowired
 	protected Environment myEnv;
 	@Resource
@@ -87,18 +89,6 @@ public class BaseConfig implements SchedulingConfigurer {
 		return new StaleSearchDeletingSvcImpl();
 	}
 
-	@Bean
-	@Lazy
-	public SubscriptionRestHookInterceptor subscriptionRestHookInterceptor() {
-		return new SubscriptionRestHookInterceptor();
-	}
-
-	@Bean
-	@Lazy
-	public SubscriptionWebsocketInterceptor subscriptionWebsocketInterceptor() {
-		return new SubscriptionWebsocketInterceptor();
-	}
-
 	/**
 	 * Note: If you're going to use this, you need to provide a bean
 	 * of type {@link ca.uhn.fhir.jpa.subscription.email.IEmailSender}
@@ -111,6 +101,18 @@ public class BaseConfig implements SchedulingConfigurer {
 	}
 
 	@Bean
+	@Lazy
+	public SubscriptionRestHookInterceptor subscriptionRestHookInterceptor() {
+		return new SubscriptionRestHookInterceptor();
+	}
+
+	@Bean
+	@Lazy
+	public SubscriptionWebsocketInterceptor subscriptionWebsocketInterceptor() {
+		return new SubscriptionWebsocketInterceptor();
+	}
+
+	@Bean(name=TASK_EXECUTOR_NAME)
 	public TaskScheduler taskScheduler() {
 		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
 		retVal.setConcurrentExecutor(scheduledExecutorService().getObject());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -18,7 +18,7 @@ import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
-import org.hl7.fhir.dstu3.utils.IResourceValidator.BestPracticeWarningLevel;
+import org.hl7.fhir.r4.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -66,7 +66,7 @@ public class BaseDstu3Config extends BaseConfig {
 	@Lazy
 	public IValidatorModule instanceValidatorDstu3() {
 		FhirInstanceValidator val = new FhirInstanceValidator();
-		val.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
 		val.setValidationSupport(validationSupportChainDstu3());
 		return val;
 	}

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

@@ -50,6 +50,7 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.*;
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Sets;
@@ -60,9 +61,14 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.utils.URLEncodedUtils;
+import org.hibernate.Session;
+import org.hibernate.internal.SessionImpl;
 import org.hl7.fhir.instance.model.api.*;
 import org.hl7.fhir.r4.model.BaseResource;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Reference;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 
@@ -75,18 +81,17 @@ import javax.xml.stream.events.Characters;
 import javax.xml.stream.events.XMLEvent;
 import java.io.CharArrayWriter;
 import java.io.UnsupportedEncodingException;
-import java.io.Writer;
-import java.nio.CharBuffer;
 import java.text.Normalizer;
 import java.util.*;
 import java.util.Map.Entry;
 
 import static org.apache.commons.lang3.StringUtils.*;
 
+@SuppressWarnings("WeakerAccess")
 public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
-	public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
+	public static final long INDEX_STATUS_INDEXED = 1L;
-	public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
+	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
 	public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
 	public static final String OO_SEVERITY_ERROR = "error";
 	public static final String OO_SEVERITY_INFO = "information";
@@ -104,6 +109,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirDao.class);
 	private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<FhirVersionEnum, FhirContext>();
 	private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
+	private static boolean ourValidationDisabledForUnitTest;
 
 	static {
 		Map<String, Class<? extends IQueryParameterType>> resourceMetaParams = new HashMap<String, Class<? extends IQueryParameterType>>();
@@ -310,6 +316,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					nextObject = ((IBaseExtension<?, ?>) nextObject).getValue();
 				}
 
+				if (nextObject instanceof CanonicalType) {
+					nextObject = new Reference(((CanonicalType) nextObject).getValueAsString());
+				}
+
 				IIdType nextId;
 				if (nextObject instanceof IBaseReference) {
 					IBaseReference nextValue = (IBaseReference) nextObject;
@@ -379,7 +389,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					} else {
 						ResourceLink resourceLink = new ResourceLink(nextPathAndRef.getPath(), theEntity, nextId, theUpdateTime);
 						if (theLinks.add(resourceLink)) {
-							ourLog.info("Indexing remote resource reference URL: {}", nextId);
+							ourLog.debug("Indexing remote resource reference URL: {}", nextId);
 						}
 						continue;
 					}
@@ -417,7 +427,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 						IBaseResource newResource = missingResourceDef.newInstance();
 						newResource.setId(resName + "/" + id);
 						IFhirResourceDao<IBaseResource> placeholderResourceDao = (IFhirResourceDao<IBaseResource>) getDao(newResource.getClass());
-						ourLog.info("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
+						ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
 						valueOf = placeholderResourceDao.update(newResource).getEntity().getId();
 					} else {
 						throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
@@ -632,6 +642,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 	}
 
+	protected void flushJpaSession() {
+		SessionImpl session = (SessionImpl) myEntityManager.unwrap(Session.class);
+		int insertionCount = session.getActionQueue().numberOfInsertions();
+		int updateCount = session.getActionQueue().numberOfUpdates();
+
+		StopWatch sw = new StopWatch();
+		myEntityManager.flush();
+		ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
+	}
+
 	private Set<TagDefinition> getAllTagDefinitions(ResourceTable theEntity) {
 		HashSet<TagDefinition> retVal = Sets.newHashSet();
 		for (ResourceTag next : theEntity.getTags()) {
@@ -673,7 +693,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@SuppressWarnings("unchecked")
 	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
 		if (myResourceTypeToDao == null) {
-			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<Class<? extends IBaseResource>, IFhirResourceDao<?>>();
+			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
 			for (IFhirResourceDao<?> next : myResourceDaos) {
 				theResourceTypeToDao.put(next.getResourceType(), next);
 			}
@@ -1213,6 +1233,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		retVal.removeAll(theToRemove);
 		return retVal;
 	}
+
 	private void setUpdatedTime(Collection<? extends BaseResourceIndexedSearchParam> theParams, Date theUpdateTime) {
 		for (BaseResourceIndexedSearchParam nextSearchParam : theParams) {
 			nextSearchParam.setUpdated(theUpdateTime);
@@ -1377,7 +1398,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		 */
 		if (theResource != null) {
 			if (thePerformIndexing) {
-				validateResourceForStorage((T) theResource, theEntity);
+				if (!ourValidationDisabledForUnitTest) {
+					validateResourceForStorage((T) theResource, theEntity);
+				}
 			}
 			String resourceType = myContext.getResourceDefinition(theResource).getName();
 			if (isNotBlank(theEntity.getResourceType()) && !theEntity.getResourceType().equals(resourceType)) {
@@ -1546,7 +1569,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 							}
 							Long next = matches.iterator().next();
 							String newId = translatePidIdToForcedId(resourceTypeString, next);
-							ourLog.info("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
+							ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
 							nextRef.setReference(newId);
 						}
 					}
@@ -1612,7 +1635,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 
 		if (!changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
-			ourLog.info("Resource {} has not changed", theEntity.getIdDt().toUnqualified().getValue());
+			ourLog.debug("Resource {} has not changed", theEntity.getIdDt().toUnqualified().getValue());
 			if (theResource != null) {
 				populateResourceIdFromEntity(theEntity, theResource);
 			}
@@ -1654,7 +1677,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			historyEntry.setEncoding(changed.getEncoding());
 			historyEntry.setResource(changed.getResource());
 
-			ourLog.info("Saving history entry {}", historyEntry.getIdDt());
+			ourLog.debug("Saving history entry {}", historyEntry.getIdDt());
 			myResourceHistoryTableDao.save(historyEntry);
 		}
 
@@ -1691,6 +1714,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			for (ResourceIndexedSearchParamString next : removeCommon(existingStringParams, stringParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsString().remove(next);
 			}
 			for (ResourceIndexedSearchParamString next : removeCommon(stringParams, existingStringParams)) {
 				myEntityManager.persist(next);
@@ -1698,6 +1722,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			for (ResourceIndexedSearchParamToken next : removeCommon(existingTokenParams, tokenParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsToken().remove(next);
 			}
 			for (ResourceIndexedSearchParamToken next : removeCommon(tokenParams, existingTokenParams)) {
 				myEntityManager.persist(next);
@@ -1705,6 +1730,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			for (ResourceIndexedSearchParamNumber next : removeCommon(existingNumberParams, numberParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsNumber().remove(next);
 			}
 			for (ResourceIndexedSearchParamNumber next : removeCommon(numberParams, existingNumberParams)) {
 				myEntityManager.persist(next);
@@ -1712,6 +1738,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			for (ResourceIndexedSearchParamQuantity next : removeCommon(existingQuantityParams, quantityParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsQuantity().remove(next);
 			}
 			for (ResourceIndexedSearchParamQuantity next : removeCommon(quantityParams, existingQuantityParams)) {
 				myEntityManager.persist(next);
@@ -1720,6 +1747,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			// Store date SP's
 			for (ResourceIndexedSearchParamDate next : removeCommon(existingDateParams, dateParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsDate().remove(next);
 			}
 			for (ResourceIndexedSearchParamDate next : removeCommon(dateParams, existingDateParams)) {
 				myEntityManager.persist(next);
@@ -1728,6 +1756,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			// Store URI SP's
 			for (ResourceIndexedSearchParamUri next : removeCommon(existingUriParams, uriParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsUri().remove(next);
 			}
 			for (ResourceIndexedSearchParamUri next : removeCommon(uriParams, existingUriParams)) {
 				myEntityManager.persist(next);
@@ -1736,6 +1765,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			// Store Coords SP's
 			for (ResourceIndexedSearchParamCoords next : removeCommon(existingCoordsParams, coordsParams)) {
 				myEntityManager.remove(next);
+				theEntity.getParamsCoords().remove(next);
 			}
 			for (ResourceIndexedSearchParamCoords next : removeCommon(coordsParams, existingCoordsParams)) {
 				myEntityManager.persist(next);
@@ -1744,6 +1774,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			// Store resource links
 			for (ResourceLink next : removeCommon(existingResourceLinks, links)) {
 				myEntityManager.remove(next);
+				theEntity.getResourceLinks().remove(next);
 			}
 			for (ResourceLink next : removeCommon(links, existingResourceLinks)) {
 				myEntityManager.persist(next);
@@ -1753,23 +1784,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			// Store composite string uniques
 			if (getConfig().isUniqueIndexesEnabled()) {
-				for (ResourceIndexedCompositeStringUnique next : existingCompositeStringUniques) {
+				for (ResourceIndexedCompositeStringUnique next : removeCommon(existingCompositeStringUniques, compositeStringUniques)) {
-					if (!compositeStringUniques.contains(next)) {
+					ourLog.debug("Removing unique index: {}", next);
-						ourLog.debug("Removing unique index: {}", next);
+					myEntityManager.remove(next);
-						myEntityManager.remove(next);
+					theEntity.getParamsCompositeStringUnique().remove(next);
-					}
 				}
-				for (ResourceIndexedCompositeStringUnique next : compositeStringUniques) {
+				for (ResourceIndexedCompositeStringUnique next : removeCommon(compositeStringUniques, existingCompositeStringUniques)) {
-					if (!existingCompositeStringUniques.contains(next)) {
+					if (myConfig.isUniqueIndexesCheckedBeforeSave()) {
-						if (myConfig.isUniqueIndexesCheckedBeforeSave()) {
+						ResourceIndexedCompositeStringUnique existing = myResourceIndexedCompositeStringUniqueDao.findByQueryString(next.getIndexString());
-							ResourceIndexedCompositeStringUnique existing = myResourceIndexedCompositeStringUniqueDao.findByQueryString(next.getIndexString());
+						if (existing != null) {
-							if (existing != null) {
+							throw new PreconditionFailedException("Can not create resource of type " + theEntity.getResourceType() + " as it would create a duplicate index matching query: " + next.getIndexString() + " (existing index belongs to " + existing.getResource().getIdDt().toUnqualifiedVersionless().getValue() + ")");
-								throw new PreconditionFailedException("Can not create resource of type " + theEntity.getResourceType() + " as it would create a duplicate index matching query: " + next.getIndexString() + " (existing index belongs to " + existing.getResource().getIdDt().toUnqualifiedVersionless().getValue() + ")");
-							}
 						}
-						ourLog.debug("Persisting unique index: {}", next);
-						myEntityManager.persist(next);
 					}
+					ourLog.debug("Persisting unique index: {}", next);
+					myEntityManager.persist(next);
 				}
 			}
 
@@ -1813,7 +1841,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			if (nextChildDef instanceof RuntimeChildResourceDefinition) {
 				RuntimeChildResourceDefinition nextChildDefRes = (RuntimeChildResourceDefinition) nextChildDef;
-				Set<String> validTypes = new HashSet<String>();
+				Set<String> validTypes = new HashSet<>();
 				boolean allowAny = false;
 				for (Class<? extends IBaseResource> nextValidType : nextChildDefRes.getResourceTypes()) {
 					if (nextValidType.isInterface()) {
@@ -2105,6 +2133,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return b.toString();
 	}
 
+	/**
+	 * Do not call this method outside of unit tests
+	 */
+	@VisibleForTesting
+	public static void setValidationDisabledForUnitTest(boolean theValidationDisabledForUnitTest) {
+		ourValidationDisabledForUnitTest = theValidationDisabledForUnitTest;
+	}
+
 	private static List<BaseCodingDt> toBaseCodingList(List<IBaseCoding> theSecurityLabels) {
 		ArrayList<BaseCodingDt> retVal = new ArrayList<BaseCodingDt>(theSecurityLabels.size());
 		for (IBaseCoding next : theSecurityLabels) {
@@ -2131,7 +2167,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 
 			if (forcedId.isEmpty() == false) {
-				List<Long> retVal = new ArrayList<Long>(forcedId.size());
+				List<Long> retVal = new ArrayList<>(forcedId.size());
 				for (ForcedId next : forcedId) {
 					retVal.add(next.getResourcePid());
 				}

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

@@ -32,7 +32,7 @@ import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
 import ca.uhn.fhir.model.api.*;
@@ -56,6 +56,7 @@ import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Required;
+import org.springframework.lang.NonNull;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
@@ -126,7 +127,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
-		ourLog.info("Processed addTag {}/{} on {} in {}ms", new Object[]{theScheme, theTerm, theId, w.getMillisAndRestart()});
+		ourLog.debug("Processed addTag {}/{} on {} in {}ms", theScheme, theTerm, theId, w.getMillisAndRestart());
 	}
 
 	@Override
@@ -272,7 +273,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
-		ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
+		ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
 		return retVal;
 	}
 
@@ -349,7 +350,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
 		}
 
-		ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[]{theUrl, deletedResources.size(), w.getMillis()});
+		ourLog.debug("Processed delete on {} (matched {} resource(s)) in {}ms", theUrl, deletedResources.size(), w.getMillis());
 
 		DeleteMethodOutcome retVal = new DeleteMethodOutcome();
 		retVal.setDeletedEntities(deletedResources);
@@ -461,7 +462,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart());
 		outcome.setOperationOutcome(createInfoOperationOutcome(msg));
 
