Merge branch 'master' into kh_2526_Add_Operation_Section_to_Conformance_Statements_resource_section

.editorconfig

@@ -31,6 +31,7 @@ charset = utf-8
 indent_style = tab
 tab_width = 3
 indent_size = 3
+continuation_indent_size=3
 ij_java_align_consecutive_assignments = false
 ij_java_align_consecutive_variable_declarations = false
 ij_java_align_group_field_declarations = false

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.context;
 
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -60,7 +61,7 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
 		myElementName = theElementName;
 		if (theDescriptionAnnotation != null) {
 			myShortDefinition = theDescriptionAnnotation.shortDefinition();
-			myFormalDefinition = theDescriptionAnnotation.formalDefinition();
+			myFormalDefinition = ParametersUtil.extractDescription(theDescriptionAnnotation);
 		} else {
 			myShortDefinition = null;
 			myFormalDefinition = null;

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

@@ -0,0 +1,38 @@
+package ca.uhn.fhir.context.phonetic;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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 com.google.common.base.CharMatcher;
+
+// Useful for numerical identifiers like phone numbers, address parts etc.
+// This should not be used where decimals are important.  A new "quantity encoder" should be added to handle cases like that.
+public class NumericEncoder implements IPhoneticEncoder {
+	@Override
+	public String name() {
+		return "NUMERIC";
+	}
+
+	@Override
+	public String encode(String theString) {
+		// Remove everything but the numbers
+		return CharMatcher.inRange('0', '9').retainFrom(theString);
+	}
+}

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

@@ -39,7 +39,8 @@ public enum PhoneticEncoderEnum {
 	METAPHONE(new ApacheEncoder("METAPHONE", new Metaphone())),
 	NYSIIS(new ApacheEncoder("NYSIIS", new Nysiis())),
 	REFINED_SOUNDEX(new ApacheEncoder("REFINED_SOUNDEX", new RefinedSoundex())),
-	SOUNDEX(new ApacheEncoder("SOUNDEX", new Soundex()));
+	SOUNDEX(new ApacheEncoder("SOUNDEX", new Soundex())),
+	NUMERIC(new NumericEncoder());
 
 	private final IPhoneticEncoder myPhoneticEncoder;
 

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

@@ -33,6 +33,13 @@ import java.lang.annotation.Target;
 @Target(value = {ElementType.FIELD, ElementType.TYPE, ElementType.PARAMETER, ElementType.METHOD})
 public @interface Description {
 
+	/**
+	 * A description of this method or parameter
+	 *
+	 * @since 5.4.0
+	 */
+	String value() default "";
+
 	/**
 	 * Optional short name for this child
 	 */
@@ -40,7 +47,16 @@ public @interface Description {
 
 	/**
 	 * Optional formal definition for this child
+	 *
+	 * @deprecated Use {@link #value()} instead. Deprecated in 5.4.0.
 	 */
+	@Deprecated
 	String formalDefinition() default "";
 
+	/**
+	 * May be used to supply example values for this
+	 *
+	 * @since 5.4.0
+	 */
+	String[] example() default {};
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/AddTags.java

@@ -78,4 +78,13 @@ public @interface AddTags {
 	 */
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Create.java

@@ -47,4 +47,13 @@ public @interface Create {
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Delete.java

@@ -48,4 +48,15 @@ public @interface Delete {
 	 */
 	// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
 	Class<? extends IBaseResource> type() default IBaseResource.class;
+
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/DeleteTags.java

@@ -74,4 +74,14 @@ public @interface DeleteTags {
 	 */
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/History.java

@@ -81,4 +81,14 @@ public @interface History {
 	 */
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Operation.java

@@ -132,7 +132,10 @@ public @interface Operation {
 
 	/**
 	 * If this is set to <code>true</code>, this method will be a <b>global operation</b>
-	 * meaning that it applies to all resource types
+	 * meaning that it applies to all resource types. Operations with this flag set should be
+	 * placed in Plain Providers (i.e. they don't need to be placed in a resource-type-specific
+	 * <code>IResourceProvider</code> instance) and should have a parameter annotated with
+	 * {@link IdParam}.
 	 */
 	boolean global() default false;
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/OperationParam.java

@@ -39,7 +39,7 @@ public @interface OperationParam {
 	/**
 	 * Value for {@link OperationParam#max()} indicating no maximum
 	 */
-	final int MAX_UNLIMITED = -1;
+	int MAX_UNLIMITED = -1;
 
 
 	/**
@@ -57,7 +57,7 @@ public @interface OperationParam {
 	 * 
 	 * @since 1.5
 	 */
-	final int MAX_DEFAULT = -2;
+	int MAX_DEFAULT = -2;
 	
 	/**
 	 * The name of the parameter

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Patch.java

@@ -50,4 +50,13 @@ public @interface Patch {
 	// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Search.java

@@ -78,6 +78,16 @@ public @interface Search {
 	// NB: Read, Search (maybe others) share this annotation method, so update the javadocs everywhere
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 	/**
 	 * In a REST server, should this method be invoked even if it does not have method parameters 
 	 * which correspond to all of the URL parameters passed in by the client (default is <code>false</code>).
@@ -91,4 +101,5 @@ public @interface Search {
 	 * </p>
 	 */
 	boolean allowUnknownParams() default false;
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Update.java

@@ -49,4 +49,14 @@ public @interface Update {
 	// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
 	Class<? extends IResource> type() default IResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 * <p>
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Validate.java

@@ -53,6 +53,16 @@ public @interface Validate {
 	// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This method allows the return type for this method to be specified in a
+	 * non-type-specific way, using the text name of the resource, e.g. "Patient".
+	 *
+	 * This attribute should be populate, or {@link #type()} should be, but not both.
+	 *
+	 * @since 5.4.0
+	 */
+	String typeName() default "";
+
 	/**
 	 * Validation mode parameter annotation for the validation mode parameter (only supported
 	 * in FHIR DSTU2+). Parameter must be of type {@link ValidationModeEnum}.

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

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.primitive.IdDt;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@@ -156,7 +157,8 @@ public class BundleBuilder {
 
 		// Bundle.entry.request.url
 		IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		url.setValueAsString(theResource.getIdElement().toUnqualifiedVersionless().getValue());
+		String resourceType = myContext.getResourceType(theResource);
+		url.setValueAsString(theResource.getIdElement().toUnqualifiedVersionless().withResourceType(resourceType).getValue());
 		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
 		// Bundle.entry.request.url
@@ -193,6 +195,45 @@ public class BundleBuilder {
 		return new CreateBuilder(request);
 	}
 
