Integrate Bulk Export (#1487)

* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java

@@ -8,6 +8,7 @@ import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.Date;
 
+import ca.uhn.fhir.rest.api.PreferHeader;
 import org.hl7.fhir.dstu3.model.*;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
@@ -20,7 +21,6 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
@@ -246,7 +246,7 @@ public class GenericClientDstu3IT {
 		Patient pt = new Patient();
 		pt.getText().setDivAsString("A PATIENT");
 
-		MethodOutcome outcome = client.create().resource(pt).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		MethodOutcome outcome = client.create().resource(pt).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 
 		assertNull(outcome.getOperationOutcome());
 		assertNotNull(outcome.getResource());

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

@@ -220,17 +220,31 @@ public class Constants {
 	public static final String CASCADE_DELETE = "delete";
 	public static final int MAX_RESOURCE_NAME_LENGTH = 100;
 	public static final String CACHE_CONTROL_PRIVATE = "private";
+	public static final String CT_FHIR_NDJSON = "application/fhir+ndjson";
+	public static final String CT_APP_NDJSON = "application/ndjson";
+	public static final String CT_NDJSON = "ndjson";
+	public static final Set<String> CTS_NDJSON;
+	public static final String HEADER_PREFER_RESPOND_ASYNC = "respond-async";
 	public static final int STATUS_HTTP_412_PAYLOAD_TOO_LARGE = 413;
 	public static final String OPERATION_NAME_GRAPHQL = "$graphql";
 	/**
 	 * Note that this constant is used in a number of places including DB column lengths! Be careful if you decide to change it.
 	 */
 	public static final int REQUEST_ID_LENGTH = 16;
+	public static final int STATUS_HTTP_202_ACCEPTED = 202;
+	public static final String HEADER_X_PROGRESS = "X-Progress";
+	public static final String HEADER_RETRY_AFTER = "Retry-After";
 
 	static {
 		CHARSET_UTF8 = StandardCharsets.UTF_8;
 		CHARSET_US_ASCII = StandardCharsets.ISO_8859_1;
 
+		HashSet<String> ctsNdjson = new HashSet<>();
+		ctsNdjson.add(CT_FHIR_NDJSON);
+		ctsNdjson.add(CT_APP_NDJSON);
+		ctsNdjson.add(CT_NDJSON);
+		CTS_NDJSON = Collections.unmodifiableSet(ctsNdjson);
+
 		HashMap<Integer, String> statusNames = new HashMap<>();
 		statusNames.put(200, "OK");
 		statusNames.put(201, "Created");

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

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.rest.api;
+
+import javax.annotation.Nullable;
+import java.util.HashMap;
+
+public class PreferHeader {
+
+	private PreferReturnEnum myReturn;
+	private boolean myRespondAsync;
+
+	public @Nullable
+	PreferReturnEnum getReturn() {
+		return myReturn;
+	}
+
+	public PreferHeader setReturn(PreferReturnEnum theReturn) {
+		myReturn = theReturn;
+		return this;
+	}
+
+	public boolean getRespondAsync() {
+		return myRespondAsync;
+	}
+
+	public PreferHeader setRespondAsync(boolean theRespondAsync) {
+		myRespondAsync = theRespondAsync;
+		return this;
+	}
+
+	/**
+	 * Represents values for "return" value as provided in the the <a href="https://tools.ietf.org/html/rfc7240#section-4.2">HTTP Prefer header</a>.
+	 */
+	public enum PreferReturnEnum {
+
+		REPRESENTATION("representation"), MINIMAL("minimal"), OPERATION_OUTCOME("OperationOutcome");
+
+		private static HashMap<String, PreferReturnEnum> ourValues;
+		private String myHeaderValue;
+
+		PreferReturnEnum(String theHeaderValue) {
+			myHeaderValue = theHeaderValue;
+		}
+
+		public String getHeaderValue() {
+			return myHeaderValue;
+		}
+
+		public static PreferReturnEnum fromHeaderValue(String theHeaderValue) {
+			if (ourValues == null) {
+				HashMap<String, PreferReturnEnum> values = new HashMap<>();
+				for (PreferReturnEnum next : PreferReturnEnum.values()) {
+					values.put(next.getHeaderValue(), next);
+				}
+				ourValues = values;
+			}
+			return ourValues.get(theHeaderValue);
+		}
+
+	}
+
+}

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

@@ -1,54 +0,0 @@
-package ca.uhn.fhir.rest.api;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 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.util.HashMap;
-
-/**
- * Represents values for "return" value as provided in the the <a href="https://tools.ietf.org/html/rfc7240#section-4.2">HTTP Prefer header</a>.
- */
-public enum PreferReturnEnum {
-
-	REPRESENTATION("representation"), MINIMAL("minimal"), OPERATION_OUTCOME("OperationOutcome");
-
-	private String myHeaderValue;
-	private static HashMap<String, PreferReturnEnum> ourValues;
-
-	private PreferReturnEnum(String theHeaderValue) {
-		myHeaderValue = theHeaderValue;
-	}
-
-	public static PreferReturnEnum fromHeaderValue(String theHeaderValue) {
-		if (ourValues == null) {
-			HashMap<String, PreferReturnEnum> values = new HashMap<String, PreferReturnEnum>();
-			for (PreferReturnEnum next : PreferReturnEnum.values()) {
-				values.put(next.getHeaderValue(), next);
-			}
-			ourValues = values;
-		}
-		return ourValues.get(theHeaderValue);
-	}
-
-	public String getHeaderValue() {
-		return myHeaderValue;
-	}
-
-}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ICreateTyped.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.rest.gclient;
  */
 
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.PreferHeader;
 
 public interface ICreateTyped extends IClientExecutable<ICreateTyped, MethodOutcome> {
 	
@@ -47,6 +47,6 @@ public interface ICreateTyped extends IClientExecutable<ICreateTyped, MethodOutc
 	 * 
 	 * @since HAPI 1.1
 	 */
-	ICreateTyped prefer(PreferReturnEnum theReturn);
+	ICreateTyped prefer(PreferHeader.PreferReturnEnum theReturn);
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IPatchExecutable.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.rest.gclient;
  */
 
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.PreferHeader;
 
 public interface IPatchExecutable extends IClientExecutable<IPatchExecutable, MethodOutcome>{
 
@@ -32,6 +32,6 @@ public interface IPatchExecutable extends IClientExecutable<IPatchExecutable, Me
 	 * 
 	 * @since HAPI 1.1
 	 */
-	IPatchExecutable prefer(PreferReturnEnum theReturn);
+	IPatchExecutable prefer(PreferHeader.PreferReturnEnum theReturn);
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IUpdateExecutable.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.rest.gclient;
  */
 
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.PreferHeader;
 
 public interface IUpdateExecutable extends IClientExecutable<IUpdateExecutable, MethodOutcome>{
 
@@ -32,6 +32,6 @@ public interface IUpdateExecutable extends IClientExecutable<IUpdateExecutable,
 	 * 
 	 * @since HAPI 1.1
 	 */
-	IUpdateExecutable prefer(PreferReturnEnum theReturn);
+	IUpdateExecutable prefer(PreferHeader.PreferReturnEnum theReturn);
 
 }

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

@@ -0,0 +1,25 @@
+package ca.uhn.fhir.util;
+
+import java.util.Arrays;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.StringUtils.*;
+
+public class ArrayUtil {
+
+	/** Non instantiable */
+	private ArrayUtil() {}
+
+	/**
+	 * Takes in a list like "foo, bar,, baz" and returns a set containing only ["foo", "bar", "baz"]
+	 */
+	public static Set<String> commaSeparatedListToCleanSet(String theValueAsString) {
+		Set<String> resourceTypes;
+		resourceTypes = Arrays.stream(split(theValueAsString, ","))
+			.map(t->trim(t))
+			.filter(t->isNotBlank(t))
+			.collect(Collectors.toSet());
+		return resourceTypes;
+	}
+}

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

@@ -63,6 +63,9 @@ public class StopWatch {
 		myStarted = theStart.getTime();
 	}
 
+	public StopWatch(long theL) {
+	}
+
 	private void addNewlineIfContentExists(StringBuilder theB) {
 		if (theB.length() > 0) {
 			theB.append("\n");
@@ -231,7 +234,12 @@ public class StopWatch {
 
 		double denominator = ((double) millisElapsed) / ((double) periodMillis);
 
-		return (double) theNumOperations / denominator;
+		double throughput = (double) theNumOperations / denominator;
+		if (throughput > theNumOperations) {
+			throughput = theNumOperations;
+		}
+
+		return throughput;
 	}
 
 	public void restart() {

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

@@ -5,9 +5,9 @@
 		if you are using this file as a basis for your own project. -->
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<artifactId>hapi-fhir-cli</artifactId>
+		<artifactId>hapi-deployable-pom</artifactId>
 		<version>4.1.0-SNAPSHOT</version>
-		<relativePath>../pom.xml</relativePath>
+		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 
 	<artifactId>hapi-fhir-cli-jpaserver</artifactId>
@@ -131,6 +131,10 @@
 					<artifactId>Saxon-HE</artifactId>
 					<groupId>net.sf.saxon</groupId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.glassfish.jaxb</groupId>
+					<artifactId>jaxb-core</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 	</dependencies>
@@ -183,15 +187,6 @@
 				</configuration>
 			</plugin>
 
-			<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-deploy-plugin</artifactId>
-				<configuration>
-					<skip>true</skip>
-				</configuration>
-			</plugin>
-
 			<!-- This is to run the integration tests -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.jpa.dao.DaoConfig;
 import org.apache.commons.cli.ParseException;

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.jpa.config.BaseJavaConfigDstu3;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.jpa.config.BaseJavaConfigR4;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.demo;
 
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - Server WAR
+ * %%
+ * Copyright (C) 2014 - 2019 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.interceptor.api.IInterceptorBroadcaster;

hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java

@@ -364,11 +364,11 @@ public class GenericOkHttpClientDstu2Test {
 		Patient p = new Patient();
 		p.addName().addFamily("FOOFAMILY");
 
-		client.create().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 
-		client.create().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 	}
@@ -1735,11 +1735,11 @@ public class GenericOkHttpClientDstu2Test {
 		p.setId(new IdDt("1"));
 		p.addName().addFamily("FOOFAMILY");
 
-		client.update().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 
-		client.update().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 	}

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

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.rest.client.apache;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.Constants;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.nio.charset.UnsupportedCharsetException;
+
+/**
+ * Apache HttpClient request content entity where the body is a FHIR resource, that will
+ * be encoded as JSON by default
+ */
+public class ResourceEntity extends StringEntity {
+
+	public ResourceEntity(FhirContext theContext, IBaseResource theResource) throws UnsupportedCharsetException {
+		super(theContext.newJsonParser().encodeResourceToString(theResource), ContentType.parse(Constants.CT_FHIR_JSON_NEW));
+	}
+}

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

@@ -533,7 +533,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 	private class CreateInternal extends BaseSearch<ICreateTyped, ICreateWithQueryTyped, MethodOutcome> implements ICreate, ICreateTyped, ICreateWithQuery, ICreateWithQueryTyped {
 
 		private boolean myConditional;
-		private PreferReturnEnum myPrefer;
+		private PreferHeader.PreferReturnEnum myPrefer;
 		private IBaseResource myResource;
 		private String myResourceBody;
 		private String mySearchUrl;
@@ -580,7 +580,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 
 		@Override
-		public ICreateTyped prefer(PreferReturnEnum theReturn) {
+		public ICreateTyped prefer(PreferHeader.PreferReturnEnum theReturn) {
 			myPrefer = theReturn;
 			return this;
 		}
@@ -1380,13 +1380,13 @@ public class GenericClient extends BaseClient implements IGenericClient {
 	}
 
 	private final class OutcomeResponseHandler implements IClientResponseHandler<MethodOutcome> {
-		private PreferReturnEnum myPrefer;
+		private PreferHeader.PreferReturnEnum myPrefer;
 
 		private OutcomeResponseHandler() {
 			super();
 		}
 
-		private OutcomeResponseHandler(PreferReturnEnum thePrefer) {
+		private OutcomeResponseHandler(PreferHeader.PreferReturnEnum thePrefer) {
 			this();
 			myPrefer = thePrefer;
 		}
@@ -1396,7 +1396,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			MethodOutcome response = MethodUtil.process2xxResponse(myContext, theResponseStatusCode, theResponseMimeType, theResponseInputStream, theHeaders);
 			response.setCreatedUsingStatusCode(theResponseStatusCode);
 
-			if (myPrefer == PreferReturnEnum.REPRESENTATION) {
+			if (myPrefer == PreferHeader.PreferReturnEnum.REPRESENTATION) {
 				if (response.getResource() == null) {
 					if (response.getId() != null && isNotBlank(response.getId().getValue()) && response.getId().hasBaseUrl()) {
 						ourLog.info("Server did not return resource for Prefer-representation, going to fetch: {}", response.getId().getValue());
@@ -1418,7 +1418,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		private IIdType myId;
 		private String myPatchBody;
 		private PatchTypeEnum myPatchType;
-		private PreferReturnEnum myPrefer;
+		private PreferHeader.PreferReturnEnum myPrefer;
 		private String myResourceType;
 		private String mySearchUrl;
 
@@ -1476,7 +1476,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 
 		@Override
-		public IPatchExecutable prefer(PreferReturnEnum theReturn) {
+		public IPatchExecutable prefer(PreferHeader.PreferReturnEnum theReturn) {
 			myPrefer = theReturn;
 			return this;
 		}
@@ -2048,7 +2048,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 
 		private boolean myConditional;
 		private IIdType myId;
-		private PreferReturnEnum myPrefer;
+		private PreferHeader.PreferReturnEnum myPrefer;
 		private IBaseResource myResource;
 		private String myResourceBody;
 		private String mySearchUrl;
@@ -2102,7 +2102,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 
 		@Override
-		public IUpdateExecutable prefer(PreferReturnEnum theReturn) {
+		public IUpdateExecutable prefer(PreferHeader.PreferReturnEnum theReturn) {
 			myPrefer = theReturn;
 			return this;
 		}
@@ -2282,7 +2282,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		params.get(parameterName).add(parameterValue);
 	}
 
-	private static void addPreferHeader(PreferReturnEnum thePrefer, BaseHttpClientInvocation theInvocation) {
+	private static void addPreferHeader(PreferHeader.PreferReturnEnum thePrefer, BaseHttpClientInvocation theInvocation) {
 		if (thePrefer != null) {
 			theInvocation.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RETURN + '=' + thePrefer.getHeaderValue());
 		}

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

@@ -112,8 +112,8 @@ public abstract class AbstractJaxRsPageProvider extends AbstractJaxRsProvider im
 	}
 
 	@Override
-	public PreferReturnEnum getDefaultPreferReturn() {
+	public PreferHeader.PreferReturnEnum getDefaultPreferReturn() {
-		return PreferReturnEnum.REPRESENTATION;
+		return PreferHeader.PreferReturnEnum.REPRESENTATION;
 	}
 
 }

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

@@ -28,7 +28,6 @@ import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
-import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -371,8 +370,8 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
     }
 
 	@Override
-	public PreferReturnEnum getDefaultPreferReturn() {
+	public PreferHeader.PreferReturnEnum getDefaultPreferReturn() {
-		return PreferReturnEnum.REPRESENTATION;
+		return PreferHeader.PreferReturnEnum.REPRESENTATION;
 	}
 
 	/**

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu2Test.java

@@ -301,12 +301,12 @@ public class GenericJaxRsClientDstu2Test {
 		Patient p = new Patient();
 		p.addName().addFamily("FOOFAMILY");
 
-		client.create().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
 
-		client.create().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
@@ -1927,12 +1927,12 @@ public class GenericJaxRsClientDstu2Test {
 		p.setId(new IdDt("1"));
 		p.addName().addFamily("FOOFAMILY");
 
-		client.update().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
 
-		client.update().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu3Test.java

@@ -321,12 +321,12 @@ public class GenericJaxRsClientDstu3Test {
 		Patient p = new Patient();
 		p.addName().setFamily("FOOFAMILY");
 
-		client.create().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
 
-		client.create().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.create().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
@@ -1980,12 +1980,12 @@ public class GenericJaxRsClientDstu3Test {
 		p.setId(new IdType("1"));
 		p.addName().setFamily("FOOFAMILY");
 
-		client.update().resource(p).prefer(PreferReturnEnum.MINIMAL).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.MINIMAL).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_MINIMAL, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		
 
-		client.update().resource(p).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		client.update().resource(p).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		assertEquals(1, ourRequestHeaders.get(Constants.HEADER_PREFER).size());
 		assertEquals(Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_REPRESENTATION, ourRequestHeaders.get(Constants.HEADER_PREFER).get(0).getValue());
 		

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProviderDstu3Test.java

@@ -7,10 +7,7 @@ import ca.uhn.fhir.jaxrs.server.test.TestJaxRsConformanceRestProviderDstu3;
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPageProviderDstu3;
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu3;
 import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
-import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
@@ -138,7 +135,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 		client.setEncoding(EncodingEnum.JSON);
 
 		MethodOutcome response = client.create().resource(toCreate).conditional()
-				.where(Patient.IDENTIFIER.exactly().identifier("2")).prefer(PreferReturnEnum.REPRESENTATION).execute();
+				.where(Patient.IDENTIFIER.exactly().identifier("2")).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 
 		assertEquals("myIdentifier", patientCaptor.getValue().getIdentifier().get(0).getValue());
 		IBaseResource resource = response.getResource();
@@ -161,7 +158,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 
 		when(mock.create(patientCaptor.capture(), isNull(String.class))).thenReturn(outcome);
 		client.setEncoding(EncodingEnum.JSON);
-		final MethodOutcome response = client.create().resource(toCreate).prefer(PreferReturnEnum.REPRESENTATION)
+		final MethodOutcome response = client.create().resource(toCreate).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION)
 				.execute();
 		IBaseResource resource = response.getResource();
 		compareResultId(1, resource);

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

@@ -13,10 +13,7 @@ import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
-import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
@@ -134,7 +131,7 @@ public class AbstractJaxRsResourceProviderTest {
 		client.setEncoding(EncodingEnum.JSON);
 
 		MethodOutcome response = client.create().resource(toCreate).conditional()
-				.where(Patient.IDENTIFIER.exactly().identifier("2")).prefer(PreferReturnEnum.REPRESENTATION).execute();
+				.where(Patient.IDENTIFIER.exactly().identifier("2")).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 
 		assertEquals("myIdentifier", patientCaptor.getValue().getIdentifierFirstRep().getValue());
 		IResource resource = (IResource) response.getResource();
@@ -157,7 +154,7 @@ public class AbstractJaxRsResourceProviderTest {
 
 		when(mock.create(patientCaptor.capture(), isNull(String.class))).thenReturn(outcome);
 		client.setEncoding(EncodingEnum.JSON);
-		final MethodOutcome response = client.create().resource(toCreate).prefer(PreferReturnEnum.REPRESENTATION)
+		final MethodOutcome response = client.create().resource(toCreate).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION)
 				.execute();
 		IResource resource = (IResource) response.getResource();
 		compareResultId(1, resource);

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderDstu3Test.java

@@ -138,7 +138,7 @@ public class JaxRsPatientProviderDstu3Test {
         existing.setId((IdType) null);
         existing.getName().add(new HumanName().setFamily("Created Patient 54"));
         client.setEncoding(EncodingEnum.JSON);
-        final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+        final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
         System.out.println(results.getId());
         final Patient patient = (Patient) results.getResource();
         System.out.println(patient);
@@ -154,7 +154,7 @@ public class JaxRsPatientProviderDstu3Test {
         existing.setId((IdType) null);
         existing.getName().add(new HumanName().setFamily("Created Patient 54"));
         client.setEncoding(EncodingEnum.XML);
-        final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+        final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
         System.out.println(results.getId());
         final Patient patient = (Patient) results.getResource();
 
@@ -187,7 +187,7 @@ public class JaxRsPatientProviderDstu3Test {
     public void testDeletePatient() {
         final Patient existing = new Patient();
         existing.getName().add(new HumanName().setFamily("Created Patient XYZ"));
-        final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+        final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
         System.out.println(results.getId());
         final Patient patient = (Patient) results.getResource();
         client.delete().resourceById(patient.getIdElement()).execute();

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderR4Test.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.PreferHeader;
 import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
@@ -152,7 +152,7 @@ public class JaxRsPatientProviderR4Test {
 		existing.setId((IdDt) null);
 		existing.getNameFirstRep().setFamily("Created Patient 54");
 		client.setEncoding(EncodingEnum.JSON);
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 		System.out.println(patient);
@@ -167,7 +167,7 @@ public class JaxRsPatientProviderR4Test {
 		existing.setId((IdDt) null);
 		existing.getNameFirstRep().setFamily("Created Patient 54");
 		client.setEncoding(EncodingEnum.XML);
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 
@@ -199,7 +199,7 @@ public class JaxRsPatientProviderR4Test {
 	public void testDeletePatient() {
 		final Patient existing = new Patient();
 		existing.getNameFirstRep().setFamily("Created Patient XYZ");
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 		client.delete().resource(patient).execute();

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderTest.java

@@ -149,7 +149,7 @@ public class JaxRsPatientProviderTest {
 		existing.setId((IdDt) null);
 		existing.getNameFirstRep().addFamily("Created Patient 54");
 		client.setEncoding(EncodingEnum.JSON);
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 		System.out.println(patient);
@@ -164,7 +164,7 @@ public class JaxRsPatientProviderTest {
 		existing.setId((IdDt) null);
 		existing.getNameFirstRep().addFamily("Created Patient 54");
 		client.setEncoding(EncodingEnum.XML);
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 
@@ -196,7 +196,7 @@ public class JaxRsPatientProviderTest {
 	public void testDeletePatient() {
 		final Patient existing = new Patient();
 		existing.getNameFirstRep().addFamily("Created Patient XYZ");
-		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute();
 		System.out.println(results.getId());
 		final Patient patient = (Patient) results.getResource();
 		client.delete().resourceById(patient.getId()).execute();

hapi-fhir-jpaserver-base/pom.xml

@@ -309,6 +309,11 @@
 			<scope>provided</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>org.quartz-scheduler</groupId>
+			<artifactId>quartz</artifactId>
+		</dependency>
+
 
 		<!-- <dependency> <groupId>org.hsqldb</groupId> <artifactId>hsqldb</artifactId> <version>2.3.2</version> </dependency> -->
 