-		ourLog.info(msg);
+		ourLog.debug(msg);
 		return outcome;
 	}
 
@@ -529,7 +530,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		StopWatch w = new StopWatch();
 		TagList tags = super.getTags(myResourceType, null);
-		ourLog.info("Processed getTags on {} in {}ms", myResourceName, w.getMillisAndRestart());
+		ourLog.debug("Processed getTags on {} in {}ms", myResourceName, w.getMillisAndRestart());
 		return tags;
 	}
 
@@ -556,7 +557,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		StopWatch w = new StopWatch();
 		TagList retVal = super.getTags(myResourceType, theResourceId);
-		ourLog.info("Processed getTags on {} in {}ms", theResourceId, w.getMillisAndRestart());
+		ourLog.debug("Processed getTags on {} in {}ms", theResourceId, w.getMillisAndRestart());
 		return retVal;
 	}
 
@@ -568,7 +569,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		StopWatch w = new StopWatch();
 		IBundleProvider retVal = super.history(myResourceName, null, theSince, theUntil);
-		ourLog.info("Processed history on {} in {}ms", myResourceName, w.getMillisAndRestart());
+		ourLog.debug("Processed history on {} in {}ms", myResourceName, w.getMillisAndRestart());
 		return retVal;
 	}
 
@@ -585,7 +586,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IBundleProvider retVal = super.history(myResourceName, entity.getId(), theSince, theUntil);
 
-		ourLog.info("Processed history on {} in {}ms", id, w.getMillisAndRestart());
+		ourLog.debug("Processed history on {} in {}ms", id, w.getMillisAndRestart());
 		return retVal;
 	}
 
@@ -612,25 +613,31 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return theRequestDetails.getServer().getPagingProvider() instanceof DatabaseBackedPagingProvider;
 	}
 
-	protected void markResourcesMatchingExpressionAsNeedingReindexing(String theExpression) {
+	protected void markResourcesMatchingExpressionAsNeedingReindexing(Boolean theCurrentlyReindexing, String theExpression) {
+		// Avoid endless loops
+		if (Boolean.TRUE.equals(theCurrentlyReindexing)) {
+			return;
+		}
+
 		if (myDaoConfig.isMarkResourcesForReindexingUponSearchParameterChange()) {
 			if (isNotBlank(theExpression)) {
 				final String resourceType = theExpression.substring(0, theExpression.indexOf('.'));
-				ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", resourceType, theExpression);
+				ourLog.debug("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", resourceType, theExpression);
 
 				TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
 				txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-				int updatedCount = txTemplate.execute(new TransactionCallback<Integer>() {
+				Integer updatedCount = txTemplate.execute(new TransactionCallback<Integer>() {
 					@Override
-					public Integer doInTransaction(TransactionStatus theStatus) {
+					public @NonNull Integer doInTransaction(TransactionStatus theStatus) {
 						return myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType);
 					}
 				});
 
-				ourLog.info("Marked {} resources for reindexing", updatedCount);
+				ourLog.debug("Marked {} resources for reindexing", updatedCount);
 			}
 		}
-		mySearchParamRegistry.forceRefresh();
+
+		mySearchParamRegistry.requestRefresh();
 	}
 
 	@Override
@@ -658,7 +665,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			doMetaAdd(theMetaAdd, history);
 		}
 
-		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[]{theResourceId, w.getMillisAndRestart()});
+		ourLog.debug("Processed metaAddOperation on {} in {}ms", new Object[]{theResourceId, w.getMillisAndRestart()});
 
 		@SuppressWarnings("unchecked")
 		MT retVal = (MT) metaGetOperation(theMetaAdd.getClass(), theResourceId, theRequestDetails);
@@ -692,7 +699,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		myEntityManager.flush();
 
-		ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[]{theResourceId.getValue(), w.getMillisAndRestart()});
+		ourLog.debug("Processed metaDeleteOperation on {} in {}ms", new Object[]{theResourceId.getValue(), w.getMillisAndRestart()});
 
 		@SuppressWarnings("unchecked")
 		MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails);
@@ -707,7 +714,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			notifyInterceptors(RestOperationTypeEnum.META, requestDetails);
 		}
 
-		Set<TagDefinition> tagDefs = new HashSet<TagDefinition>();
+		Set<TagDefinition> tagDefs = new HashSet<>();
 		BaseHasResource entity = readEntity(theId);
 		for (BaseTag next : entity.getTags()) {
 			tagDefs.add(next.getTag());
@@ -733,9 +740,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		q.setParameter("res_type", myResourceName);
 		List<TagDefinition> tagDefinitions = q.getResultList();
 
-		MT retVal = toMetaDt(theType, tagDefinitions);
+		return toMetaDt(theType, tagDefinitions);
-
-		return retVal;
 	}
 
 	@Override
@@ -859,15 +864,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw new ResourceGoneException("Resource was deleted at " + deleted.getValueAsString());
 		}
 
-		ourLog.info("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
+		ourLog.debug("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
 		return retVal;
 	}
 
 	@Override
 	public BaseHasResource readEntity(IIdType theId) {
-		BaseHasResource entity = readEntity(theId, true);
 
-		return entity;
+		return readEntity(theId, true);
 	}
 
 	@Override
@@ -885,7 +889,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			if (theId.isVersionIdPartValidLong() == false) {
 				throw new ResourceNotFoundException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless()));
 			}
-			if (entity.getVersion() != theId.getVersionIdPartAsLong().longValue()) {
+			if (entity.getVersion() != theId.getVersionIdPartAsLong()) {
 				entity = null;
 			}
 		}
@@ -925,7 +929,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Override
 	public void reindex(T theResource, ResourceTable theEntity) {
 		ourLog.debug("Indexing resource {} - PID {}", theResource.getIdElement().getValue(), theEntity.getId());
+		CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
 		updateEntity(theResource, theEntity, null, true, false, theEntity.getUpdatedDate(), true, false);
+		CURRENTLY_REINDEXING.put(theResource, null);
 	}
 
 	@Override
@@ -962,7 +968,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		myEntityManager.merge(entity);
 
-		ourLog.info("Processed remove tag {}/{} on {} in {}ms", new Object[]{theScheme, theTerm, theId.getValue(), w.getMillisAndRestart()});
+		ourLog.debug("Processed remove tag {}/{} on {} in {}ms", theScheme, theTerm, theId.getValue(), w.getMillisAndRestart());
 	}
 
 	@Transactional(propagation = Propagation.SUPPORTS)
@@ -1276,7 +1282,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart());
 		outcome.setOperationOutcome(createInfoOperationOutcome(msg));
 
-		ourLog.info(msg);
+		ourLog.debug(msg);
 		return outcome;
 	}
 
@@ -1333,7 +1339,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		if (myDaoConfig.isEnforceReferentialIntegrityOnDelete() == false && !theForValidate) {
-			ourLog.info("Deleting {} resource dependencies which can no longer be satisfied", resultList.size());
+			ourLog.debug("Deleting {} resource dependencies which can no longer be satisfied", resultList.size());
 			myResourceLinkDao.delete(resultList);
 			return;
 		}

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

@@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
 import ca.uhn.fhir.jpa.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.util.ReindexFailureException;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -66,13 +66,21 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 
 	@Autowired
 	private ITermConceptDao myTermConceptDao;
-
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
 	@Autowired
 	private PlatformTransactionManager myTxManager;
 	@Autowired
 	private IResourceTableDao myResourceTableDao;
 
 	private int doPerformReindexingPass(final Integer theCount) {
+		/*
+		 * If any search parameters have been recently added or changed,
+		 * this makes sure that the cache has been reloaded to reflect
+		 * them.
+		 */
+		mySearchParamRegistry.refreshCacheIfNecessary();
+
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
 		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
 		return doPerformReindexingPassForResources(theCount, txTemplate);

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

@@ -24,17 +24,25 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.util.SearchParameterUtil;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.annotation.Scheduled;
 
 import javax.annotation.PostConstruct;
 import java.util.*;
 
-public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
+public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implements ISearchParamRegistry {
+
+	private static final int MAX_MANAGED_PARAM_COUNT = 10000;
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseSearchParamRegistry.class);
 	private Map<String, Map<String, RuntimeSearchParam>> myBuiltInSearchParams;
 	private volatile Map<String, List<JpaRuntimeSearchParam>> myActiveUniqueSearchParams = Collections.emptyMap();
@@ -43,14 +51,26 @@ public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
 	private FhirContext myCtx;
 	@Autowired
 	private Collection<IFhirResourceDao<?>> myDaos;
+	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
+	@Autowired
+	private DaoConfig myDaoConfig;
+	private volatile long myLastRefresh;
 
 	public BaseSearchParamRegistry() {
 		super();
 	}
 
+	@Override
+	public void requestRefresh() {
+		synchronized (this) {
+			myLastRefresh = 0;
+		}
+	}
+
 	@Override
 	public void forceRefresh() {
-		// nothing by default
+		requestRefresh();
+		refreshCacheIfNecessary();
 	}
 
 	@Override
@@ -63,21 +83,19 @@ public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
 		return retVal;
 	}
 
+
 	@Override
 	public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
-		return myBuiltInSearchParams;
+		return myActiveSearchParams;
 	}
 
 	@Override
 	public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
-		Validate.notBlank(theResourceName, "theResourceName must not be blank or null");
+		return myActiveSearchParams.get(theResourceName);
-
-		return myBuiltInSearchParams.get(theResourceName);
 	}
 
 	@Override
 	public List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName) {
-		refreshCacheIfNecessary();
 		List<JpaRuntimeSearchParam> retVal = myActiveUniqueSearchParams.get(theResourceName);
 		if (retVal == null) {
 			retVal = Collections.emptyList();
@@ -87,7 +105,6 @@ public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
 
 	@Override
 	public List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName, Set<String> theParamNames) {
-		refreshCacheIfNecessary();
 
 		Map<Set<String>, List<JpaRuntimeSearchParam>> paramNamesToParams = myActiveParamNamesToUniqueSearchParams.get(theResourceName);
 		if (paramNamesToParams == null) {
@@ -105,7 +122,18 @@ public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
 		return myBuiltInSearchParams;
 	}
 
-	public void populateActiveSearchParams(Map<String, Map<String, RuntimeSearchParam>> theActiveSearchParams) {
+	private Map<String, RuntimeSearchParam> getSearchParamMap(Map<String, Map<String, RuntimeSearchParam>> searchParams, String theResourceName) {
+		Map<String, RuntimeSearchParam> retVal = searchParams.get(theResourceName);
+		if (retVal == null) {
+			retVal = new HashMap<>();
+			searchParams.put(theResourceName, retVal);
+		}
+		return retVal;
+	}
+
+	public abstract IFhirResourceDao<SP> getSearchParameterDao();
+
+	private void populateActiveSearchParams(Map<String, Map<String, RuntimeSearchParam>> theActiveSearchParams) {
 		Map<String, List<JpaRuntimeSearchParam>> activeUniqueSearchParams = new HashMap<>();
 		Map<String, Map<Set<String>, List<JpaRuntimeSearchParam>>> activeParamNamesToUniqueSearchParams = new HashMap<>();
 
@@ -196,8 +224,100 @@ public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
 		}
 
 		myBuiltInSearchParams = Collections.unmodifiableMap(resourceNameToSearchParams);
+
+		refreshCacheIfNecessary();
 	}
 
-	protected abstract void refreshCacheIfNecessary();
+	@Override
+	public void refreshCacheIfNecessary() {
+		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
+		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
+			synchronized (this) {
+				if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
+					StopWatch sw = new StopWatch();
+
+					Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
+					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
+						for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
+							String nextResourceName = nextBuiltInEntry.getKey();
+							getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
+						}
+					}
+
+					SearchParameterMap params = new SearchParameterMap();
+					params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
+
+					IBundleProvider allSearchParamsBp = getSearchParameterDao().search(params);
+					int size = allSearchParamsBp.size();
+
+					// Just in case..
+					if (size >= MAX_MANAGED_PARAM_COUNT) {
+						ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
+						size = MAX_MANAGED_PARAM_COUNT;
+					}
+
+					List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
+					for (IBaseResource nextResource : allSearchParams) {
+						SP nextSp = (SP) nextResource;
+						RuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
+						if (runtimeSp == null) {
+							continue;
+						}
+
+						for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myCtx, nextSp)) {
+							if (isBlank(nextBaseName)) {
+								continue;
+							}
+
+							Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, nextBaseName);
+							String name = runtimeSp.getName();
+							if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
+								searchParamMap.put(name, runtimeSp);
+							}
+
+						}
+					}
+
+					Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
+					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
+						for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
+							String nextName = nextSp.getName();
+							if (nextSp.getStatus() != RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE) {
+								nextSp = null;
+							}
+
+							if (!activeSearchParams.containsKey(nextEntry.getKey())) {
+								activeSearchParams.put(nextEntry.getKey(), new HashMap<String, RuntimeSearchParam>());
+							}
+							if (activeSearchParams.containsKey(nextEntry.getKey())) {
+								ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
+							}
+
+							if (nextSp != null) {
+								activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
+							} else {
+								activeSearchParams.get(nextEntry.getKey()).remove(nextName);
+							}
+						}
+					}
+
+					myActiveSearchParams = activeSearchParams;
+
+					populateActiveSearchParams(activeSearchParams);
+
+					myLastRefresh = System.currentTimeMillis();
+					ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
+				}
+			}
+		}
+	}
+
+	@Scheduled(fixedDelay = 10 * DateUtils.MILLIS_PER_SECOND)
+	public void refreshCacheOnSchedule() {
+		refreshCacheIfNecessary();
+	}
+
+	protected abstract RuntimeSearchParam toRuntimeSp(SP theNextSp);
+
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java

@@ -45,7 +45,9 @@ public class FhirResourceDaoSearchParameterDstu2 extends FhirResourceDaoDstu2<Se
 	private IFhirSystemDao<Bundle, MetaDt> mySystemDao;
 
 	protected void markAffectedResources(SearchParameter theResource) {
-		markResourcesMatchingExpressionAsNeedingReindexing(theResource != null ? theResource.getXpath() : null);
+		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
+		String expression = theResource != null ? theResource.getXpath() : null;
+		markResourcesMatchingExpressionAsNeedingReindexing(reindex, expression);
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -25,6 +25,7 @@ import java.util.*;
 
 import javax.persistence.TypedQuery;
 
+import ca.uhn.fhir.model.primitive.UriDt;
 import org.apache.http.NameValuePair;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -453,6 +454,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				continue;
 			}
 
+			// References
 			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
 			for (BaseResourceReferenceDt nextRef : allRefs) {
 				IdDt nextId = nextRef.getReference();
@@ -461,13 +463,30 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				}
 				if (idSubstitutions.containsKey(nextId)) {
 					IdDt newId = idSubstitutions.get(nextId);
-					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
 					nextRef.setReference(newId);
 				} else {
 					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
 				}
 			}
 