+	/**
+	 * Adds an entry containing a delete (DELETE) request.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 *
+	 * Note that the resource is only used to extract its ID and type, and the body of the resource is not included in the entry,
+	 *
+	 * @param theResource The resource to delete.
+	 */
+	public void addTransactionDeleteEntry(IBaseResource theResource) {
+		String resourceType = myContext.getResourceType(theResource);
+		String idPart = theResource.getIdElement().toUnqualifiedVersionless().getIdPart();
+		addTransactionDeleteEntry(resourceType, idPart);
+	}
+
+	/**
+	 * Adds an entry containing a delete (DELETE) request.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 *
+	 * @param theResourceType The type resource to delete.
+	 * @param theIdPart  the ID of the resource to delete.
+	 */
+	public void addTransactionDeleteEntry(String theResourceType, String theIdPart) {
+		setBundleField("type", "transaction");
+		IBase request = addEntryAndReturnRequest();
+		IdDt idDt = new IdDt(theIdPart);
+		
+		// Bundle.entry.request.url
+		IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
+		url.setValueAsString(idDt.toUnqualifiedVersionless().withResourceType(theResourceType).getValue());
+		myEntryRequestUrlChild.getMutator().setValue(request, url);
+
+		// Bundle.entry.request.method
+		IPrimitiveType<?> method = (IPrimitiveType<?>) myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
+		method.setValueAsString("DELETE");
+		myEntryRequestMethodChild.getMutator().setValue(request, method);
+	}
+
+
+
 	/**
 	 * Adds an entry for a Collection bundle type
 	 */
@@ -250,6 +291,16 @@ public class BundleBuilder {
 		return request;
 	}
 
+	public IBase addEntryAndReturnRequest() {
+		IBase entry = addEntry();
+
+		// Bundle.entry.request
+		IBase request = myEntryRequestDef.newInstance();
+		myEntryRequestChild.getMutator().setValue(entry, request);
+		return request;
+
+	}
+
 
 	public IBaseBundle getBundle() {
 		return myBundle;

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

@@ -36,6 +36,13 @@ import java.util.stream.Collectors;
  */
 public class ExtensionUtil {
 
+	/**
+	 * Non instantiable
+	 */
+	private ExtensionUtil() {
+		// nothing
+	}
+
 	/**
 	 * Returns an extension with the specified URL creating one if it doesn't exist.
 	 *
@@ -46,7 +53,7 @@ public class ExtensionUtil {
 	 */
 	public static IBaseExtension<?, ?> getOrCreateExtension(IBase theBase, String theUrl) {
 		IBaseHasExtensions baseHasExtensions = validateExtensionSupport(theBase);
-		IBaseExtension extension = getExtensionByUrl(baseHasExtensions, theUrl);
+		IBaseExtension<?,?> extension = getExtensionByUrl(baseHasExtensions, theUrl);
 		if (extension == null) {
 			extension = baseHasExtensions.addExtension();
 			extension.setUrl(theUrl);
@@ -75,13 +82,27 @@ public class ExtensionUtil {
 	 */
 	public static IBaseExtension<?, ?> addExtension(IBase theBase, String theUrl) {
 		IBaseHasExtensions baseHasExtensions = validateExtensionSupport(theBase);
-		IBaseExtension extension = baseHasExtensions.addExtension();
+		IBaseExtension<?,?> extension = baseHasExtensions.addExtension();
 		if (theUrl != null) {
 			extension.setUrl(theUrl);
 		}
 		return extension;
 	}
 
+	/**
+	 * Adds an extension with the specified value
+	 *
+	 * @param theBase        The resource to update extension on
+	 * @param theUrl         Extension URL
+	 * @param theValueType   Type of the value to set in the extension
+	 * @param theValue       Extension value
+	 * @param theFhirContext The context containing FHIR resource definitions
+	 */
+	public static void addExtension(FhirContext theFhirContext, IBase theBase, String theUrl, String theValueType, Object theValue) {
+		IBaseExtension<?,?> ext = addExtension(theBase, theUrl);
+		setExtension(theFhirContext, ext, theValueType, theValue);
+	}
+
 	private static IBaseHasExtensions validateExtensionSupport(IBase theBase) {
 		if (!(theBase instanceof IBaseHasExtensions)) {
 			throw new IllegalArgumentException(String.format("Expected instance that supports extensions, but got %s", theBase));
@@ -118,7 +139,7 @@ public class ExtensionUtil {
 		if (!hasExtension(theBase, theExtensionUrl)) {
 			return false;
 		}
-		IBaseDatatype value = getExtensionByUrl((IBaseHasExtensions) theBase, theExtensionUrl).getValue();
+		IBaseDatatype value = getExtensionByUrl(theBase, theExtensionUrl).getValue();
 		if (value == null) {
 			return theExtensionValue == null;
 		}
@@ -133,7 +154,7 @@ public class ExtensionUtil {
 	 * @return Returns the first available extension with the specified URL, or null if such extension doesn't exist
 	 */
 	public static IBaseExtension<?, ?> getExtensionByUrl(IBase theBase, String theExtensionUrl) {
-		Predicate<IBaseExtension> filter;
+		Predicate<IBaseExtension<?,?>> filter;
 		if (theExtensionUrl == null) {
 			filter = (e -> true);
 		} else {
@@ -153,7 +174,7 @@ public class ExtensionUtil {
 	 * @param theFilter Predicate to match the extension against
 	 * @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
 	 */
-	public static List<IBaseExtension<?, ?>> getExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
+	public static List<IBaseExtension<?, ?>> getExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension<?,?>> theFilter) {
 		return validateExtensionSupport(theBase)
 			.getExtension()
 			.stream()
@@ -189,7 +210,7 @@ public class ExtensionUtil {
 	 * @param theFilter Defines which extensions should be cleared
 	 * @return Returns all extension that were removed
 	 */
-	private static List<IBaseExtension<?, ?>> clearExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
+	private static List<IBaseExtension<?, ?>> clearExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension<?,?>> theFilter) {
 		List<IBaseExtension<?, ?>> retVal = getExtensionsMatchingPredicate(theBase, theFilter);
 		validateExtensionSupport(theBase)
 			.getExtension()
@@ -205,7 +226,7 @@ public class ExtensionUtil {
 	 * @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
 	 */
 	public static List<IBaseExtension<?, ?>> getExtensionsByUrl(IBaseHasExtensions theBase, String theExtensionUrl) {
-		Predicate<IBaseExtension> urlEqualityPredicate = e -> theExtensionUrl.equals(e.getUrl());
+		Predicate<IBaseExtension<?,?>> urlEqualityPredicate = e -> theExtensionUrl.equals(e.getUrl());
 		return getExtensionsMatchingPredicate(theBase, urlEqualityPredicate);
 	}
 
@@ -216,8 +237,8 @@ public class ExtensionUtil {
 	 * @param theValue       The value to set
 	 * @param theFhirContext The context containing FHIR resource definitions
 	 */
-	public static void setExtension(FhirContext theFhirContext, IBaseExtension theExtension, String theValue) {
+	public static void setExtension(FhirContext theFhirContext, IBaseExtension<?,?> theExtension, String theValue) {
-		setExtension(theFhirContext, theExtension, "string", (Object) theValue);
+		setExtension(theFhirContext, theExtension, "string", theValue);
 	}
 
 	/**
@@ -228,7 +249,7 @@ public class ExtensionUtil {
 	 * @param theValue         The value to set
 	 * @param theFhirContext   The context containing FHIR resource definitions
 	 */
-	public static void setExtension(FhirContext theFhirContext, IBaseExtension theExtension, String theExtensionType, Object theValue) {
+	public static void setExtension(FhirContext theFhirContext, IBaseExtension<?,?> theExtension, String theExtensionType, Object theValue) {
 		theExtension.setValue(TerserUtil.newElement(theFhirContext, theExtensionType, theValue));
 	}
 