@@ -700,7 +705,7 @@
 							<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
 							<packageBase>ca.uhn.fhir.jpa.rp.dstu2</packageBase>
 							<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml</targetResourceSpringBeansFile>
-							<baseResourceNames></baseResourceNames>
+							<baseResourceNames/>
 							<excludeResourceNames>
 								<!-- <excludeResourceName>OperationDefinition</excludeResourceName> <excludeResourceName>OperationOutcome</excludeResourceName> -->
 							</excludeResourceNames>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProvider.java

@@ -0,0 +1,158 @@
+package ca.uhn.fhir.jpa.bulk;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.util.JsonUtil;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.PreferHeader;
+import ca.uhn.fhir.rest.server.RestfulServerUtils;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.ArrayUtil;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.InstantType;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+import java.util.Date;
+import java.util.Set;
+
+public class BulkDataExportProvider {
+
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
+	@Autowired
+	private FhirContext myFhirContext;
+
+	@VisibleForTesting
+	public void setFhirContextForUnitTest(FhirContext theFhirContext) {
+		myFhirContext = theFhirContext;
+	}
+
+	@VisibleForTesting
+	public void setBulkDataExportSvcForUnitTests(IBulkDataExportSvc theBulkDataExportSvc) {
+		myBulkDataExportSvc = theBulkDataExportSvc;
+	}
+
+	/**
+	 * $export
+	 */
+	@Operation(name = JpaConstants.OPERATION_EXPORT, global = false /* set to true once we can handle this */, manualResponse = true, idempotent = true)
+	public void export(
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
+		ServletRequestDetails theRequestDetails
+	) {
+
+		String preferHeader = theRequestDetails.getHeader(Constants.HEADER_PREFER);
+		PreferHeader prefer = RestfulServerUtils.parsePreferHeader(null, preferHeader);
+		if (prefer.getRespondAsync() == false) {
+			throw new InvalidRequestException("Must request async processing for $export");
+		}
+
+		String outputFormat = theOutputFormat != null ? theOutputFormat.getValueAsString() : null;
+
+		Set<String> resourceTypes = null;
+		if (theType != null) {
+			resourceTypes = ArrayUtil.commaSeparatedListToCleanSet(theType.getValueAsString());
+		}
+
+		Date since = null;
+		if (theSince != null) {
+			since = theSince.getValue();
+		}
+
+		Set<String> filters = null;
+		if (theTypeFilter != null) {
+			filters = ArrayUtil.commaSeparatedListToCleanSet(theTypeFilter.getValueAsString());
+		}
+
+		IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(outputFormat, resourceTypes, since, filters);
+
+		String serverBase = getServerBase(theRequestDetails);
+		String pollLocation = serverBase + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" + JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + outcome.getJobId();
+
+		HttpServletResponse response = theRequestDetails.getServletResponse();
+
+		// Add standard headers
+		theRequestDetails.getServer().addHeadersToResponse(response);
+
+		// Successful 202 Accepted
+		response.addHeader(Constants.HEADER_CONTENT_LOCATION, pollLocation);
+		response.setStatus(Constants.STATUS_HTTP_202_ACCEPTED);
+	}
+
+	/**
+	 * $export-poll-status
+	 */
+	@Operation(name = JpaConstants.OPERATION_EXPORT_POLL_STATUS, manualResponse = true, idempotent = true)
+	public void exportPollStatus(
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID, typeName = "string", min = 0, max = 1) IPrimitiveType<String> theJobId,
+		ServletRequestDetails theRequestDetails
+	) throws IOException {
+
+		HttpServletResponse response = theRequestDetails.getServletResponse();
+		theRequestDetails.getServer().addHeadersToResponse(response);
+
+		IBulkDataExportSvc.JobInfo status = myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(theJobId.getValueAsString());
+
+		switch (status.getStatus()) {
+			case SUBMITTED:
+			case BUILDING:
+
+				response.setStatus(Constants.STATUS_HTTP_202_ACCEPTED);
+				response.addHeader(Constants.HEADER_X_PROGRESS, "Build in progress - Status set to " + status.getStatus() + " at " + new InstantType(status.getStatusTime()).getValueAsString());
+				response.addHeader(Constants.HEADER_RETRY_AFTER, "120");
+				break;
+
+			case COMPLETE:
+
+				response.setStatus(Constants.STATUS_HTTP_200_OK);
+				response.setContentType(Constants.CT_JSON);
+
+				// Create a JSON response
+				BulkExportResponseJson bulkResponseDocument = new BulkExportResponseJson();
+				bulkResponseDocument.setTransactionTime(status.getStatusTime());
+				bulkResponseDocument.setRequest(status.getRequest());
+				for (IBulkDataExportSvc.FileEntry nextFile : status.getFiles()) {
+					String serverBase = getServerBase(theRequestDetails);
+					String nextUrl = serverBase + "/" + nextFile.getResourceId().toUnqualifiedVersionless().getValue();
+					bulkResponseDocument
+						.addOutput()
+						.setType(nextFile.getResourceType())
+						.setUrl(nextUrl);
+				}
+				JsonUtil.serialize(bulkResponseDocument, response.getWriter());
+				response.getWriter().close();
+				break;
+
+			case ERROR:
+
+				response.setStatus(Constants.STATUS_HTTP_500_INTERNAL_ERROR);
+				response.setContentType(Constants.CT_FHIR_JSON);
+
+				// Create an OperationOutcome response
+				IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(myFhirContext);
+				OperationOutcomeUtil.addIssue(myFhirContext, oo, "error", status.getStatusMessage(), null, null);
+				myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToWriter(oo, response.getWriter());
+				response.getWriter().close();
+
+		}
+
+
+	}
+
+	private String getServerBase(ServletRequestDetails theRequestDetails) {
+		return StringUtils.removeEnd(theRequestDetails.getServerBaseForRequest(), "/");
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImpl.java

@@ -0,0 +1,447 @@
+package ca.uhn.fhir.jpa.bulk;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IResultIterator;
+import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
+import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
+import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
+import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.util.ExpungeOptions;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.BinaryUtil;
+import ca.uhn.fhir.util.StopWatch;
+import com.google.common.collect.Sets;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.InstantType;
+import org.quartz.DisallowConcurrentExecution;
+import org.quartz.JobExecutionContext;
+import org.quartz.PersistJobDataAfterExecution;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Slice;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.PostConstruct;
+import javax.transaction.Transactional;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.*;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static ca.uhn.fhir.util.UrlUtil.escapeUrlParam;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
+
+	private static final long REFRESH_INTERVAL = 10 * DateUtils.MILLIS_PER_SECOND;
+	private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportSvcImpl.class);
+	private int myReuseBulkExportForMillis = (int) (60 * DateUtils.MILLIS_PER_MINUTE);
+
+	@Autowired
+	private IBulkExportJobDao myBulkExportJobDao;
+	@Autowired
+	private IBulkExportCollectionDao myBulkExportCollectionDao;
+	@Autowired
+	private IBulkExportCollectionFileDao myBulkExportCollectionFileDao;
+	@Autowired
+	private ISchedulerService mySchedulerService;
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private FhirContext myContext;
+	@Autowired
+	private PlatformTransactionManager myTxManager;
+	private TransactionTemplate myTxTemplate;
+
+	private long myFileMaxChars = 500 * FileUtils.ONE_KB;
+	private int myRetentionPeriod = (int) DateUtils.MILLIS_PER_DAY;
+
+	/**
+	 * This method is called by the scheduler to run a pass of the
+	 * generator
+	 */
+	@Transactional(value = Transactional.TxType.NEVER)
+	@Override
+	public synchronized void buildExportFiles() {
+
+		Optional<BulkExportJobEntity> jobToProcessOpt = myTxTemplate.execute(t -> {
+			Pageable page = PageRequest.of(0, 1);
+			Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByStatus(page, BulkJobStatusEnum.SUBMITTED);
+			if (submittedJobs.isEmpty()) {
+				return Optional.empty();
+			}
+			return Optional.of(submittedJobs.getContent().get(0));
+		});
+
+		if (!jobToProcessOpt.isPresent()) {
+			return;
+		}
+
+		String jobUuid = jobToProcessOpt.get().getJobId();
+
+		try {
+			myTxTemplate.execute(t -> {
+				processJob(jobUuid);
+				return null;
+			});
+		} catch (Exception e) {
+			ourLog.error("Failure while preparing bulk export extract", e);
+			myTxTemplate.execute(t -> {
+				Optional<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByJobId(jobUuid);
+				if (submittedJobs.isPresent()) {
+					BulkExportJobEntity jobEntity = submittedJobs.get();
+					jobEntity.setStatus(BulkJobStatusEnum.ERROR);
+					jobEntity.setStatusMessage(e.getMessage());
+					myBulkExportJobDao.save(jobEntity);
+				}
+				return null;
+			});
+		}
+
+	}
+
+
+	/**
+	 * This method is called by the scheduler to run a pass of the
+	 * generator
+	 */
+	@Transactional(value = Transactional.TxType.NEVER)
+	@Override
+	public void purgeExpiredFiles() {
+		Optional<BulkExportJobEntity> jobToDelete = myTxTemplate.execute(t -> {
+			Pageable page = PageRequest.of(0, 1);
+			Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByExpiry(page, new Date());
+			if (submittedJobs.isEmpty()) {
+				return Optional.empty();
+			}
+			return Optional.of(submittedJobs.getContent().get(0));
+		});
+
+		if (jobToDelete.isPresent()) {
+
+			ourLog.info("Deleting bulk export job: {}", jobToDelete.get().getJobId());
+
+			myTxTemplate.execute(t -> {
+
+				BulkExportJobEntity job = myBulkExportJobDao.getOne(jobToDelete.get().getId());
+				for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
+					for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
+
+						ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
+						getBinaryDao().delete(toId(nextFile.getResourceId()));
+						getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), null);
+						myBulkExportCollectionFileDao.delete(nextFile);
+
+					}
+
+					myBulkExportCollectionDao.delete(nextCollection);
+				}
+
+				myBulkExportJobDao.delete(job);
+				return null;
+			});
+
+		}
+
+	}
+
+	private void processJob(String theJobUuid) {
+
+		Optional<BulkExportJobEntity> jobOpt = myBulkExportJobDao.findByJobId(theJobUuid);
+		if (!jobOpt.isPresent()) {
+			ourLog.info("Job appears to be deleted");
+			return;
+		}
+
+		StopWatch jobStopwatch = new StopWatch();
+		AtomicInteger jobResourceCounter = new AtomicInteger();
+
+		BulkExportJobEntity job = jobOpt.get();
+		ourLog.info("Bulk export starting generation for batch export job: {}", job);
+
+		for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
+
+			String nextType = nextCollection.getResourceType();
+			IFhirResourceDao dao = myDaoRegistry.getResourceDao(nextType);
+
+			ourLog.info("Bulk export assembling export of type {} for job {}", nextType, theJobUuid);
+
+			ISearchBuilder sb = dao.newSearchBuilder();
+			Class<? extends IBaseResource> nextTypeClass = myContext.getResourceDefinition(nextType).getImplementingClass();
+			sb.setType(nextTypeClass, nextType);
+
+			SearchParameterMap map = new SearchParameterMap();
+			map.setLoadSynchronous(true);
+			if (job.getSince() != null) {
+				map.setLastUpdated(new DateRangeParam(job.getSince(), null));
+			}
+
+			IResultIterator resultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, theJobUuid), null);
+			storeResultsToFiles(nextCollection, sb, resultIterator, jobResourceCounter, jobStopwatch);
+
+
+		}
+
+		job.setStatus(BulkJobStatusEnum.COMPLETE);
+		updateExpiry(job);
+		myBulkExportJobDao.save(job);
+
+		ourLog.info("Bulk export completed job in {}: {}", jobStopwatch, job);
+
+	}
+
+	private void storeResultsToFiles(BulkExportCollectionEntity theExportCollection, ISearchBuilder theSearchBuilder, IResultIterator theResultIterator, AtomicInteger theJobResourceCounter, StopWatch theJobStopwatch) {
+
+		try (IResultIterator query = theResultIterator) {
+			if (!query.hasNext()) {
+				return;
+			}
+
+			AtomicInteger fileCounter = new AtomicInteger(0);
+			ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+			OutputStreamWriter writer = new OutputStreamWriter(outputStream, Constants.CHARSET_UTF8);
+			IParser parser = myContext.newJsonParser().setPrettyPrint(false);
+
+			List<Long> pidsSpool = new ArrayList<>();
+			List<IBaseResource> resourcesSpool = new ArrayList<>();
+			while (query.hasNext()) {
+				pidsSpool.add(query.next());
+				fileCounter.incrementAndGet();
+				theJobResourceCounter.incrementAndGet();
+
+				if (pidsSpool.size() >= 10 || !query.hasNext()) {
+
+					theSearchBuilder.loadResourcesByPid(pidsSpool, Collections.emptyList(), resourcesSpool, false, null);
+
+					for (IBaseResource nextFileResource : resourcesSpool) {
+						parser.encodeResourceToWriter(nextFileResource, writer);
+						writer.append("\n");
+					}
+
+					pidsSpool.clear();
+					resourcesSpool.clear();
+
+					if (outputStream.size() >= myFileMaxChars || !query.hasNext()) {
+						Optional<IIdType> createdId = flushToFiles(theExportCollection, fileCounter, outputStream);
+						createdId.ifPresent(theIIdType -> ourLog.info("Created resource {} for bulk export file containing {} resources of type {} - Total {} resources ({}/sec)", theIIdType.toUnqualifiedVersionless().getValue(), fileCounter.get(), theExportCollection.getResourceType(), theJobResourceCounter.get(), theJobStopwatch.formatThroughput(theJobResourceCounter.get(), TimeUnit.SECONDS)));
+						fileCounter.set(0);
+					}
+
+				}
+			}
+
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
+		}
+	}
+
+	private Optional<IIdType> flushToFiles(BulkExportCollectionEntity theCollection, AtomicInteger theCounter, ByteArrayOutputStream theOutputStream) {
+		if (theOutputStream.size() > 0) {
+			IBaseBinary binary = BinaryUtil.newBinary(myContext);
+			binary.setContentType(Constants.CT_FHIR_NDJSON);
+			binary.setContent(theOutputStream.toByteArray());
+
+			IIdType createdId = getBinaryDao().create(binary).getResource().getIdElement();
+
+			BulkExportCollectionFileEntity file = new BulkExportCollectionFileEntity();
+			theCollection.getFiles().add(file);
+			file.setCollection(theCollection);
+			file.setResource(createdId.getIdPart());
+			myBulkExportCollectionFileDao.saveAndFlush(file);
+			theOutputStream.reset();
+
+			return Optional.of(createdId);
+		}
+
+		return Optional.empty();
+	}
+
+	@SuppressWarnings("unchecked")
+	private IFhirResourceDao<IBaseBinary> getBinaryDao() {
+		return myDaoRegistry.getResourceDao("Binary");
+	}
+
+	@PostConstruct
+	public void start() {
+		ourLog.info("Bulk export service starting with refresh interval {}", StopWatch.formatMillis(REFRESH_INTERVAL));
+		myTxTemplate = new TransactionTemplate(myTxManager);
+
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(BulkDataExportSvcImpl.class.getName());
+		jobDetail.setJobClass(BulkDataExportSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(REFRESH_INTERVAL, true, jobDetail);
+	}
+
+	@Transactional
+	@Override
+	public JobInfo submitJob(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters) {
+		String outputFormat = Constants.CT_FHIR_NDJSON;
+		if (isNotBlank(theOutputFormat)) {
+			outputFormat = theOutputFormat;
+		}
+		if (!Constants.CTS_NDJSON.contains(outputFormat)) {
+			throw new InvalidRequestException("Invalid output format: " + theOutputFormat);
+		}
+
+		StringBuilder requestBuilder = new StringBuilder();
+		requestBuilder.append("/").append(JpaConstants.OPERATION_EXPORT);
+		requestBuilder.append("?").append(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT).append("=").append(escapeUrlParam(outputFormat));
+		Set<String> resourceTypes = theResourceTypes;
+		if (resourceTypes != null) {
+			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE).append("=").append(String.join(",", resourceTypes));
+		}
+		Date since = theSince;
+		if (since != null) {
+			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_SINCE).append("=").append(new InstantType(since).setTimeZoneZulu(true).getValueAsString());
+		}
+		if (theFilters != null && theFilters.size() > 0) {
+			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE).append("=").append(String.join(",", theFilters));
+		}
+		String request = requestBuilder.toString();
+
+		Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis);
+		Pageable page = PageRequest.of(0, 10);
+		Slice<BulkExportJobEntity> existing = myBulkExportJobDao.findExistingJob(page, request, cutoff, BulkJobStatusEnum.ERROR);
+		if (existing.isEmpty() == false) {
+			return toSubmittedJobInfo(existing.iterator().next());
+		}
+
+		if (theResourceTypes == null || resourceTypes.isEmpty()) {
+			// This is probably not a useful default, but having the default be "download the whole
+			// server" seems like a risky default too. We'll deal with that by having the default involve
+			// only returning a small time span
+			resourceTypes = myContext.getResourceNames();
+			if (since == null) {
+				since = DateUtils.addDays(new Date(), -1);
+			}
+		}
+
+		BulkExportJobEntity job = new BulkExportJobEntity();
+		job.setJobId(UUID.randomUUID().toString());
+		job.setStatus(BulkJobStatusEnum.SUBMITTED);
+		job.setSince(since);
+		job.setCreated(new Date());
+		job.setRequest(request);
+
+		updateExpiry(job);
+		myBulkExportJobDao.save(job);
+
+		for (String nextType : resourceTypes) {
+			if (!myDaoRegistry.isResourceTypeSupported(nextType)) {
+				throw new InvalidRequestException("Unknown or unsupported resource type: " + nextType);
+			}
+
+			BulkExportCollectionEntity collection = new BulkExportCollectionEntity();
+			collection.setJob(job);
+			collection.setResourceType(nextType);
+			job.getCollections().add(collection);
+			myBulkExportCollectionDao.save(collection);
+		}
+
+		ourLog.info("Bulk export job submitted: {}", job.toString());
+
+		return toSubmittedJobInfo(job);
+	}
+
+	private JobInfo toSubmittedJobInfo(BulkExportJobEntity theJob) {
+		return new JobInfo().setJobId(theJob.getJobId());
+	}
+
+
+	private void updateExpiry(BulkExportJobEntity theJob) {
+		theJob.setExpiry(DateUtils.addMilliseconds(new Date(), myRetentionPeriod));
+	}
+
+	@Transactional
+	@Override
+	public JobInfo getJobStatusOrThrowResourceNotFound(String theJobId) {
+		BulkExportJobEntity job = myBulkExportJobDao
+			.findByJobId(theJobId)
+			.orElseThrow(() -> new ResourceNotFoundException(theJobId));
+
+		JobInfo retVal = new JobInfo();
+		retVal.setJobId(theJobId);
+		retVal.setStatus(job.getStatus());
+		retVal.setStatus(job.getStatus());
+		retVal.setStatusTime(job.getStatusTime());
+		retVal.setStatusMessage(job.getStatusMessage());
+		retVal.setRequest(job.getRequest());
+
+		if (job.getStatus() == BulkJobStatusEnum.COMPLETE) {
+			for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
+				for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
+					retVal.addFile()
+						.setResourceType(nextCollection.getResourceType())
+						.setResourceId(toQualifiedBinaryId(nextFile.getResourceId()));
+				}
+			}
+		}
+
+		return retVal;
+	}
+
+	private IIdType toId(String theResourceId) {
+		IIdType retVal = myContext.getVersion().newIdType();
+		retVal.setValue(theResourceId);
+		return retVal;
+	}
+
+	private IIdType toQualifiedBinaryId(String theIdPart) {
+		IIdType retVal = myContext.getVersion().newIdType();
+		retVal.setParts(null, "Binary", theIdPart, null);
+
+		return retVal;
+	}
+
+	@Override
+	@Transactional
+	public synchronized void cancelAndPurgeAllJobs() {
+		myBulkExportCollectionFileDao.deleteAll();
+		myBulkExportCollectionDao.deleteAll();
+		myBulkExportJobDao.deleteAll();
+	}
+
+	@DisallowConcurrentExecution
+	@PersistJobDataAfterExecution
+	public static class SubmitJob extends FireAtIntervalJob {
+		@Autowired
+		private IBulkDataExportSvc myTarget;
+
+		public SubmitJob() {
+			super(REFRESH_INTERVAL);
+		}
+
+		@Override
+		protected void doExecute(JobExecutionContext theContext) {
+			myTarget.buildExportFiles();
+		}
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/BulkExportResponseJson.java

@@ -0,0 +1,110 @@
+package ca.uhn.fhir.jpa.bulk;
+
+
+import ca.uhn.fhir.jpa.util.JsonDateDeserializer;
+import ca.uhn.fhir.jpa.util.JsonDateSerializer;
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_DEFAULT)
+@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
+public class BulkExportResponseJson {
+
+	@JsonProperty("transactionTime")
+	@JsonSerialize(using = JsonDateSerializer.class)
+	@JsonDeserialize(using = JsonDateDeserializer.class)
+	private Date myTransactionTime;
+
+	@JsonProperty("request")
+	private String myRequest;
+	@JsonProperty("requiresAccessToken")
+	private Boolean myRequiresAccessToken;
+	@JsonProperty("output")
+	private List<Output> myOutput;
+	@JsonProperty("error")
+	private List<Output> myError;
+
+	public Date getTransactionTime() {
+		return myTransactionTime;
+	}
+
+	public BulkExportResponseJson setTransactionTime(Date theTransactionTime) {
+		myTransactionTime = theTransactionTime;
+		return this;
+	}
+
+	public String getRequest() {
+		return myRequest;
+	}
+
+	public BulkExportResponseJson setRequest(String theRequest) {
+		myRequest = theRequest;
+		return this;
+	}
+
+	public Boolean getRequiresAccessToken() {
+		return myRequiresAccessToken;
+	}
+
+	public BulkExportResponseJson setRequiresAccessToken(Boolean theRequiresAccessToken) {
+		myRequiresAccessToken = theRequiresAccessToken;
+		return this;
+	}
+
+	public List<Output> getOutput() {
+		if (myOutput == null) {
+			myOutput = new ArrayList<>();
+		}
+		return myOutput;
+	}
+
+	public List<Output> getError() {
+		if (myError == null) {
+			myError = new ArrayList<>();
+		}
+		return myError;
+	}
+
+	public Output addOutput() {
+		Output retVal = new Output();
+		getOutput().add(retVal);
+		return retVal;
+	}
+
+	@JsonInclude(JsonInclude.Include.NON_NULL)
+	@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
+	public static class Output {
+
+		@JsonProperty("type")
+		private String myType;
+		@JsonProperty("url")
+		private String myUrl;
+
+		public String getType() {
+			return myType;
+		}
+
+		public Output setType(String theType) {
+			myType = theType;
+			return this;
+		}
+
+		public String getUrl() {
+			return myUrl;
+		}
+
+		public Output setUrl(String theUrl) {
+			myUrl = theUrl;
+			return this;
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/BulkJobStatusEnum.java