+			// URIs
+			List<UriDt> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriDt.class);
+			for (UriDt nextRef : allUris) {
+				if (nextRef instanceof IIdType) {
+					continue; // No substitution on the resource ID itself!
+				}
+				IdDt nextUriString = new IdDt(nextRef.getValueAsString());
+				if (idSubstitutions.containsKey(nextUriString)) {
+					IdDt newId = idSubstitutions.get(nextUriString);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
+					nextRef.setValue(newId.getValue());
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
+				}
+			}
+
+
 			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
@@ -503,7 +522,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 			if (replacement.equals(next)) {
 				continue;
 			}
-			ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
+			ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
 		}
 
 		/*
@@ -532,7 +551,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				}
 				for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
 					String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
-					requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
+					requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
 				}
 				url = url.substring(0, qIndex);
 			}

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

@@ -1,17 +1,15 @@
 package ca.uhn.fhir.jpa.dao;
 
-import java.util.Collection;
-import java.util.Set;
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupportingAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.util.Collection;
+import java.util.Set;
 
 /*
  * #%L
@@ -35,7 +33,9 @@ import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupporti
 
 public interface IDao {
 
-	ResourceMetadataKeySupportingAnyResource<Long, Long> RESOURCE_PID = new MetadataKeyResourcePid("RESOURCE_PID");
+	MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid("RESOURCE_PID");
+
+	MetadataKeyCurrentlyReindexing CURRENTLY_REINDEXING = new MetadataKeyCurrentlyReindexing("CURRENTLY_REINDEXING");
 
 	FhirContext getContext();
 

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

@@ -29,6 +29,9 @@ import java.util.Set;
 
 public interface ISearchParamRegistry {
 
+	/**
+	 * Request that the cache be refreshed now, in the current thread
+	 */
 	void forceRefresh();
 
 	/**
@@ -36,11 +39,18 @@ public interface ISearchParamRegistry {
 	 */
 	RuntimeSearchParam getActiveSearchParam(String theResourceName, String theParamName);
 
+	Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams();
+
 	Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName);
 
-	Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams();
+	List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName, Set<String> theParamNames);
 
 	List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName);
 
-	List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName, Set<String> theParamNames);
+	void refreshCacheIfNecessary();
+
+	/**
+	 * Request that the cache be refreshed at the next convenient time (in a different thread)
+	 */
+	void requestRefresh();
 }

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

@@ -0,0 +1,70 @@
+package ca.uhn.fhir.jpa.dao;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupportingAnyResource;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public final class MetadataKeyCurrentlyReindexing extends ResourceMetadataKeySupportingAnyResource<Boolean, Boolean> {
+	private static final long serialVersionUID = 1L;
+
+	MetadataKeyCurrentlyReindexing(String theValue) {
+		super(theValue);
+	}
+
+	@Override
+	public Boolean get(IAnyResource theResource) {
+		return (Boolean) theResource.getUserData(IDao.CURRENTLY_REINDEXING.name());
+	}
+
+	@Override
+	public Boolean get(IResource theResource) {
+		return (Boolean) theResource.getResourceMetadata().get(IDao.CURRENTLY_REINDEXING);
+	}
+
+	public Boolean get(IBaseResource theResource) {
+		if (theResource instanceof IAnyResource) {
+			return get((IAnyResource) theResource);
+		} else {
+			return get((IResource) theResource);
+		}
+	}
+
+	@Override
+	public void put(IAnyResource theResource, Boolean theObject) {
+		theResource.setUserData(IDao.CURRENTLY_REINDEXING.name(), theObject);
+	}
+
+	public void put(IBaseResource theResource, Boolean theValue) {
+		if (theResource instanceof IAnyResource) {
+			put((IAnyResource) theResource, theValue);
+		} else {
+			put((IResource) theResource, theValue);
+		}
+	}
+
+	@Override
+	public void put(IResource theResource, Boolean theObject) {
+		theResource.getResourceMetadata().put(IDao.CURRENTLY_REINDEXING, theObject);
+	}
+}

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

@@ -28,7 +28,7 @@ import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.jpa.util.BaseIterator;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.model.api.*;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
@@ -83,7 +83,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 	private static final List<Long> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<Long>());
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
-	private static Long NO_MORE = Long.valueOf(-1);
+	private static Long NO_MORE = -1L;
 	private static HandlerTypeEnum ourLastHandlerMechanismForUnitTest;
 	private List<Long> myAlsoIncludePids;
 	private CriteriaBuilder myBuilder;
@@ -331,10 +331,9 @@ public class SearchBuilder implements ISearchBuilder {
 		List<Predicate> codePredicates = new ArrayList<Predicate>();
 
 		for (IQueryParameterType nextOr : theList) {
-			IQueryParameterType params = nextOr;
 
-			if (params instanceof ReferenceParam) {
+			if (nextOr instanceof ReferenceParam) {
-				ReferenceParam ref = (ReferenceParam) params;
+				ReferenceParam ref = (ReferenceParam) nextOr;
 
 				if (isBlank(ref.getChain())) {
 					IIdType dt = new IdDt(ref.getBaseUrl(), ref.getResourceType(), ref.getIdPart(), null);
@@ -471,7 +470,7 @@ public class SearchBuilder implements ISearchBuilder {
 						IQueryParameterType chainValue;
 						if (remainingChain != null) {
 							if (param == null || param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
-								ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", new Object[]{nextType.getSimpleName(), chain, remainingChain});
+								ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", new Object[] {nextType.getSimpleName(), chain, remainingChain});
 								continue;
 							}
 
@@ -533,7 +532,7 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 
 			} else {
-				throw new IllegalArgumentException("Invalid token type (expecting ReferenceParam): " + params.getClass());
+				throw new IllegalArgumentException("Invalid token type (expecting ReferenceParam): " + nextOr.getClass());
 			}
 
 		}
@@ -771,12 +770,11 @@ public class SearchBuilder implements ISearchBuilder {
 			return;
 		}
 
-		List<Predicate> codePredicates = new ArrayList<Predicate>();
+		List<Predicate> codePredicates = new ArrayList<>();
 		for (IQueryParameterType nextOr : theList) {
-			IQueryParameterType params = nextOr;
 
-			if (params instanceof UriParam) {
+			if (nextOr instanceof UriParam) {
-				UriParam param = (UriParam) params;
+				UriParam param = (UriParam) nextOr;
 
 				String value = param.getValue();
 				if (value == null) {
@@ -821,7 +819,7 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 				codePredicates.add(predicate);
 			} else {
-				throw new IllegalArgumentException("Invalid URI type: " + params.getClass());
+				throw new IllegalArgumentException("Invalid URI type: " + nextOr.getClass());
 			}
 
 		}
@@ -838,9 +836,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 		Predicate orPredicate = myBuilder.or(toArray(codePredicates));
 
-		Predicate paramNamePredicate = myBuilder.equal(join.get("myParamName"), theParamName);
+		Predicate outerPredicate = combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, join, orPredicate);
-		Predicate outerPredicate = myBuilder.and(paramNamePredicate, orPredicate);
-
 		myPredicates.add(outerPredicate);
 	}
 
@@ -1196,7 +1192,7 @@ public class SearchBuilder implements ISearchBuilder {
 				for (VersionIndependentConcept nextCode : codes) {
 					List<VersionIndependentConcept> systemCodes = map.get(nextCode.getSystem());
 					if (null == systemCodes) {
-						systemCodes = new ArrayList<VersionIndependentConcept>();
+						systemCodes = new ArrayList<>();
 						map.put(nextCode.getSystem(), systemCodes);
 					}
 					systemCodes.add(nextCode);
@@ -1343,7 +1339,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 		}
 
-		myPredicates = new ArrayList<Predicate>();
+		myPredicates = new ArrayList<>();
 
 		if (myParams.getEverythingMode() != null) {
 			Join<ResourceTable, ResourceLink> join = myResourceTableRoot.join("myResourceLinks", JoinType.LEFT);
@@ -1352,7 +1348,7 @@ public class SearchBuilder implements ISearchBuilder {
 				StringParam idParm = (StringParam) myParams.get(BaseResource.SP_RES_ID).get(0).get(0);
 				Long pid = BaseHapiFhirDao.translateForcedIdToPid(myResourceName, idParm.getValue(), myForcedIdDao);
 				if (myAlsoIncludePids == null) {
-					myAlsoIncludePids = new ArrayList<Long>(1);
+					myAlsoIncludePids = new ArrayList<>(1);
 				}
 				myAlsoIncludePids.add(pid);
 				myPredicates.add(myBuilder.equal(join.get("myTargetResourcePid").as(Long.class), pid));
@@ -1475,37 +1471,37 @@ public class SearchBuilder implements ISearchBuilder {
 		switch (param.getParamType()) {
 			case STRING:
 				joinAttrName = "myParamsString";
-				sortAttrName = new String[]{"myValueExact"};
+				sortAttrName = new String[] {"myValueExact"};
 				joinType = JoinEnum.STRING;
 				break;
 			case DATE:
 				joinAttrName = "myParamsDate";
-				sortAttrName = new String[]{"myValueLow"};
+				sortAttrName = new String[] {"myValueLow"};
 				joinType = JoinEnum.DATE;
 				break;
 			case REFERENCE:
 				joinAttrName = "myResourceLinks";
-				sortAttrName = new String[]{"myTargetResourcePid"};
+				sortAttrName = new String[] {"myTargetResourcePid"};
 				joinType = JoinEnum.REFERENCE;
 				break;
 			case TOKEN:
 				joinAttrName = "myParamsToken";
-				sortAttrName = new String[]{"mySystem", "myValue"};
+				sortAttrName = new String[] {"mySystem", "myValue"};
 				joinType = JoinEnum.TOKEN;
 				break;
 			case NUMBER:
 				joinAttrName = "myParamsNumber";
-				sortAttrName = new String[]{"myValue"};
+				sortAttrName = new String[] {"myValue"};
 				joinType = JoinEnum.NUMBER;
 				break;
 			case URI:
 				joinAttrName = "myParamsUri";
-				sortAttrName = new String[]{"myUri"};
+				sortAttrName = new String[] {"myUri"};
 				joinType = JoinEnum.URI;
 				break;
 			case QUANTITY:
 				joinAttrName = "myParamsQuantity";
-				sortAttrName = new String[]{"myValue"};
+				sortAttrName = new String[] {"myValue"};
 				joinType = JoinEnum.QUANTITY;
 				break;
 			default:
@@ -1780,7 +1776,7 @@ public class SearchBuilder implements ISearchBuilder {
 			nextRoundMatches = pidsToInclude;
 		} while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound);
 
-		ourLog.info("Loaded {} {} in {} rounds and {} ms", new Object[]{allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart()});
+		ourLog.info("Loaded {} {} in {} rounds and {} ms", new Object[] {allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart()});
 
 		return allAdded;
 	}
@@ -2006,8 +2002,17 @@ public class SearchBuilder implements ISearchBuilder {
 		RuntimeResourceDefinition resourceDef = theContext.getResourceDefinition(theResourceType);
 		RuntimeSearchParam param = theCallingDao.getSearchParamByName(resourceDef, theParamName);
 		List<String> path = param.getPathsSplit();
-		Predicate type = theFrom.get("mySourcePath").in(path);
+
-		return type;
+		/*
+		 * SearchParameters can declare paths on multiple resources
+		 * types. Here we only want the ones that actually apply.
+		 */
+		for (Iterator<String> iter = path.iterator(); iter.hasNext(); ) {
+			if (!iter.next().startsWith(theResourceType + ".")) {
+				iter.remove();
+			}
+		}
+		return theFrom.get("mySourcePath").in(path);
 	}
 
 	private static List<Long> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<Long> thePids) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamRegistryDstu2.java

@@ -21,17 +21,12 @@ package ca.uhn.fhir.jpa.dao;
  */
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
-import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.util.JpaConstants;
-import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.dstu2.resource.SearchParameter;
-import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.util.DatatypeUtil;
-import org.apache.commons.lang3.time.DateUtils;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -39,134 +34,19 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.util.*;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-public class SearchParamRegistryDstu2 extends BaseSearchParamRegistry {
+public class SearchParamRegistryDstu2 extends BaseSearchParamRegistry<SearchParameter> {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamRegistryDstu3.class);
-	public static final int MAX_MANAGED_PARAM_COUNT = 10000;
-
-	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
-
-	@Autowired
-	private DaoConfig myDaoConfig;
-
-	private volatile long myLastRefresh;
 
 	@Autowired
 	private IFhirResourceDao<SearchParameter> mySpDao;
 
 	@Override
-	public void forceRefresh() {
+	public IFhirResourceDao<SearchParameter> getSearchParameterDao() {
-		synchronized (this) {
+		return mySpDao;
-			myLastRefresh = 0;
-		}
 	}
 
 	@Override
-	public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
+	protected JpaRuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams;
-	}
-
-	@Override
-	public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams.get(theResourceName);
-	}
-
-	private Map<String, RuntimeSearchParam> getSearchParamMap(Map<String, Map<String, RuntimeSearchParam>> searchParams, String theResourceName) {
-		Map<String, RuntimeSearchParam> retVal = searchParams.get(theResourceName);
-		if (retVal == null) {
-			retVal = new HashMap<>();
-			searchParams.put(theResourceName, retVal);
-		}
-		return retVal;
-	}
-
-	protected void refreshCacheIfNecessary() {
-		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
-		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-			synchronized (this) {
-				if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-					StopWatch sw = new StopWatch();
-
-					Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
-					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
-						for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
-							String nextResourceName = nextBuiltInEntry.getKey();
-							getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
-						}
-					}
-
-					SearchParameterMap params = new SearchParameterMap();
-					params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
-
-					IBundleProvider allSearchParamsBp = mySpDao.search(params);
-					int size = allSearchParamsBp.size();
-
-					// Just in case..
-					if (size > MAX_MANAGED_PARAM_COUNT) {
-						ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
-						size = MAX_MANAGED_PARAM_COUNT;
-					}
-
-					List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
-					for (IBaseResource nextResource : allSearchParams) {
-						SearchParameter nextSp = (SearchParameter) nextResource;
-						JpaRuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
-						if (runtimeSp == null) {
-							continue;
-						}
-
-						CodeDt nextBaseName = nextSp.getBaseElement();
-							String resourceType = nextBaseName.getValue();
-							if (isBlank(resourceType)) {
-								continue;
-							}
-
-							Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, resourceType);
-							String name = runtimeSp.getName();
-							if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
-								searchParamMap.put(name, runtimeSp);
-							}
-
-					}
-
-					Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
-					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
-						for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
-							String nextName = nextSp.getName();
-							if (nextSp.getStatus() != RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE) {
-								nextSp = null;
-							}
-
-							if (!activeSearchParams.containsKey(nextEntry.getKey())) {
-								activeSearchParams.put(nextEntry.getKey(), new HashMap<String, RuntimeSearchParam>());
-							}
-							if (activeSearchParams.containsKey(nextEntry.getKey())) {
-								ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
-							}
-
-							if (nextSp != null) {
-								activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
-							} else {
-								activeSearchParams.get(nextEntry.getKey()).remove(nextName);
-							}
-						}
-					}
-
-					myActiveSearchParams = activeSearchParams;
-
-					super.populateActiveSearchParams(activeSearchParams);
-
-					myLastRefresh = System.currentTimeMillis();
-					ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
-				}
-			}
-		}
-	}
-
-	private JpaRuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
 		String name = theNextSp.getCode();
 		String description = theNextSp.getDescription();
 		String path = theNextSp.getXpath();
@@ -212,9 +92,9 @@ public class SearchParamRegistryDstu2 extends BaseSearchParamRegistry {
 			}
 		}
 		Set<String> providesMembershipInCompartments = Collections.emptySet();
-		Set<String> targets = toStrings(theNextSp.getTarget());
+		Set<String> targets = DatatypeUtil.toStringSet(theNextSp.getTarget());
 