@@ -241,7 +262,7 @@ public class ExtensionUtil {
 	 * @param theFhirContext The context containing FHIR resource definitions
 	 */
 	public static void setExtensionAsString(FhirContext theFhirContext, IBase theBase, String theUrl, String theValue) {
-		IBaseExtension ext = getOrCreateExtension(theBase, theUrl);
+		IBaseExtension<?,?> ext = getOrCreateExtension(theBase, theUrl);
 		setExtension(theFhirContext, ext, theValue);
 	}
 
@@ -255,7 +276,7 @@ public class ExtensionUtil {
 	 * @param theFhirContext The context containing FHIR resource definitions
 	 */
 	public static void setExtension(FhirContext theFhirContext, IBase theBase, String theUrl, String theValueType, Object theValue) {
-		IBaseExtension ext = getOrCreateExtension(theBase, theUrl);
+		IBaseExtension<?,?> ext = getOrCreateExtension(theBase, theUrl);
 		setExtension(theFhirContext, ext, theValueType, theValue);
 	}
 
@@ -266,7 +287,7 @@ public class ExtensionUtil {
 	 * @param theRightExtension : Extension to be evaluated #2
 	 * @return Result of the comparison
 	 */
-	public static boolean equals(IBaseExtension theLeftExtension, IBaseExtension theRightExtension) {
+	public static boolean equals(IBaseExtension<?,?> theLeftExtension, IBaseExtension<?,?> theRightExtension) {
 		return TerserUtil.equals(theLeftExtension, theRightExtension);
 	}
 }

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

@@ -116,6 +116,12 @@ public class HapiExtensions {
 	 */
     public static final String ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL = "https://hapifhir.org/associated-patient-golden-resource/";
 
+	/**
+	 * This extension provides an example value for a parameter value for
+	 * a REST operation (eg for an OperationDefinition)
+	 */
+	public static final String EXT_OP_PARAMETER_EXAMPLE_VALUE = "http://hapifhir.io/fhir/StructureDefinition/op-parameter-example-value";
+
 	/**
 	 * Non instantiable
 	 */

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.primitive.StringDt;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -34,8 +35,13 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import javax.annotation.Nullable;
+import java.lang.annotation.Annotation;
+import java.lang.reflect.AnnotatedElement;
+import java.lang.reflect.Method;
 import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
@@ -43,6 +49,7 @@ import java.util.function.Function;
 import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 /**
  * Utilities for dealing with parameters resources in a version indepenedent way
@@ -418,4 +425,60 @@ public class ParametersUtil {
 			.findFirst();
 	}
 
+	@Nullable
+	public static String extractDescription(AnnotatedElement theType) {
+		Description description = theType.getAnnotation(Description.class);
+		if (description != null) {
+			return extractDescription(description);
+		} else {
+			return null;
+		}
+	}
+
+	@Nullable
+	public static String extractDescription(Description desc) {
+		String description = desc.value();
+		if (isBlank(description)) {
+			description = desc.formalDefinition();
+		}
+		if (isBlank(description)) {
+			description = desc.shortDefinition();
+		}
+		return defaultIfBlank(description, null);
+	}
+
+	@Nullable
+	public static String extractShortDefinition(AnnotatedElement theType) {
+		Description description = theType.getAnnotation(Description.class);
+		if (description != null) {
+			return defaultIfBlank(description.shortDefinition(), null);
+		} else {
+			return null;
+		}
+	}
+
+	public static String extractDescription(Annotation[] theParameterAnnotations) {
+		for (Annotation next : theParameterAnnotations) {
+			if (next instanceof Description) {
+				return extractDescription((Description)next);
+			}
+		}
+		return null;
+	}
+
+	public static List<String> extractExamples(Annotation[] theParameterAnnotations) {
+		ArrayList<String> retVal = null;
+		for (Annotation next : theParameterAnnotations) {
+			if (next instanceof Description) {
+				String[] examples = ((Description) next).example();
+				if (examples.length > 0) {
+					if (retVal == null) {
+						retVal = new ArrayList<>();
+					}
+					retVal.addAll(Arrays.asList(examples));
+				}
+			}
+		}
+		return retVal;
+	}
 }

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import org.apache.commons.lang3.tuple.Triple;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
@@ -48,9 +49,15 @@ public final class TerserUtil {
 
 	private static final String EQUALS_DEEP = "equalsDeep";
 
+	/**
+	 * Exclude for id, identifier and meta fields of a resource.
+	 */
 	public static final Collection<String> IDS_AND_META_EXCLUDES =
 		Collections.unmodifiableSet(Stream.of("id", "identifier", "meta").collect(Collectors.toSet()));
 
+	/**
+	 * Exclusion predicate for id, identifier, meta fields.
+	 */
 	public static final Predicate<String> EXCLUDE_IDS_AND_META = new Predicate<String>() {
 		@Override
 		public boolean test(String s) {
@@ -58,6 +65,25 @@ public final class TerserUtil {
 		}
 	};
 
+	/**
+	 * Exclusion predicate for id/identifier, meta and fields with empty values. This ensures that source / target resources,
+	 * empty source fields will not results in erasure of target fields.
+	 */
+	public static final Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> EXCLUDE_IDS_META_AND_EMPTY = new Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>>() {
+		@Override
+		public boolean test(Triple<BaseRuntimeChildDefinition, IBase, IBase> theTriple) {
+			if (!EXCLUDE_IDS_AND_META.test(theTriple.getLeft().getElementName())) {
+				return false;
+			}
+			BaseRuntimeChildDefinition childDefinition = theTriple.getLeft();
+			boolean isSourceFieldEmpty = childDefinition.getAccessor().getValues(theTriple.getMiddle()).isEmpty();
+			return !isSourceFieldEmpty;
+		}
+	};
+
+	/**
+	 * Exclusion predicate for keeping all fields.
+	 */
 	public static final Predicate<String> INCLUDE_ALL = new Predicate<String>() {
 		@Override
 		public boolean test(String s) {
@@ -235,26 +261,37 @@ public final class TerserUtil {
 	}
 
 	/**
-	 * Replaces all fields that test positive by the given inclusion strategy. <code>theTo</code> will contain a copy of the
+	 * Replaces all fields that have matching field names by the given inclusion strategy. <code>theTo</code> will contain a copy of the
 	 * values from <code>theFrom</code> instance.
 	 *
 	 * @param theFhirContext        Context holding resource definition
 	 * @param theFrom               The resource to merge the fields from
 	 * @param theTo                 The resource to merge the fields into
-	 * @param inclusionStrategy Inclusion strategy that checks if a given field should be replaced by checking {@link Predicate#test(Object)}
+	 * @param theFieldNameInclusion Inclusion strategy that checks if a given field should be replaced
 	 */
-	public static void replaceFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> inclusionStrategy) {
+	public static void replaceFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> theFieldNameInclusion) {
-		FhirTerser terser = theFhirContext.newTerser();
+		Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> predicate
-
+			= (t) -> theFieldNameInclusion.test(t.getLeft().getElementName());
-		RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
+		replaceFieldsByPredicate(theFhirContext, theFrom, theTo, predicate);
-		for (BaseRuntimeChildDefinition childDefinition : definition.getChildrenAndExtension()) {
-			if (!inclusionStrategy.test(childDefinition.getElementName())) {
-				continue;
 	}
 