@@ -0,0 +1,10 @@
+package ca.uhn.fhir.jpa.bulk;
+
+public enum BulkJobStatusEnum {
+
+	SUBMITTED,
+	BUILDING,
+	COMPLETE,
+	ERROR
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/IBulkDataExportSvc.java

@@ -0,0 +1,114 @@
+package ca.uhn.fhir.jpa.bulk;
+
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import javax.transaction.Transactional;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Set;
+
+public interface IBulkDataExportSvc {
+	void buildExportFiles();
+
+	@Transactional(value = Transactional.TxType.NEVER)
+	void purgeExpiredFiles();
+
+	JobInfo submitJob(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters);
+
+	JobInfo getJobStatusOrThrowResourceNotFound(String theJobId);
+
+	void cancelAndPurgeAllJobs();
+
+	class JobInfo {
+		private String myJobId;
+		private BulkJobStatusEnum myStatus;
+		private List<FileEntry> myFiles;
+		private String myRequest;
+		private Date myStatusTime;
+		private String myStatusMessage;
+
+		public String getRequest() {
+			return myRequest;
+		}
+
+		public void setRequest(String theRequest) {
+			myRequest = theRequest;
+		}
+
+		public Date getStatusTime() {
+			return myStatusTime;
+		}
+
+		public JobInfo setStatusTime(Date theStatusTime) {
+			myStatusTime = theStatusTime;
+			return this;
+		}
+
+		public String getJobId() {
+			return myJobId;
+		}
+
+		public JobInfo setJobId(String theJobId) {
+			myJobId = theJobId;
+			return this;
+		}
+
+		public List<FileEntry> getFiles() {
+			if (myFiles == null) {
+				myFiles = new ArrayList<>();
+			}
+			return myFiles;
+		}
+
+		public BulkJobStatusEnum getStatus() {
+			return myStatus;
+		}
+
+		public JobInfo setStatus(BulkJobStatusEnum theStatus) {
+			myStatus = theStatus;
+			return this;
+		}
+
+		public String getStatusMessage() {
+			return myStatusMessage;
+		}
+
+		public JobInfo setStatusMessage(String theStatusMessage) {
+			myStatusMessage = theStatusMessage;
+			return this;
+		}
+
+		public FileEntry addFile() {
+			FileEntry retVal = new FileEntry();
+			getFiles().add(retVal);
+			return retVal;
+		}
+	}
+
+
+	class FileEntry {
+		private String myResourceType;
+		private IIdType myResourceId;
+
+		public String getResourceType() {
+			return myResourceType;
+		}
+
+		public FileEntry setResourceType(String theResourceType) {
+			myResourceType = theResourceType;
+			return this;
+		}
+
+		public IIdType getResourceId() {
+			return myResourceId;
+		}
+
+		public FileEntry setResourceId(IIdType theResourceId) {
+			myResourceId = theResourceId;
+			return this;
+		}
+	}
+
+
+}

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

@@ -6,11 +6,17 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
 import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
+import ca.uhn.fhir.jpa.bulk.BulkDataExportSvcImpl;
+import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
 import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory;
+import ca.uhn.fhir.jpa.sched.SchedulerServiceImpl;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
@@ -29,7 +35,6 @@ import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
-import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.*;
 import org.springframework.core.env.Environment;
@@ -38,15 +43,10 @@ import org.springframework.dao.annotation.PersistenceExceptionTranslationPostPro
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.scheduling.TaskScheduler;
-import org.springframework.scheduling.annotation.EnableScheduling;
-import org.springframework.scheduling.annotation.SchedulingConfigurer;
 import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
 import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
-import org.springframework.scheduling.config.ScheduledTaskRegistrar;
 import org.springframework.web.socket.config.annotation.WebSocketConfigurer;
 
-import javax.annotation.Nonnull;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -69,7 +69,6 @@ import javax.annotation.Nonnull;
 
 
 @Configuration
-@EnableScheduling
 @EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
 @ComponentScan(basePackages = "ca.uhn.fhir.jpa", excludeFilters = {
 	@ComponentScan.Filter(type = FilterType.ASSIGNABLE_TYPE, value = BaseConfig.class),
@@ -77,8 +76,7 @@ import javax.annotation.Nonnull;
 	@ComponentScan.Filter(type = FilterType.REGEX, pattern = ".*\\.test\\..*"),
 	@ComponentScan.Filter(type = FilterType.REGEX, pattern = ".*Test.*"),
 	@ComponentScan.Filter(type = FilterType.REGEX, pattern = "ca.uhn.fhir.jpa.subscription.module.standalone.*")})
-
+public abstract class BaseConfig {
-public abstract class BaseConfig implements SchedulingConfigurer {
 
 	public static final String TASK_EXECUTOR_NAME = "hapiJpaTaskExecutor";
 	public static final String GRAPHQL_PROVIDER_NAME = "myGraphQLProvider";
@@ -86,18 +84,12 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 	@Autowired
 	protected Environment myEnv;
 
-
-	@Override
-	public void configureTasks(@Nonnull ScheduledTaskRegistrar theTaskRegistrar) {
-		theTaskRegistrar.setTaskScheduler(taskScheduler());
-	}
-
 	@Bean("myDaoRegistry")
 	public DaoRegistry daoRegistry() {
 		return new DaoRegistry();
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
 		return new DatabaseBackedPagingProvider();
 	}
@@ -226,7 +218,7 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 	 * Subclasses may override
 	 */
 	protected boolean isSupported(String theResourceType) {
-		return daoRegistry().getResourceDaoIfExists(theResourceType) != null;
+		return daoRegistry().getResourceDaoOrNull(theResourceType) != null;
 	}
 
 	@Bean
@@ -241,6 +233,30 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 		return retVal;
 	}
 
+	@Bean
+	public ISchedulerService schedulerService() {
+		return new SchedulerServiceImpl();
+	}
+
+	@Bean
+	public AutowiringSpringBeanJobFactory schedulerJobFactory() {
+		return new AutowiringSpringBeanJobFactory();
+	}
+
+	@Bean
+	@Lazy
+	public IBulkDataExportSvc bulkDataExportSvc() {
+		return new BulkDataExportSvcImpl();
+	}
+
+	@Bean
+	@Lazy
+	public BulkDataExportProvider bulkDataExportProvider() {
+		return new BulkDataExportProvider();
+	}
+
+
+
 	public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
 		theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
 		theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

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

@@ -80,7 +80,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 @Transactional(propagation = Propagation.REQUIRED)
 public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
 
-	private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
 
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
@@ -551,10 +551,22 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		myEntityManager.merge(entity);
 	}
 
+    private void validateExpungeEnabled() {
+        if (!myDaoConfig.isExpungeEnabled()) {
+            throw new MethodNotAllowedException("$expunge is not enabled on this server");
+        }
+    }
+    
 	@Override
 	@Transactional(propagation = Propagation.NEVER)
 	public ExpungeOutcome expunge(IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
+		validateExpungeEnabled();
+		return forceExpungeInExistingTransaction(theId, theExpungeOptions, theRequest);
+	}
 
+	@Override
+	@Transactional(propagation = Propagation.SUPPORTS)
+	public ExpungeOutcome forceExpungeInExistingTransaction(IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
 
 		BaseHasResource entity = txTemplate.execute(t -> readEntity(theId, theRequest));

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

@@ -41,6 +41,9 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
 
 	@Autowired
 	private FhirContext myContext;
+	private volatile Map<String, IFhirResourceDao<?>> myResourceNameToResourceDao;
+	private volatile IFhirSystemDao<?, ?> mySystemDao;
+	private Set<String> mySupportedResourceTypes;
 
 	/**
 	 * Constructor
@@ -49,11 +52,6 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
 		super();
 	}
 
-	private volatile Map<String, IFhirResourceDao<?>> myResourceNameToResourceDao;
-	private volatile IFhirSystemDao<?, ?> mySystemDao;
-
-	private Set<String> mySupportedResourceTypes;
-
 	public void setSupportedResourceTypes(Collection<String> theSupportedResourceTypes) {
 		HashSet<String> supportedResourceTypes = new HashSet<>();
 		if (theSupportedResourceTypes != null) {
@@ -138,7 +136,10 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
 
 	@Override
 	public boolean isResourceTypeSupported(String theResourceType) {
-		return mySupportedResourceTypes == null || mySupportedResourceTypes.contains(theResourceType);
+		if (mySupportedResourceTypes == null) {
+			return getResourceDaoOrNull(theResourceType) != null;
+		}
+		return mySupportedResourceTypes.contains(theResourceType);
 	}
 
 	private void init() {

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

@@ -116,6 +116,8 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	ExpungeOutcome expunge(IIdType theIIdType, ExpungeOptions theExpungeOptions, RequestDetails theRequest);
 
+	ExpungeOutcome forceExpungeInExistingTransaction(IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest);
+
 	Class<T> getResourceType();
 
 	IBundleProvider history(Date theSince, Date theUntil, RequestDetails theRequestDetails);

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

@@ -185,9 +185,9 @@ public class TransactionProcessor<BUNDLE extends IBaseBundle, BUNDLEENTRY> {
 		if (theRequestDetails != null) {
 			if (outcome.getResource() != null) {
 				String prefer = theRequestDetails.getHeader(Constants.HEADER_PREFER);
-				PreferReturnEnum preferReturn = RestfulServerUtils.parsePreferHeader(null, prefer);
+				PreferHeader.PreferReturnEnum preferReturn = RestfulServerUtils.parsePreferHeader(null, prefer).getReturn();
 				if (preferReturn != null) {
-					if (preferReturn == PreferReturnEnum.REPRESENTATION) {
+					if (preferReturn == PreferHeader.PreferReturnEnum.REPRESENTATION) {
 						outcome.fireResourceViewCallbacks();
 						myVersionAdapter.setResource(newEntry, outcome.getResource());
 					}
@@ -211,7 +211,10 @@ public class TransactionProcessor<BUNDLE extends IBaseBundle, BUNDLEENTRY> {
 				String nextReplacementIdPart = nextReplacementId.getValueAsString();
 				if (isUrn(nextTemporaryId) && nextTemporaryIdPart.length() > URN_PREFIX.length()) {
 					matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
-					matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
+					String escapedUrlParam = UrlUtil.escapeUrlParam(nextTemporaryIdPart);
+					if (isNotBlank(escapedUrlParam)) {
+						matchUrl = matchUrl.replace(escapedUrlParam, nextReplacementIdPart);
+					}
 				}
 			}
 		}

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

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
+import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
+import org.springframework.data.domain.Slice;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import java.util.Optional;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 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 interface IBulkExportCollectionDao extends JpaRepository<BulkExportCollectionEntity, Long> {
+	// nothing currently
+}

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

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 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 interface IBulkExportCollectionFileDao extends JpaRepository<BulkExportCollectionFileEntity, Long> {
+	// nothing currently
+}

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

@@ -0,0 +1,47 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import ca.uhn.fhir.jpa.bulk.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Slice;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import java.util.Date;
+import java.util.Optional;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 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 interface IBulkExportJobDao extends JpaRepository<BulkExportJobEntity, Long> {
+
+	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myJobId = :jobid")
+	Optional<BulkExportJobEntity> findByJobId(@Param("jobid") String theUuid);
+
+	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myStatus = :status")
+	Slice<BulkExportJobEntity> findByStatus(Pageable thePage, @Param("status") BulkJobStatusEnum theSubmitted);
+
+	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myExpiry < :cutoff")
+	Slice<BulkExportJobEntity> findByExpiry(Pageable thePage, @Param("cutoff") Date theCutoff);
+
+	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myRequest = :request AND j.myCreated > :createdAfter AND j.myStatus <> :status")
+	Slice<BulkExportJobEntity> findExistingJob(Pageable thePage, @Param("request") String theRequest, @Param("createdAfter") Date theCreatedAfter, @Param("status") BulkJobStatusEnum theNotStatus);
+}

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

@@ -37,11 +37,11 @@ public interface ISearchDao extends JpaRepository<Search, Long> {
 	@Query("SELECT s FROM Search s LEFT OUTER JOIN FETCH s.myIncludes WHERE s.myUuid = :uuid")
 	Optional<Search> findByUuidAndFetchIncludes(@Param("uuid") String theUuid);
 
-	@Query("SELECT s.myId FROM Search s WHERE s.mySearchLastReturned < :cutoff")
+	@Query("SELECT s.myId FROM Search s WHERE (s.mySearchLastReturned < :cutoff) AND (s.myExpiryOrNull IS NULL OR s.myExpiryOrNull < :now)")
-	Slice<Long> findWhereLastReturnedBefore(@Param("cutoff") Date theCutoff, Pageable thePage);
+	Slice<Long> findWhereLastReturnedBefore(@Param("cutoff") Date theCutoff, @Param("now") Date theNow, Pageable thePage);
 
-	@Query("SELECT s FROM Search s WHERE s.myResourceType = :type AND mySearchQueryStringHash = :hash AND s.myCreated > :cutoff AND s.myDeleted = false")
+	@Query("SELECT s FROM Search s WHERE s.myResourceType = :type AND mySearchQueryStringHash = :hash AND (s.myCreated > :cutoff) AND s.myDeleted = false")
-	Collection<Search> find(@Param("type") String theResourceType, @Param("hash") int theHashCode, @Param("cutoff") Date theCreatedCutoff);
+	Collection<Search> findWithCutoffOrExpiry(@Param("type") String theResourceType, @Param("hash") int theHashCode, @Param("cutoff") Date theCreatedCutoff);
 
 	@Modifying
 	@Query("UPDATE Search s SET s.mySearchLastReturned = :last WHERE s.myId = :pid")

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

@@ -49,10 +49,6 @@ public abstract class ExpungeService {
 	public ExpungeOutcome expunge(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
 		ourLog.info("Expunge: ResourceName[{}] Id[{}] Version[{}] Options[{}]", theResourceName, theResourceId, theVersion, theExpungeOptions);
 
-		if (!myConfig.isExpungeEnabled()) {
-			throw new MethodNotAllowedException("$expunge is not enabled on this server");
-		}
-
 		if (theExpungeOptions.getLimit() < 1) {
 			throw new InvalidRequestException("Expunge limit may not be less than 1.  Received expunge limit " + theExpungeOptions.getLimit() + ".");
 		}

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

@@ -55,6 +55,16 @@ public class PartitionRunner {
 			return;
 		}
 
+		if (callableTasks.size() == 1) {
+			try {
+				callableTasks.get(0).call();
+				return;
+			} catch (Exception e) {
+				ourLog.error("Error while expunging.", e);
+				throw new InternalErrorException(e);
+			}
+		}
+
 		ExecutorService executorService = buildExecutor(callableTasks.size());
 		try {
 			List<Future<Void>> futures = executorService.invokeAll(callableTasks);

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

@@ -0,0 +1,65 @@
+package ca.uhn.fhir.jpa.entity;
+
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+
+import javax.persistence.*;
+import java.util.ArrayList;
+import java.util.Collection;
+
+@Entity
+@Table(name = "HFJ_BLK_EXPORT_COLLECTION")
+public class BulkExportCollectionEntity {
+
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_BLKEXCOL_PID")
+	@SequenceGenerator(name = "SEQ_BLKEXCOL_PID", sequenceName = "SEQ_BLKEXCOL_PID")
+	@Column(name = "PID")
+	private Long myId;
+	@ManyToOne
+	@JoinColumn(name = "JOB_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name="FK_BLKEXCOL_JOB"))
+	private BulkExportJobEntity myJob;
+	@Column(name = "RES_TYPE", length = ResourceTable.RESTYPE_LEN, nullable = false)
+	private String myResourceType;
+	@Column(name = "TYPE_FILTER", length = 1000, nullable = true)
+	private String myFilter;
+	@Version
+	@Column(name = "OPTLOCK", nullable = false)
+	private int myVersion;
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCollection")
+	private Collection<BulkExportCollectionFileEntity> myFiles;
+
+	public void setJob(BulkExportJobEntity theJob) {
+		myJob = theJob;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getFilter() {
+		return myFilter;
+	}
+
+	public void setFilter(String theFilter) {
+		myFilter = theFilter;
+	}
+
+	public int getVersion() {
+		return myVersion;
+	}
+
+	public void setVersion(int theVersion) {
+		myVersion = theVersion;
+	}
+
+	public Collection<BulkExportCollectionFileEntity> getFiles() {
+		if (myFiles == null) {
+			myFiles = new ArrayList<>();
+		}
+		return myFiles;
+	}
+}

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

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.entity;
+
+import ca.uhn.fhir.jpa.model.entity.ForcedId;
+
+import javax.persistence.*;
+
+@Entity
+@Table(name = "HFJ_BLK_EXPORT_COLFILE")
+public class BulkExportCollectionFileEntity {
+
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_BLKEXCOLFILE_PID")
+	@SequenceGenerator(name = "SEQ_BLKEXCOLFILE_PID", sequenceName = "SEQ_BLKEXCOLFILE_PID")
+	@Column(name = "PID")
+	private Long myId;
+	@ManyToOne(fetch = FetchType.LAZY)
+	@JoinColumn(name = "COLLECTION_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name="FK_BLKEXCOLFILE_COLLECT"))
+	private BulkExportCollectionEntity myCollection;
+	@Column(name = "RES_ID", length = ForcedId.MAX_FORCED_ID_LENGTH, nullable = false)
+	private String myResourceId;
+
+	public void setCollection(BulkExportCollectionEntity theCollection) {
+		myCollection = theCollection;
+	}
+
+	public void setResource(String theResourceId) {
+		myResourceId = theResourceId;
+	}
+
+	public String getResourceId() {
+		return myResourceId;
+	}
+}

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

@@ -0,0 +1,157 @@
+package ca.uhn.fhir.jpa.entity;
+
+import ca.uhn.fhir.jpa.bulk.BulkJobStatusEnum;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.hl7.fhir.r5.model.InstantType;
+
+import javax.persistence.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+@Entity
+@Table(name = "HFJ_BLK_EXPORT_JOB", uniqueConstraints = {
+	@UniqueConstraint(name = "IDX_BLKEX_JOB_ID", columnNames = "JOB_ID")
+}, indexes = {
+	@Index(name = "IDX_BLKEX_EXPTIME", columnList = "EXP_TIME")
+})
+public class BulkExportJobEntity {
+
+	public static final int REQUEST_LENGTH = 500;
+	public static final int STATUS_MESSAGE_LEN = 500;
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_BLKEXJOB_PID")
+	@SequenceGenerator(name = "SEQ_BLKEXJOB_PID", sequenceName = "SEQ_BLKEXJOB_PID")
+	@Column(name = "PID")
+	private Long myId;
+
+	@Column(name = "JOB_ID", length = Search.UUID_COLUMN_LENGTH, nullable = false)
+	private String myJobId;
+
+	@Enumerated(EnumType.STRING)
+	@Column(name = "JOB_STATUS", length = 10, nullable = false)
+	private BulkJobStatusEnum myStatus;
+	@Temporal(TemporalType.TIMESTAMP)
+	@Column(name = "CREATED_TIME", nullable = false)
+	private Date myCreated;
+	@Temporal(TemporalType.TIMESTAMP)
+	@Column(name = "STATUS_TIME", nullable = false)
+	private Date myStatusTime;
+	@Temporal(TemporalType.TIMESTAMP)
+	@Column(name = "EXP_TIME", nullable = false)
+	private Date myExpiry;
+	@Column(name = "REQUEST", nullable = false, length = REQUEST_LENGTH)
+	private String myRequest;
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myJob")
+	private Collection<BulkExportCollectionEntity> myCollections;
+	@Version
+	@Column(name = "OPTLOCK", nullable = false)
+	private int myVersion;
+	@Temporal(TemporalType.TIMESTAMP)
+	@Column(name = "EXP_SINCE", nullable = true)
+	private Date mySince;
+	@Column(name = "STATUS_MESSAGE", nullable = true, length = STATUS_MESSAGE_LEN)
+	private String myStatusMessage;
+
+	public Date getCreated() {
+		return myCreated;
+	}
+
+	public void setCreated(Date theCreated) {
+		myCreated = theCreated;
+	}
+
+	public String getStatusMessage() {
+		return myStatusMessage;
+	}
+
+	public void setStatusMessage(String theStatusMessage) {
+		myStatusMessage = theStatusMessage;
+	}
+
+	public String getRequest() {
+		return myRequest;
+	}
+
+	public void setRequest(String theRequest) {
+		myRequest = theRequest;
+	}
+
+	public void setExpiry(Date theExpiry) {
+		myExpiry = theExpiry;
+	}
+
+	public Collection<BulkExportCollectionEntity> getCollections() {
+		if (myCollections == null) {
+			myCollections = new ArrayList<>();
+		}
+		return myCollections;
+	}
+
+	public String getJobId() {
+		return myJobId;
+	}
+
+	public void setJobId(String theJobId) {
+		myJobId = theJobId;
+	}
+
+	@Override
+	public String toString() {
+		ToStringBuilder b = new ToStringBuilder(this);
+		if (isNotBlank(myJobId)) {
+			b.append("jobId", myJobId);
+		}
+		if (myStatus != null) {
+			b.append("status", myStatus + " " + new InstantType(myStatusTime).getValueAsString());
+		}
+		b.append("created", new InstantType(myExpiry).getValueAsString());
+		b.append("expiry", new InstantType(myExpiry).getValueAsString());
+		b.append("request", myRequest);
+		b.append("since", mySince);
+		if (isNotBlank(myStatusMessage)) {
+			b.append("statusMessage", myStatusMessage);
+		}
+		return b.toString();
+	}
+
+	public BulkJobStatusEnum getStatus() {
+		return myStatus;
+	}
+
+	public void setStatus(BulkJobStatusEnum theStatus) {
+		if (myStatus != theStatus) {
+			myStatusTime = new Date();
+			myStatus = theStatus;
+		}
+	}
+
+	public Date getStatusTime() {
+		return myStatusTime;
+	}
+
+	public int getVersion() {
+		return myVersion;
+	}
+
+	public void setVersion(int theVersion) {
+		myVersion = theVersion;
+	}
+
+	public Long getId() {
+		return myId;
+	}
+
+	public Date getSince() {
+		if (mySince != null) {
+			return new Date(mySince.getTime());
+		}
+		return null;
+	}
+
+	public void setSince(Date theSince) {
+		mySince = theSince;
+	}
+}