-		if (isBlank(name) || isBlank(path) || paramType == null) {
+		if (isBlank(name) || isBlank(path)) {
 			if (paramType != RestSearchParameterTypeEnum.COMPOSITE) {
 				return null;
 			}
@@ -235,19 +115,8 @@ public class SearchParamRegistryDstu2 extends BaseSearchParamRegistry {
 		}
 
 		List<JpaRuntimeSearchParam.Component> components = Collections.emptyList();
-		Collection<? extends IPrimitiveType<String>> base = Arrays.asList(theNextSp.getBaseElement());
+		Collection<? extends IPrimitiveType<String>> base = Collections.singletonList(theNextSp.getBaseElement());
-		JpaRuntimeSearchParam retVal = new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, base);
+		return new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, base);
-		return retVal;
-	}
-
-	private Set<String> toStrings(List<? extends CodeDt> theTarget) {
-		HashSet<String> retVal = new HashSet<String>();
-		for (CodeDt next : theTarget) {
-			if (isNotBlank(next.getValue())) {
-				retVal.add(next.getValue());
-			}
-		}
-		return retVal;
 	}
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -50,7 +50,9 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 
 	protected void markAffectedResources(SearchParameter theResource) {
-		markResourcesMatchingExpressionAsNeedingReindexing(theResource != null ? theResource.getExpression() : null);
+		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
+		String expression = theResource != null ? theResource.getExpression() : null;
+		markResourcesMatchingExpressionAsNeedingReindexing(reindex, expression);
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.SubscriptionTable;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import org.apache.commons.lang3.ObjectUtils;
 import org.hl7.fhir.dstu3.model.Subscription;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
@@ -108,6 +109,16 @@ public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subsc
 	}
 
 	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
+		switch (ObjectUtils.defaultIfNull(theResource.getStatus(), SubscriptionStatus.OFF)) {
+			case REQUESTED:
+			case ACTIVE:
+				break;
+			case ERROR:
+			case OFF:
+			case NULL:
+				return null;
+		}
+
 		String query = theResource.getCriteria();
 		if (isBlank(query)) {
 			throw new UnprocessableEntityException("Subscription.criteria must be populated");
@@ -144,6 +155,9 @@ public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subsc
 		super.validateResourceForStorage(theResource, theEntityToSave);
 
 		RuntimeResourceDefinition resDef = validateCriteriaAndReturnResourceDefinition(theResource);
+		if (resDef == null) {
+			return;
+		}
 
 		IFhirResourceDao<? extends IBaseResource> dao = getDao(resDef.getImplementingClass());
 		if (dao == null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -28,7 +28,7 @@ import java.util.Map.Entry;
 
 import javax.persistence.TypedQuery;
 
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
@@ -260,7 +260,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				}
 				for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
 					String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
-					requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
+					requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
 				}
 				url = url.substring(0, qIndex);
 			}
@@ -311,7 +311,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 	
 	@SuppressWarnings("unchecked")
 	private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date updateTime, Set<IdType> allIds,
-			Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder, List<BundleEntryComponent> theEntries) {
+			Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder, List<BundleEntryComponent> theEntries) {
 		Set<String> deletedResources = new HashSet<String>();
 		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
 		Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<BundleEntryComponent, ResourceTable>();
@@ -379,10 +379,10 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				res.setId((String) null);
 				DaoMethodOutcome outcome;
 				String matchUrl = nextReqEntry.getRequest().getIfNoneExist();
-				matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+				matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 				outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
 				if (nextResourceId != null) {
-					handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
+					handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
 				}
 				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				if (outcome.getCreated() == false) {
@@ -412,7 +412,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 					}
 				} else {
 					String matchUrl = parts.getResourceType() + '?' + parts.getParams();
-					matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+					matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 					DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequestDetails);
 					List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
 					for (ResourceTable deleted : allDeleted) {
@@ -453,14 +453,14 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 					} else {
 						matchUrl = parts.getResourceType();
 					}
-					matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+					matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 					outcome = resourceDao.update(res, matchUrl, false, theRequestDetails);
 					if (Boolean.TRUE.equals(outcome.getCreated())) {
 						conditionalRequestUrls.put(matchUrl, res.getClass());
 					}
 				}
 
-				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
+				handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
 				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				break;
 			}
@@ -496,15 +496,16 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				continue;
 			}
 
+			// Refererences
 			List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
 			for (IBaseReference nextRef : allRefs) {
 				IIdType nextId = nextRef.getReferenceElement();
 				if (!nextId.hasIdPart()) {
 					continue;
 				}
-				if (idSubstitutions.containsKey(nextId)) {
+				if (theIdSubstitutions.containsKey(nextId)) {
-					IdType newId = idSubstitutions.get(nextId);
+					IdType newId = theIdSubstitutions.get(nextId);
-					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
 					nextRef.setReference(newId.getValue());
 				} else if (nextId.getValue().startsWith("urn:")) {
 					throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
@@ -513,6 +514,22 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				}
 			}
 
+			// URIs
+			List<UriType> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriType.class);
+			for (UriType nextRef : allUris) {
+				if (nextRef instanceof IIdType) {
+					continue; // No substitution on the resource ID itself!
+				}
+				IdType nextUriString = new IdType(nextRef.getValueAsString());
+				if (theIdSubstitutions.containsKey(nextUriString)) {
+					IdType newId = theIdSubstitutions.get(nextUriString);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
+					nextRef.setValue(newId.getValue());
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
+				}
+			}
+
 			IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
@@ -521,13 +538,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 			}
 		}
 
-		SessionImpl session = (SessionImpl) myEntityManager.unwrap(Session.class);
+		flushJpaSession();
-		int insertionCount = session.getActionQueue().numberOfInsertions();
-		int updateCount = session.getActionQueue().numberOfUpdates();
-
-		StopWatch sw = new StopWatch();
-		myEntityManager.flush();
-		ourLog.info("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
 
 		/*
 		 * Double check we didn't allow any duplicates we shouldn't have
@@ -546,14 +557,14 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		}
 
 		for (IdType next : allIds) {
-			IdType replacement = idSubstitutions.get(next);
+			IdType replacement = theIdSubstitutions.get(next);
 			if (replacement == null) {
 				continue;
 			}
 			if (replacement.equals(next)) {
 				continue;
 			}
-			ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
+			ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
 		}
 		return entriesToProcess;
 	}
@@ -603,6 +614,23 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		return retVal;
 	}
 
+	private String performIdSubstitutionsInMatchUrl(Map<IdType, IdType> theIdSubstitutions, String theMatchUrl) {
+		String matchUrl = theMatchUrl;
+		if (isNotBlank(matchUrl)) {
+			for (Entry<IdType, IdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
+				IdType nextTemporaryId = nextSubstitutionEntry.getKey();
+				IdType nextReplacementId = nextSubstitutionEntry.getValue();
+				String nextTemporaryIdPart = nextTemporaryId.getIdPart();
+				String nextReplacementIdPart = nextReplacementId.getValueAsString();
+				if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
+					matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
+					matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
+				}
+			}
+		}
+		return matchUrl;
+	}
+
 	private void populateEntryWithOperationOutcome(BaseServerResponseException caughtEx, BundleEntryComponent nextEntry) {
 		OperationOutcome oo = new OperationOutcome();
 		oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
@@ -664,27 +692,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
 	}
 
-
-
-	private String performIdSubstitutionsInMatchUrl(Map<IdType, IdType> theIdSubstitutions, String theMatchUrl) {
-		String matchUrl = theMatchUrl;
-		if (isNotBlank(matchUrl)) {
-			for (Entry<IdType, IdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
-				IdType nextTemporaryId = nextSubstitutionEntry.getKey();
-				IdType nextReplacementId = nextSubstitutionEntry.getValue();
-				String nextTemporaryIdPart = nextTemporaryId.getIdPart();
-				String nextReplacementIdPart = nextReplacementId.getValueAsString();
-				if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
-					matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
-					matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
-				}
-			}
-		}
-		return matchUrl;
-	}
-
-
-
 	private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
 		super.markRequestAsProcessingSubRequest(theRequestDetails);
 		try {
@@ -742,23 +749,9 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
 	}
 
-	private static class BaseServerResponseExceptionHolder
-	{
-		private BaseServerResponseException myException;
-
-		public BaseServerResponseException getException() {
-			return myException;
-		}
-
-		public void setException(BaseServerResponseException myException) {
-			this.myException = myException;
-		}
-	}
-
-	//@formatter:off
 	/**
 	 * Transaction Order, per the spec:
-	 * 
+	 *
 	 * Process any DELETE interactions
 	 * Process any POST interactions
 	 * Process any PUT interactions
@@ -859,4 +852,19 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 	}
 
+	//@formatter:off
+
+	private static class BaseServerResponseExceptionHolder
+	{
+		private BaseServerResponseException myException;
+
+		public BaseServerResponseException getException() {
+			return myException;
+		}
+
+		public void setException(BaseServerResponseException myException) {
+			this.myException = myException;
+		}
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamExtractorDstu3.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  */
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 import java.math.BigDecimal;
 import java.util.*;
@@ -478,8 +479,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 				multiType = true;
 			}
 
-			List<String> systems = new ArrayList<String>();
+			List<String> systems = new ArrayList<>();
-			List<String> codes = new ArrayList<String>();
+			List<String> codes = new ArrayList<>();
 
 			// String needContactPointSystem = null;
 			// if (nextPath.contains(".where(system='phone')")) {
@@ -693,11 +694,11 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 		IWorkerContext worker = new org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext(getContext(), myValidationSupport);
 		FHIRPathEngine fp = new FHIRPathEngine(worker);
 
-		List<Object> values = new ArrayList<Object>();
+		List<Object> values = new ArrayList<>();
 		try {
 			String[] nextPathsSplit = SPLIT.split(thePaths);
 			for (String nextPath : nextPathsSplit) {
-				List<Base> allValues = fp.evaluate((Base) theResource, nextPath);
+				List<Base> allValues = fp.evaluate((Base) theResource, trim(nextPath));
 				if (allValues.isEmpty() == false) {
 					values.addAll(allValues);
 				}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java

@@ -20,210 +20,91 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
+import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.jpa.dao.BaseSearchParamRegistry;
-
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import java.util.*;
-import java.util.Map.Entry;
-
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.util.JpaConstants;
-import org.apache.commons.lang3.time.DateUtils;
+import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-import org.hl7.fhir.dstu3.model.CodeType;
+import ca.uhn.fhir.util.DatatypeUtil;
 import org.hl7.fhir.dstu3.model.Extension;
 import org.hl7.fhir.dstu3.model.SearchParameter;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import ca.uhn.fhir.context.RuntimeSearchParam;
+import java.util.ArrayList;
-import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
+import java.util.Collections;
-import ca.uhn.fhir.jpa.dao.*;
+import java.util.List;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import java.util.Set;
-import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
 
-public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
+import static org.apache.commons.lang3.StringUtils.isBlank;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamRegistryDstu3.class);
-	public static final int MAX_MANAGED_PARAM_COUNT = 10000;
 
-	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
+public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry<SearchParameter> {
-
-	@Autowired
-	private DaoConfig myDaoConfig;
-
-	private volatile long myLastRefresh;
 
 	@Autowired
 	private IFhirResourceDao<SearchParameter> mySpDao;
 
 	@Override
-	public void forceRefresh() {
+	public IFhirResourceDao<SearchParameter> getSearchParameterDao() {
-		synchronized (this) {
+		return mySpDao;
-			myLastRefresh = 0;
-		}
 	}
 