+	/**
+	 * Replaces fields on theTo resource that test positive by the given predicate. <code>theTo</code> will contain a copy of the
+	 * values from <code>theFrom</code> for which predicate tests positive. Please note that composite fields will be replaced fully.
+	 *
+	 * @param theFhirContext Context holding resource definition
+	 * @param theFrom        The resource to merge the fields from
+	 * @param theTo          The resource to merge the fields into
+	 * @param thePredicate   Predicate that checks if a given field should be replaced
+	 */
+	public static void replaceFieldsByPredicate(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> thePredicate) {
+		RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
+		for (BaseRuntimeChildDefinition childDefinition : definition.getChildrenAndExtension()) {
+			if (thePredicate.test(Triple.of(childDefinition, theFrom, theTo))) {
 				replaceField(theFrom, theTo, childDefinition);
 			}
 		}
+	}
 
 	/**
 	 * Checks if the field exists on the resource
@@ -277,14 +314,11 @@ public final class TerserUtil {
 	 * @param theTo          The resource to replace the field on
 	 */
 	public static void replaceField(FhirContext theFhirContext, String theFieldName, IBaseResource theFrom, IBaseResource theTo) {
-		replaceField(theFhirContext, theFhirContext.newTerser(), theFieldName, theFrom, theTo);
+		RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
+		if (definition == null) {
+			throw new IllegalArgumentException(String.format("Field %s does not exist in %s", theFieldName, theFrom));
 		}
-
+		replaceField(theFrom, theTo, theFhirContext.getResourceDefinition(theFrom).getChildByName(theFieldName));
-	/**
-	 * @deprecated Use {@link #replaceField(FhirContext, String, IBaseResource, IBaseResource)} instead
-	 */
-	public static void replaceField(FhirContext theFhirContext, FhirTerser theTerser, String theFieldName, IBaseResource theFrom, IBaseResource theTo) {
-		replaceField(theFrom, theTo, getBaseRuntimeChildDefinition(theFhirContext, theFieldName, theFrom));
 	}
 
 	/**
@@ -301,7 +335,7 @@ public final class TerserUtil {
 
 	/**
 	 * Sets the provided field with the given values. This method will add to the collection of existing field values
-	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
+	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, String, IBaseResource)}
 	 * to remove values before setting
 	 *
 	 * @param theFhirContext Context holding resource definition
@@ -315,7 +349,7 @@ public final class TerserUtil {
 
 	/**
 	 * Sets the provided field with the given values. This method will add to the collection of existing field values
-	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
+	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, String, IBaseResource)}
 	 * to remove values before setting
 	 *
 	 * @param theFhirContext Context holding resource definition
@@ -370,10 +404,26 @@ public final class TerserUtil {
 		setFieldByFhirPath(theFhirContext.newTerser(), theFhirPath, theResource, theValue);
 	}
 
+	/**
+	 * Returns field values ant the specified FHIR path from the resource.
+	 *
+	 * @param theFhirContext Context holding resource definition
+	 * @param theFhirPath    The FHIR path to get the field from
+	 * @param theResource    The resource from which the value should be retrieved
+	 * @return Returns the list of field values at the given FHIR path
+	 */
 	public static List<IBase> getFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
 		return theFhirContext.newTerser().getValues(theResource, theFhirPath, false, false);
 	}
 
+	/**
+	 * Returns the first available field value at the specified FHIR path from the resource.
+	 *
+	 * @param theFhirContext Context holding resource definition
+	 * @param theFhirPath    The FHIR path to get the field from
+	 * @param theResource    The resource from which the value should be retrieved
+	 * @return Returns the first available value or null if no values can be retrieved
+	 */
 	public static IBase getFirstFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
 		List<IBase> values = getFieldByFhirPath(theFhirContext, theFhirPath, theResource);
 		if (values == null || values.isEmpty()) {

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

@@ -68,7 +68,11 @@ public enum VersionEnum {
 	V5_2_0,
 	V5_2_1,
 	V5_3_0,
-	V5_4_0;
+	V5_3_1,
+	V5_3_2,
+	V5_3_3,
+	V5_4_0,
+	;
 
 	public static VersionEnum latestVersion() {
 		VersionEnum[] values = VersionEnum.values();

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java

@@ -51,6 +51,7 @@ public class SchemaBaseValidator implements IValidatorModule {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SchemaBaseValidator.class);
 	private static final Set<String> SCHEMA_NAMES;
+	private static boolean ourJaxp15Supported;
 
 	static {
 		HashSet<String> sn = new HashSet<>();
@@ -132,7 +133,9 @@ public class SchemaBaseValidator implements IValidatorModule {
 					 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
 					 */
 					schemaFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
+					ourJaxp15Supported = true;
 				} catch (SAXNotRecognizedException e) {
+					ourJaxp15Supported = false;
 					ourLog.warn("Jaxp 1.5 Support not found.", e);
 				}
 				schema = schemaFactory.newSchema(new Source[]{baseSource});
@@ -216,4 +219,8 @@ public class SchemaBaseValidator implements IValidatorModule {
 
 	}
 
+	public static boolean isJaxp15Supported() {
+		return ourJaxp15Supported;
+	}
+
 }

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

@@ -68,8 +68,8 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
 
 # JPA Messages
 
-ca.uhn.fhir.jpa.bulk.svc.BulkDataExportSvcImpl.onlyBinarySelected=Binary resources may not be exported with bulk export
+ca.uhn.fhir.jpa.bulk.export.svc.BulkDataExportSvcImpl.onlyBinarySelected=Binary resources may not be exported with bulk export
-ca.uhn.fhir.jpa.bulk.svc.BulkDataExportSvcImpl.unknownResourceType=Unknown or unsupported resource type: {0} 
+ca.uhn.fhir.jpa.bulk.export.svc.BulkDataExportSvcImpl.unknownResourceType=Unknown or unsupported resource type: {0} 
 ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFailure=The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.
 ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
 ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected.

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/phonetic/PhoneticEncoderTest.java

@@ -1,14 +1,14 @@
 package ca.uhn.fhir.context.phonetic;
 
-import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.EnumSource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.hamcrest.Matchers.startsWith;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.startsWith;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 class PhoneticEncoderTest {
 	private static final Logger ourLog = LoggerFactory.getLogger(PhoneticEncoderTest.class);
@@ -23,7 +23,11 @@ class PhoneticEncoderTest {
 	public void testEncodeAddress(PhoneticEncoderEnum thePhoneticEncoderEnum) {
 		String encoded = thePhoneticEncoderEnum.getPhoneticEncoder().encode(ADDRESS_LINE);
 		ourLog.info("{}: {}", thePhoneticEncoderEnum.name(), encoded);
+		if (thePhoneticEncoderEnum == PhoneticEncoderEnum.NUMERIC) {
+			assertEquals(NUMBER + SUITE, encoded);
+		} else {
 			assertThat(encoded, startsWith(NUMBER + " "));
 			assertThat(encoded, endsWith(" " + SUITE));
 		}
 	}
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/validation/PlaceholderTest.java