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

@@ -59,6 +59,9 @@ public class Search implements ICachedSearchDetails, Serializable {
 	private Integer myFailureCode;
 	@Column(name = "FAILURE_MESSAGE", length = FAILURE_MESSAGE_LENGTH, nullable = true)
 	private String myFailureMessage;
+	@Temporal(TemporalType.TIMESTAMP)
+	@Column(name = "EXPIRY_OR_NULL", nullable = true)
+	private Date myExpiryOrNull;
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SEARCH")
 	@SequenceGenerator(name = "SEQ_SEARCH", sequenceName = "SEQ_SEARCH")
@@ -108,7 +111,6 @@ public class Search implements ICachedSearchDetails, Serializable {
 	@Lob
 	@Column(name = "SEARCH_PARAM_MAP", nullable = true)
 	private byte[] mySearchParameterMap;
-
 	/**
 	 * Constructor
 	 */
@@ -116,6 +118,14 @@ public class Search implements ICachedSearchDetails, Serializable {
 		super();
 	}
 
+	public Date getExpiryOrNull() {
+		return myExpiryOrNull;
+	}
+
+	public void setExpiryOrNull(Date theExpiryOrNull) {
+		myExpiryOrNull = theExpiryOrNull;
+	}
+
 	public Boolean getDeleted() {
 		return myDeleted;
 	}
@@ -230,11 +240,15 @@ public class Search implements ICachedSearchDetails, Serializable {
 	}
 
 	public void setSearchQueryString(String theSearchQueryString) {
-		if (theSearchQueryString != null && theSearchQueryString.length() > MAX_SEARCH_QUERY_STRING) {
+		if (theSearchQueryString == null || theSearchQueryString.length() > MAX_SEARCH_QUERY_STRING) {
-			mySearchQueryString = null;
+			// We want this field to always have a wide distribution of values in order
+			// to avoid optimizers avoiding using it if it has lots of nulls, so in the
+			// case of null, just put a value that will never be hit
+			mySearchQueryString = UUID.randomUUID().toString();
 		} else {
 			mySearchQueryString = theSearchQueryString;
 		}
+		mySearchQueryStringHash = mySearchQueryString.hashCode();
 	}
 
 	public SearchTypeEnum getSearchType() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sched/AutowiringSpringBeanJobFactory.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.sched;
+
+import org.quartz.spi.TriggerFiredBundle;
+import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.scheduling.quartz.SpringBeanJobFactory;
+
+public class AutowiringSpringBeanJobFactory extends SpringBeanJobFactory implements ApplicationContextAware {
+
+	private transient AutowireCapableBeanFactory myBeanFactory;
+	private ApplicationContext myAppCtx;
+
+	@Override
+	public void setApplicationContext(final ApplicationContext theApplicationContext) {
+		myAppCtx = theApplicationContext;
+		myBeanFactory = theApplicationContext.getAutowireCapableBeanFactory();
+	}
+
+	@Override
+	protected Object createJobInstance(final TriggerFiredBundle bundle) throws Exception {
+		Object job = super.createJobInstance(bundle);
+		myBeanFactory.autowireBean(job);
+		if (job instanceof ApplicationContextAware) {
+			((ApplicationContextAware) job).setApplicationContext(myAppCtx);
+		}
+		return job;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sched/QuartzTableSeeder.java

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jpa.sched;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+import javax.annotation.PostConstruct;
+
+public class QuartzTableSeeder {
+
+	@Autowired
+	private LocalContainerEntityManagerFactoryBean myEntityManagerFactory;
+
+	@PostConstruct
+	public void start() {
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImpl.java

@@ -0,0 +1,559 @@
+package ca.uhn.fhir.jpa.sched;
+
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import com.google.common.collect.Sets;
+import org.apache.commons.lang3.Validate;
+import org.quartz.Calendar;
+import org.quartz.*;
+import org.quartz.impl.JobDetailImpl;
+import org.quartz.impl.StdSchedulerFactory;
+import org.quartz.impl.matchers.GroupMatcher;
+import org.quartz.spi.JobFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.EventListener;
+import org.springframework.core.env.Environment;
+
+import javax.annotation.PostConstruct;
+import javax.annotation.PreDestroy;
+import java.util.*;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.stream.Collectors;
+
+import static org.quartz.impl.StdSchedulerFactory.PROP_SCHED_INSTANCE_NAME;
+
+/**
+ * This class provides task scheduling for the entire module using the Quartz library.
+ * Inside here, we have two schedulers:
+ * <ul>
+ * <li>
+ * The <b>Local Scheduler</b> handles tasks that need to execute locally. This
+ * typically means things that should happen on all nodes in a clustered
+ * environment.
+ * </li>
+ * <li>
+ * The <b>Cluster Scheduler</b> handles tasks that are distributed and should be
+ * handled by only one node in the cluster (assuming a clustered server). If the
+ * server is not clustered, this scheduler acts the same way as the
+ * local scheduler.
+ * </li>
+ * </ul>
+ */
+public class SchedulerServiceImpl implements ISchedulerService {
+	public static final String SCHEDULING_DISABLED = "scheduling_disabled";
+	public static final String SCHEDULING_DISABLED_EQUALS_TRUE = SCHEDULING_DISABLED + "=true";
+
+	private static final Logger ourLog = LoggerFactory.getLogger(SchedulerServiceImpl.class);
+	private static int ourNextSchedulerId = 0;
+	private Scheduler myLocalScheduler;
+	private Scheduler myClusteredScheduler;
+	private String myThreadNamePrefix;
+	private boolean myLocalSchedulingEnabled;
+	private boolean myClusteredSchedulingEnabled;
+	@Autowired
+	private AutowiringSpringBeanJobFactory mySpringBeanJobFactory;
+	private AtomicBoolean myStopping = new AtomicBoolean(false);
+	@Autowired
+	private Environment myEnvironment;
+
+	/**
+	 * Constructor
+	 */
+	public SchedulerServiceImpl() {
+		setThreadNamePrefix("hapi-fhir-jpa-scheduler");
+		setLocalSchedulingEnabled(true);
+		setClusteredSchedulingEnabled(true);
+	}
+
+	public boolean isLocalSchedulingEnabled() {
+		return myLocalSchedulingEnabled;
+	}
+
+	public void setLocalSchedulingEnabled(boolean theLocalSchedulingEnabled) {
+		myLocalSchedulingEnabled = theLocalSchedulingEnabled;
+	}
+
+	public boolean isClusteredSchedulingEnabled() {
+		return myClusteredSchedulingEnabled;
+	}
+
+	public void setClusteredSchedulingEnabled(boolean theClusteredSchedulingEnabled) {
+		myClusteredSchedulingEnabled = theClusteredSchedulingEnabled;
+	}
+
+	public String getThreadNamePrefix() {
+		return myThreadNamePrefix;
+	}
+
+	public void setThreadNamePrefix(String theThreadNamePrefix) {
+		myThreadNamePrefix = theThreadNamePrefix;
+	}
+
+	@PostConstruct
+	public void start() throws SchedulerException {
+		myLocalScheduler = createLocalScheduler();
+		myClusteredScheduler = createClusteredScheduler();
+		myStopping.set(false);
+	}
+
+	/**
+	 * We defer startup of executing started tasks until we're sure we're ready for it
+	 * and the startup is completely done
+	 */
+	@EventListener
+	public void contextStarted(ContextRefreshedEvent theEvent) throws SchedulerException {
+		try {
+			ourLog.info("Starting task schedulers for context {}", theEvent != null ? theEvent.getApplicationContext().getId() : "null");
+			if (myLocalScheduler != null) {
+				myLocalScheduler.start();
+			}
+			if (myClusteredScheduler != null) {
+				myClusteredScheduler.start();
+			}
+		} catch (Exception e) {
+			ourLog.error("Failed to start context", e);
+			throw new SchedulerException(e);
+		}
+	}
+
+	private Scheduler createLocalScheduler() throws SchedulerException {
+		if (!isLocalSchedulingEnabled() || isSchedulingDisabledForUnitTests()) {
+			return new NullScheduler();
+		}
+		Properties localProperties = new Properties();
+		localProperties.setProperty(PROP_SCHED_INSTANCE_NAME, "local-" + ourNextSchedulerId++);
+		quartzPropertiesCommon(localProperties);
+		quartzPropertiesLocal(localProperties);
+		StdSchedulerFactory factory = new StdSchedulerFactory();
+		factory.initialize(localProperties);
+		Scheduler scheduler = factory.getScheduler();
+		configureSchedulerCommon(scheduler);
+		scheduler.standby();
+		return scheduler;
+	}
+
+	private Scheduler createClusteredScheduler() throws SchedulerException {
+		if (!isClusteredSchedulingEnabled() || isSchedulingDisabledForUnitTests()) {
+			return new NullScheduler();
+		}
+		Properties clusteredProperties = new Properties();
+		clusteredProperties.setProperty(PROP_SCHED_INSTANCE_NAME, "clustered-" + ourNextSchedulerId++);
+		quartzPropertiesCommon(clusteredProperties);
+		quartzPropertiesClustered(clusteredProperties);
+		StdSchedulerFactory factory = new StdSchedulerFactory();
+		factory.initialize(clusteredProperties);
+		Scheduler scheduler = factory.getScheduler();
+		configureSchedulerCommon(scheduler);
+		scheduler.standby();
+		return scheduler;
+	}
+
+	private void configureSchedulerCommon(Scheduler theScheduler) throws SchedulerException {
+		theScheduler.setJobFactory(mySpringBeanJobFactory);
+	}
+
+	@PreDestroy
+	public void stop() throws SchedulerException {
+		ourLog.info("Shutting down task scheduler...");
+
+		myStopping.set(true);
+		myLocalScheduler.shutdown(true);
+		myClusteredScheduler.shutdown(true);
+	}
+
+	@Override
+	public void purgeAllScheduledJobsForUnitTest() throws SchedulerException {
+		myLocalScheduler.clear();
+		myClusteredScheduler.clear();
+	}
+
+	@Override
+	public void logStatus() {
+		try {
+			Set<JobKey> keys = myLocalScheduler.getJobKeys(GroupMatcher.anyGroup());
+			String keysString = keys.stream().map(t -> t.getName()).collect(Collectors.joining(", "));
+			ourLog.info("Local scheduler has jobs: {}", keysString);
+
+			keys = myClusteredScheduler.getJobKeys(GroupMatcher.anyGroup());
+			keysString = keys.stream().map(t -> t.getName()).collect(Collectors.joining(", "));
+			ourLog.info("Clustered scheduler has jobs: {}", keysString);
+		} catch (SchedulerException e) {
+			throw new InternalErrorException(e);
+		}
+	}
+
+	@Override
+	public void scheduleFixedDelay(long theIntervalMillis, boolean theClusteredTask, ScheduledJobDefinition theJobDefinition) {
+		Validate.isTrue(theIntervalMillis >= 100);
+
+		Validate.notNull(theJobDefinition);
+		Validate.notNull(theJobDefinition.getJobClass());
+		Validate.notBlank(theJobDefinition.getId());
+
+		JobKey jobKey = new JobKey(theJobDefinition.getId());
+
+		JobDetailImpl jobDetail = new NonConcurrentJobDetailImpl();
+		jobDetail.setJobClass(theJobDefinition.getJobClass());
+		jobDetail.setKey(jobKey);
+		jobDetail.setName(theJobDefinition.getId());
+		jobDetail.setJobDataMap(new JobDataMap(theJobDefinition.getJobData()));
+
+		ScheduleBuilder<? extends Trigger> schedule = SimpleScheduleBuilder
+			.simpleSchedule()
+			.withIntervalInMilliseconds(theIntervalMillis)
+			.repeatForever();
+
+		Trigger trigger = TriggerBuilder.newTrigger()
+			.forJob(jobDetail)
+			.startNow()
+			.withSchedule(schedule)
+			.build();
+
+		Set<? extends Trigger> triggers = Sets.newHashSet(trigger);
+		try {
+			Scheduler scheduler;
+			if (theClusteredTask) {
+				scheduler = myClusteredScheduler;
+			} else {
+				scheduler = myLocalScheduler;
+			}
+			scheduler.scheduleJob(jobDetail, triggers, true);
+		} catch (SchedulerException e) {
+			ourLog.error("Failed to schedule job", e);
+			throw new InternalErrorException(e);
+		}
+
+	}
+
+	@Override
+	public boolean isStopping() {
+		return myStopping.get();
+	}
+
+	/**
+	 * Properties for the local scheduler (see the class docs to learn what this means)
+	 */
+	protected void quartzPropertiesLocal(Properties theProperties) {
+		// nothing
+	}
+
+	/**
+	 * Properties for the cluster scheduler (see the class docs to learn what this means)
+	 */
+	protected void quartzPropertiesClustered(Properties theProperties) {
+//		theProperties.put("org.quartz.jobStore.tablePrefix", "QRTZHFJC_");
+	}
+
+	protected void quartzPropertiesCommon(Properties theProperties) {
+		theProperties.put("org.quartz.threadPool.threadCount", "4");
+		theProperties.put("org.quartz.threadPool.threadNamePrefix", getThreadNamePrefix() + "-" + theProperties.get(PROP_SCHED_INSTANCE_NAME));
+	}
+
+	private boolean isSchedulingDisabledForUnitTests() {
+		String schedulingDisabled = myEnvironment.getProperty(SCHEDULING_DISABLED);
+		return "true".equals(schedulingDisabled);
+	}
+
+	private static class NonConcurrentJobDetailImpl extends JobDetailImpl {
+		private static final long serialVersionUID = 5716197221121989740L;
+
+		// All HAPI FHIR jobs shouldn't allow concurrent execution
+		@Override
+		public boolean isConcurrentExectionDisallowed() {
+			return true;
+		}
+	}
+
+	private static class NullScheduler implements Scheduler {
+		@Override
+		public String getSchedulerName() {
+			return null;
+		}
+
+		@Override
+		public String getSchedulerInstanceId() {
+			return null;
+		}
+
+		@Override
+		public SchedulerContext getContext() {
+			return null;
+		}
+
+		@Override
+		public void start() {
+
+		}
+
+		@Override
+		public void startDelayed(int seconds) {
+
+		}
+
+		@Override
+		public boolean isStarted() {
+			return false;
+		}
+
+		@Override
+		public void standby() {
+
+		}
+
+		@Override
+		public boolean isInStandbyMode() {
+			return false;
+		}
+
+		@Override
+		public void shutdown() {
+
+		}
+
+		@Override
+		public void shutdown(boolean waitForJobsToComplete) {
+
+		}
+
+		@Override
+		public boolean isShutdown() {
+			return false;
+		}
+
+		@Override
+		public SchedulerMetaData getMetaData() {
+			return null;
+		}
+
+		@Override
+		public List<JobExecutionContext> getCurrentlyExecutingJobs() {
+			return null;
+		}
+
+		@Override
+		public void setJobFactory(JobFactory factory) {
+
+		}
+
+		@Override
+		public ListenerManager getListenerManager() {
+			return null;
+		}
+
+		@Override
+		public Date scheduleJob(JobDetail jobDetail, Trigger trigger) {
+			return null;
+		}
+
+		@Override
+		public Date scheduleJob(Trigger trigger) {
+			return null;
+		}
+
+		@Override
+		public void scheduleJobs(Map<JobDetail, Set<? extends Trigger>> triggersAndJobs, boolean replace) {
+
+		}
+
+		@Override
+		public void scheduleJob(JobDetail jobDetail, Set<? extends Trigger> triggersForJob, boolean replace) {
+
+		}
+
+		@Override
+		public boolean unscheduleJob(TriggerKey triggerKey) {
+			return false;
+		}
+
+		@Override
+		public boolean unscheduleJobs(List<TriggerKey> triggerKeys) {
+			return false;
+		}
+
+		@Override
+		public Date rescheduleJob(TriggerKey triggerKey, Trigger newTrigger) {
+			return null;
+		}
+
+		@Override
+		public void addJob(JobDetail jobDetail, boolean replace) {
+
+		}
+
+		@Override
+		public void addJob(JobDetail jobDetail, boolean replace, boolean storeNonDurableWhileAwaitingScheduling) {
+
+		}
+
+		@Override
+		public boolean deleteJob(JobKey jobKey) {
+			return false;
+		}
+
+		@Override
+		public boolean deleteJobs(List<JobKey> jobKeys) {
+			return false;
+		}
+
+		@Override
+		public void triggerJob(JobKey jobKey) {
+
+		}
+
+		@Override
+		public void triggerJob(JobKey jobKey, JobDataMap data) {
+
+		}
+
+		@Override
+		public void pauseJob(JobKey jobKey) {
+
+		}
+
+		@Override
+		public void pauseJobs(GroupMatcher<JobKey> matcher) {
+
+		}
+
+		@Override
+		public void pauseTrigger(TriggerKey triggerKey) {
+
+		}
+
+		@Override
+		public void pauseTriggers(GroupMatcher<TriggerKey> matcher) {
+
+		}
+
+		@Override
+		public void resumeJob(JobKey jobKey) {
+
+		}
+
+		@Override
+		public void resumeJobs(GroupMatcher<JobKey> matcher) {
+
+		}
+
+		@Override
+		public void resumeTrigger(TriggerKey triggerKey) {
+
+		}
+
+		@Override
+		public void resumeTriggers(GroupMatcher<TriggerKey> matcher) {
+
+		}
+
+		@Override
+		public void pauseAll() {
+
+		}
+
+		@Override
+		public void resumeAll() {
+
+		}
+
+		@Override
+		public List<String> getJobGroupNames() {
+			return null;
+		}
+
+		@Override
+		public Set<JobKey> getJobKeys(GroupMatcher<JobKey> matcher) {
+			return null;
+		}
+
+		@Override
+		public List<? extends Trigger> getTriggersOfJob(JobKey jobKey) {
+			return null;
+		}
+
+		@Override
+		public List<String> getTriggerGroupNames() {
+			return null;
+		}
+
+		@Override
+		public Set<TriggerKey> getTriggerKeys(GroupMatcher<TriggerKey> matcher) {
+			return null;
+		}
+
+		@Override
+		public Set<String> getPausedTriggerGroups() {
+			return null;
+		}
+
+		@Override
+		public JobDetail getJobDetail(JobKey jobKey) {
+			return null;
+		}
+
+		@Override
+		public Trigger getTrigger(TriggerKey triggerKey) {
+			return null;
+		}
+
+		@Override
+		public Trigger.TriggerState getTriggerState(TriggerKey triggerKey) {
+			return null;
+		}
+
+		@Override
+		public void resetTriggerFromErrorState(TriggerKey triggerKey) {
+
+		}
+
+		@Override
+		public void addCalendar(String calName, Calendar calendar, boolean replace, boolean updateTriggers) {
+
+		}
+
+		@Override
+		public boolean deleteCalendar(String calName) {
+			return false;
+		}
+
+		@Override
+		public Calendar getCalendar(String calName) {
+			return null;
+		}
+
+		@Override
+		public List<String> getCalendarNames() {
+			return null;
+		}
+
+		@Override
+		public boolean interrupt(JobKey jobKey) throws UnableToInterruptJobException {
+			return false;
+		}
+
+		@Override
+		public boolean interrupt(String fireInstanceId) throws UnableToInterruptJobException {
+			return false;
+		}
+
+		@Override
+		public boolean checkExists(JobKey jobKey) {
+			return false;
+		}
+
+		@Override
+		public boolean checkExists(TriggerKey triggerKey) {
+			return false;
+		}
+
+		@Override
+		public void clear() {
+
+		}
+	}
+
+
+}

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

@@ -21,12 +21,17 @@ package ca.uhn.fhir.jpa.search;
  */
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import javax.annotation.PostConstruct;
+
 import static ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl.DEFAULT_CUTOFF_SLACK;
 
 /**
@@ -43,6 +48,8 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 	private DaoConfig myDaoConfig;
 	@Autowired
 	private ISearchCacheSvc mySearchCacheSvc;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	@Override
 	@Transactional(propagation = Propagation.NEVER)
@@ -50,7 +57,14 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 		mySearchCacheSvc.pollForStaleSearchesAndDeleteThem();
 	}
 
-	@Scheduled(fixedDelay = DEFAULT_CUTOFF_SLACK)
+	@PostConstruct
+	public void registerScheduledJob() {
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(StaleSearchDeletingSvcImpl.class.getName());
+		jobDetail.setJobClass(StaleSearchDeletingSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(DEFAULT_CUTOFF_SLACK, true, jobDetail);
+	}
+
 	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public synchronized void schedulePollForStaleSearches() {
@@ -58,4 +72,14 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 			pollForStaleSearchesAndDeleteThem();
 		}
 	}
+
+	public static class SubmitJob implements Job {
+		@Autowired
+		private IStaleSearchDeletingSvc myTarget;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTarget.schedulePollForStaleSearches();
+		}
+	}
 }

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

@@ -0,0 +1,8 @@
+package ca.uhn.fhir.jpa.search;
+
+public class WarmSearchDefinition {
+
+	private String mySearchUrl;
+	private long myRefreshPeriodMillis;
+
+}

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

@@ -21,12 +21,16 @@ package ca.uhn.fhir.jpa.search.cache;
  */
 
 import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import org.apache.commons.lang3.time.DateUtils;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.PostConstruct;
 import java.util.Date;
 import java.util.Iterator;
 import java.util.Map;
@@ -36,6 +40,8 @@ public abstract class BaseSearchCacheSvcImpl implements ISearchCacheSvc {
 
 	@Autowired
 	private PlatformTransactionManager myTxManager;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	private ConcurrentHashMap<Long, Date> myUnsyncedLastUpdated = new ConcurrentHashMap<>();
 
@@ -44,11 +50,18 @@ public abstract class BaseSearchCacheSvcImpl implements ISearchCacheSvc {
 		myUnsyncedLastUpdated.put(theSearch.getId(), theDate);
 	}
 
+	@PostConstruct
+	public void registerScheduledJob() {
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(BaseSearchCacheSvcImpl.class.getName());
+		jobDetail.setJobClass(BaseSearchCacheSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_SECOND, false, jobDetail);
+	}
+
 	@Override
-	@Scheduled(fixedDelay = 10 * DateUtils.MILLIS_PER_SECOND)
 	public void flushLastUpdated() {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-		txTemplate.execute(t->{
+		txTemplate.execute(t -> {
 			for (Iterator<Map.Entry<Long, Date>> iter = myUnsyncedLastUpdated.entrySet().iterator(); iter.hasNext(); ) {
 				Map.Entry<Long, Date> next = iter.next();
 				flushLastUpdated(next.getKey(), next.getValue());
@@ -60,5 +73,15 @@ public abstract class BaseSearchCacheSvcImpl implements ISearchCacheSvc {
 
 	protected abstract void flushLastUpdated(Long theSearchId, Date theLastUpdated);
 
+	public static class SubmitJob implements Job {
+		@Autowired
+		private ISearchCacheSvc myTarget;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTarget.flushLastUpdated();
+		}
+	}
+
 
 }

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

@@ -136,7 +136,7 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
 	@Override
 	public Collection<Search> findCandidatesForReuse(String theResourceType, String theQueryString, int theQueryStringHash, Date theCreatedAfter) {
 		int hashCode = theQueryString.hashCode();
-		return mySearchDao.find(theResourceType, hashCode, theCreatedAfter);
+		return mySearchDao.findWithCutoffOrExpiry(theResourceType, hashCode, theCreatedAfter);
 
 	}
 
@@ -166,7 +166,7 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
 
 		TransactionTemplate tt = new TransactionTemplate(myTxManager);
 		final Slice<Long> toDelete = tt.execute(theStatus ->
-			mySearchDao.findWhereLastReturnedBefore(cutoff, PageRequest.of(0, 2000))
+			mySearchDao.findWhereLastReturnedBefore(cutoff, new Date(), PageRequest.of(0, 2000))
 		);
 		for (final Long nextSearchToDelete : toDelete) {
 			ourLog.debug("Deleting search with PID {}", nextSearchToDelete);

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

@@ -36,11 +36,6 @@ public interface IResourceReindexingSvc {
 	 */
 	Long markAllResourcesForReindexing(String theType);
 
-	/**
-	 * Called automatically by the job scheduler
-	 */
-	void scheduleReindexingPass();
-
 	/**
 	 * @return Returns null if the system did not attempt to perform a pass because one was
 	 * already proceeding. Otherwise, returns the number of resources affected.