 	@Override
-	public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
+	protected JpaRuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams;
-	}
-
-	@Override
-	public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams.get(theResourceName);
-	}
-
-	private Map<String, RuntimeSearchParam> getSearchParamMap(Map<String, Map<String, RuntimeSearchParam>> searchParams, String theResourceName) {
-		Map<String, RuntimeSearchParam> retVal = searchParams.get(theResourceName);
-		if (retVal == null) {
-			retVal = new HashMap<>();
-			searchParams.put(theResourceName, retVal);
-		}
-		return retVal;
-	}
-
-	protected void refreshCacheIfNecessary() {
-		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
-		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-			synchronized (this) {
-				if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-					StopWatch sw = new StopWatch();
-
-					Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
-					for (Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
-						for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
-							String nextResourceName = nextBuiltInEntry.getKey();
-							getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
-						}
-					}
-
-					SearchParameterMap params = new SearchParameterMap();
-					params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
-
-					IBundleProvider allSearchParamsBp = mySpDao.search(params);
-					int size = allSearchParamsBp.size();
-
-					// Just in case..
-					if (size > MAX_MANAGED_PARAM_COUNT) {
-						ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
-						size = MAX_MANAGED_PARAM_COUNT;
-					}
-
-					List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
-					for (IBaseResource nextResource : allSearchParams) {
-						SearchParameter nextSp = (SearchParameter) nextResource;
-						JpaRuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
-						if (runtimeSp == null) {
-							continue;
-						}
-
-						for (org.hl7.fhir.dstu3.model.CodeType nextBaseName : nextSp.getBase()) {
-							String resourceType = nextBaseName.getValue();
-							if (isBlank(resourceType)) {
-								continue;
-							}
-
-							Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, resourceType);
-							String name = runtimeSp.getName();
-							if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
-								searchParamMap.put(name, runtimeSp);
-							}
-
-						}
-					}
-
-					Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
-					for (Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
-						for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
-							String nextName = nextSp.getName();
-							if (nextSp.getStatus() != RuntimeSearchParamStatusEnum.ACTIVE) {
-								nextSp = null;
-							}
-
-							if (!activeSearchParams.containsKey(nextEntry.getKey())) {
-								activeSearchParams.put(nextEntry.getKey(), new HashMap<String, RuntimeSearchParam>());
-							}
-							if (activeSearchParams.containsKey(nextEntry.getKey())) {
-								ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
-							}
-
-							if (nextSp != null) {
-								activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
-							} else {
-								activeSearchParams.get(nextEntry.getKey()).remove(nextName);
-							}
-						}
-					}
-
-					myActiveSearchParams = activeSearchParams;
-
-					super.populateActiveSearchParams(activeSearchParams);
-
-					myLastRefresh = System.currentTimeMillis();
-					ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
-				}
-			}
-		}
-	}
-
-	private JpaRuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
 		String name = theNextSp.getCode();
 		String description = theNextSp.getDescription();
 		String path = theNextSp.getExpression();
 		RestSearchParameterTypeEnum paramType = null;
 		RuntimeSearchParamStatusEnum status = null;
 		switch (theNextSp.getType()) {
-		case COMPOSITE:
+			case COMPOSITE:
-			paramType = RestSearchParameterTypeEnum.COMPOSITE;
+				paramType = RestSearchParameterTypeEnum.COMPOSITE;
-			break;
-		case DATE:
-			paramType = RestSearchParameterTypeEnum.DATE;
-			break;
-		case NUMBER:
-			paramType = RestSearchParameterTypeEnum.NUMBER;
-			break;
-		case QUANTITY:
-			paramType = RestSearchParameterTypeEnum.QUANTITY;
-			break;
-		case REFERENCE:
-			paramType = RestSearchParameterTypeEnum.REFERENCE;
-			break;
-		case STRING:
-			paramType = RestSearchParameterTypeEnum.STRING;
-			break;
-		case TOKEN:
-			paramType = RestSearchParameterTypeEnum.TOKEN;
-			break;
-		case URI:
-			paramType = RestSearchParameterTypeEnum.URI;
-			break;
-		case NULL:
-			break;
-		}
-		if (theNextSp.getStatus() != null) {
-			switch (theNextSp.getStatus()) {
-			case ACTIVE:
-				status = RuntimeSearchParamStatusEnum.ACTIVE;
 				break;
-			case DRAFT:
+			case DATE:
-				status = RuntimeSearchParamStatusEnum.DRAFT;
+				paramType = RestSearchParameterTypeEnum.DATE;
 				break;
-			case RETIRED:
+			case NUMBER:
-				status = RuntimeSearchParamStatusEnum.RETIRED;
+				paramType = RestSearchParameterTypeEnum.NUMBER;
 				break;
-			case UNKNOWN:
+			case QUANTITY:
-				status = RuntimeSearchParamStatusEnum.UNKNOWN;
+				paramType = RestSearchParameterTypeEnum.QUANTITY;
+				break;
+			case REFERENCE:
+				paramType = RestSearchParameterTypeEnum.REFERENCE;
+				break;
+			case STRING:
+				paramType = RestSearchParameterTypeEnum.STRING;
+				break;
+			case TOKEN:
+				paramType = RestSearchParameterTypeEnum.TOKEN;
+				break;
+			case URI:
+				paramType = RestSearchParameterTypeEnum.URI;
 				break;
 			case NULL:
 				break;
+		}
+		if (theNextSp.getStatus() != null) {
+			switch (theNextSp.getStatus()) {
+				case ACTIVE:
+					status = RuntimeSearchParamStatusEnum.ACTIVE;
+					break;
+				case DRAFT:
+					status = RuntimeSearchParamStatusEnum.DRAFT;
+					break;
+				case RETIRED:
+					status = RuntimeSearchParamStatusEnum.RETIRED;
+					break;
+				case UNKNOWN:
+					status = RuntimeSearchParamStatusEnum.UNKNOWN;
+					break;
+				case NULL:
+					break;
 			}
 		}
 		Set<String> providesMembershipInCompartments = Collections.emptySet();
-		Set<String> targets = toStrings(theNextSp.getTarget());
+		Set<String> targets = DatatypeUtil.toStringSet(theNextSp.getTarget());
 
 		if (isBlank(name) || isBlank(path) || paramType == null) {
 			if (paramType != RestSearchParameterTypeEnum.COMPOSITE) {
@@ -250,18 +131,7 @@ public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
 			components.add(new JpaRuntimeSearchParam.Component(next.getExpression(), next.getDefinition()));
 		}
 
-		JpaRuntimeSearchParam retVal = new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, theNextSp.getBase());
+		return new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, theNextSp.getBase());
-		return retVal;
-	}
-
-	private Set<String> toStrings(List<CodeType> theTarget) {
-		HashSet<String> retVal = new HashSet<String>();
-		for (CodeType next : theTarget) {
-			if (isNotBlank(next.getValue())) {
-				retVal.add(next.getValue());
-			}
-		}
-		return retVal;
 	}
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java

@@ -40,14 +40,13 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoSearchParameterR4.class);
-
-
 	@Autowired
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 
 	protected void markAffectedResources(SearchParameter theResource) {
-		markResourcesMatchingExpressionAsNeedingReindexing(theResource != null ? theResource.getExpression() : null);
+		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
+		String expression = theResource != null ? theResource.getExpression() : null;
+		markResourcesMatchingExpressionAsNeedingReindexing(reindex, expression);
 	}
 
 	/**
@@ -128,7 +127,6 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
 			theExpression = theExpression.trim();
 
 			String[] expressionSplit = BaseSearchParamExtractor.SPLIT.split(theExpression);
-			String allResourceName = null;
 			for (String nextPath : expressionSplit) {
 				nextPath = nextPath.trim();
 
@@ -144,14 +142,6 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
 					throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\": " + e.getMessage());
 				}
 
-				if (allResourceName == null) {
-					allResourceName = resourceName;
-				} else {
-					if (!allResourceName.equals(resourceName)) {
-						throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
-					}
-				}
-
 			}
 
 		} // if have expression

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.SubscriptionTable;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import org.apache.commons.lang3.ObjectUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Subscription;
@@ -37,20 +38,16 @@ import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 
+import javax.annotation.Nullable;
 import java.util.Date;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoSubscriptionR4.class);
-
 	@Autowired
 	private ISubscriptionTableDao mySubscriptionTableDao;
 
-	@Autowired
-	private PlatformTransactionManager myTxManager;
-
 	private void createSubscriptionTable(ResourceTable theEntity, Subscription theSubscription) {
 		SubscriptionTable subscriptionEntity = new SubscriptionTable();
 		subscriptionEntity.setCreated(new Date());
@@ -108,7 +105,18 @@ public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscriptio
 		}
 	}
 
+	@Nullable
 	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
+		switch (ObjectUtils.defaultIfNull(theResource.getStatus(), Subscription.SubscriptionStatus.OFF)) {
+			case REQUESTED:
+			case ACTIVE:
+				break;
+			case ERROR:
+			case OFF:
+			case NULL:
+				return null;
+		}
+
 		String query = theResource.getCriteria();
 		if (isBlank(query)) {
 			throw new UnprocessableEntityException("Subscription.criteria must be populated");
@@ -145,6 +153,9 @@ public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscriptio
 		super.validateResourceForStorage(theResource, theEntityToSave);
 
 		RuntimeResourceDefinition resDef = validateCriteriaAndReturnResourceDefinition(theResource);
+		if (resDef == null) {
+			return;
+		}
 
 		IFhirResourceDao<? extends IBaseResource> dao = getDao(resDef.getImplementingClass());
 		if (dao == null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
@@ -144,7 +145,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		}
 
 		long delay = System.currentTimeMillis() - start;
-		ourLog.info("Batch completed in {}ms", new Object[]{delay});
+		ourLog.info("Batch completed in {}ms", new Object[] {delay});
 
 		return resp;
 	}
@@ -169,9 +170,9 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		long start = System.currentTimeMillis();
 		final Date updateTime = new Date();
 
-		final Set<IdType> allIds = new LinkedHashSet<IdType>();
+		final Set<IdType> allIds = new LinkedHashSet<>();
-		final Map<IdType, IdType> idSubstitutions = new HashMap<IdType, IdType>();
+		final Map<IdType, IdType> idSubstitutions = new HashMap<>();
-		final Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdType, DaoMethodOutcome>();
+		final Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
 
 		// Do all entries have a verb?
 		for (int i = 0; i < theRequest.getEntry().size(); i++) {
@@ -193,8 +194,8 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		 * we want the GET processing to use the final indexing state
 		 */
 		final Bundle response = new Bundle();
-		List<BundleEntryComponent> getEntries = new ArrayList<BundleEntryComponent>();
+		List<BundleEntryComponent> getEntries = new ArrayList<>();
-		final IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<Bundle.BundleEntryComponent, Integer>();
+		final IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<>();
 		for (int i = 0; i < theRequest.getEntry().size(); i++) {
 			originalRequestOrder.put(theRequest.getEntry().get(i), i);
 			response.addEntry();
@@ -265,8 +266,8 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 					paramValues.put(next.getName(), next.getValue());
 				}
 				for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
-					String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
+					String[] nextValue = nextParamEntry.getValue().toArray(new String[ nextParamEntry.getValue().size() ]);
-					requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
+					requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
 				}
 				url = url.substring(0, qIndex);
 			}
@@ -290,7 +291,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
 			}
 
-			Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
+			Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {0}", url);
 			try {
 				IBaseResource resource = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
 				if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
@@ -309,20 +310,20 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		}
 
 		long delay = System.currentTimeMillis() - start;
-		ourLog.info(theActionName + " completed in {}ms", new Object[]{delay});
+		ourLog.info(theActionName + " completed in {}ms", new Object[] {delay});
 
 		response.setType(BundleType.TRANSACTIONRESPONSE);
 		return response;
 	}
 
 	@SuppressWarnings("unchecked")
-	private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date updateTime, Set<IdType> allIds,
+	private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date theUpdateTime, Set<IdType> theAllIds,
-																											Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder, List<BundleEntryComponent> theEntries) {
+																											Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<BundleEntryComponent, Integer> theOriginalRequestOrder, List<BundleEntryComponent> theEntries) {
-		Set<String> deletedResources = new HashSet<String>();
+		Set<String> deletedResources = new HashSet<>();
-		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
+		List<DeleteConflict> deleteConflicts = new ArrayList<>();
-		Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<BundleEntryComponent, ResourceTable>();
+		Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<>();
-		Set<ResourceTable> nonUpdatedEntities = new HashSet<ResourceTable>();
+		Set<ResourceTable> nonUpdatedEntities = new HashSet<>();
-		Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<String, Class<? extends IBaseResource>>();
+		Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
 
 		/*
 		 * Loop through the request and process any entries of type
@@ -341,7 +342,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 				nextResourceId = res.getIdElement();
 
-				if (nextResourceId.hasIdPart() == false) {
+				if (!nextResourceId.hasIdPart()) {
 					if (isNotBlank(nextReqEntry.getFullUrl())) {
 						nextResourceId = new IdType(nextReqEntry.getFullUrl());
 					}
@@ -360,12 +361,12 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
 				 */
 				if (isPlaceholder(nextResourceId)) {
-					if (!allIds.add(nextResourceId)) {
+					if (!theAllIds.add(nextResourceId)) {
 						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
 					}
 				} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
 					IdType nextId = nextResourceId.toUnqualifiedVersionless();
-					if (!allIds.add(nextId)) {
+					if (!theAllIds.add(nextId)) {
 						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
 					}
 				}
@@ -375,7 +376,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 			HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
 
 			String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
-			BundleEntryComponent nextRespEntry = response.getEntry().get(originalRequestOrder.get(nextReqEntry));
+			BundleEntryComponent nextRespEntry = theResponse.getEntry().get(theOriginalRequestOrder.get(nextReqEntry));
 
 			switch (verb) {
 				case POST: {
@@ -385,10 +386,10 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 					res.setId((String) null);
 					DaoMethodOutcome outcome;
 					String matchUrl = nextReqEntry.getRequest().getIfNoneExist();
-					matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+					matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 					outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
 					if (nextResourceId != null) {
-						handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
+						handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
 					}
 					entriesToProcess.put(nextRespEntry, outcome.getEntity());
 					if (outcome.getCreated() == false) {
@@ -418,7 +419,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 						}
 					} else {
 						String matchUrl = parts.getResourceType() + '?' + parts.getParams();
-						matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+						matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 						DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequestDetails);
 						List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
 						for (ResourceTable deleted : allDeleted) {
@@ -459,14 +460,14 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 						} else {
 							matchUrl = parts.getResourceType();
 						}
-						matchUrl = performIdSubstitutionsInMatchUrl(idSubstitutions, matchUrl);
+						matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 						outcome = resourceDao.update(res, matchUrl, false, theRequestDetails);
 						if (Boolean.TRUE.equals(outcome.getCreated())) {
 							conditionalRequestUrls.put(matchUrl, res.getClass());
 						}
 					}
 
-					handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
+					handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
 					entriesToProcess.put(nextRespEntry, outcome.getEntity());
 					break;
 				}
@@ -499,21 +500,22 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		 */
 
 		FhirTerser terser = getContext().newTerser();
-		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
+		for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
 			IBaseResource nextResource = nextOutcome.getResource();
 			if (nextResource == null) {
 				continue;
 			}
 
+			// References
 			List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
 			for (IBaseReference nextRef : allRefs) {
 				IIdType nextId = nextRef.getReferenceElement();
 				if (!nextId.hasIdPart()) {
 					continue;
 				}
-				if (idSubstitutions.containsKey(nextId)) {
+				if (theIdSubstitutions.containsKey(nextId)) {
-					IdType newId = idSubstitutions.get(nextId);
+					IdType newId = theIdSubstitutions.get(nextId);
-					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
 					nextRef.setReference(newId.getValue());
 				} else if (nextId.getValue().startsWith("urn:")) {
 					throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
@@ -522,15 +524,31 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				}
 			}
 
+			// URIs
+			List<UriType> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriType.class);
+			for (UriType nextRef : allUris) {
+				if (nextRef instanceof IIdType) {
+					continue; // No substitution on the resource ID itself!
+				}
+				IdType nextUriString = new IdType(nextRef.getValueAsString());
+				if (theIdSubstitutions.containsKey(nextUriString)) {
+					IdType newId = theIdSubstitutions.get(nextUriString);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
+					nextRef.setValue(newId.getValue());
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
+				}
+			}
+
 			IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
 			if (shouldUpdate) {
-				updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, shouldUpdate, false, updateTime, false, true);
+				updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, shouldUpdate, false, theUpdateTime, false, true);
 			}
 		}
 
-		myEntityManager.flush();
+		flushJpaSession();
 
 		/*
 		 * Double check we didn't allow any duplicates we shouldn't have
@@ -548,15 +566,15 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 			}
 		}
 
-		for (IdType next : allIds) {
+		for (IdType next : theAllIds) {
-			IdType replacement = idSubstitutions.get(next);
+			IdType replacement = theIdSubstitutions.get(next);
 			if (replacement == null) {
 				continue;
 			}
 			if (replacement.equals(next)) {
 				continue;
 			}
-			ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
+			ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
 		}
 		return entriesToProcess;
 	}
@@ -601,9 +619,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
 		List<TagDefinition> tagDefinitions = q.getResultList();
 
-		Meta retVal = toMeta(tagDefinitions);
+		return toMeta(tagDefinitions);
-
-		return retVal;
 	}
 
 	private String performIdSubstitutionsInMatchUrl(Map<IdType, IdType> theIdSubstitutions, String theMatchUrl) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamRegistryR4.java