@@ -11,5 +11,4 @@ public class PlaceholderTest {
 	public void testPass() {
 		// nothing
 	}
-	
 }

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>5.4.0-PRE5-SNAPSHOT</version>
+    <version>5.4.0-PRE8-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
     <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>5.4.0-PRE5-SNAPSHOT</version>
+      <version>5.4.0-PRE8-SNAPSHOT</version>
       <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
     
@@ -41,6 +41,11 @@
 				  <artifactId>hapi-fhir-server-mdm</artifactId>
 				  <version>${project.version}</version>
 			  </dependency>
+            <dependency>
+                <groupId>${project.groupId}</groupId>
+                <artifactId>hapi-fhir-server-openapi</artifactId>
+                <version>${project.version}</version>
+            </dependency>
             <dependency>
                 <groupId>${project.groupId}</groupId>
                 <artifactId>hapi-fhir-validation</artifactId>

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -31,6 +31,7 @@ import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
@@ -70,6 +71,9 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 	protected static final String VERBOSE_LOGGING_PARAM = "l";
 	protected static final String VERBOSE_LOGGING_PARAM_LONGOPT = "logging";
 	protected static final String VERBOSE_LOGGING_PARAM_DESC = "If specified, verbose logging will be used.";
+	protected static final int DEFAULT_THREAD_COUNT = 10;
+	protected static final String THREAD_COUNT = "thread-count";
+
 	// TODO: Don't use qualified names for loggers in HAPI CLI.
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseCommand.class);
 	protected FhirContext myFhirCtx;
@@ -87,6 +91,11 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		addOptionalOption(theOptions, null, BEARER_TOKEN_PARAM_LONGOPT, BEARER_TOKEN_PARAM_NAME, BEARER_TOKEN_PARAM_DESC);
 	}
 
+	protected void addThreadCountOption(Options theOptions) {
+		addOptionalOption(theOptions, null, THREAD_COUNT, "count", "If specified, this argument specifies the number of worker threads used (default is " + DEFAULT_THREAD_COUNT + ")");
+	}
+
+
 	protected String promptUser(String thePrompt) throws ParseException {
 		System.out.print(ansi().bold().fgBrightDefault());
 		System.out.print(thePrompt);
@@ -309,6 +318,12 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		return getFhirContext().getResourceDefinition("Bundle").getImplementingClass(IBaseBundle.class);
 	}
 
+	protected int getThreadCount(CommandLine theCommandLine) throws ParseException {
+		Integer parallelismThreadCount = getAndParsePositiveIntegerParam(theCommandLine, THREAD_COUNT);
+		parallelismThreadCount = ObjectUtils.defaultIfNull(parallelismThreadCount, DEFAULT_THREAD_COUNT);
+		return parallelismThreadCount.intValue();
+	}
+
 	public abstract String getCommandDescription();
 
 	public abstract String getCommandName();

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/OperationMethodBinding.java

@@ -30,6 +30,7 @@ import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.ParametersUtil;
 import org.hl7.fhir.instance.model.api.*;
 
 import java.lang.reflect.Method;
@@ -64,10 +65,7 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 
 		Description description = theMethod.getAnnotation(Description.class);
 		if (description != null) {
-			myDescription = description.formalDefinition();
+			myDescription = ParametersUtil.extractDescription(description);
-			if (isBlank(myDescription)) {
-				myDescription = description.shortDefinition();
-			}
 		}
 		if (isBlank(myDescription)) {
 			myDescription = null;

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/SearchMethodBinding.java

@@ -33,6 +33,7 @@ import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.ParametersUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -59,15 +60,7 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 		this.myQueryName = StringUtils.defaultIfBlank(search.queryName(), null);
 		this.myCompartmentName = StringUtils.defaultIfBlank(search.compartmentName(), null);
 		this.myIdParamIndex = ParameterUtil.findIdParameterIndex(theMethod, getContext());
-
+		this.myDescription = ParametersUtil.extractDescription(theMethod);
-		Description desc = theMethod.getAnnotation(Description.class);
-		if (desc != null) {
-			if (isNotBlank(desc.formalDefinition())) {
-				myDescription = StringUtils.defaultIfBlank(desc.formalDefinition(), null);
-			} else {
-				myDescription = StringUtils.defaultIfBlank(desc.shortDefinition(), null);
-			}
-		}
 
 		/*
 		 * Check for parameter combinations and names that are invalid

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -55,6 +55,11 @@
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-server-openapi</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 
 		<dependency>
 			<groupId>com.fasterxml.jackson.dataformat</groupId>
@@ -78,13 +83,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>5.4.0-PRE5-SNAPSHOT</version>
+			<version>5.4.0-PRE8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
-			<version>5.4.0-PRE5-SNAPSHOT</version>
+			<version>5.4.0-PRE8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -101,7 +106,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-testpage-overlay</artifactId>
-			<version>5.4.0-PRE5-SNAPSHOT</version>
+			<version>5.4.0-PRE8-SNAPSHOT</version>
 			<classifier>classes</classifier>
 		</dependency>
 		<dependency>

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/CreateCompositionAndGenerateDocument.java

@@ -0,0 +1,73 @@
+package ca.uhn.hapi.fhir.docs;
+
+/*-
+ * #%L
+ * HAPI FHIR - Docs
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.rest.client.api.IGenericClient;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Composition;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Reference;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class CreateCompositionAndGenerateDocument {
+
+  private static final Logger ourLog = LoggerFactory.getLogger(CreateCompositionAndGenerateDocument.class);
+
+  public static void main(String[] args) {
+
+    // START SNIPPET: CreateCompositionAndGenerateDocument
+    FhirContext ctx = FhirContext.forR4();
+    IGenericClient client = ctx.newRestfulGenericClient("http://hapi.fhir.org/baseR4");
+
+    Patient patient = new Patient();
+    patient.setId("PATIENT-ABC");
+    patient.setActive(true);
+    client.update().resource(patient).execute();
+
+    Observation observation = new Observation();
+    observation.setId("OBSERVATION-ABC");
+    observation.setSubject(new Reference("Patient/PATIENT-ABC"));
+    observation.setStatus(Observation.ObservationStatus.FINAL);
+    client.update().resource(observation).execute();
+
+    Composition composition = new Composition();
+    composition.setId("COMPOSITION-ABC");
+    composition.setSubject(new Reference("Patient/PATIENT-ABC"));
+    composition.addSection().setFocus(new Reference("Observation/OBSERVATION-ABC"));
+    client.update().resource(composition).execute();
+
+    Bundle document = client
+       .operation()
+       .onInstance("Composition/COMPOSITION-ABC")
+       .named("$document")
+       .withNoParameters(Parameters.class)
+       .returnResourceType(Bundle.class)
+       .execute();
+
+    ourLog.info("Document bundle: {}", ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(document));
+    // END SNIPPET: CreateCompositionAndGenerateDocument
+
+  }
+}

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServletExamples.java

@@ -23,6 +23,7 @@ package ca.uhn.hapi.fhir.docs;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.rest.api.PreferHandlingEnum;
+import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.interceptor.*;
@@ -65,6 +66,24 @@ public class ServletExamples {
    }
    // END SNIPPET: loggingInterceptor
 