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

@@ -33,6 +33,8 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
 import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
@@ -44,12 +46,13 @@ import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.search.util.impl.Executors;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.InstantType;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Slice;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.support.TransactionCallback;
@@ -101,6 +104,8 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	private EntityManager myEntityManager;
 	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	@VisibleForTesting
 	void setReindexJobDaoForUnitTest(IResourceReindexJobDao theReindexJobDao) {
@@ -182,11 +187,12 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		return job.getId();
 	}
 
-	@Override
+	@PostConstruct
-	@Transactional(Transactional.TxType.NEVER)
+	public void registerScheduledJob() {
-	@Scheduled(fixedDelay = 10 * DateUtils.MILLIS_PER_SECOND)
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
-	public void scheduleReindexingPass() {
+		jobDetail.setId(ResourceReindexingSvcImpl.class.getName());
-		runReindexingPass();
+		jobDetail.setJobClass(ResourceReindexingSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_SECOND, true, jobDetail);
 	}
 
 	@Override
@@ -223,6 +229,8 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	@Override
 	public void cancelAndPurgeAllJobs() {
 		ourLog.info("Cancelling and purging all resource reindexing jobs");
+		myIndexingLock.lock();
+		try {
 		myTxTemplate.execute(t -> {
 			myReindexJobDao.markAllOfTypeAsDeleted();
 			return null;
@@ -232,6 +240,9 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		initExecutor();
 
 		expungeJobsMarkedAsDeleted();
+		} finally {
+			myIndexingLock.unlock();
+		}
 	}
 
 	private int runReindexJobs() {
@@ -277,7 +288,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	}
 
 	@VisibleForTesting
-	public void setSearchParamRegistryForUnitTest(ISearchParamRegistry theSearchParamRegistry) {
+	void setSearchParamRegistryForUnitTest(ISearchParamRegistry theSearchParamRegistry) {
 		mySearchParamRegistry = theSearchParamRegistry;
 	}
 
@@ -306,7 +317,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		Date low = theJob.getThresholdLow() != null ? theJob.getThresholdLow() : BEGINNING_OF_TIME;
 		Date high = theJob.getThresholdHigh();
 
-		// SqlQuery for resources within threshold
+		// Query for resources within threshold
 		StopWatch pageSw = new StopWatch();
 		Slice<Long> range = myTxTemplate.execute(t -> {
 			PageRequest page = PageRequest.of(0, PASS_SIZE);
@@ -529,4 +540,14 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 			return myUpdated;
 		}
 	}
+
+	public static class SubmitJob implements Job {
+		@Autowired
+		private IResourceReindexingSvc myTarget;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTarget.runReindexingPass();
+		}
+	}
 }

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

@@ -26,22 +26,29 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.util.UrlUtil;
+import org.apache.commons.lang3.time.DateUtils;
+import org.quartz.DisallowConcurrentExecution;
+import org.quartz.JobExecutionContext;
+import org.quartz.PersistJobDataAfterExecution;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.stereotype.Component;
 
 import javax.annotation.PostConstruct;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
 
 @Component
 public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
 
+	public static final long SCHEDULED_JOB_INTERVAL = 10 * DateUtils.MILLIS_PER_SECOND;
+	private static final Logger ourLog = LoggerFactory.getLogger(CacheWarmingSvcImpl.class);
 	@Autowired
 	private DaoConfig myDaoConfig;
 	private Map<WarmCacheEntry, Long> myCacheEntryToNextRefresh = new LinkedHashMap<>();
@@ -51,10 +58,12 @@ public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
 	private DaoRegistry myDaoRegistry;
 	@Autowired
 	private MatchUrlService myMatchUrlService;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	@Override
-	@Scheduled(fixedDelay = 1000)
 	public synchronized void performWarmingPass() {
+		ourLog.trace("Starting cache warming pass for {} tasks", myCacheEntryToNextRefresh.size());
 
 		for (WarmCacheEntry nextCacheEntry : new ArrayList<>(myCacheEntryToNextRefresh.keySet())) {
 
@@ -74,6 +83,14 @@ public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
 
 	}
 
+	@PostConstruct
+	public void registerScheduledJob() {
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(CacheWarmingSvcImpl.class.getName());
+		jobDetail.setJobClass(CacheWarmingSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(SCHEDULED_JOB_INTERVAL, true, jobDetail);
+	}
+
 	private void refreshNow(WarmCacheEntry theCacheEntry) {
 		String nextUrl = theCacheEntry.getUrl();
 
@@ -98,7 +115,7 @@ public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
 		initCacheMap();
 	}
 
-	public synchronized void initCacheMap() {
+	public synchronized Set<WarmCacheEntry> initCacheMap() {
 
 		myCacheEntryToNextRefresh.clear();
 		List<WarmCacheEntry> warmCacheEntries = myDaoConfig.getWarmCacheEntries();
@@ -110,6 +127,24 @@ public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
 
 			myCacheEntryToNextRefresh.put(next, 0L);
 		}
-		
+
+		return Collections.unmodifiableSet(myCacheEntryToNextRefresh.keySet());
+
+	}
+
+	@DisallowConcurrentExecution
+	@PersistJobDataAfterExecution
+	public static class SubmitJob extends FireAtIntervalJob {
+		@Autowired
+		private ICacheWarmingSvc myTarget;
+
+		public SubmitJob() {
+			super(SCHEDULED_JOB_INTERVAL);
+		}
+
+		@Override
+		protected void doExecute(JobExecutionContext theContext) {
+			myTarget.performWarmingPass();
+		}
 	}
 }

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

@@ -20,9 +20,6 @@ package ca.uhn.fhir.jpa.search.warm;
  * #L%
  */
 
-import org.springframework.scheduling.annotation.Scheduled;
-
 public interface ICacheWarmingSvc {
-	@Scheduled(fixedDelay = 1000)
 	void performWarmingPass();
 }

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

@@ -30,4 +30,6 @@ import java.util.List;
 
 public interface ISubscriptionTriggeringSvc {
 	IBaseParameters triggerSubscription(List<UriParam> theResourceIds, List<StringParam> theSearchUrls, @IdParam IIdType theSubscriptionId);
+
+	void runDeliveryPass();
 }

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

@@ -25,6 +25,9 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
@@ -53,10 +56,12 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
 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.quartz.DisallowConcurrentExecution;
+import org.quartz.JobExecutionContext;
+import org.quartz.PersistJobDataAfterExecution;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.stereotype.Service;
 
 import javax.annotation.PostConstruct;
@@ -73,10 +78,10 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @Service
 public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc {
+	public static final long SCHEDULE_DELAY = DateUtils.MILLIS_PER_SECOND;
 	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTriggeringProvider.class);
-
 	private static final int DEFAULT_MAX_SUBMIT = 10000;
-
+	private final List<SubscriptionTriggeringJobDetails> myActiveJobs = new ArrayList<>();
 	@Autowired
 	private FhirContext myFhirContext;
 	@Autowired
@@ -89,10 +94,10 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 	private MatchUrlService myMatchUrlService;
 	@Autowired
 	private IResourceModifiedConsumer myResourceModifiedConsumer;
-
-	private final List<SubscriptionTriggeringJobDetails> myActiveJobs = new ArrayList<>();
 	private int myMaxSubmitPerPass = DEFAULT_MAX_SUBMIT;
 	private ExecutorService myExecutorService;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	@Override
 	public IBaseParameters triggerSubscription(List<UriParam> theResourceIds, List<StringParam> theSearchUrls, @IdParam IIdType theSubscriptionId) {
@@ -143,8 +148,8 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 		// Submit job for processing
 		synchronized (myActiveJobs) {
 			myActiveJobs.add(jobDetails);
+			ourLog.info("Subscription triggering requested for {} resource and {} search - Gave job ID: {} and have {} jobs", resourceIds.size(), searchUrls.size(), jobDetails.getJobId(), myActiveJobs.size());
 		}
-		ourLog.info("Subscription triggering requested for {} resource and {} search - Gave job ID: {}", resourceIds.size(), searchUrls.size(), jobDetails.getJobId());
 
 		// Create a parameters response
 		IBaseParameters retVal = ParametersUtil.newInstance(myFhirContext);
@@ -154,10 +159,19 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 		return retVal;
 	}
 
-	@Scheduled(fixedDelay = DateUtils.MILLIS_PER_SECOND)
+	@PostConstruct
+	public void registerScheduledJob() {
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(SubscriptionTriggeringSvcImpl.class.getName());
+		jobDetail.setJobClass(SubscriptionTriggeringSvcImpl.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(SCHEDULE_DELAY, false, jobDetail);
+	}
+
+	@Override
 	public void runDeliveryPass() {
 
 		synchronized (myActiveJobs) {
+
 			if (myActiveJobs.isEmpty()) {
 				return;
 			}
@@ -305,7 +319,7 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 		return myExecutorService.submit(() -> {
 			for (int i = 0; ; i++) {
 				try {
-						myResourceModifiedConsumer.submitResourceModified(msg);
+					myResourceModifiedConsumer.submitResourceModified(msg);
 					break;
 				} catch (Exception e) {
 					if (i >= 3) {
@@ -375,6 +389,22 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 
 	}
 
+	@DisallowConcurrentExecution
+	@PersistJobDataAfterExecution
+	public static class SubmitJob extends FireAtIntervalJob {
+		@Autowired
+		private ISubscriptionTriggeringSvc myTarget;
+
+		public SubmitJob() {
+			super(SCHEDULE_DELAY);
+		}
+
+		@Override
+		protected void doExecute(JobExecutionContext theContext) {
+			myTarget.runDeliveryPass();
+		}
+	}
+
 	private static class SubscriptionTriggeringJobDetails {
 
 		private String myJobId;

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

@@ -28,6 +28,9 @@ 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.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -61,6 +64,8 @@ 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.*;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
 import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -162,6 +167,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	private PlatformTransactionManager myTxManager;
 	@Autowired
 	private ITermValueSetConceptViewDao myTermValueSetConceptViewDao;
+    @Autowired
+    private ISchedulerService mySchedulerService;
 
 	private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
 		String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
@@ -1529,7 +1536,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		}
 	}
 
-	@Scheduled(fixedRate = 5000)
 	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public synchronized void saveDeferred() {
@@ -1616,6 +1622,24 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		myTxTemplate = new TransactionTemplate(myTransactionManager);
 	}
 
+	@PostConstruct
+	public void registerScheduledJob() {
+		// Register scheduled job to save deferred concepts
+		// In the future it would be great to make this a cluster-aware task somehow
+		ScheduledJobDefinition jobDefinition = new ScheduledJobDefinition();
+		jobDefinition.setId(BaseHapiTerminologySvcImpl.class.getName() + "_saveDeferred");
+		jobDefinition.setJobClass(SaveDeferredJob.class);
+		mySchedulerService.scheduleFixedDelay(5000, false, jobDefinition);
+
+		// Register scheduled job to save deferred concepts
+		// In the future it would be great to make this a cluster-aware task somehow
+		ScheduledJobDefinition vsJobDefinition = new ScheduledJobDefinition();
+		vsJobDefinition.setId(BaseHapiTerminologySvcImpl.class.getName() + "_preExpandValueSets");
+		vsJobDefinition.setJobClass(PreExpandValueSetsJob.class);
+		mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_MINUTE, true, vsJobDefinition);
+
+	}
+
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
 	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion) {
@@ -1696,7 +1720,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 		ourLog.info("Saving {} concepts...", totalCodeCount);
 
-		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<TermConcept, Object>();
+		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
 		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
 			persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
 		}
@@ -1939,7 +1963,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		ourLog.info("Done storing TermConceptMap[{}]", termConceptMap.getId());
 	}
 
-	@Scheduled(fixedDelay = 600000) // 10 minutes.
 	@Override
 	public synchronized void preExpandDeferredValueSetsToTerminologyTables() {
 		if (isNotSafeToPreExpandValueSets()) {
@@ -2497,6 +2520,28 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		return new VersionIndependentConcept(system, code);
 	}
 
+	public static class SaveDeferredJob implements Job {
+
+		@Autowired
+		private IHapiTerminologySvc myTerminologySvc;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTerminologySvc.saveDeferred();
+		}
+	}
+
+	public static class PreExpandValueSetsJob implements Job {
+
+		@Autowired
+		private IHapiTerminologySvc myTerminologySvc;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTerminologySvc.preExpandDeferredValueSetsToTerminologyTables();
+		}
+	}
+
 	/**
 	 * This method is present only for unit tests, do not call from client code
 	 */

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

@@ -0,0 +1,75 @@
+package ca.uhn.fhir.jpa.util;
+
+/*-
+ * #%L
+ * Smile CDR - CDR
+ * %%
+ * Copyright (C) 2016 - 2018 Simpatico Intelligent Systems Inc
+ * %%
+ * All rights reserved.
+ * #L%
+ */
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+
+import javax.annotation.Nonnull;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.io.Writer;
+
+public class JsonUtil {
+
+	private static final ObjectMapper ourMapperPrettyPrint;
+	private static final ObjectMapper ourMapperNonPrettyPrint;
+
+	static {
+		ourMapperPrettyPrint = new ObjectMapper();
+		ourMapperPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+		ourMapperPrettyPrint.enable(SerializationFeature.INDENT_OUTPUT);
+
+		ourMapperNonPrettyPrint = new ObjectMapper();
+		ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+		ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
+	}
+
+	/**
+	 * Parse JSON
+	 */
+	public static <T> T deserialize(@Nonnull String theInput, @Nonnull Class<T> theType) throws IOException {
+		return ourMapperPrettyPrint.readerFor(theType).readValue(theInput);
+	}
+
+	/**
+	 * Encode JSON
+	 */
+	public static String serialize(@Nonnull Object theInput) throws IOException {
+		return serialize(theInput, true);
+	}
+
+	/**
+	 * Encode JSON
+	 */
+	public static String serialize(@Nonnull Object theInput, boolean thePrettyPrint) throws IOException {
+		StringWriter sw = new StringWriter();
+		if (thePrettyPrint) {
+			ourMapperPrettyPrint.writeValue(sw, theInput);
+		} else {
+			ourMapperNonPrettyPrint.writeValue(sw, theInput);
+		}
+		return sw.toString();
+	}
+
+	/**
+	 * Encode JSON
+	 */
+	public static void serialize(@Nonnull Object theInput, @Nonnull Writer theWriter) throws IOException {
+		// Note: We append a string here rather than just having ourMapper write directly
+		// to the Writer because ourMapper seems to close the writer for some stupid
+		// reason.. There's probably a way of preventing that bit I'm not sure what that
+		// is and it's not a big deal here.
+		theWriter.append(serialize(theInput));
+	}
+
+}

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

@@ -20,14 +20,106 @@ package ca.uhn.fhir.jpa.util;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.time.DateUtils;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.PostConstruct;
 import java.util.Map;
 import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicReference;
+
+public class ResourceCountCache {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceCountCache.class);
+	private static Long ourNowForUnitTest;
+	private final Callable<Map<String, Long>> myFetcher;
+	private volatile long myCacheMillis;
+	private AtomicReference<Map<String, Long>> myCapabilityStatement = new AtomicReference<>();
+	private long myLastFetched;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
-public class ResourceCountCache extends SingleItemLoadingCache<Map<String, Long>> {
 	/**
 	 * Constructor
 	 */
 	public ResourceCountCache(Callable<Map<String, Long>> theFetcher) {
-		super(theFetcher);
+		myFetcher = theFetcher;
 	}
+
+	public synchronized void clear() {
+		ourLog.info("Clearing cache");
+		myCapabilityStatement.set(null);
+		myLastFetched = 0;
+	}
+
+	public synchronized Map<String, Long> get() {
+		return myCapabilityStatement.get();
+	}
+
+	private Map<String, Long> refresh() {
+		Map<String, Long> retVal;
+		try {
+			retVal = myFetcher.call();
+		} catch (Exception e) {
+			throw new InternalErrorException(e);
+		}
+
+		myCapabilityStatement.set(retVal);
+		myLastFetched = now();
+		return retVal;
+	}
+
+	public void setCacheMillis(long theCacheMillis) {
+		myCacheMillis = theCacheMillis;
+	}
+
+	public void update() {
+		if (myCacheMillis > 0) {
+			long now = now();
+			long expiry = now - myCacheMillis;
+			if (myLastFetched < expiry) {
+				refresh();
+			}
+		}
+	}
+
+	@PostConstruct
+	public void registerScheduledJob() {
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(ResourceCountCache.class.getName());
+		jobDetail.setJobClass(ResourceCountCache.SubmitJob.class);
+		mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_MINUTE, false, jobDetail);
+	}
+
+	public static class SubmitJob implements Job {
+		@Autowired
+		private ResourceCountCache myTarget;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			myTarget.update();
+		}
+	}
+
+	private static long now() {
+		if (ourNowForUnitTest != null) {
+			return ourNowForUnitTest;
+		}
+		return System.currentTimeMillis();
+	}
+
+	@VisibleForTesting
+	static void setNowForUnitTest(Long theNowForUnitTest) {
+		ourNowForUnitTest = theNowForUnitTest;
+	}
+
+
 }

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

@@ -1,101 +0,0 @@
-package ca.uhn.fhir.jpa.util;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2019 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.server.exceptions.InternalErrorException;
-import com.google.common.annotations.VisibleForTesting;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.scheduling.annotation.Scheduled;
-
-import java.util.concurrent.Callable;
-import java.util.concurrent.atomic.AtomicReference;
-
-/**
- * This is a simple cache for CapabilityStatement resources to
- * be returned as server metadata.
- */
-public class SingleItemLoadingCache<T> {
-	private static final Logger ourLog = LoggerFactory.getLogger(SingleItemLoadingCache.class);
-	private static Long ourNowForUnitTest;
-	private final Callable<T> myFetcher;
-	private volatile long myCacheMillis;
-	private AtomicReference<T> myCapabilityStatement = new AtomicReference<>();
-	private long myLastFetched;
-
-	/**
-	 * Constructor
-	 */
-	public SingleItemLoadingCache(Callable<T> theFetcher) {
-		myFetcher = theFetcher;
-	}
-
-	public synchronized void clear() {
-		ourLog.info("Clearing cache");
-		myCapabilityStatement.set(null);
-		myLastFetched = 0;
-	}
-
-	public synchronized T get() {
-		return myCapabilityStatement.get();
-	}
-
-	private T refresh() {
-		T retVal;
-		try {
-			retVal = myFetcher.call();
-		} catch (Exception e) {
-			throw new InternalErrorException(e);
-		}
-
-		myCapabilityStatement.set(retVal);
-		myLastFetched = now();
-		return retVal;
-	}
-
-	public void setCacheMillis(long theCacheMillis) {
-		myCacheMillis = theCacheMillis;
-	}
-
-	@Scheduled(fixedDelay = 60000)
-	public void update() {
-		if (myCacheMillis > 0) {
-			long now = now();
-			long expiry = now - myCacheMillis;
-			if (myLastFetched < expiry) {
-				refresh();
-			}
-		}
-	}
-
-	private static long now() {
-		if (ourNowForUnitTest != null) {
-			return ourNowForUnitTest;
-		}
-		return System.currentTimeMillis();
-	}
-
-	@VisibleForTesting
-	static void setNowForUnitTest(Long theNowForUnitTest) {
-		ourNowForUnitTest = theNowForUnitTest;
-	}
-
-}

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

@@ -259,7 +259,7 @@ public class TestUtil {
 		}
 	}
 
-	public static void sleepAtLeast(int theMillis) {
+	public static void sleepAtLeast(long theMillis) {
 		long start = System.currentTimeMillis();
 		while (System.currentTimeMillis() <= start + theMillis) {
 			try {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java