@@ -20,211 +20,93 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.defaultString;
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.util.*;
-import java.util.Map.Entry;
-
-import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
-import ca.uhn.fhir.jpa.util.JpaConstants;
-import org.apache.commons.lang3.time.DateUtils;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.CodeType;
-import org.hl7.fhir.r4.model.Extension;
-import org.hl7.fhir.r4.model.SearchParameter;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.springframework.beans.factory.annotation.Autowired;
-
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
-import ca.uhn.fhir.jpa.dao.*;
+import ca.uhn.fhir.jpa.dao.BaseSearchParamRegistry;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
+import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.util.DatatypeUtil;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
+import org.springframework.beans.factory.annotation.Autowired;
 
-public class SearchParamRegistryR4 extends BaseSearchParamRegistry {
+import java.util.ArrayList;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamRegistryR4.class);
+import java.util.Collections;
-	public static final int MAX_MANAGED_PARAM_COUNT = 10000;
+import java.util.List;
+import java.util.Set;
 
-	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
-	@Autowired
+public class SearchParamRegistryR4 extends BaseSearchParamRegistry<SearchParameter> {
-	private DaoConfig myDaoConfig;
-
-	private volatile long myLastRefresh;
 
 	@Autowired
 	private IFhirResourceDao<SearchParameter> mySpDao;
 
 	@Override
-	public void forceRefresh() {
+	public IFhirResourceDao<SearchParameter> getSearchParameterDao() {
-		synchronized (this) {
+		return mySpDao;
-			myLastRefresh = 0;
-		}
 	}
 
 	@Override
-	public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
+	protected RuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams;
-	}
-
-	@Override
-	public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
-		refreshCacheIfNecessary();
-		return myActiveSearchParams.get(theResourceName);
-	}
-
-	private Map<String, RuntimeSearchParam> getSearchParamMap(Map<String, Map<String, RuntimeSearchParam>> searchParams, String theResourceName) {
-		Map<String, RuntimeSearchParam> retVal = searchParams.get(theResourceName);
-		if (retVal == null) {
-			retVal = new HashMap<>();
-			searchParams.put(theResourceName, retVal);
-		}
-		return retVal;
-	}
-
-	protected void refreshCacheIfNecessary() {
-		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
-		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-			synchronized (this) {
-				if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
-					StopWatch sw = new StopWatch();
-
-					Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
-					for (Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
-						for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
-							String nextResourceName = nextBuiltInEntry.getKey();
-							getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
-						}
-					}
-
-					SearchParameterMap params = new SearchParameterMap();
-					params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
-
-					IBundleProvider allSearchParamsBp = mySpDao.search(params);
-					int size = allSearchParamsBp.size();
-
-					// Just in case..
-					if (size >= MAX_MANAGED_PARAM_COUNT) {
-						ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
-						size = MAX_MANAGED_PARAM_COUNT;
-					}
-
-					List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
-					for (IBaseResource nextResource : allSearchParams) {
-						SearchParameter nextSp = (SearchParameter) nextResource;
-						RuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
-						if (runtimeSp == null) {
-							continue;
-						}
-
-						for (CodeType nextBaseName : nextSp.getBase()) {
-							String resourceType = nextBaseName.getValue();
-							if (isBlank(resourceType)) {
-								continue;
-							}
-
-							Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, resourceType);
-							String name = runtimeSp.getName();
-							if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
-								searchParamMap.put(name, runtimeSp);
-							}
-
-						}
-					}
-
-					Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
-					for (Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
-						for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
-							String nextName = nextSp.getName();
-							if (nextSp.getStatus() != RuntimeSearchParamStatusEnum.ACTIVE) {
-								nextSp = null;
-							}
-
-							if (!activeSearchParams.containsKey(nextEntry.getKey())) {
-								activeSearchParams.put(nextEntry.getKey(), new HashMap<String, RuntimeSearchParam>());
-							}
-							if (activeSearchParams.containsKey(nextEntry.getKey())) {
-								ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
-							}
-
-							if (nextSp != null) {
-								activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
-							} else {
-								activeSearchParams.get(nextEntry.getKey()).remove(nextName);
-							}
-						}
-					}
-
-					myActiveSearchParams = activeSearchParams;
-
-					super.populateActiveSearchParams(activeSearchParams);
-
-					myLastRefresh = System.currentTimeMillis();
-					ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
-				}
-			}
-		}
-	}
-
-	private RuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
 		String name = theNextSp.getCode();
 		String description = theNextSp.getDescription();
 		String path = theNextSp.getExpression();
 		RestSearchParameterTypeEnum paramType = null;
 		RuntimeSearchParamStatusEnum status = null;
 		switch (theNextSp.getType()) {
-		case COMPOSITE:
+			case COMPOSITE:
-			paramType = RestSearchParameterTypeEnum.COMPOSITE;
+				paramType = RestSearchParameterTypeEnum.COMPOSITE;
-			break;
-		case DATE:
-			paramType = RestSearchParameterTypeEnum.DATE;
-			break;
-		case NUMBER:
-			paramType = RestSearchParameterTypeEnum.NUMBER;
-			break;
-		case QUANTITY:
-			paramType = RestSearchParameterTypeEnum.QUANTITY;
-			break;
-		case REFERENCE:
-			paramType = RestSearchParameterTypeEnum.REFERENCE;
-			break;
-		case STRING:
-			paramType = RestSearchParameterTypeEnum.STRING;
-			break;
-		case TOKEN:
-			paramType = RestSearchParameterTypeEnum.TOKEN;
-			break;
-		case URI:
-			paramType = RestSearchParameterTypeEnum.URI;
-			break;
-		case NULL:
-			break;
-		}
-		if (theNextSp.getStatus() != null) {
-			switch (theNextSp.getStatus()) {
-			case ACTIVE:
-				status = RuntimeSearchParamStatusEnum.ACTIVE;
 				break;
-			case DRAFT:
+			case DATE:
-				status = RuntimeSearchParamStatusEnum.DRAFT;
+				paramType = RestSearchParameterTypeEnum.DATE;
 				break;
-			case RETIRED:
+			case NUMBER:
-				status = RuntimeSearchParamStatusEnum.RETIRED;
+				paramType = RestSearchParameterTypeEnum.NUMBER;
 				break;
-			case UNKNOWN:
+			case QUANTITY:
-				status = RuntimeSearchParamStatusEnum.UNKNOWN;
+				paramType = RestSearchParameterTypeEnum.QUANTITY;
+				break;
+			case REFERENCE:
+				paramType = RestSearchParameterTypeEnum.REFERENCE;
+				break;
+			case STRING:
+				paramType = RestSearchParameterTypeEnum.STRING;
+				break;
+			case TOKEN:
+				paramType = RestSearchParameterTypeEnum.TOKEN;
+				break;
+			case URI:
+				paramType = RestSearchParameterTypeEnum.URI;
 				break;
 			case NULL:
 				break;
+		}
+		if (theNextSp.getStatus() != null) {
+			switch (theNextSp.getStatus()) {
+				case ACTIVE:
+					status = RuntimeSearchParamStatusEnum.ACTIVE;
+					break;
+				case DRAFT:
+					status = RuntimeSearchParamStatusEnum.DRAFT;
+					break;
+				case RETIRED:
+					status = RuntimeSearchParamStatusEnum.RETIRED;
+					break;
+				case UNKNOWN:
+					status = RuntimeSearchParamStatusEnum.UNKNOWN;
+					break;
+				case NULL:
+					break;
 			}
 		}
 		Set<String> providesMembershipInCompartments = Collections.emptySet();
-		Set<String> targets = toStrings(theNextSp.getTarget());
+		Set<String> targets = DatatypeUtil.toStringSet(theNextSp.getTarget());
 
 		if (isBlank(name) || isBlank(path) || paramType == null) {
 			if (paramType != RestSearchParameterTypeEnum.COMPOSITE) {
@@ -248,21 +130,11 @@ public class SearchParamRegistryR4 extends BaseSearchParamRegistry {
 
 		List<JpaRuntimeSearchParam.Component> components = new ArrayList<>();
 		for (org.hl7.fhir.r4.model.SearchParameter.SearchParameterComponentComponent next : theNextSp.getComponent()) {
-			components.add(new JpaRuntimeSearchParam.Component(next.getExpression(), next.getDefinition()));
+			components.add(new JpaRuntimeSearchParam.Component(next.getExpression(), new Reference(next.getDefinition())));
 		}
 
-		RuntimeSearchParam retVal = new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, theNextSp.getBase());
+		return new JpaRuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, theNextSp.getBase());
-		return retVal;
 	}
 
-	private Set<String> toStrings(List<CodeType> theTarget) {
-		HashSet<String> retVal = new HashSet<>();
-		for (CodeType next : theTarget) {
-			if (isNotBlank(next.getValue())) {
-				retVal.add(next.getValue());
-			}
-		}
-		return retVal;
-	}
 
 }

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

@@ -36,6 +36,7 @@ public abstract class BaseHasResource {
 	@Temporal(TemporalType.TIMESTAMP)
 	private Date myDeleted;
 
+	// TODO: move to resource history table
 	@Column(name = "RES_VERSION", nullable = true, length = 7)
 	@Enumerated(EnumType.STRING)
 	@OptimisticLock(excluded = true)

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

@@ -20,24 +20,15 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
-import javax.persistence.Column;
-import javax.persistence.Embeddable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-
 import ca.uhn.fhir.model.api.IQueryParameterType;
-import com.sun.prism.image.Coords;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.search.annotations.Field;
 
+import javax.persistence.*;
+
 //@formatter:off
 @Embeddable
 @Entity

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/ServletSubRequestDetails.java

@@ -29,13 +29,13 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 
 public class ServletSubRequestDetails extends ServletRequestDetails {
 
-	private Map<String, ArrayList<String>> myHeaders = new HashMap<String, ArrayList<String>>();
+	private Map<String, ArrayList<String>> myHeaders = new HashMap<>();
 
 	public void addHeader(String theName, String theValue) {
 		String lowerCase = theName.toLowerCase();
 		ArrayList<String> list = myHeaders.get(lowerCase);
 		if (list == null) {
-			list = new ArrayList<String>();
+			list = new ArrayList<>();
 			myHeaders.put(lowerCase, list);
 		}
 		list.add(theValue);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -29,7 +29,7 @@ import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.Constants;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java

@@ -37,6 +37,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.Date;
@@ -95,17 +96,24 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 		ourLog.debug("Searching for searches which are before {}", cutoff);
 
 		TransactionTemplate tt = new TransactionTemplate(myTransactionManager);
-		int count = tt.execute(new TransactionCallback<Integer>() {
+		final Slice<Long> toDelete = tt.execute(new TransactionCallback<Slice<Long>>() {
 			@Override
-			public Integer doInTransaction(TransactionStatus theStatus) {
+			public Slice<Long> doInTransaction(TransactionStatus theStatus) {
-				Slice<Long> toDelete = mySearchDao.findWhereLastReturnedBefore(cutoff, new PageRequest(0, 1000));
+				return mySearchDao.findWhereLastReturnedBefore(cutoff, new PageRequest(0, 1000));
-				for (final Long next : toDelete) {
-					deleteSearch(next);
-				}
-				return toDelete.getContent().size();
 			}
 		});
 
+		for (final Long nextSearchToDelete : toDelete) {
+			ourLog.debug("Deleting search with PID {}", nextSearchToDelete);
+			tt.execute(new TransactionCallbackWithoutResult() {
+				@Override
+				protected void doInTransactionWithoutResult(TransactionStatus status) {
+					deleteSearch(nextSearchToDelete);
+				}
+			});
+		}
+
+		int count = toDelete.getContent().size();
 		if (count > 0) {
 			long total = tt.execute(new TransactionCallback<Long>() {
 				@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionDeliverySubscriber.java

@@ -21,6 +21,9 @@ package ca.uhn.fhir.jpa.subscription;
  */
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Subscription;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -29,6 +32,7 @@ import org.springframework.messaging.MessagingException;
 
 public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptionSubscriber {
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseSubscriptionDeliverySubscriber.class);
+	private boolean myReloadResourceBeforeDelivery = true;
 
 	public BaseSubscriptionDeliverySubscriber(IFhirResourceDao<?> theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor) {
 		super(theSubscriptionDao, theChannelType, theSubscriptionInterceptor);
@@ -40,24 +44,54 @@ public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptio
 			ourLog.warn("Unexpected payload type: {}", theMessage.getPayload());
 			return;
 		}
+
+		String subscriptionId = "(unknown?)";
+
 		try {
 			ResourceDeliveryMessage msg = (ResourceDeliveryMessage) theMessage.getPayload();
+			subscriptionId = msg.getPayload(getContext()).getIdElement().getValue();
+
 			if (!subscriptionTypeApplies(getContext(), msg.getSubscription().getBackingSubscription(getContext()))) {
 				return;
 			}
 
-			CanonicalSubscription updatedSubscription = (CanonicalSubscription)getSubscriptionInterceptor().getIdToSubscription().get(msg.getSubscription().getIdElement(getContext()).getIdPart());
+			CanonicalSubscription updatedSubscription = (CanonicalSubscription) getSubscriptionInterceptor().getIdToSubscription().get(msg.getSubscription().getIdElement(getContext()).getIdPart());
 			if (updatedSubscription != null) {
 				msg.setSubscription(updatedSubscription);
 			}
 
+			if (myReloadResourceBeforeDelivery) {
+				// Reload the payload just in case any interceptors modified
+				// it before it was saved to the database. This is also
+				// useful for resources created in a transaction, since they
+				// can have placeholder IDs in them.
+				IIdType payloadId = msg.getPayloadId(getContext());
+				Class type = getContext().getResourceDefinition(payloadId.getResourceType()).getImplementingClass();
+				IFhirResourceDao dao = getSubscriptionDao().getDao(type);
+				IBaseResource loadedPayload;
+				try {
+					loadedPayload = dao.read(payloadId);
+				} catch (ResourceNotFoundException e) {
+					// This can happen if a last minute failure happens when saving a resource,
+					// eg a constraint causes the transaction to roll back on commit
+					ourLog.warn("Unable to find resource {} - Aborting delivery", payloadId.getValue());
+					return;
+				}
+				msg.setPayload(getContext(), loadedPayload);
+			}
+
 			handleMessage(msg);
 		} catch (Exception e) {
-			ourLog.error("Failure handling subscription payload", e);
+			String msg = "Failure handling subscription payload for subscription: " + subscriptionId;
-			throw new MessagingException(theMessage, "Failure handling subscription payload", e);
+			ourLog.error(msg, e);
+			throw new MessagingException(theMessage, msg, e);
 		}
 	}
 
 	public abstract void handleMessage(ResourceDeliveryMessage theMessage) throws Exception;
 
+	public void setReloadResourceBeforeDelivery(boolean theReloadResourceBeforeDelivery) {
+		myReloadResourceBeforeDelivery = theReloadResourceBeforeDelivery;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionInterceptor.java