+   // START SNIPPET: OpenApiInterceptor
+	@WebServlet(urlPatterns = { "/fhir/*" }, displayName = "FHIR Server")
+   public class RestfulServerWithOpenApi extends RestfulServer {
+
+      @Override
+      protected void initialize() throws ServletException {
+
+         // ... define your resource providers here ...
+
+         // Now register the interceptor
+			OpenApiInterceptor openApiInterceptor = new OpenApiInterceptor();
+         registerInterceptor(openApiInterceptor);
+
+      }
+
+   }
+   // END SNIPPET: OpenApiInterceptor
+
    // START SNIPPET: validatingInterceptor
    @WebServlet(urlPatterns = { "/fhir/*" }, displayName = "FHIR Server")
    public class ValidatingServerWithLogging extends RestfulServer {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_1/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2021-03-11"
+codename: "Odyssey"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2021-04-14"
+codename: "Odyssey"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_3/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2021-04-26"
+codename: "Odyssey"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2407-allow-partition-date-for-nonpartitionable.yaml

@@ -4,3 +4,4 @@ issue: 2407
 title: "When using the JPA server in partitioned mode with a partition interceptor, the interceptor is now called even for
    resource types that can not be placed in a non-default partition (e.g. SearchParameter, CodeSystem, etc.). The interceptor
    may return null or default in this case, but can include a non-null partition date if needed."
+backport: 5.3.1

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2417-avoid-npe-indexing-timing.yaml

@@ -3,3 +3,4 @@ type: fix
 issue: 2417
 title: "A NullPointerException was corrected when indexing resources containing an indexed Period field that
   had a start but not an end defined."
+backport: 5.3.3

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2515-mdm-survivorship-rules-application.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2515
+title: "Fixed issues with application of survivorship rules when matching golden record to a single resource"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2533-fix-issue-with-reference-resources-not-being-returned-in-search-queries.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 2533
+title: "When issuing a request for a specific Resource and also specifying an _include param, 
+the referenced resource is not returned when there is only 1 version of the referenced resource available. 
+When there are more than 1 versions available, the referenced resource is returned in the response bundle."
+backport: 5.3.2

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2535-do-not-create-snapshot-for-logical-structuredefinition.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 2535
+title: "An issue with package installer involving logical StructureDefinition resources was fixed. Package registry will no
+    longer attempt to generate a snapshot for logical StructureDefinition resources if one is not already provided in the
+    resource definition."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2543-fix-issue-where-versionned-references-are-not-being-returned-properly.yaml

@@ -0,0 +1,9 @@
+---
+type: fix
+issue: 2543
+title: "When issuing a request for a specific Resource and also specifying an _include param, 
+the proper historical referenced resource is not returned when there are more than 1 versions of the 
+referenced resource available, after the reference has been changed from the original version 1 to some other version. 
+When there are more than 1 versions available, and the referring resource had previously referred to version 1 
+but now refers to version 4, the resource returned in the response bundle is for version 1."
+backport: 5.3.2

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2547-mdm-add-numeric-matcher.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2547
+title: "Added new NUMERIC mdm matcher for matching phone numbers.  Also added NUMERIC phonetic encoder to support
+adding NUMERIC encoded search parameter (e.g. if searching for matching phone numbers is required by mdm candidate searching)."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2556-prevent-bulk-failure-while-partitioned.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2556
+title: "Fixed a bug which would cause Bulk Export to fail when run in a partitioned environment."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2560-openapi-support.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2560
+title: "A new interceptor called `OpenApiInterceptor` has been added. This interceptor can be registered against FHIR Servers to
+   automatically add support for OpenAPI / Swagger."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2571-add-delete-to-bundle-builder.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2571
+title: "Added support for deleting resources to BundleBuilder via method `addTransactionDeleteEntry`."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/changes.yaml

@@ -0,0 +1,27 @@
+---
+- item:
+    type: "add"
+    title: "The version of a few dependencies have been bumped to the latest versions
+(dependent HAPI modules listed in brackets):
+<ul>
+<li>Commons-Lang3 (Core): 3.9 -> 3.12.0</li>
+<li>Commons-Text (Core): 1.7 -> 1.9</li>
+<li>Commons-Codec (Core): 1.14 -> 1.15</li>
+<li>Commons-IO (Core): 2.6 -> 2.8.0</li>
+<li>Guava (Core): 30.1-jre -> 30.1.1-jre</li>
+<li>Jackson (Core): 2.12.1 -> 2.12.3</li>
+<li>Woodstox (Core): 6.2.3 -> 6.2.5</li>
+<li>Apache Jena (Core/RDF): 3.16.0 -> 3.17.0</li>
+<li>Gson (JPA): 2.8.5 -> 2.8.6</li>
+<li>Caffeine (JPA): 2.7.0 -> 3.0.1</li>
+<li>Hibernate (JPA): 5.4.26.Final -> 5.4.30.Final</li>
+<li>Hibernate Search (JPA): 6.0.0.Final -> 6.0.2.Final</li>
+<li>Spring (JPA): 5.3.3 -> 5.3.6</li>
+<li>Spring Batch (JPA): 4.2.3.RELEASE -> 4.3.2</li>
+<li>Spring Data (JPA): 2.4.2 -> 2.4.7</li>
+<li>Commons DBCP2 (JPA): 2.7.0 -> 2.8.0</li>
+<li>Thymeleaf (Testpage Overlay): 3.0.11.RELEASE -> 3.0.12.RELEASE</li>
+<li>JAnsi (CLI): 2.1.1 -> 2.3.2</li>
+<li>JArchivelib (CLI): 1.0.0 -> 1.1.0</li>
+</ul>
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