@@ -0,0 +1,242 @@
+package ca.uhn.fhir.jpa.bulk;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.util.JsonUtil;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.client.apache.ResourceEntity;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+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.r4.model.IdType;
+import org.hl7.fhir.r4.model.InstantType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.util.Date;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.*;
+
+@RunWith(MockitoJUnitRunner.class)
+public class BulkDataExportProviderTest {
+
+	private static final String A_JOB_ID = "0000000-AAAAAA";
+	private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportProviderTest.class);
+	private Server myServer;
+	private FhirContext myCtx = FhirContext.forR4();
+	private int myPort;
+	@Mock
+	private IBulkDataExportSvc myBulkDataExportSvc;
+	private CloseableHttpClient myClient;
+	@Captor
+	private ArgumentCaptor<String> myOutputFormatCaptor;
+	@Captor
+	private ArgumentCaptor<Set<String>> myResourceTypesCaptor;
+	@Captor
+	private ArgumentCaptor<Date> mySinceCaptor;
+	@Captor
+	private ArgumentCaptor<Set<String>> myFiltersCaptor;
+
+	@After
+	public void after() throws Exception {
+		JettyUtil.closeServer(myServer);
+		myClient.close();
+	}
+
+	@Before
+	public void start() throws Exception {
+		myServer = new Server(0);
+
+		BulkDataExportProvider provider = new BulkDataExportProvider();
+		provider.setBulkDataExportSvcForUnitTests(myBulkDataExportSvc);
+		provider.setFhirContextForUnitTest(myCtx);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(myCtx);
+		servlet.registerProvider(provider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		myServer.setHandler(proxyHandler);
+		JettyUtil.startServer(myServer);
+		myPort = JettyUtil.getPortForStartedServer(myServer);
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		myClient = builder.build();
+
+	}
+
+	@Test
+	public void testSuccessfulInitiateBulkRequest() throws IOException {
+
+		IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
+			.setJobId(A_JOB_ID);
+		when(myBulkDataExportSvc.submitJob(any(), any(), any(), any())).thenReturn(jobInfo);
+
+		InstantType now = InstantType.now();
+
+		Parameters input = new Parameters();
+		input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
+		input.addParameter(JpaConstants.PARAM_EXPORT_TYPE, new StringType("Patient, Practitioner"));
+		input.addParameter(JpaConstants.PARAM_EXPORT_SINCE, now);
+		input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Patient?identifier=foo"));
+
+		HttpPost post = new HttpPost("http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT);
+		post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		post.setEntity(new ResourceEntity(myCtx, input));
+		try (CloseableHttpResponse response = myClient.execute(post)) {
+			ourLog.info("Response: {}", response.toString());
+
+			assertEquals(202, response.getStatusLine().getStatusCode());
+			assertEquals("Accepted", response.getStatusLine().getReasonPhrase());
+			assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
+		}
+
+		verify(myBulkDataExportSvc, times(1)).submitJob(myOutputFormatCaptor.capture(), myResourceTypesCaptor.capture(), mySinceCaptor.capture(), myFiltersCaptor.capture());
+		assertEquals(Constants.CT_FHIR_NDJSON, myOutputFormatCaptor.getValue());
+		assertThat(myResourceTypesCaptor.getValue(), containsInAnyOrder("Patient", "Practitioner"));
+		assertThat(mySinceCaptor.getValue(), notNullValue());
+		assertThat(myFiltersCaptor.getValue(), containsInAnyOrder("Patient?identifier=foo"));
+
+	}
+
+	@Test
+	public void testPollForStatus_BUILDING() throws IOException {
+
+		IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
+			.setJobId(A_JOB_ID)
+			.setStatus(BulkJobStatusEnum.BUILDING)
+			.setStatusTime(InstantType.now().getValue());
+		when(myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(eq(A_JOB_ID))).thenReturn(jobInfo);
+
+		String url = "http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" +
+			JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + A_JOB_ID;
+		HttpGet get = new HttpGet(url);
+		get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		try (CloseableHttpResponse response = myClient.execute(get)) {
+			ourLog.info("Response: {}", response.toString());
+
+			assertEquals(202, response.getStatusLine().getStatusCode());
+			assertEquals("Accepted", response.getStatusLine().getReasonPhrase());
+			assertEquals("120", response.getFirstHeader(Constants.HEADER_RETRY_AFTER).getValue());
+			assertThat(response.getFirstHeader(Constants.HEADER_X_PROGRESS).getValue(), containsString("Build in progress - Status set to BUILDING at 20"));
+		}
+
+	}
+
+	@Test
+	public void testPollForStatus_ERROR() throws IOException {
+
+		IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
+			.setJobId(A_JOB_ID)
+			.setStatus(BulkJobStatusEnum.ERROR)
+			.setStatusTime(InstantType.now().getValue())
+			.setStatusMessage("Some Error Message");
+		when(myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(eq(A_JOB_ID))).thenReturn(jobInfo);
+
+		String url = "http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" +
+			JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + A_JOB_ID;
+		HttpGet get = new HttpGet(url);
+		get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		try (CloseableHttpResponse response = myClient.execute(get)) {
+			ourLog.info("Response: {}", response.toString());
+
+			assertEquals(500, response.getStatusLine().getStatusCode());
+			assertEquals("Server Error", response.getStatusLine().getReasonPhrase());
+
+			String responseContent = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info("Response content: {}", responseContent);
+			assertThat(responseContent, containsString("\"diagnostics\": \"Some Error Message\""));
+		}
+
+	}
+
+	@Test
+	public void testPollForStatus_COMPLETED() throws IOException {
+
+		IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
+			.setJobId(A_JOB_ID)
+			.setStatus(BulkJobStatusEnum.COMPLETE)
+			.setStatusTime(InstantType.now().getValue());
+		jobInfo.addFile().setResourceType("Patient").setResourceId(new IdType("Binary/111"));
+		jobInfo.addFile().setResourceType("Patient").setResourceId(new IdType("Binary/222"));
+		jobInfo.addFile().setResourceType("Patient").setResourceId(new IdType("Binary/333"));
+		when(myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(eq(A_JOB_ID))).thenReturn(jobInfo);
+
+		String url = "http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" +
+			JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + A_JOB_ID;
+		HttpGet get = new HttpGet(url);
+		get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		try (CloseableHttpResponse response = myClient.execute(get)) {
+			ourLog.info("Response: {}", response.toString());
+
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			assertEquals("OK", response.getStatusLine().getReasonPhrase());
+			assertEquals(Constants.CT_JSON, response.getEntity().getContentType().getValue());
+
+			String responseContent = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info("Response content: {}", responseContent);
+			BulkExportResponseJson responseJson = JsonUtil.deserialize(responseContent, BulkExportResponseJson.class);
+			assertEquals(3, responseJson.getOutput().size());
+			assertEquals("Patient", responseJson.getOutput().get(0).getType());
+			assertEquals("http://localhost:" + myPort + "/Binary/111", responseJson.getOutput().get(0).getUrl());
+			assertEquals("Patient", responseJson.getOutput().get(1).getType());
+			assertEquals("http://localhost:" + myPort + "/Binary/222", responseJson.getOutput().get(1).getUrl());
+			assertEquals("Patient", responseJson.getOutput().get(2).getType());
+			assertEquals("http://localhost:" + myPort + "/Binary/333", responseJson.getOutput().get(2).getUrl());
+		}
+
+	}
+
+	@Test
+	public void testPollForStatus_Gone() throws IOException {
+
+		when(myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(eq(A_JOB_ID))).thenThrow(new ResourceNotFoundException("Unknown job: AAA"));
+
+		String url = "http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" +
+			JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + A_JOB_ID;
+		HttpGet get = new HttpGet(url);
+		get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		try (CloseableHttpResponse response = myClient.execute(get)) {
+			ourLog.info("Response: {}", response.toString());
+			String responseContent = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info("Response content: {}", responseContent);
+
+			assertEquals(404, response.getStatusLine().getStatusCode());
+			assertEquals(Constants.CT_FHIR_JSON_NEW, response.getEntity().getContentType().getValue().replaceAll(";.*", "").trim());
+			assertThat(responseContent, containsString("\"diagnostics\":\"Unknown job: AAA\""));
+		}
+
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java

@@ -0,0 +1,254 @@
+package ca.uhn.fhir.jpa.bulk;
+
+import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
+import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
+import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
+import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
+import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
+import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
+import com.google.common.collect.Sets;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Binary;
+import org.hl7.fhir.r4.model.InstantType;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.TestPropertySource;
+
+import java.util.Date;
+import java.util.UUID;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.junit.Assert.*;
+
+@TestPropertySource(properties = {
+	UnregisterScheduledProcessor.SCHEDULING_DISABLED_EQUALS_TRUE
+})
+public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportSvcImplR4Test.class);
+	@Autowired
+	private IBulkExportJobDao myBulkExportJobDao;
+	@Autowired
+	private IBulkExportCollectionDao myBulkExportCollectionDao;
+	@Autowired
+	private IBulkExportCollectionFileDao myBulkExportCollectionFileDao;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
+
+
+	@Test
+	public void testPurgeExpiredJobs() {
+
+		// Create an expired job
+		runInTransaction(() -> {
+
+			Binary b = new Binary();
+			b.setContent(new byte[]{0, 1, 2, 3});
+			String binaryId = myBinaryDao.create(b).getId().toUnqualifiedVersionless().getValue();
+
+			BulkExportJobEntity job = new BulkExportJobEntity();
+			job.setStatus(BulkJobStatusEnum.COMPLETE);
+			job.setExpiry(DateUtils.addHours(new Date(), -1));
+			job.setJobId(UUID.randomUUID().toString());
+			job.setRequest("$export");
+			myBulkExportJobDao.save(job);
+
+			BulkExportCollectionEntity collection = new BulkExportCollectionEntity();
+			job.getCollections().add(collection);
+			collection.setResourceType("Patient");
+			collection.setJob(job);
+			myBulkExportCollectionDao.save(collection);
+
+			BulkExportCollectionFileEntity file = new BulkExportCollectionFileEntity();
+			collection.getFiles().add(file);
+			file.setCollection(collection);
+			file.setResource(binaryId);
+			myBulkExportCollectionFileDao.save(file);
+
+		});
+
+		// Check that things were created
+		runInTransaction(() -> {
+			assertEquals(1, myResourceTableDao.count());
+			assertEquals(1, myBulkExportJobDao.count());
+			assertEquals(1, myBulkExportCollectionDao.count());
+			assertEquals(1, myBulkExportCollectionFileDao.count());
+		});
+
+		// Run a purge pass
+		myBulkDataExportSvc.purgeExpiredFiles();
+
+		// Check that things were deleted
+		runInTransaction(() -> {
+			assertEquals(0, myResourceTableDao.count());
+			assertEquals(0, myBulkExportJobDao.count());
+			assertEquals(0, myBulkExportCollectionDao.count());
+			assertEquals(0, myBulkExportCollectionFileDao.count());
+		});
+
+	}
+
+	@Test
+	public void testCreateBulkLoad_InvalidOutputFormat() {
+		try {
+			myBulkDataExportSvc.submitJob(Constants.CT_FHIR_JSON_NEW, Sets.newHashSet("Patient", "Observation"), null, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid output format: application/fhir+json", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateBulkLoad_NoResourceTypes() {
+		try {
+			myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet(), null, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("No resource types specified", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateBulkLoad_InvalidResourceTypes() {
+		try {
+			myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient", "FOO"), null, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Unknown or unsupported resource type: FOO", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateBulkLoad() {
+
+		// Create some resources to load
+		createResources();
+
+		// Create a bulk job
+		IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
+		assertNotNull(jobDetails.getJobId());
+
+		// Check the status
+		IBulkDataExportSvc.JobInfo status = myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(jobDetails.getJobId());
+		assertEquals(BulkJobStatusEnum.SUBMITTED, status.getStatus());
+		assertEquals("/$export?_outputFormat=application%2Ffhir%2Bndjson&_type=Observation,Patient", status.getRequest());
+
+		// Run a scheduled pass to build the export
+		myBulkDataExportSvc.buildExportFiles();
+
+		// Fetch the job again
+		status = myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(jobDetails.getJobId());
+		assertEquals(BulkJobStatusEnum.COMPLETE, status.getStatus());
+		assertEquals(2, status.getFiles().size());
+
+		// Iterate over the files
+		for (IBulkDataExportSvc.FileEntry next : status.getFiles()) {
+			Binary nextBinary = myBinaryDao.read(next.getResourceId());
+			assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
+			String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
+			ourLog.info("Next contents for type {}:\n{}", next.getResourceType(), nextContents);
+
+			if ("Patient".equals(next.getResourceType())) {
+				assertThat(nextContents, containsString("\"value\":\"PAT0\"}]}\n"));
+				assertEquals(10, nextContents.split("\n").length);
+			} else if ("Observation".equals(next.getResourceType())) {
+				assertThat(nextContents, containsString("\"subject\":{\"reference\":\"Patient/PAT0\"}}\n"));
+				assertEquals(10, nextContents.split("\n").length);
+			} else {
+				fail(next.getResourceType());
+			}
+
+		}
+	}
+
+	@Test
+	public void testSubmitReusesExisting() {
+
+		// Submit
+		IBulkDataExportSvc.JobInfo jobDetails1 = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
+		assertNotNull(jobDetails1.getJobId());
+
+		// Submit again
+		IBulkDataExportSvc.JobInfo jobDetails2 = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
+		assertNotNull(jobDetails2.getJobId());
+
+		assertEquals(jobDetails1.getJobId(), jobDetails2.getJobId());
+	}
+
+
+		@Test
+	public void testCreateBulkLoad_WithSince() throws InterruptedException {
+
+		// Create some resources to load
+		createResources();
+
+		sleepUntilTimeChanges();
+		InstantType cutoff = InstantType.now();
+		sleepUntilTimeChanges();
+
+		for (int i = 10; i < 12; i++) {
+			Patient patient = new Patient();
+			patient.setId("PAT" + i);
+			patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
+			myPatientDao.update(patient).getId().toUnqualifiedVersionless();
+		}
+
+		// Create a bulk job
+		IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), cutoff.getValue(), null);
+		assertNotNull(jobDetails.getJobId());
+
+		// Check the status
+		IBulkDataExportSvc.JobInfo status = myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(jobDetails.getJobId());
+		assertEquals(BulkJobStatusEnum.SUBMITTED, status.getStatus());
+		assertEquals("/$export?_outputFormat=application%2Ffhir%2Bndjson&_type=Observation,Patient&_since=" + cutoff.setTimeZoneZulu(true).getValueAsString(), status.getRequest());
+
+		// Run a scheduled pass to build the export
+		myBulkDataExportSvc.buildExportFiles();
+
+		// Fetch the job again
+		status = myBulkDataExportSvc.getJobStatusOrThrowResourceNotFound(jobDetails.getJobId());
+		assertEquals(BulkJobStatusEnum.COMPLETE, status.getStatus());
+		assertEquals(1, status.getFiles().size());
+
+		// Iterate over the files
+		for (IBulkDataExportSvc.FileEntry next : status.getFiles()) {
+			Binary nextBinary = myBinaryDao.read(next.getResourceId());
+			assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
+			String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
+			ourLog.info("Next contents for type {}:\n{}", next.getResourceType(), nextContents);
+
+			if ("Patient".equals(next.getResourceType())) {
+				assertThat(nextContents, containsString("\"id\":\"PAT10\""));
+				assertThat(nextContents, containsString("\"id\":\"PAT11\""));
+				assertEquals(2, nextContents.split("\n").length);
+			} else {
+				fail(next.getResourceType());
+			}
+
+		}
+	}
+
+	private void createResources() {
+		for (int i = 0; i < 10; i++) {
+			Patient patient = new Patient();
+			patient.setId("PAT" + i);
+			patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
+			IIdType patId = myPatientDao.update(patient).getId().toUnqualifiedVersionless();
+
+			Observation obs = new Observation();
+			obs.setId("OBS" + i);
+			obs.setStatus(Observation.ObservationStatus.FINAL);
+			obs.getSubject().setReference(patId.getValue());
+			myObservationDao.update(obs);
+		}
+	}
+}

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

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
@@ -389,9 +390,10 @@ public abstract class BaseJpaTest {
 		return IOUtils.toString(bundleRes, Constants.CHARSET_UTF8);
 	}
 
-	protected static void purgeDatabase(DaoConfig theDaoConfig, IFhirSystemDao<?, ?> theSystemDao, IResourceReindexingSvc theResourceReindexingSvc, ISearchCoordinatorSvc theSearchCoordinatorSvc, ISearchParamRegistry theSearchParamRegistry) {
+	protected static void purgeDatabase(DaoConfig theDaoConfig, IFhirSystemDao<?, ?> theSystemDao, IResourceReindexingSvc theResourceReindexingSvc, ISearchCoordinatorSvc theSearchCoordinatorSvc, ISearchParamRegistry theSearchParamRegistry, IBulkDataExportSvc theBulkDataExportSvc) {
 		theSearchCoordinatorSvc.cancelAllActiveSearches();
 		theResourceReindexingSvc.cancelAndPurgeAllJobs();
+		theBulkDataExportSvc.cancelAndPurgeAllJobs();
 
 		boolean expungeEnabled = theDaoConfig.isExpungeEnabled();
 		theDaoConfig.setExpungeEnabled(true);

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestDstu2Config;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
@@ -185,6 +186,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
 	@Autowired
 	protected SubscriptionLoader mySubscriptionLoader;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@Before
 	public void beforeFlushFT() {
@@ -202,7 +205,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Before
 	@Transactional()
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestDstu3Config;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.*;
@@ -256,6 +257,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;
 	@Autowired
 	private JpaValidationSupportChainDstu3 myJpaValidationSupportChainDstu3;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@After()
 	public void afterCleanupDao() {
@@ -302,7 +305,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Before
 	@Transactional()
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ReferentialIntegrityTest.java

@@ -1,8 +1,9 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.junit.Assert.assertEquals;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-import static org.junit.Assert.fail;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Reference;
@@ -11,18 +12,11 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import static org.junit.Assert.assertEquals;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import static org.junit.Assert.fail;
-import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
-import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu3ReferentialIntegrityTest extends BaseJpaDstu3Test {
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
 	@After
 	public void afterResetConfig() {
 		myDaoConfig.setEnforceReferentialIntegrityOnWrite(new DaoConfig().isEnforceReferentialIntegrityOnWrite());
@@ -46,11 +40,11 @@ public class FhirResourceDaoDstu3ReferentialIntegrityTest extends BaseJpaDstu3Te
 	@Test
 	public void testCreateUnknownReferenceAllow() throws Exception {
 		myDaoConfig.setEnforceReferentialIntegrityOnWrite(false);
-		
+
 		Patient p = new Patient();
 		p.setManagingOrganization(new Reference("Organization/AAA"));
 		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-		
+
 		p = myPatientDao.read(id);
 		assertEquals("Organization/AAA", p.getManagingOrganization().getReference());
 
@@ -61,11 +55,11 @@ public class FhirResourceDaoDstu3ReferentialIntegrityTest extends BaseJpaDstu3Te
 		Organization o = new Organization();
 		o.setName("FOO");
 		IIdType oid = myOrganizationDao.create(o).getId().toUnqualifiedVersionless();
-		
+
 		Patient p = new Patient();
 		p.setManagingOrganization(new Reference(oid));
 		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-		
+
 		try {
 			myOrganizationDao.delete(oid);
 			fail();
@@ -81,19 +75,24 @@ public class FhirResourceDaoDstu3ReferentialIntegrityTest extends BaseJpaDstu3Te
 	@Test
 	public void testDeleteAllow() throws Exception {
 		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
-		
+
 		Organization o = new Organization();
 		o.setName("FOO");
 		IIdType oid = myOrganizationDao.create(o).getId().toUnqualifiedVersionless();
-		
+
 		Patient p = new Patient();
 		p.setManagingOrganization(new Reference(oid));
 		IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-		
+
 		myOrganizationDao.delete(oid);
 		myPatientDao.delete(pid);
 
 	}
 
-	
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestDstu3WithoutLuceneConfig;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
@@ -149,10 +150,12 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private IResourceReindexingSvc myResourceReindexingSvc;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@Before
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

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

@@ -73,7 +73,7 @@ public class PartitionRunnerTest {
 		myLatch.setExpectedCount(1);
 		myPartitionRunner.runInPartitionedThreads(resourceIds, partitionConsumer);
 		PartitionCall partitionCall = (PartitionCall) PointcutLatch.getLatchInvocationParameter(myLatch.awaitExpected());
-		assertEquals(EXPUNGE_THREADNAME_1, partitionCall.threadName);
+		assertEquals("main", partitionCall.threadName);
 		assertEquals(1, partitionCall.size);
 	}
 
@@ -86,7 +86,7 @@ public class PartitionRunnerTest {
 		myLatch.setExpectedCount(1);
 		myPartitionRunner.runInPartitionedThreads(resourceIds, partitionConsumer);
 		PartitionCall partitionCall = (PartitionCall) PointcutLatch.getLatchInvocationParameter(myLatch.awaitExpected());
-		assertEquals(EXPUNGE_THREADNAME_1, partitionCall.threadName);
+		assertEquals("main", partitionCall.threadName);
 		assertEquals(2, partitionCall.size);
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestR4Config;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.*;
@@ -315,6 +316,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	private List<Object> mySystemInterceptors;
 	@Autowired
 	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@After()
 	public void afterCleanupDao() {
@@ -376,7 +379,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Before
 	@Transactional()
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ConsentEventsDaoR4Test.java

@@ -13,7 +13,6 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import com.google.common.collect.Lists;
 import org.apache.commons.collections4.ListUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -32,7 +31,6 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import javax.servlet.ServletException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
@@ -54,9 +52,9 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 	private InterceptorService myInterceptorService;
 	private List<String> myObservationIdsOddOnly;
 	private List<String> myObservationIdsEvenOnly;
-	private List<String> myObservationIdsEvenOnlyBackwards;
+	private List<String> myObservationIdsWithVersions;
-	private List<String> myObservationIdsBackwards;
 	private List<String> myPatientIdsEvenOnly;
+	private List<String> myObservationIdsEvenOnlyWithVersions;
 
 	@After
 	public void after() {
@@ -313,9 +311,9 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 		 * Note: Each observation in the observation list will appear twice in the actual
 		 * returned results because we create it then update it in create50Observations()
 		 */
-		assertEquals(sort(myObservationIdsEvenOnlyBackwards.subList(0, 3), myObservationIdsEvenOnlyBackwards.subList(0, 3)), sort(returnedIdValues));
 		assertEquals(1, hitCount.get());
-		assertEquals(sort(myObservationIdsBackwards.subList(0, 5), myObservationIdsBackwards.subList(0, 5)), sort(interceptedResourceIds));
+		assertEquals(myObservationIdsWithVersions.subList(90, myObservationIdsWithVersions.size()), sort(interceptedResourceIds));
+		assertEquals(myObservationIdsEvenOnlyWithVersions.subList(44, 50), sort(returnedIdValues));
 