@@ -23,11 +23,12 @@ package ca.uhn.fhir.jpa.subscription;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.config.BaseConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
 import ca.uhn.fhir.jpa.util.JpaConstants;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -48,6 +49,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.core.task.AsyncTaskExecutor;
 import org.springframework.messaging.MessageHandler;
 import org.springframework.messaging.SubscribableChannel;
 import org.springframework.messaging.support.ExecutorSubscribableChannel;
@@ -92,8 +94,11 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 	@Autowired(required = false)
 	@Qualifier("myEventDefinitionDaoR4")
 	private IFhirResourceDao<org.hl7.fhir.r4.model.EventDefinition> myEventDefinitionDaoR4;
-	@Autowired
+	@Autowired()
 	private PlatformTransactionManager myTxManager;
+	@Autowired
+	@Qualifier(BaseConfig.TASK_EXECUTOR_NAME)
+	private AsyncTaskExecutor myAsyncTaskExecutor;
 
 	/**
 	 * Constructor
@@ -364,6 +369,11 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 		});
 	}
 
+	@VisibleForTesting
+	public void setAsyncTaskExecutorForUnitTest(AsyncTaskExecutor theAsyncTaskExecutor) {
+		myAsyncTaskExecutor = theAsyncTaskExecutor;
+	}
+
 	public void setFhirContext(FhirContext theCtx) {
 		myCtx = theCtx;
 	}
@@ -455,7 +465,7 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 		}
 
 		if (mySubscriptionActivatingSubscriber == null) {
-			mySubscriptionActivatingSubscriber = new SubscriptionActivatingSubscriber(getSubscriptionDao(), getChannelType(), this, myTxManager);
+			mySubscriptionActivatingSubscriber = new SubscriptionActivatingSubscriber(getSubscriptionDao(), getChannelType(), this, myTxManager, myAsyncTaskExecutor);
 		}
 
 		registerSubscriptionCheckingSubscriber();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionSubscriber.java

@@ -26,7 +26,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Subscription;
 import org.springframework.messaging.MessageHandler;
-import org.springframework.messaging.MessagingException;
 
 public abstract class BaseSubscriptionSubscriber implements MessageHandler {
 
@@ -60,14 +59,6 @@ public abstract class BaseSubscriptionSubscriber implements MessageHandler {
 	}
 
 
-	/**
-	 * Does this subscription type (e.g. rest hook, websocket, etc) apply to this interceptor?
-	 */
-	protected boolean subscriptionTypeApplies(IBaseResource theSubscription) {
-		FhirContext ctx = mySubscriptionDao.getContext();
-		return subscriptionTypeApplies(ctx, theSubscription);
-	}
-
 	/**
 	 * Does this subscription type (e.g. rest hook, websocket, etc) apply to this interceptor?
 	 */
@@ -80,10 +71,12 @@ public abstract class BaseSubscriptionSubscriber implements MessageHandler {
 	 * Does this subscription type (e.g. rest hook, websocket, etc) apply to this interceptor?
 	 */
 	static boolean subscriptionTypeApplies(FhirContext theCtx, IBaseResource theSubscription, Subscription.SubscriptionChannelType theChannelType) {
-		IPrimitiveType<?> status = theCtx.newTerser().getSingleValueOrNull(theSubscription, BaseSubscriptionInterceptor.SUBSCRIPTION_TYPE, IPrimitiveType.class);
+		IPrimitiveType<?> subscriptionType = theCtx.newTerser().getSingleValueOrNull(theSubscription, BaseSubscriptionInterceptor.SUBSCRIPTION_TYPE, IPrimitiveType.class);
 		boolean subscriptionTypeApplies = false;
-		if (theChannelType.toCode().equals(status.getValueAsString())) {
+ 		if (subscriptionType != null) {
-			subscriptionTypeApplies = true;
+			if (theChannelType.toCode().equals(subscriptionType.getValueAsString())) {
+				subscriptionTypeApplies = true;
+			}
 		}
 		return subscriptionTypeApplies;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionActivatingSubscriber.java

@@ -23,13 +23,19 @@ package ca.uhn.fhir.jpa.subscription;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.SubscriptionUtil;
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Subscription;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.core.task.AsyncTaskExecutor;
 import org.springframework.messaging.MessagingException;
+import org.springframework.scheduling.TaskScheduler;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@@ -37,24 +43,33 @@ import org.springframework.transaction.support.TransactionSynchronizationAdapter
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import java.util.Date;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+
 @SuppressWarnings("unchecked")
 public class SubscriptionActivatingSubscriber {
+	private static boolean ourWaitForSubscriptionActivationSynchronouslyForUnitTest;
 	private final IFhirResourceDao mySubscriptionDao;
 	private final BaseSubscriptionInterceptor mySubscriptionInterceptor;
 	private final PlatformTransactionManager myTransactionManager;
+	private final AsyncTaskExecutor myTaskExecutor;
 	private Logger ourLog = LoggerFactory.getLogger(SubscriptionActivatingSubscriber.class);
 	private FhirContext myCtx;
 	private Subscription.SubscriptionChannelType myChannelType;
 
+
 	/**
 	 * Constructor
 	 */
-	public SubscriptionActivatingSubscriber(IFhirResourceDao<? extends IBaseResource> theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor, PlatformTransactionManager theTransactionManager) {
+	public SubscriptionActivatingSubscriber(IFhirResourceDao<? extends IBaseResource> theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor, PlatformTransactionManager theTransactionManager, AsyncTaskExecutor theTaskExecutor) {
 		mySubscriptionDao = theSubscriptionDao;
 		mySubscriptionInterceptor = theSubscriptionInterceptor;
 		myChannelType = theChannelType;
 		myCtx = theSubscriptionDao.getContext();
 		myTransactionManager = theTransactionManager;
+		myTaskExecutor = theTaskExecutor;
+		Validate.notNull(theTaskExecutor);
 	}
 
 	public void activateAndRegisterSubscriptionIfRequired(final IBaseResource theSubscription) {
@@ -70,14 +85,40 @@ public class SubscriptionActivatingSubscriber {
 		final String activeStatus = Subscription.SubscriptionStatus.ACTIVE.toCode();
 		if (requestedStatus.equals(statusString)) {
 			if (TransactionSynchronizationManager.isSynchronizationActive()) {
+				/*
+				 * If we're in a transaction, we don't want to try and change the status from
+				 * requested to active within the same transaction because it's too late by
+				 * the time we get here to make modifications to the payload.
+				 *
+				 * So, we register a synchronization, meaning that when the transaction is
+				 * finished, we'll schedule a task to do this in a separate worker thread
+				 * to avoid any possibility of conflict.
+				 */
 				TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
 					@Override
 					public void afterCommit() {
-						activateSubscription(status, activeStatus, theSubscription, requestedStatus);
+						Future<?> activationFuture = myTaskExecutor.submit(new Runnable() {
+							@Override
+							public void run() {
+								activateSubscription(activeStatus, theSubscription, requestedStatus);
+							}
+						});
+
+						/*
+						 * If we're running in a unit test, it's nice to be predictable in
+						 * terms of order... In the real world it's a recipe for deadlocks
+						 */
+						if (ourWaitForSubscriptionActivationSynchronouslyForUnitTest) {
+							try {
+								activationFuture.get(5, TimeUnit.SECONDS);
+							} catch (Exception e) {
+								ourLog.error("Failed to activate subscription", e);
+							}
+						}
 					}
 				});
 			} else {
-				activateSubscription(status, activeStatus, theSubscription, requestedStatus);
+				activateSubscription(activeStatus, theSubscription, requestedStatus);
 			}
 		} else if (activeStatus.equals(statusString)) {
 			if (!mySubscriptionInterceptor.hasSubscription(theSubscription.getIdElement())) {
@@ -92,13 +133,21 @@ public class SubscriptionActivatingSubscriber {
 		}
 	}
 
-	private void activateSubscription(IPrimitiveType<?> theStatus, String theActiveStatus, IBaseResource theSubscription, String theRequestedStatus) {
+	private void activateSubscription(String theActiveStatus, final IBaseResource theSubscription, String theRequestedStatus) {
-		theStatus.setValueAsString(theActiveStatus);
+		IBaseResource subscription = mySubscriptionDao.read(theSubscription.getIdElement());
-		ourLog.info("Activating and registering subscription {} from status {} to {}", theSubscription.getIdElement().toUnqualified().getValue(), theRequestedStatus, theActiveStatus);
-		mySubscriptionDao.update(theSubscription);
-		mySubscriptionInterceptor.registerSubscription(theSubscription.getIdElement(), theSubscription);
-	}
 
+		ourLog.info("Activating and registering subscription {} from status {} to {}", subscription.getIdElement().toUnqualified().getValue(), theRequestedStatus, theActiveStatus);
+		try {
+			SubscriptionUtil.setStatus(myCtx, subscription, theActiveStatus);
+			mySubscriptionDao.update(subscription);
+			mySubscriptionInterceptor.registerSubscription(subscription.getIdElement(), subscription);
+		} catch (final UnprocessableEntityException e) {
+			ourLog.info("Changing status of {} to ERROR", subscription.getIdElement());
+			SubscriptionUtil.setStatus(myCtx, subscription, "error");
+			SubscriptionUtil.setReason(myCtx, subscription, e.getMessage());
+			mySubscriptionDao.update(subscription);
+		}
+	}
 
 	public void handleMessage(RestOperationTypeEnum theOperationType, IIdType theId, final IBaseResource theSubscription) throws MessagingException {
 
@@ -125,4 +174,9 @@ public class SubscriptionActivatingSubscriber {
 
 	}
 
+	@VisibleForTesting
+	public static void setWaitForSubscriptionActivationSynchronouslyForUnitTest(boolean theWaitForSubscriptionActivationSynchronouslyForUnitTest) {
+		ourWaitForSubscriptionActivationSynchronouslyForUnitTest = theWaitForSubscriptionActivationSynchronouslyForUnitTest;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionCheckingSubscriber.java

@@ -102,25 +102,22 @@ public class SubscriptionCheckingSubscriber extends BaseSubscriptionSubscriber {
 
 			IBundleProvider results = performSearch(criteria);
 
-			ourLog.info("Subscription check found {} results for query: {}", results.size(), criteria);
+			ourLog.debug("Subscription check found {} results for query: {}", results.size(), criteria);
 
 			if (results.size() == 0) {
 				continue;
 			}
 
-			// should just be one resource as it was filtered by the id
+			ourLog.debug("Found match: queueing rest-hook notification for resource: {}", id.toUnqualifiedVersionless().getValue());
-			for (IBaseResource nextBase : results.getResources(0, results.size())) {
-				ourLog.info("Found match: queueing rest-hook notification for resource: {}", nextBase.getIdElement());
 
-				ResourceDeliveryMessage deliveryMsg = new ResourceDeliveryMessage();
+			ResourceDeliveryMessage deliveryMsg = new ResourceDeliveryMessage();
-				deliveryMsg.setPayload(getContext(), nextBase);
+			deliveryMsg.setPayload(getContext(), msg.getNewPayload(getContext()));
-				deliveryMsg.setSubscription(nextSubscription);
+			deliveryMsg.setSubscription(nextSubscription);
-				deliveryMsg.setOperationType(msg.getOperationType());
+			deliveryMsg.setOperationType(msg.getOperationType());
-				deliveryMsg.setPayloadId(msg.getId(getContext()));
+			deliveryMsg.setPayloadId(msg.getId(getContext()));
 
-				ResourceDeliveryJsonMessage wrappedMsg = new ResourceDeliveryJsonMessage(deliveryMsg);
+			ResourceDeliveryJsonMessage wrappedMsg = new ResourceDeliveryJsonMessage(deliveryMsg);
-				getSubscriptionInterceptor().getDeliveryChannel().send(wrappedMsg);
+			getSubscriptionInterceptor().getDeliveryChannel().send(wrappedMsg);
-			}
 		}
 
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/email/JavaMailEmailSender.java

@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.subscription.email;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.StringUtils;
@@ -95,7 +95,6 @@ public class JavaMailEmailSender implements IEmailSender {
 	@Override
 	public void send(EmailDetails theDetails) {
 		String subscriptionId = theDetails.getSubscription().toUnqualifiedVersionless().getValue();
-		ourLog.info("Sending email for subscription {} to recipients: {}", subscriptionId, theDetails.getTo());
 		StopWatch sw = new StopWatch();
 
 		StringTemplateResolver templateResolver = new StringTemplateResolver();
@@ -116,15 +115,18 @@ public class JavaMailEmailSender implements IEmailSender {
 
 		MimeMessage email = mySender.createMimeMessage();
 
+		String from = trim(theDetails.getFrom());
+		ourLog.info("Sending email for subscription {} from [{}] to recipients: [{}]", subscriptionId, from, theDetails.getTo());
+
 		try {
-			email.setFrom(trim(theDetails.getFrom()));
+			email.setFrom(from);
 			email.setRecipients(Message.RecipientType.TO, toTrimmedCommaSeparatedString(theDetails.getTo()));
 			email.setSubject(subject);
 			email.setText(body);
 			email.setSentDate(new Date());
 			email.addHeader("X-FHIR-Subscription", subscriptionId);
 		} catch (MessagingException e) {
-			throw new InternalErrorException("Failed to create email messaage", e);
+			throw new InternalErrorException("Failed to create email message", e);
 		}
 
 		mySender.send(email);

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

@@ -47,7 +47,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.ObjectUtil;

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

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;

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

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StopWatch.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.util;
 
-import org.apache.commons.lang3.time.DateUtils;
-
-import java.util.Date;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -24,91 +20,10 @@ import java.util.Date;
  * #L%
  */
 
-public class StopWatch {
+/**
-
+ * @deprecated Use {@link ca.uhn.fhir.util.StopWatch} instead
-	private long myStarted = System.currentTimeMillis();
+ */
-
+@Deprecated
-	/**
+public class StopWatch extends ca.uhn.fhir.util.StopWatch {
-	 * Constructor
+	// this just exists since existing code may depend on it
-	 */
-	public StopWatch() {
-		super();
-	}
-
-	/**
-	 * Constructor
-	 */
-	public StopWatch(Date theNow) {
-		myStarted = theNow.getTime();
-	}
-
-	public long getMillisAndRestart() {
-		long now = System.currentTimeMillis();
-		long retVal = now - myStarted;
-		myStarted = now;
-		return retVal;
-	}
-
-	public long getMillis() {
-		long now = System.currentTimeMillis();
-		long retVal = now - myStarted;
-		return retVal;
-	}
-
-	public long getMillis(Date theNow) {
-		long retVal = theNow.getTime() - myStarted;
-		return retVal;
-	}
-
-	public Date getStartedDate() {
-		return new Date(myStarted);
-	}
-
-	/**
-	 * Formats value in the format [DD d ]HH:mm:ss.SSSS
-	 */
-	@Override
-	public String toString() {
-		return formatMillis(getMillis());
-	}
-
-	static public String formatMillis(long val) {
-		StringBuilder buf = new StringBuilder(20);
-		if (val >= DateUtils.MILLIS_PER_DAY) {
-			long days = val / DateUtils.MILLIS_PER_DAY;
-			append(buf, "", 1, days);
-			if (days > 1) {
-				buf.append(" days ");
-			} else if (days == 1) {
-				buf.append(" day ");
-			}
-			append(buf, "", 2, ((val % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
-		} else {
-			append(buf, "", 2, ((val % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
-		}
-		append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
-		append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
-		append(buf, ".", 3, (val % DateUtils.MILLIS_PER_SECOND));
-		return buf.toString();
-	}
-
-	/** Append a right-aligned and zero-padded numeric value to a `StringBuilder`. */
-	static private void append(StringBuilder tgt, String pfx, int dgt, long val) {
-		tgt.append(pfx);
-		if (dgt > 1) {
-			int pad = (dgt - 1);
-			for (long xa = val; xa > 9 && pad > 0; xa /= 10) {
-				pad--;
-			}
-			for (int xa = 0; xa < pad; xa++) {
-				tgt.append('0');
-			}
-		}
-		tgt.append(val);
-	}
-
-	public int getMillisPerOperation(int theNumOperations) {
-		return (int)(((double) getMillis()) / Math.max(1.0, theNumOperations));
-	}
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorDstu2.java