@@ -161,3 +161,13 @@ This following example shows how to load all pages of a bundle by fetching each
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/BundleFetcher.java|loadAll}}
 ```
+
+# Create Composition and Generate Document
+
+This example shows how to generate a Composition resource with two linked resources, then apply the server `$document` operation to generate a document based on this composition.
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/CreateCompositionAndGenerateDocument.java|CreateCompositionAndGenerateDocument}}
+```
+
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties

@@ -47,6 +47,7 @@ page.server_plain.web_testpage_overlay=Web Testpage Overlay
 page.server_plain.multitenancy=Multitenancy
 page.server_plain.jax_rs=JAX-RS Support
 page.server_plain.customizing_the_capabilitystatement=Customizing the CapabilityStatement
+page.server_plain.openapi=OpenAPI / Swagger
 
 section.server_jpa.title=JPA Server
 page.server_jpa.introduction=Introduction

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/built_in_server_interceptors.md

@@ -196,6 +196,11 @@ Some security audit tools require that servers return an HTTP 405 if an unsuppor
 * [BanUnsupportedHttpMethodsInterceptor JavaDoc](/apidocs/hapi-fhir-server/ca/uhn/fhir/rest/server/interceptor/BanUnsupportedHttpMethodsInterceptor.html)
 * [BanUnsupportedHttpMethodsInterceptor Source](https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BanUnsupportedHttpMethodsInterceptor.java)
 
+# Server: OpenAPI / Swagger Support
+
+An interceptor can be registered against your server that enables support for OpenAPI (aka Swagger) automatically. See [OpenAPI](/docs/server_plain/openapi.html) for more information.
+
+
 # Subscription: Subscription Debug Log Interceptor
 
 When using Subscriptions, the debug log interceptor can be used to add a number of additional lines to the server logs showing the internals of the subscription processing pipeline.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_rules.md

@@ -292,10 +292,10 @@ The following algorithms are currently supported:
             <td>Gail = Gael, Gail != Gale, Thomas != Tom</td>
         </tr>
         <tr>
-            <td>CAVERPHONE1</td>
+            <td>CAVERPHONE2</td>
             <td>matcher</td>
             <td>
-              <a href="https://commons.apache.org/proper/commons-codec/apidocs/org/apache/commons/codec/language/Caverphone1.html">Apache Caverphone1</a>          
+              <a href="https://commons.apache.org/proper/commons-codec/apidocs/org/apache/commons/codec/language/Caverphone2.html">Apache Caverphone2</a>          
             </td>
             <td>Gail = Gael, Gail = Gale, Thomas != Tom</td>
         </tr>
@@ -379,6 +379,14 @@ The following algorithms are currently supported:
             </td>
             <td>2019-12,Month = 2019-12-19,Day</td>
         </tr>
+        <tr>
+            <td>NUMERIC</td>
+            <td>matcher</td>
+            <td>
+               Remove all non-numeric characters from the string before comparing.
+            </td>
+            <td>4169671111 = (416) 967-1111</td>
+        </tr>
         <tr>
             <td>NAME_ANY_ORDER</td>
             <td>matcher</td>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

@@ -0,0 +1,39 @@
+# OpenAPI / Swagger Support
+
+In HAPI FHIR, support for OpenAPI (aka Swagger) is supported via the [OpenApiInterceptor](/hapi-fhir/apidocs/hapi-fhir-server-openapi/ca/uhn/fhir/rest/openapi/OpenApiInterceptor.html).
+
+Note that this interceptor supports servers using the RestfulServer (aka HAPI FHIR Plain Server and JPA Server), and does not currently support JAX-RS servers. 
+
+When this interceptor is registered against the server, it performs the following 3 tasks:
+
+### System Functionality
+
+* OpenAPI 3.0 Documentation will be served at `[baseUrl]/api-docs`. This documentation is generated by the interceptor using information from the server's CapabilityStatement as well as from its automatically generated OperationDefinitions.  
+
+### User Functionality
+
+* Anytime a user using a browser navigates to the Base URL of the server, they will be automatically redirected to `[baseUrl]/swagger-ui/`
+
+* A customized version of the [Swagger UI](https://swagger.io/tools/swagger-ui/) tool will be served at `[baseUrl]/swagger-ui/`
+
+# Enabling OpenAPI
+
+The HAPI FHIR OpenAPI functionality is supplied in a dedicated module called `hapi-fhir-server-openapi`. To enable this functionality you must first include this module in your project. For example, Maven users should include the following dependency:
+
+```xml
+<dependency>
+	<groupId>ca.uhn.hapi.fhir</groupId>
+	<artifactId>hapi-fhir-server-openapi</artifactId>
+	<version>VERSION</version>
+</dependency>
+```
+
+You then simply have to register the interceptor against your RestfulServer instance.
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/ServletExamples.java|OpenApiInterceptor}}
+```
+
+# Demonstration
+
+See the HAPI FHIR Test Server for a demonstration of HAPI FHIR OpenAPI functionality: http://hapi.fhir.org/baseR4/swagger-ui/

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -36,6 +36,11 @@
 			<artifactId>hapi-fhir-server-mdm</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-server-openapi</artifactId>
+            <version>${project.version}</version>
+        </dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-client</artifactId>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirSystemDao.java

@@ -67,6 +67,18 @@ public interface IFhirSystemDao<T, MT> extends IDao {
 	 */
 	IBaseBundle processMessage(RequestDetails theRequestDetails, IBaseBundle theMessage);
 
+	/**
+	 * Executes a FHIR transaction using a new database transaction. This method must
+	 * not be called from within a DB transaction.
+	 */
 	T transaction(RequestDetails theRequestDetails, T theResources);
 
+	/**
+	 * Executes a FHIR transaction nested inside the current database transaction.
+	 * This form of the transaction processor can handle write operations only (no reads)
+	 */
+	default T transactionNested(RequestDetails theRequestDetails, T theResources) {
+		throw new UnsupportedOperationException();
+	}
+
 }

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE5-SNAPSHOT</version>
+		<version>5.4.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -577,6 +577,13 @@
 			<scope>test</scope>
 		</dependency>
 
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-server-openapi</artifactId>
+            <version>${project.version}</version>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
 			<groupId>com.github.ben-manes.caffeine</groupId>
 			<artifactId>caffeine</artifactId>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java

@@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.batch;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 
@@ -28,9 +29,11 @@ import org.springframework.context.annotation.Import;
 //When you define a new batch job, add it here.
 @Import({
 		  CommonBatchJobConfig.class,
-	BulkExportJobConfig.class
+		  BulkExportJobConfig.class,
+		  BulkImportJobConfig.class
 })
 public class BatchJobsConfig {
+	public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
 	public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
 	public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
 	public static final String PATIENT_BULK_EXPORT_JOB_NAME = "patientBulkExportJob";

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/GoldenResourceAnnotatingProcessor.java

@@ -24,7 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.fhirpath.IFhirPath;
 import ca.uhn.fhir.jpa.batch.log.Logs;
-import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
 import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
 import ca.uhn.fhir.util.ExtensionUtil;
 import ca.uhn.fhir.util.HapiExtensions;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/api/BulkDataExportOptions.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.api;
+package ca.uhn.fhir.jpa.bulk.export.api;
 
 /*-
  * #%L

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.api;
+package ca.uhn.fhir.jpa.bulk.export.api;
 
 /*-
  * #%L
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.api;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
 import org.hl7.fhir.instance.model.api.IIdType;
 
 import javax.transaction.Transactional;
@@ -50,7 +50,7 @@ public interface IBulkDataExportSvc {
 
 	class JobInfo {
 		private String myJobId;
-		private BulkJobStatusEnum myStatus;
+		private BulkExportJobStatusEnum myStatus;
 		private List<FileEntry> myFiles;
 		private String myRequest;
 		private Date myStatusTime;
@@ -90,11 +90,11 @@ public interface IBulkDataExportSvc {
 
 		}
 
-		public BulkJobStatusEnum getStatus() {
+		public BulkExportJobStatusEnum getStatus() {
 			return myStatus;
 		}
 
-		public JobInfo setStatus(BulkJobStatusEnum theStatus) {
+		public JobInfo setStatus(BulkExportJobStatusEnum theStatus) {
 			myStatus = theStatus;
 			return this;
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -30,7 +30,6 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
 import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
-import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -102,7 +101,7 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