 	}
 
@@ -349,6 +347,7 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 	private void create50Observations() {
 		myPatientIds = new ArrayList<>();
 		myObservationIds = new ArrayList<>();
+		myObservationIdsWithVersions = new ArrayList<>();
 
 		Patient p = new Patient();
 		p.setActive(true);
@@ -370,6 +369,7 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 			obs1.addIdentifier().setSystem("urn:system").setValue("I" + leftPad("" + i, 5, '0'));
 			IIdType obs1id = myObservationDao.create(obs1).getId().toUnqualifiedVersionless();
 			myObservationIds.add(obs1id.toUnqualifiedVersionless().getValue());
+			myObservationIdsWithVersions.add(obs1id.toUnqualifiedVersionless().getValue());
 
 			obs1.setId(obs1id);
 			if (obs1id.getIdPartAsLong() % 2 == 0) {
@@ -378,6 +378,8 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 				obs1.getSubject().setReference(oddPid);
 			}
 			myObservationDao.update(obs1);
+			myObservationIdsWithVersions.add(obs1id.toUnqualifiedVersionless().getValue());
+
 		}
 
 		myPatientIdsEvenOnly =
@@ -391,10 +393,13 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
 				.stream()
 				.filter(t -> Long.parseLong(t.substring(t.indexOf('/') + 1)) % 2 == 0)
 				.collect(Collectors.toList());
+		myObservationIdsEvenOnlyWithVersions =
+			myObservationIdsWithVersions
+				.stream()
+				.filter(t -> Long.parseLong(t.substring(t.indexOf('/') + 1)) % 2 == 0)
+				.collect(Collectors.toList());
 
 		myObservationIdsOddOnly = ListUtils.removeAll(myObservationIds, myObservationIdsEvenOnly);
-		myObservationIdsBackwards = Lists.reverse(myObservationIds);
-		myObservationIdsEvenOnlyBackwards = Lists.reverse(myObservationIdsEvenOnly);
 	}
 
 	static class PreAccessInterceptorCounting implements IAnonymousInterceptor {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CacheWarmingTest.java

@@ -78,7 +78,7 @@ public class FhirResourceDaoR4CacheWarmingTest extends BaseJpaR4Test {
 				.setUrl("Patient?name=smith")
 		);
 		CacheWarmingSvcImpl cacheWarmingSvc = (CacheWarmingSvcImpl) myCacheWarmingSvc;
-		cacheWarmingSvc.initCacheMap();
+		ourLog.info("Have {} tasks", cacheWarmingSvc.initCacheMap().size());
 
 		Patient p1 = new Patient();
 		p1.setId("p1");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestR4Config;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestR4WithoutLuceneConfig;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
@@ -37,7 +38,6 @@ import java.util.List;
 
 import static org.junit.Assert.*;
 import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.when;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(classes = {TestR4WithoutLuceneConfig.class})
@@ -110,11 +110,13 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 	@Autowired
 	private IResourceReindexingSvc myResourceReindexingSvc;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@Before
 	@Transactional()
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java

@@ -696,7 +696,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 		myResourceReindexingSvc.markAllResourcesForReindexing("Observation");
 		assertEquals(1, myResourceReindexingSvc.forceReindexingPass());
-		assertEquals(0, myResourceReindexingSvc.forceReindexingPass());
+		myResourceReindexingSvc.forceReindexingPass();
+		myResourceReindexingSvc.forceReindexingPass();
 		assertEquals(0, myResourceReindexingSvc.forceReindexingPass());
 
 		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4Test.java

@@ -48,6 +48,11 @@ public class SearchParamExtractorR4Test {
 				return getActiveSearchParams(theResourceName).get(theParamName);
 			}
 
+			@Override
+			public void refreshCacheIfNecessary() {
+				// nothing
+			}
+
 			@Override
 			public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
 				throw new UnsupportedOperationException();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
+import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestR5Config;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.*;
@@ -315,6 +316,8 @@ public abstract class BaseJpaR5Test extends BaseJpaTest {
 	private List<Object> mySystemInterceptors;
 	@Autowired
 	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private IBulkDataExportSvc myBulkDataExportSvc;
 
 	@After()
 	public void afterCleanupDao() {
@@ -376,7 +379,7 @@ public abstract class BaseJpaR5Test extends BaseJpaTest {
 	@Before
 	@Transactional()
 	public void beforePurgeDatabase() {
-		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
+		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4Test.java

@@ -4,7 +4,7 @@ import ca.uhn.fhir.jpa.config.BaseConfig;
 import ca.uhn.fhir.jpa.config.TestR4Config;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.PreferHeader;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@@ -349,7 +349,7 @@ public class ConsentInterceptorResourceProviderR4Test extends BaseResourceProvid
 
 		Patient patient = new Patient();
 		patient.setActive(true);
-		IIdType id = ourClient.create().resource(patient).prefer(PreferReturnEnum.REPRESENTATION).execute().getId().toUnqualifiedVersionless();
+		IIdType id = ourClient.create().resource(patient).prefer(PreferHeader.PreferReturnEnum.REPRESENTATION).execute().getId().toUnqualifiedVersionless();
 
 		DelegatingConsentService consentService = new DelegatingConsentService();
 		myConsentInterceptor = new ConsentInterceptor(consentService, IConsentContextServices.NULL_IMPL);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderOnlySomeResourcesProvidedR4Test.java

@@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.util.TestUtil;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
@@ -10,16 +9,18 @@ import org.junit.AfterClass;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
+import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
 
 import javax.annotation.PostConstruct;
+import javax.annotation.PreDestroy;
 
 import static org.hamcrest.CoreMatchers.containsString;
-import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
 @SuppressWarnings("Duplicates")
 @ContextConfiguration(classes = {ResourceProviderOnlySomeResourcesProvidedR4Test.OnlySomeResourcesProvidedCtxConfig.class})
+@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
 public class ResourceProviderOnlySomeResourcesProvidedR4Test extends BaseResourceProviderR4Test {
 
 	@Test
@@ -62,6 +63,13 @@ public class ResourceProviderOnlySomeResourcesProvidedR4Test extends BaseResourc
 			}
 
 		}
+
+		@PreDestroy
+		public void stop() {
+			myDaoRegistry.setSupportedResourceTypes();
+		}
+
+
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -31,6 +31,7 @@ import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.time.DateUtils;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
 import org.apache.http.client.methods.*;
@@ -491,13 +492,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	private void checkParamMissing(String paramName) throws IOException {
 		HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
 		CloseableHttpResponse resp = ourHttpClient.execute(get);
-		IOUtils.closeQuietly(resp.getEntity().getContent());
+		resp.getEntity().getContent().close();
 		assertEquals(200, resp.getStatusLine().getStatusCode());
 	}
 
 
 	private ArrayList<IBaseResource> genResourcesOfType(Bundle theRes, Class<? extends IBaseResource> theClass) {
-		ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
+		ArrayList<IBaseResource> retVal = new ArrayList<>();
 		for (BundleEntryComponent next : theRes.getEntry()) {
 			if (next.getResource() != null) {
 				if (theClass.isAssignableFrom(next.getResource().getClass())) {
@@ -531,14 +532,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		ourLog.info("About to perform search for: {}", theUri);
 
-		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
 			ids = toUnqualifiedIdValues(bundle);
-		} finally {
-			IOUtils.closeQuietly(response);
 		}
 		return ids;
 	}
@@ -547,14 +545,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		List<String> ids;
 		HttpGet get = new HttpGet(uri);
 
-		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
 			ids = toUnqualifiedVersionlessIdValues(bundle);
-		} finally {
-			IOUtils.closeQuietly(response);
 		}
 		return ids;
 	}
@@ -589,7 +584,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		String resBody = IOUtils.toString(ResourceProviderR4Test.class.getResource("/r4/document-father.json"), StandardCharsets.UTF_8);
 		resBody = resBody.replace("\"type\": \"document\"", "\"type\": \"transaction\"");
 		try {
-			client.create().resource(resBody).execute().getId();
+			client.create().resource(resBody).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Unable to store a Bundle resource on this server with a Bundle.type value of: transaction"));
@@ -688,7 +683,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.create()
 			.resource(p)
 			.conditionalByUrl("Patient?identifier=foo|bar")
-			.prefer(PreferReturnEnum.REPRESENTATION)
+			.prefer(PreferHeader.PreferReturnEnum.REPRESENTATION)
 			.execute();
 
 		assertEquals(id.getIdPart(), outcome.getId().getIdPart());
@@ -721,7 +716,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(200, resp.getStatusLine().getStatusCode());
 			assertEquals(resource.withVersion("2").getValue(), resp.getFirstHeader("Content-Location").getValue());
 		} finally {
-			IOUtils.closeQuietly(resp);
+			resp.close();
 		}
 
 		fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
@@ -737,7 +732,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(200, resp.getStatusLine().getStatusCode());
 			assertEquals(resource.withVersion("3").getValue(), resp.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
 		} finally {
-			IOUtils.closeQuietly(resp);
+			resp.close();
 		}
 
 		fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
@@ -754,7 +749,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			assertEquals(400, resp.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(resp);
+			resp.close();
 		}
 
 		fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
@@ -769,7 +764,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testCreateBundle() throws IOException {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/bryn-bundle.json"), StandardCharsets.UTF_8);
 		Validate.notNull(input);
-		ourClient.create().resource(input).execute().getResource();
+		ourClient.create().resource(input).execute();
 	}
 
 	@Test
@@ -1659,7 +1654,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		b = parser.parseResource(Bundle.class, new InputStreamReader(ResourceProviderR4Test.class.getResourceAsStream("/r4/bug147-bundle.json")));
 
 		Bundle resp = ourClient.transaction().withBundle(b).execute();
-		List<IdType> ids = new ArrayList<IdType>();
+		List<IdType> ids = new ArrayList<>();
 		for (BundleEntryComponent next : resp.getEntry()) {
 			IdType toAdd = new IdType(next.getResponse().getLocation()).toUnqualifiedVersionless();
 			ids.add(toAdd);
@@ -1673,7 +1668,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			Parameters output = ourClient.operation().onInstance(patientId).named("everything").withNoParameters(Parameters.class).execute();
 			b = (Bundle) output.getParameter().get(0).getResource();
 
-			ids = new ArrayList<IdType>();
+			ids = new ArrayList<>();
 			boolean dupes = false;
 			for (BundleEntryComponent next : b.getEntry()) {
 				IdType toAdd = next.getResource().getIdElement().toUnqualifiedVersionless();
@@ -1694,7 +1689,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			Parameters output = ourClient.operation().onInstance(patientId).named("everything").withParameters(input).execute();
 			b = (Bundle) output.getParameter().get(0).getResource();
 
-			ids = new ArrayList<IdType>();
+			ids = new ArrayList<>();
 			boolean dupes = false;
 			for (BundleEntryComponent next : b.getEntry()) {
 				IdType toAdd = next.getResource().getIdElement().toUnqualifiedVersionless();
@@ -1760,7 +1755,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Parameters output = ourClient.operation().onInstance(patientId).named("everything").withNoParameters(Parameters.class).execute();
 		b = (Bundle) output.getParameter().get(0).getResource();
 
-		List<IdType> ids = new ArrayList<IdType>();
+		List<IdType> ids = new ArrayList<>();
 		for (BundleEntryComponent next : b.getEntry()) {
 			IdType toAdd = next.getResource().getIdElement().toUnqualifiedVersionless();
 			ids.add(toAdd);
@@ -1892,7 +1887,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			ourLog.info(output);
 			List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
 			ourLog.info(ids.toString());
@@ -1907,7 +1902,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			ourLog.info(output);
 			List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
 			ourLog.info(ids.toString());
@@ -1926,7 +1921,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		// try {
 		// assertEquals(200, response.getStatusLine().getStatusCode());
 		// String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-		// IOUtils.closeQuietly(response.getEntity().getContent());
+		// response.getEntity().getContent().close();
 		// ourLog.info(output);
 		// List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
 		// ourLog.info(ids.toString());
@@ -1940,7 +1935,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		// try {
 		// assertEquals(200, response.getStatusLine().getStatusCode());
 		// String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-		// IOUtils.closeQuietly(response.getEntity().getContent());
+		// response.getEntity().getContent().close();
 		// ourLog.info(output);
 		// List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
 		// ourLog.info(ids.toString());
@@ -1964,7 +1959,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		assertEquals(53, inputBundle.getEntry().size());
 
-		Set<String> allIds = new TreeSet<String>();
+		Set<String> allIds = new TreeSet<>();
 		for (BundleEntryComponent nextEntry : inputBundle.getEntry()) {
 			nextEntry.getRequest().setMethod(HTTPVerb.PUT);
 			nextEntry.getRequest().setUrl(nextEntry.getResource().getId());
@@ -1986,7 +1981,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(responseBundle));
 
-		List<String> ids = new ArrayList<String>();
+		List<String> ids = new ArrayList<>();
 		for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
 			ids.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
 		}
@@ -1995,7 +1990,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		assertThat(responseBundle.getEntry().size(), lessThanOrEqualTo(25));
 
-		TreeSet<String> idsSet = new TreeSet<String>();
+		TreeSet<String> idsSet = new TreeSet<>();
 		for (int i = 0; i < responseBundle.getEntry().size(); i++) {
 			for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
 				idsSet.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
@@ -2118,13 +2113,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/" + JpaConstants.OPERATION_VALIDATE);
 		post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
 
-		CloseableHttpResponse resp = ourHttpClient.execute(post);
+		try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
-		try {
 			String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
 			ourLog.info(respString);
 			assertEquals(200, resp.getStatusLine().getStatusCode());
-		} finally {
-			IOUtils.closeQuietly(resp);
 		}
 	}
 
@@ -2144,14 +2136,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
 			post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
 
-			CloseableHttpResponse resp = ourHttpClient.execute(post);
+			try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
-			try {
 				String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
 				ourLog.info(respString);
 				assertThat(respString, containsString("Unknown extension http://hl7.org/fhir/ValueSet/v3-ActInvoiceGroupCode"));
 				assertEquals(200, resp.getStatusLine().getStatusCode());
-			} finally {
-				IOUtils.closeQuietly(resp);
 			}
 		} finally {
 			ourRestServer.unregisterInterceptor(interceptor);
@@ -2247,15 +2236,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		myResourceCountsCache.update();
 
 		HttpGet get = new HttpGet(ourServerBase + "/$get-resource-counts");
-		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
-		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			ourLog.info(output);
 			assertThat(output, containsString("<parameter><name value=\"Patient\"/><valueInteger value=\""));
-		} finally {
-			response.close();
 		}
 	}
 
@@ -2300,13 +2286,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testHasParameterNoResults() throws Exception {
 
 		HttpGet get = new HttpGet(ourServerBase + "/AllergyIntolerance?_has=Provenance:target:userID=12345");
-		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			assertThat(resp, containsString("Invalid _has parameter syntax: _has"));
-		} finally {
-			IOUtils.closeQuietly(response);
 		}
 
 	}
@@ -2644,7 +2627,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			assertThat(resp, stringContainsInOrder("THIS IS THE DESC"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -2798,7 +2781,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			assertThat(resp, containsString("Underweight"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 
@@ -2820,14 +2803,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		patch.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_OPERATION_OUTCOME);
 		patch.setEntity(new StringEntity("[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]", ContentType.parse(Constants.CT_JSON_PATCH + Constants.CHARSET_UTF8_CTSUFFIX)));
 
-		CloseableHttpResponse response = ourHttpClient.execute(patch);
+		try (CloseableHttpResponse response = ourHttpClient.execute(patch)) {
-		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			assertThat(responseString, containsString("<OperationOutcome"));
 			assertThat(responseString, containsString("INFORMATION"));
-		} finally {
-			response.close();
 		}
 
 		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
@@ -2851,14 +2831,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		patch.setEntity(new StringEntity("[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]", ContentType.parse(Constants.CT_JSON_PATCH + Constants.CHARSET_UTF8_CTSUFFIX)));
 		patch.addHeader("If-Match", "W/\"9\"");
 
-		CloseableHttpResponse response = ourHttpClient.execute(patch);
+		try (CloseableHttpResponse response = ourHttpClient.execute(patch)) {
-		try {
 			assertEquals(409, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			assertThat(responseString, containsString("<OperationOutcome"));
 			assertThat(responseString, containsString("<diagnostics value=\"Version 9 is not the most recent version of this resource, unable to apply patch\"/>"));
-		} finally {
-			response.close();
 		}
 
 		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
@@ -2883,14 +2860,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		patch.addHeader("If-Match", "W/\"1\"");
 		patch.setEntity(new StringEntity("[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]", ContentType.parse(Constants.CT_JSON_PATCH + Constants.CHARSET_UTF8_CTSUFFIX)));
 
-		CloseableHttpResponse response = ourHttpClient.execute(patch);
+		try (CloseableHttpResponse response = ourHttpClient.execute(patch)) {
-		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			assertThat(responseString, containsString("<OperationOutcome"));
 			assertThat(responseString, containsString("INFORMATION"));
-		} finally {
-			response.close();
 		}
 
 		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
@@ -2915,14 +2889,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		patch.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RETURN + '=' + Constants.HEADER_PREFER_RETURN_OPERATION_OUTCOME);
 		patch.setEntity(new StringEntity(patchString, ContentType.parse(Constants.CT_XML_PATCH + Constants.CHARSET_UTF8_CTSUFFIX)));
 
-		CloseableHttpResponse response = ourHttpClient.execute(patch);
+		try (CloseableHttpResponse response = ourHttpClient.execute(patch)) {
-		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			assertThat(responseString, containsString("<OperationOutcome"));
 			assertThat(responseString, containsString("INFORMATION"));
-		} finally {
-			response.close();
 		}
 
 		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
@@ -2987,11 +2958,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		pat = new Patient();
 		pat.addIdentifier().setSystem("urn:system").setValue("testReadAllInstancesOfType_01");
-		ourClient.create().resource(pat).prettyPrint().encodedXml().execute().getId();
+		ourClient.create().resource(pat).prettyPrint().encodedXml().execute();
 
 		pat = new Patient();
 		pat.addIdentifier().setSystem("urn:system").setValue("testReadAllInstancesOfType_02");
-		ourClient.create().resource(pat).prettyPrint().encodedXml().execute().getId();
+		ourClient.create().resource(pat).prettyPrint().encodedXml().execute();
 
 		{
 			Bundle returned = ourClient.search().forResource(Patient.class).encodedXml().returnBundle(Bundle.class).execute();
@@ -3115,7 +3086,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Patient actual = ourClient.read(Patient.class, new UriDt(newId.getValue()));
 		assertEquals(1, actual.getContained().size());
 
-		//@formatter:off
 		Bundle b = ourClient
 			.search()
 			.forResource("Patient")
@@ -3123,7 +3093,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.prettyPrint()
 			.returnBundle(Bundle.class)
 			.execute();
-		//@formatter:on
 		assertEquals(1, b.getEntry().size());
 
 	}
@@ -3873,6 +3842,70 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertEquals(uuid1, uuid2);
 	}
 
+	@Test
+	public void testSearchReusesBeforeExpiry() {
+		List<IBaseResource> resources = new ArrayList<IBaseResource>();
+		for (int i = 0; i < 50; i++) {
+			Organization org = new Organization();
+			org.setName("HELLO");
+			resources.add(org);
+		}
+		ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
+
+		/*
+		 * First, make sure that we don't reuse a search if
+		 * it's not marked with an expiry
+		 */
+		{
+			myDaoConfig.setReuseCachedSearchResultsForMillis(10L);
+			Bundle result1 = ourClient
+				.search()
+				.forResource("Organization")
+				.returnBundle(Bundle.class)
+				.execute();
+			final String uuid1 = toSearchUuidFromLinkNext(result1);
+			sleepOneClick();
+			Bundle result2 = ourClient
+				.search()
+				.forResource("Organization")
+				.returnBundle(Bundle.class)
+				.execute();
+			final String uuid2 = toSearchUuidFromLinkNext(result2);
+			assertNotEquals(uuid1, uuid2);
+		}
+
+		/*
+		 * Now try one but mark it with an expiry time
+		 * in the future
+		 */
+		{
+			myDaoConfig.setReuseCachedSearchResultsForMillis(1000L);
+			Bundle result1 = ourClient
+				.search()
+				.forResource("Organization")
+				.returnBundle(Bundle.class)
+				.execute();
+			final String uuid1 = toSearchUuidFromLinkNext(result1);
+			runInTransaction(() -> {
+				Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid1).orElseThrow(()->new IllegalStateException());
+				search.setExpiryOrNull(DateUtils.addSeconds(new Date(), -2));
+				mySearchEntityDao.save(search);
+			});
+			sleepOneClick();
+			Bundle result2 = ourClient
+				.search()
+				.forResource("Organization")
+				.returnBundle(Bundle.class)
+				.execute();
+
+			// Expiry doesn't affect reusablility
+			final String uuid2 = toSearchUuidFromLinkNext(result2);
+			assertEquals(uuid1, uuid2);
+
+		}
+	}
+
+
 	@Test
 	public void testSearchReusesResultsDisabled() {
 		List<IBaseResource> resources = new ArrayList<>();
@@ -4995,13 +5028,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		String encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
 
 		HttpPut put = new HttpPut(ourServerBase + "/Patient/A");
-		put.setEntity(new StringEntity(encoded, "application/fhir+json", "UTF-8"));
+		put.setEntity(new StringEntity(encoded, ContentType.create("application/fhir+json", "UTF-8")));
 
 		CloseableHttpResponse response = ourHttpClient.execute(put);
 		try {
 			assertEquals(201, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response);
+			response.close();
 		}
 
 		p = new Patient();
@@ -5010,13 +5043,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
 
 		put = new HttpPut(ourServerBase + "/Patient/A");
-		put.setEntity(new StringEntity(encoded, "application/fhir+json", "UTF-8"));
+		put.setEntity(new StringEntity(encoded, ContentType.create("application/fhir+json", "UTF-8")));
 
 		response = ourHttpClient.execute(put);
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response);
+			response.close();
 		}
 
 	}
@@ -5100,8 +5133,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		HttpPut post = new HttpPut(ourServerBase + "/Patient/A2");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
-		CloseableHttpResponse response = ourHttpClient.execute(post);
+		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
-		try {
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
@@ -5109,8 +5141,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(
 				"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"A2\"",
 				oo.getIssue().get(0).getDiagnostics());
-		} finally {
-			response.close();
 		}
 	}
 