@@ -74,7 +74,7 @@ public class SubscriptionsRequireManualActivationInterceptorDstu2 extends Server
 
 		if (newStatus == null) {
 			String actualCode = subscription.getStatusElement().getValueAsString();
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated on this server" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
 		}
 
 		if (theOldResourceOrNull != null) {
@@ -108,7 +108,7 @@ public class SubscriptionsRequireManualActivationInterceptorDstu2 extends Server
 		}
 
 		if (theSubscription.getStatus() == null) {
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated");
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated on this server");
 		}
 
 		throw new UnprocessableEntityException("Subscription.status must be '" + SubscriptionStatusEnum.OFF.getCode() + "' or '" + SubscriptionStatusEnum.REQUESTED.getCode() + "' on a newly created subscription");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorDstu3.java

@@ -74,7 +74,7 @@ public class SubscriptionsRequireManualActivationInterceptorDstu3 extends Server
 
 		if (newStatus == null) {
 			String actualCode = subscription.getStatusElement().getValueAsString();
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated on this server" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
 		}
 
 		if (theOldResourceOrNull != null) {
@@ -108,7 +108,7 @@ public class SubscriptionsRequireManualActivationInterceptorDstu3 extends Server
 		}
 
 		if (theSubscription.getStatus() == null) {
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated");
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated on this server");
 		}
 
 		throw new UnprocessableEntityException("Subscription.status must be '" + SubscriptionStatus.OFF.toCode() + "' or '" + SubscriptionStatus.REQUESTED.toCode() + "' on a newly created subscription");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorR4.java

@@ -74,7 +74,7 @@ public class SubscriptionsRequireManualActivationInterceptorR4 extends ServerOpe
 
 		if (newStatus == null) {
 			String actualCode = subscription.getStatusElement().getValueAsString();
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode() + " resource: Subscription.status must be populated on this server" + ((isNotBlank(actualCode)) ? " (invalid value " + actualCode + ")" : ""));
 		}
 
 		if (theOldResourceOrNull != null) {
@@ -108,7 +108,7 @@ public class SubscriptionsRequireManualActivationInterceptorR4 extends ServerOpe
 		}
 
 		if (theSubscription.getStatus() == null) {
-			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated");
+			throw new UnprocessableEntityException("Can not " + theOperation.getCode().toLowerCase() + " resource: Subscription.status must be populated on this server");
 		}
 
 		throw new UnprocessableEntityException("Subscription.status must be '" + SubscriptionStatus.OFF.toCode() + "' or '" + SubscriptionStatus.REQUESTED.toCode() + "' on a newly created subscription");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -47,7 +47,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 
 			@Override
-			public Connection getConnection() throws SQLException {
+			public Connection getConnection() {
 				ConnectionWrapper retVal;
 				try {
 					retVal = new ConnectionWrapper(super.getConnection());

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

@@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
-import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -34,7 +34,6 @@ import org.springframework.transaction.support.TransactionTemplate;
 import javax.persistence.EntityManager;
 import java.io.IOException;
 import java.io.InputStream;
-import java.sql.SQLException;
 import java.util.*;
 import java.util.concurrent.Callable;
 
@@ -158,7 +157,7 @@ public abstract class BaseJpaTest {
 	}
 
 	protected List<IIdType> toUnqualifiedVersionlessIds(IBundleProvider theFound) {
-		List<IIdType> retVal = new ArrayList<IIdType>();
+		List<IIdType> retVal = new ArrayList<>();
 		Integer size = theFound.size();
 		StopWatch sw = new StopWatch();
 		while (size == null) {
@@ -171,6 +170,7 @@ public abstract class BaseJpaTest {
 			} catch (InterruptedException theE) {
 				//ignore
 			}
+			size = theFound.size();
 		}
 
 		ourLog.info("Found {} results", size);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -75,6 +75,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myDiagnosticReportDaoDstu2")
 	protected IFhirResourceDao<DiagnosticReport> myDiagnosticReportDao;
 	@Autowired
+	@Qualifier("myBinaryDaoDstu2")
+	protected IFhirResourceDao<Binary> myBinaryDao;
+	@Autowired
 	@Qualifier("myEncounterDaoDstu2")
 	protected IFhirResourceDao<Encounter> myEncounterDao;
 	//	@PersistenceContext()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java

@@ -19,9 +19,9 @@ import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.mockito.internal.util.collections.ListUtil;
-import org.thymeleaf.util.ListUtils;
 
 import java.util.List;
 
@@ -53,90 +53,6 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 		}
 	}
 
-	@Test
-	public void testOverrideAndDisableBuiltInSearchParametersWithOverridingEnabled() {
-		myDaoConfig.setDefaultSearchParamsCanBeOverridden(true);
-
-		SearchParameter memberSp = new SearchParameter();
-		memberSp.setCode("member");
-		memberSp.setBase(ResourceTypeEnum.GROUP);
-		memberSp.setType(SearchParamTypeEnum.REFERENCE);
-		memberSp.setXpath("Group.member.entity");
-		memberSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
-		memberSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
-		mySearchParameterDao.create(memberSp, mySrd);
-
-		SearchParameter identifierSp = new SearchParameter();
-		identifierSp.setCode("identifier");
-		identifierSp.setBase(ResourceTypeEnum.GROUP);
-		identifierSp.setType(SearchParamTypeEnum.TOKEN);
-		identifierSp.setXpath("Group.identifier");
-		identifierSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
-		identifierSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
-		mySearchParameterDao.create(identifierSp, mySrd);
-
-		mySearchParamRegsitry.forceRefresh();
-
-		Patient p = new Patient();
-		p.addName().addGiven("G");
-		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-
-		Group g = new Group();
-		g.addIdentifier().setSystem("urn:foo").setValue("bar");
-		g.addMember().getEntity().setReference(pid);
-		myGroupDao.create(g);
-
-		assertThat(myResourceLinkDao.findAll(), empty());
-		assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
-			@Override
-			public boolean isOut(ResourceIndexedSearchParamToken object) {
-				return !object.getResourceType().equals("Group") || object.isMissing();
-			}
-		}), empty());
-	}
-
-	@Test
-	public void testOverrideAndDisableBuiltInSearchParametersWithOverridingDisabled() {
-		myDaoConfig.setDefaultSearchParamsCanBeOverridden(false);
-
-		SearchParameter memberSp = new SearchParameter();
-		memberSp.setCode("member");
-		memberSp.setBase(ResourceTypeEnum.GROUP);
-		memberSp.setType(SearchParamTypeEnum.REFERENCE);
-		memberSp.setXpath("Group.member.entity");
-		memberSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
-		memberSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
-		mySearchParameterDao.create(memberSp, mySrd);
-
-		SearchParameter identifierSp = new SearchParameter();
-		identifierSp.setCode("identifier");
-		identifierSp.setBase(ResourceTypeEnum.GROUP);
-		identifierSp.setType(SearchParamTypeEnum.TOKEN);
-		identifierSp.setXpath("Group.identifier");
-		identifierSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
-		identifierSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
-		mySearchParameterDao.create(identifierSp, mySrd);
-
-		mySearchParamRegsitry.forceRefresh();
-
-		Patient p = new Patient();
-		p.addName().addGiven("G");
-		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-
-		Group g = new Group();
-		g.addIdentifier().setSystem("urn:foo").setValue("bar");
-		g.addMember().getEntity().setReference(pid);
-		myGroupDao.create(g);
-
-		assertThat(myResourceLinkDao.findAll(), not(empty()));
-		assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
-			@Override
-			public boolean isOut(ResourceIndexedSearchParamToken object) {
-				return !object.getResourceType().equals("Group") || object.isMissing();
-			}
-		}), not(empty()));
-	}
-
 	@Test
 	public void testCreateInvalidParamInvalidResourceName() {
 		SearchParameter fooSp = new SearchParameter();
@@ -154,23 +70,6 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 		}
 	}
 
-	@Test
-	public void testCreateInvalidParamMismatchedResourceName() {
-		SearchParameter fooSp = new SearchParameter();
-		fooSp.setBase(ResourceTypeEnum.PATIENT);
-		fooSp.setCode("foo");
-		fooSp.setType(SearchParamTypeEnum.TOKEN);
-		fooSp.setXpath("Patient.gender or Observation.code");
-		fooSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
-		fooSp.setStatus(ConformanceResourceStatusEnum.ACTIVE);
-		try {
-			mySearchParameterDao.create(fooSp, mySrd);
-			fail();
-		} catch (UnprocessableEntityException e) {
-			assertEquals("Invalid SearchParameter.expression value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
-		}
-	}
-
 	@Test
 	public void testCreateInvalidParamNoPath() {
 		SearchParameter fooSp = new SearchParameter();
@@ -224,7 +123,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 	}
 
 	@Test
-	public void testCustomReferenceParameter() throws Exception {
+	public void testCustomReferenceParameter() {
 		SearchParameter sp = new SearchParameter();
 		sp.setBase(ResourceTypeEnum.PATIENT);
 		sp.setCode("myDoctor");
@@ -234,6 +133,8 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 		sp.setStatus(ConformanceResourceStatusEnum.ACTIVE);
 		mySearchParameterDao.create(sp);
 
+		mySearchParamRegsitry.forceRefresh();
+
 		Practitioner pract = new Practitioner();
 		pract.setId("A");
 		pract.getName().addFamily("PRACT");
@@ -312,6 +213,90 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 
 	}
 
+	@Test
+	public void testOverrideAndDisableBuiltInSearchParametersWithOverridingDisabled() {
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(false);
+
+		SearchParameter memberSp = new SearchParameter();
+		memberSp.setCode("member");
+		memberSp.setBase(ResourceTypeEnum.GROUP);
+		memberSp.setType(SearchParamTypeEnum.REFERENCE);
+		memberSp.setXpath("Group.member.entity");
+		memberSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
+		memberSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
+		mySearchParameterDao.create(memberSp, mySrd);
+
+		SearchParameter identifierSp = new SearchParameter();
+		identifierSp.setCode("identifier");
+		identifierSp.setBase(ResourceTypeEnum.GROUP);
+		identifierSp.setType(SearchParamTypeEnum.TOKEN);
+		identifierSp.setXpath("Group.identifier");
+		identifierSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
+		identifierSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
+		mySearchParameterDao.create(identifierSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient p = new Patient();
+		p.addName().addGiven("G");
+		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		Group g = new Group();
+		g.addIdentifier().setSystem("urn:foo").setValue("bar");
+		g.addMember().getEntity().setReference(pid);
+		myGroupDao.create(g);
+
+		assertThat(myResourceLinkDao.findAll(), not(empty()));
+		assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
+			@Override
+			public boolean isOut(ResourceIndexedSearchParamToken object) {
+				return !object.getResourceType().equals("Group") || object.isMissing();
+			}
+		}), not(empty()));
+	}
+
+	@Test
+	public void testOverrideAndDisableBuiltInSearchParametersWithOverridingEnabled() {
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(true);
+
+		SearchParameter memberSp = new SearchParameter();
+		memberSp.setCode("member");
+		memberSp.setBase(ResourceTypeEnum.GROUP);
+		memberSp.setType(SearchParamTypeEnum.REFERENCE);
+		memberSp.setXpath("Group.member.entity");
+		memberSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
+		memberSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
+		mySearchParameterDao.create(memberSp, mySrd);
+
+		SearchParameter identifierSp = new SearchParameter();
+		identifierSp.setCode("identifier");
+		identifierSp.setBase(ResourceTypeEnum.GROUP);
+		identifierSp.setType(SearchParamTypeEnum.TOKEN);
+		identifierSp.setXpath("Group.identifier");
+		identifierSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
+		identifierSp.setStatus(ConformanceResourceStatusEnum.RETIRED);
+		mySearchParameterDao.create(identifierSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient p = new Patient();
+		p.addName().addGiven("G");
+		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		Group g = new Group();
+		g.addIdentifier().setSystem("urn:foo").setValue("bar");
+		g.addMember().getEntity().setReference(pid);
+		myGroupDao.create(g);
+
+		assertThat(myResourceLinkDao.findAll(), empty());
+		assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
+			@Override
+			public boolean isOut(ResourceIndexedSearchParamToken object) {
+				return !object.getResourceType().equals("Group") || object.isMissing();
+			}
+		}), empty());
+	}
+
 	@Test
 	public void testSearchForExtensionReferenceWithNonMatchingTarget() {
 		SearchParameter siblingSp = new SearchParameter();
@@ -883,6 +868,53 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 
 	}
 
+	@Test
+	@Ignore
+	public void testSearchForStringOnIdentifierWithSpecificSystem() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setBase(ResourceTypeEnum.PATIENT);
+		fooSp.setCode("foo");
+		fooSp.setType(SearchParamTypeEnum.STRING);
+		fooSp.setXpath("Patient.identifier.where(system = 'http://AAA').value");
+		fooSp.setXpathUsage(XPathUsageTypeEnum.NORMAL);
+		fooSp.setStatus(ConformanceResourceStatusEnum.ACTIVE);
+		IIdType spId = mySearchParameterDao.create(fooSp, mySrd).getId().toUnqualifiedVersionless();
+
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient pat = new Patient();
+		pat.addIdentifier().setSystem("http://AAA").setValue("BAR678");
+		pat.setGender(AdministrativeGenderEnum.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient pat2 = new Patient();
+		pat2.addIdentifier().setSystem("http://BBB").setValue("BAR678");
+		pat2.setGender(AdministrativeGenderEnum.FEMALE);
+		myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		IBundleProvider results;
+		List<String> foundResources;
+
+		// Partial match
+		map = new SearchParameterMap();
+		map.add("foo", new StringParam("bar"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, contains(patId.getValue()));
+
+		// Non match
+		map = new SearchParameterMap();
+		map.add("foo", new StringParam("zzz"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, empty());
+
+	}
+
+
 	@Test
 	public void testSearchWithCustomParam() {