@@ -5119,7 +5149,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/dstu3-person.json"), StandardCharsets.UTF_8);
 
 		try {
-			MethodOutcome resp = ourClient.update().resource(input).withId("Patient/PERSON1").execute();
+			ourClient.update().resource(input).withId("Patient/PERSON1").execute();
 		} catch (InvalidRequestException e) {
 			assertEquals("", e.getMessage());
 		}
@@ -5139,7 +5169,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(resp, containsString("No resource supplied for $validate operation (resource is required unless mode is &quot;delete&quot;)"));
 			assertEquals(400, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5163,7 +5193,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(resp, containsString("No resource supplied for $validate operation (resource is required unless mode is &quot;delete&quot;)"));
 			assertEquals(400, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5189,7 +5219,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(resp,
 				stringContainsInOrder(">ERROR<", "[Patient.contact[0]]", "<pre>SHALL at least contain a contact's details or a reference to an organization", "<issue><severity value=\"error\"/>"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5217,7 +5247,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			ourLog.info(resp);
 			assertEquals(200, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5241,7 +5271,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertEquals(412, response.getStatusLine().getStatusCode());
 			assertThat(resp, containsString("SHALL at least contain a contact's details or a reference to an organization"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5270,7 +5300,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			ourLog.info(resp);
 			assertEquals(200, response.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5298,7 +5328,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(resp, not(containsString("warn")));
 			assertThat(resp, not(containsString("error")));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5325,7 +5355,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>",
 					"</issue>"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 	}
@@ -5358,7 +5388,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(resp, containsString("</contains>"));
 			assertThat(resp, containsString("</expansion>"));
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 
@@ -5378,7 +5408,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				"<display value=\"Systolic blood pressure at First encounter\"/>"));
 			//@formatter:on
 		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.getEntity().getContent().close();
 			response.close();
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.entity.SearchResult;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
+import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
 import ca.uhn.fhir.rest.gclient.IClientExecutable;
 import ca.uhn.fhir.rest.gclient.IQuery;
@@ -28,6 +29,7 @@ import org.springframework.test.util.AopTestUtils;
 import java.util.Date;
 import java.util.UUID;
 
+import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
@@ -68,13 +70,11 @@ public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
 			myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless();
 		}
 
-		//@formatter:off
 		IClientExecutable<IQuery<Bundle>, Bundle> search = ourClient
 			.search()
 			.forResource(Patient.class)
 			.where(Patient.NAME.matches().value("Everything"))
 			.returnBundle(Bundle.class);
-		//@formatter:on
 
 		Bundle resp1 = search.execute();
 
@@ -172,6 +172,40 @@ public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testDontDeleteSearchBeforeExpiry() {
+		DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteForUnitTest(10);
+
+		runInTransaction(() -> {
+			Search search = new Search();
+
+			// Expires in one second, so it should not be deleted right away,
+			// but it should be deleted if we try again after one second...
+			search.setExpiryOrNull(DateUtils.addMilliseconds(new Date(), 1000));
+
+			search.setStatus(SearchStatusEnum.FINISHED);
+			search.setUuid(UUID.randomUUID().toString());
+			search.setCreated(DateUtils.addDays(new Date(), -10000));
+			search.setSearchType(SearchTypeEnum.SEARCH);
+			search.setResourceType("Patient");
+			search.setSearchLastReturned(DateUtils.addDays(new Date(), -10000));
+			search = mySearchEntityDao.save(search);
+
+		});
+
+		// Should not delete right now
+		assertEquals(1, mySearchEntityDao.count());
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		assertEquals(1, mySearchEntityDao.count());
+
+		sleepAtLeast(1100);
+
+		// Now it's time to delete
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		assertEquals(0, mySearchEntityDao.count());
+
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java

@@ -0,0 +1,207 @@
+package ca.uhn.fhir.jpa.sched;
+
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.quartz.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.BeanUtils;
+import org.springframework.beans.BeansException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.data.util.ProxyUtils;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.util.AopTestUtils;
+
+import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
+@ContextConfiguration(classes = SchedulerServiceImplTest.TestConfiguration.class)
+@RunWith(SpringJUnit4ClassRunner.class)
+public class SchedulerServiceImplTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(SchedulerServiceImplTest.class);
+
+	@Autowired
+	private ISchedulerService mySvc;
+	private static long ourTaskDelay;
+
+	@Before
+	public void before() {
+		ourTaskDelay = 0;
+	}
+
+	@Test
+	public void testScheduleTask() {
+
+		ScheduledJobDefinition def = new ScheduledJobDefinition()
+			.setId(CountingJob.class.getName())
+			.setJobClass(CountingJob.class);
+
+		mySvc.scheduleFixedDelay(100, false, def);
+
+		sleepAtLeast(1000);
+
+		ourLog.info("Fired {} times", CountingJob.ourCount);
+
+		assertThat(CountingJob.ourCount, greaterThan(3));
+		assertThat(CountingJob.ourCount, lessThan(20));
+	}
+
+	@Test
+	public void testStopAndStartService() throws SchedulerException {
+
+		ScheduledJobDefinition def = new ScheduledJobDefinition()
+			.setId(CountingJob.class.getName())
+			.setJobClass(CountingJob.class);
+
+		SchedulerServiceImpl svc = AopTestUtils.getTargetObject(mySvc);
+		svc.stop();
+		svc.start();
+		svc.contextStarted(null);
+
+		mySvc.scheduleFixedDelay(100, false, def);
+
+		sleepAtLeast(1000);
+
+		ourLog.info("Fired {} times", CountingJob.ourCount);
+
+		assertThat(CountingJob.ourCount, greaterThan(3));
+		assertThat(CountingJob.ourCount, lessThan(20));
+	}
+
+	@Test
+	public void testScheduleTaskLongRunningDoesntRunConcurrently() {
+
+		ScheduledJobDefinition def = new ScheduledJobDefinition()
+			.setId(CountingJob.class.getName())
+			.setJobClass(CountingJob.class);
+		ourTaskDelay = 500;
+
+		mySvc.scheduleFixedDelay(100, false, def);
+
+		sleepAtLeast(1000);
+
+		ourLog.info("Fired {} times", CountingJob.ourCount);
+
+		assertThat(CountingJob.ourCount, greaterThanOrEqualTo(1));
+		assertThat(CountingJob.ourCount, lessThan(5));
+	}
+
+	@Test
+	public void testIntervalJob() {
+
+		ScheduledJobDefinition def = new ScheduledJobDefinition()
+			.setId(CountingIntervalJob.class.getName())
+			.setJobClass(CountingIntervalJob.class);
+		ourTaskDelay = 500;
+
+		mySvc.scheduleFixedDelay(100, false, def);
+
+		sleepAtLeast(2000);
+
+		ourLog.info("Fired {} times", CountingIntervalJob.ourCount);
+
+		assertThat(CountingIntervalJob.ourCount, greaterThanOrEqualTo(2));
+		assertThat(CountingIntervalJob.ourCount, lessThan(6));
+	}
+
+	@After
+	public void after() throws SchedulerException {
+		CountingJob.ourCount = 0;
+		CountingIntervalJob.ourCount = 0;
+		mySvc.purgeAllScheduledJobsForUnitTest();
+	}
+
+	@DisallowConcurrentExecution
+	public static class CountingJob implements Job, ApplicationContextAware {
+
+		private static int ourCount;
+
+		@Autowired
+		@Qualifier("stringBean")
+		private String myStringBean;
+		private ApplicationContext myAppCtx;
+
+		@Override
+		public void execute(JobExecutionContext theContext) {
+			if (!"String beans are good.".equals(myStringBean)) {
+				fail("Did not autowire stringBean correctly, found: " + myStringBean);
+			}
+			if (myAppCtx == null) {
+				fail("Did not populate appctx");
+			}
+			if (ourTaskDelay > 0) {
+				ourLog.info("Job has fired, going to sleep for {}ms", ourTaskDelay);
+				sleepAtLeast(ourTaskDelay);
+				ourLog.info("Done sleeping");
+			} else {
+				ourLog.info("Job has fired...");
+			}
+			ourCount++;
+		}
+
+		@Override
+		public void setApplicationContext(ApplicationContext theAppCtx) throws BeansException {
+			myAppCtx = theAppCtx;
+		}
+	}
+
+
+	@DisallowConcurrentExecution
+	@PersistJobDataAfterExecution
+	public static class CountingIntervalJob extends FireAtIntervalJob {
+
+		private static int ourCount;
+
+		@Autowired
+		@Qualifier("stringBean")
+		private String myStringBean;
+		private ApplicationContext myAppCtx;
+
+		public CountingIntervalJob() {
+			super(500);
+		}
+
+		@Override
+		public void doExecute(JobExecutionContext theContext) {
+				ourLog.info("Job has fired, going to sleep for {}ms", ourTaskDelay);
+				sleepAtLeast(ourTaskDelay);
+			ourCount++;
+		}
+
+	}
+
+
+	@Configuration
+	public static class TestConfiguration {
+
+		@Bean
+		public ISchedulerService schedulerService() {
+			return new SchedulerServiceImpl();
+		}
+
+		@Bean
+		public String stringBean() {
+			return "String beans are good.";
+		}
+
+		@Bean
+		public AutowiringSpringBeanJobFactory springBeanJobFactory() {
+			return new AutowiringSpringBeanJobFactory();
+		}
+
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/SubscriptionTestUtil.java

@@ -80,7 +80,4 @@ public class SubscriptionTestUtil {
 		subscriber.setEmailSender(myEmailSender);
 	}
 
-	public IEmailSender getEmailSender() {
-		return myEmailSender;
-	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java

@@ -39,6 +39,7 @@ public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
 	@Autowired
 	private SubscriptionTestUtil mySubscriptionTestUtil;
 
+	@Override
 	@After
 	public void after() throws Exception {
 		ourLog.info("** AFTER **");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/module/matcher/InMemorySubscriptionMatcherR4Test.java

@@ -408,6 +408,19 @@ public class InMemorySubscriptionMatcherR4Test {
 		}
 	}
 
+	@Test
+	public void testReferenceAlias() {
+		Observation obs = new Observation();
+		obs.setId("Observation/123");
+		obs.getSubject().setReference("Patient/123");
+
+		SearchParameterMap params;
+
+		params = new SearchParameterMap();
+		params.add(Observation.SP_PATIENT, new ReferenceParam("Patient/123"));
+		assertMatched(obs, params);
+	}
+
 	@Test
 	public void testSearchResourceReferenceOnlyCorrectPath() {
 		Organization org = new Organization();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/SubscriptionTriggeringDstu3Test.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.subscription.resthook;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
 import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
@@ -55,6 +56,10 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
 
 	@Autowired
 	private SubscriptionTestUtil mySubscriptionTestUtil;
+	@Autowired
+	private SubscriptionTriggeringSvcImpl mySubscriptionTriggeringSvc;
+	@Autowired
+	private ISchedulerService mySchedulerService;
 
 	@After
 	public void afterUnregisterRestHookListener() {
@@ -80,9 +85,6 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
 		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
 	}
 
-	@Autowired
-	private SubscriptionTriggeringSvcImpl mySubscriptionTriggeringSvc;
-
 	@Before
 	public void beforeRegisterRestHookListener() {
 		mySubscriptionTestUtil.registerRestHookInterceptor();
@@ -98,6 +100,8 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
 		ourCreatedPatients.clear();
 		ourUpdatedPatients.clear();
 		ourContentTypes.clear();
+
+		mySchedulerService.logStatus();
 	}
 
 	private Subscription createSubscription(String theCriteria, String thePayload, String theEndpoint) throws InterruptedException {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/ResourceCountCacheTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.util;
 
-import org.hl7.fhir.dstu3.model.CapabilityStatement;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -8,29 +7,31 @@ import org.junit.runner.RunWith;
 import org.mockito.Mock;
 import org.mockito.junit.MockitoJUnitRunner;
 
+import java.util.HashMap;
+import java.util.Map;
 import java.util.concurrent.Callable;
-import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicLong;
 
 import static org.junit.Assert.assertEquals;
 import static org.mockito.Mockito.when;
 
 @RunWith(MockitoJUnitRunner.class)
-public class SingleItemLoadingCacheTest {
+public class ResourceCountCacheTest {
 
 	@Mock
-	private Callable<CapabilityStatement> myFetcher;
+	private Callable<Map<String, Long>> myFetcher;
 
 	@After
 	public void after() {
-		SingleItemLoadingCache.setNowForUnitTest(null);
+		ResourceCountCache.setNowForUnitTest(null);
 	}
 
 	@Before
 	public void before() throws Exception {
-		AtomicInteger id = new AtomicInteger();
+		AtomicLong id = new AtomicLong();
 		when(myFetcher.call()).thenAnswer(t->{
-			CapabilityStatement retVal = new CapabilityStatement();
+			Map<String, Long> retVal = new HashMap<>();
-			retVal.setId("" + id.incrementAndGet());
+			retVal.put("A", id.incrementAndGet());
 			return retVal;
 		});
 	}
@@ -38,36 +39,36 @@ public class SingleItemLoadingCacheTest {
 	@Test
 	public void testCache() {
 		long start = System.currentTimeMillis();
-		SingleItemLoadingCache.setNowForUnitTest(start);
+		ResourceCountCache.setNowForUnitTest(start);
 
 		// Cache is initialized on startup
-		SingleItemLoadingCache<CapabilityStatement> cache = new SingleItemLoadingCache<>(myFetcher);
+		ResourceCountCache cache = new ResourceCountCache(myFetcher);
 		cache.setCacheMillis(500);
 		assertEquals(null, cache.get());
 
 		// Not time to update yet
 		cache.update();
-		assertEquals("1", cache.get().getId());
+		assertEquals(Long.valueOf(1), cache.get().get("A"));
 
 		// Wait a bit, still not time to update
-		SingleItemLoadingCache.setNowForUnitTest(start + 400);
+		ResourceCountCache.setNowForUnitTest(start + 400);
 		cache.update();
-		assertEquals("1", cache.get().getId());
+		assertEquals(Long.valueOf(1), cache.get().get("A"));
 
 		// Wait a bit more and the cache is expired
-		SingleItemLoadingCache.setNowForUnitTest(start + 800);
+		ResourceCountCache.setNowForUnitTest(start + 800);
 		cache.update();
-		assertEquals("2", cache.get().getId());
+		assertEquals(Long.valueOf(2), cache.get().get("A"));
 
 	}
 
 	@Test
 	public void testCacheWithLoadingDisabled() {
 		long start = System.currentTimeMillis();
-		SingleItemLoadingCache.setNowForUnitTest(start);
+		ResourceCountCache.setNowForUnitTest(start);
 
 		// Cache of 0 means "never load"
-		SingleItemLoadingCache<CapabilityStatement> cache = new SingleItemLoadingCache<>(myFetcher);
+		ResourceCountCache cache = new ResourceCountCache(myFetcher);
 		cache.setCacheMillis(0);
 
 		/*
@@ -79,11 +80,11 @@ public class SingleItemLoadingCacheTest {
 		cache.update();
 		assertEquals(null, cache.get());
 
-		SingleItemLoadingCache.setNowForUnitTest(start + 400);
+		ResourceCountCache.setNowForUnitTest(start + 400);
 		cache.update();
 		assertEquals(null, cache.get());
 
-		SingleItemLoadingCache.setNowForUnitTest(start + 80000);
+		ResourceCountCache.setNowForUnitTest(start + 80000);
 		cache.update();
 		assertEquals(null, cache.get());
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -109,6 +109,16 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.addIndex("IDX_VS_CONCEPT_ORDER")
 			.unique(true)
 			.withColumns("VALUESET_PID", "VALUESET_ORDER");
+
+
+		// Account for RESTYPE_LEN column increasing from 30 to 35
+		version.onTable("HFJ_RESOURCE").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
+		version.onTable("HFJ_HISTORY_TAG").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
+		version.onTable("HFJ_RES_LINK").modifyColumn("SOURCE_RESOURCE_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
+		version.onTable("HFJ_RES_LINK").modifyColumn("TARGET_RESOURCE_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
+		version.onTable("HFJ_RES_TAG").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
+
+
 	}
 
 	protected void init400() {

hapi-fhir-jpaserver-model/pom.xml

@@ -112,6 +112,11 @@
 			<artifactId>commons-collections4</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.quartz-scheduler</groupId>
+			<artifactId>quartz</artifactId>
+		</dependency>
+
 		<!-- Java -->
 		<dependency>
 			<groupId>javax.annotation</groupId>

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

@@ -47,7 +47,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 	@Index(name = "IDX_INDEXSTATUS", columnList = "SP_INDEX_STATUS")
 })
 public class ResourceTable extends BaseHasResource implements Serializable {
-	static final int RESTYPE_LEN = 30;
+	public static final int RESTYPE_LEN = 35;
 	private static final int MAX_LANGUAGE_LENGTH = 20;
 	private static final int MAX_PROFILE_LENGTH = 200;
 	private static final long serialVersionUID = 1L;
@@ -199,7 +199,7 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@OneToMany(mappedBy = "myTargetResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
 	@OptimisticLock(excluded = true)
 	private Collection<ResourceLink> myResourceLinksAsTarget;
-	@Column(name = "RES_TYPE", length = RESTYPE_LEN)
+	@Column(name = "RES_TYPE", length = RESTYPE_LEN, nullable = false)
 	@Field
 	@OptimisticLock(excluded = true)
 	private String myResourceType;

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/sched/FireAtIntervalJob.java

@@ -0,0 +1,45 @@
+package ca.uhn.fhir.jpa.model.sched;
+
+import org.quartz.DisallowConcurrentExecution;
+import org.quartz.Job;
+import org.quartz.JobExecutionContext;
+import org.quartz.PersistJobDataAfterExecution;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+@DisallowConcurrentExecution
+@PersistJobDataAfterExecution
+public abstract class FireAtIntervalJob implements Job {
+
+	public static final String NEXT_EXECUTION_TIME = "NEXT_EXECUTION_TIME";
+	private static final Logger ourLog = LoggerFactory.getLogger(FireAtIntervalJob.class);
+	private final long myMillisBetweenExecutions;
+
+	public FireAtIntervalJob(long theMillisBetweenExecutions) {
+		myMillisBetweenExecutions = theMillisBetweenExecutions;
+	}
+
+	@Override
+	public final void execute(JobExecutionContext theContext) {
+		Long nextExecution = (Long) theContext.getJobDetail().getJobDataMap().get(NEXT_EXECUTION_TIME);
+
+		if (nextExecution != null) {
+			long cutoff = System.currentTimeMillis();
+			if (nextExecution >= cutoff) {
+				return;
+			}
+		}
+
+		try {
+			doExecute(theContext);
+		} catch (Throwable t) {
+			ourLog.error("Job threw uncaught exception", t);
+		} finally {
+			long newNextExecution = System.currentTimeMillis() + myMillisBetweenExecutions;
+			theContext.getJobDetail().getJobDataMap().put(NEXT_EXECUTION_TIME, newNextExecution);
+		}
+	}
+
+	protected abstract void doExecute(JobExecutionContext theContext);
+
+}

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/sched/ISchedulerService.java

@@ -0,0 +1,21 @@
+package ca.uhn.fhir.jpa.model.sched;
+
+import com.google.common.annotations.VisibleForTesting;
+import org.quartz.SchedulerException;
+
+public interface ISchedulerService {
+
+	@VisibleForTesting
+	void purgeAllScheduledJobsForUnitTest() throws SchedulerException;
+
+	void logStatus();
+
+	/**
+	 * @param theIntervalMillis How many milliseconds between passes should this job run
+	 * @param theClusteredTask  If <code>true</code>, only one instance of this task will fire across the whole cluster (when running in a clustered environment). If <code>false</code>, or if not running in a clustered environment, this task will execute locally (and should execute on all nodes of the cluster)
+	 * @param theJobDefinition  The Job to fire
+	 */
+	void scheduleFixedDelay(long theIntervalMillis, boolean theClusteredTask, ScheduledJobDefinition theJobDefinition);
+
+	boolean isStopping();
+}

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/sched/ScheduledJobDefinition.java

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.jpa.model.sched;
+
+import org.apache.commons.lang3.Validate;
+import org.quartz.Job;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ScheduledJobDefinition {
+
+
+	private Class<? extends Job> myJobClass;
+	private String myId;
+	private Map<String, String> myJobData;
+
+	public Map<String, String> getJobData() {
+		Map<String, String> retVal = myJobData;
+		if (retVal == null) {
+			retVal = Collections.emptyMap();
+		}
+		return Collections.unmodifiableMap(retVal);
+	}
+
+	public Class<? extends Job> getJobClass() {
+		return myJobClass;
+	}
+
+	public ScheduledJobDefinition setJobClass(Class<? extends Job> theJobClass) {
+		myJobClass = theJobClass;
+		return this;
+	}
+
+	public String getId() {
+		return myId;
+	}
+
+	public ScheduledJobDefinition setId(String theId) {
+		myId = theId;
+		return this;
+	}
+
+	public void addJobData(String thePropertyName, String thePropertyValue) {
+		Validate.notBlank(thePropertyName);
+		if (myJobData == null) {
+			myJobData = new HashMap<>();
+		}
+		Validate.isTrue(myJobData.containsKey(thePropertyName) == false);
+		myJobData.put(thePropertyName, thePropertyValue);
+	}
+}

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -174,6 +174,16 @@ public class JpaConstants {
 	 */
 	public static final String OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM = "$upload-external-code-system";
 
+	/**
+	 * Operation name for the "$export" operation
+	 */
+	public static final String OPERATION_EXPORT = "$export";
+
+	/**
+	 * Operation name for the "$export-poll-status" operation
+	 */
+	public static final String OPERATION_EXPORT_POLL_STATUS = "$export-poll-status";
+
 	/**
 	 * <p>
 	 * This extension should be of type <code>string</code> and should be
@@ -238,5 +248,28 @@ public class JpaConstants {
 	 */
 	public static final String EXT_META_SOURCE = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-source";
 
+	/**
+	 * Parameter for the $export operation
+	 */
+	public static final String PARAM_EXPORT_POLL_STATUS_JOB_ID = "_jobId";
 
+	/**
+	 * Parameter for the $export operation
+	 */
+	public static final String PARAM_EXPORT_OUTPUT_FORMAT = "_outputFormat";
+
+	/**
+	 * Parameter for the $export operation
+	 */
+	public static final String PARAM_EXPORT_TYPE = "_type";
+
+	/**
+	 * Parameter for the $export operation
+	 */
+	public static final String PARAM_EXPORT_SINCE = "_since";
+
+	/**
+	 * Parameter for the $export operation
+	 */
+	public static final String PARAM_EXPORT_TYPE_FILTER = "_typeFilter";
 }