 		myPidIterator = getResourcePidIterator();
 	}
 
-	abstract Iterator<ResourcePersistentId> getResourcePidIterator();
+	protected abstract Iterator<ResourcePersistentId> getResourcePidIterator();
 
 	protected List<SearchParameterMap> createSearchParameterMapsForResourceType() {
 		BulkExportJobEntity jobEntity = getJobEntity();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportCreateEntityStepListener.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,16 +20,12 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
-import org.springframework.batch.core.BatchStatus;
 import org.springframework.batch.core.ExitStatus;
 import org.springframework.batch.core.StepExecution;
 import org.springframework.batch.core.StepExecutionListener;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * Will run before and after a job to set the status to whatever is appropriate.
@@ -43,7 +39,7 @@ public class BulkExportCreateEntityStepListener implements StepExecutionListener
 	public void beforeStep(StepExecution theStepExecution) {
 		String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString("jobUUID");
 		if (jobUuid != null) {
-			myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkJobStatusEnum.BUILDING);
+			myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkExportJobStatusEnum.BUILDING);
 		}
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportGenerateResourceFilesStepListener.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import org.springframework.batch.core.ExitStatus;
 import org.springframework.batch.core.StepExecution;
 import org.springframework.batch.core.StepExecutionListener;
@@ -55,7 +55,7 @@ public class BulkExportGenerateResourceFilesStepListener implements StepExecutio
 			}
 			assert isNotBlank(jobUuid);
 			String exitDescription = theStepExecution.getExitStatus().getExitDescription();
-			myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkJobStatusEnum.ERROR, exitDescription);
+			myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkExportJobStatusEnum.ERROR, exitDescription);
 		}
 		return theStepExecution.getExitStatus();
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobCloser.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import org.springframework.batch.core.BatchStatus;
 import org.springframework.batch.core.StepContribution;
 import org.springframework.batch.core.scope.context.ChunkContext;
@@ -44,9 +44,9 @@ public class BulkExportJobCloser implements Tasklet {
 	@Override
 	public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) {
 		if (theChunkContext.getStepContext().getStepExecution().getJobExecution().getStatus() == BatchStatus.STARTED) {
-			myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkJobStatusEnum.COMPLETE);
+			myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkExportJobStatusEnum.COMPLETE);
 		} else {
-			myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkJobStatusEnum.ERROR);
+			myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkExportJobStatusEnum.ERROR);
 		}
 		return RepeatStatus.FINISHED;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobConfig.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.bulk.job;
 import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.processors.GoldenResourceAnnotatingProcessor;
 import ca.uhn.fhir.jpa.batch.processors.PidToIBaseResourceProcessor;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -35,8 +35,6 @@ import org.springframework.batch.core.configuration.annotation.JobScope;
 import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
 import org.springframework.batch.core.configuration.annotation.StepScope;
 import org.springframework.batch.item.ItemProcessor;
-import org.springframework.batch.item.ItemReader;
-import org.springframework.batch.item.ItemWriter;
 import org.springframework.batch.item.support.CompositeItemProcessor;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
@@ -59,6 +57,7 @@ public class BulkExportJobConfig {
 	public static final String GROUP_ID_PARAMETER = "groupId";
 	public static final String RESOURCE_TYPES_PARAMETER = "resourceTypes";
 	public static final int CHUNK_SIZE = 100;
+	public static final String JOB_DESCRIPTION = "jobDescription";
 
 	@Autowired
 	private StepBuilderFactory myStepBuilderFactory;
@@ -90,9 +89,9 @@ public class BulkExportJobConfig {
 	@Lazy
 	public Job bulkExportJob() {
 		return myJobBuilderFactory.get(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
-			.validator(bulkJobParameterValidator())
+			.validator(bulkExportJobParameterValidator())
 			.start(createBulkExportEntityStep())
-			.next(partitionStep())
+			.next(bulkExportPartitionStep())
 			.next(closeJobStep())
 			.build();
 	}
@@ -114,7 +113,7 @@ public class BulkExportJobConfig {
 	public Job groupBulkExportJob() {
 		return myJobBuilderFactory.get(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
 			.validator(groupBulkJobParameterValidator())
-			.validator(bulkJobParameterValidator())
+			.validator(bulkExportJobParameterValidator())
 			.start(createBulkExportEntityStep())
 			.next(groupPartitionStep())
 			.next(closeJobStep())
@@ -125,7 +124,7 @@ public class BulkExportJobConfig {
 	@Lazy
 	public Job patientBulkExportJob() {
 		return myJobBuilderFactory.get(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
-			.validator(bulkJobParameterValidator())
+			.validator(bulkExportJobParameterValidator())
 			.start(createBulkExportEntityStep())
 			.next(patientPartitionStep())
 			.next(closeJobStep())
@@ -150,8 +149,9 @@ public class BulkExportJobConfig {
 		return new CreateBulkExportEntityTasklet();
 	}
 
+
 	@Bean
-	public JobParametersValidator bulkJobParameterValidator() {
+	public JobParametersValidator bulkExportJobParameterValidator() {
 		return new BulkExportJobParameterValidator();
 	}
 
@@ -177,6 +177,7 @@ public class BulkExportJobConfig {
 			.listener(bulkExportGenerateResourceFilesStepListener())
 			.build();
 	}
+
 	@Bean
 	public Step patientBulkExportGenerateResourceFilesStep() {
 		return myStepBuilderFactory.get("patientBulkExportGenerateResourceFilesStep")
@@ -214,7 +215,7 @@ public class BulkExportJobConfig {
 	}
 
 	@Bean
-	public Step partitionStep() {
+	public Step bulkExportPartitionStep() {
 		return myStepBuilderFactory.get("partitionStep")
 			.partitioner("bulkExportGenerateResourceFilesStep", bulkExportResourceTypePartitioner())
 			.step(bulkExportGenerateResourceFilesStep())

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
 import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
 import ca.uhn.fhir.rest.api.Constants;
 import org.apache.commons.lang3.StringUtils;
-import org.slf4j.Logger;
 import org.springframework.batch.core.JobParameters;
 import org.springframework.batch.core.JobParametersInvalidException;
 import org.springframework.batch.core.JobParametersValidator;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParametersBuilder.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
+import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
 import ca.uhn.fhir.rest.api.Constants;
 import org.springframework.batch.core.JobParametersBuilder;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkItemReader.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -29,7 +29,6 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import org.slf4j.Logger;
 
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -43,7 +42,7 @@ public class BulkItemReader extends BaseBulkItemReader {
 	private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
 
 	@Override
-	Iterator<ResourcePersistentId> getResourcePidIterator() {
+	protected Iterator<ResourcePersistentId> getResourcePidIterator() {
 		ourLog.info("Bulk export assembling export of type {} for job {}", myResourceType, myJobUUID);
 		Set<ResourcePersistentId> myReadPids = new HashSet<>();
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
+import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
-import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
+import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
 import org.apache.commons.lang3.StringUtils;
@@ -87,7 +87,7 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
 		}
 	}
 
-	private void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
+	public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
 		theChunkContext
 			.getStepContext()
 			.getStepExecution()

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkExportJobParametersBuilder.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkItemReader.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@@ -36,7 +37,6 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.ReferenceOrListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
-import com.google.common.collect.Multimaps;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -81,7 +81,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	private MdmExpansionCacheSvc myMdmExpansionCacheSvc;
 
 	@Override
-	Iterator<ResourcePersistentId> getResourcePidIterator() {
+	protected Iterator<ResourcePersistentId> getResourcePidIterator() {
 		Set<ResourcePersistentId> myReadPids = new HashSet<>();
 
 		//Short circuit out if we detect we are attempting to extract patients
@@ -119,7 +119,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 		Set<Long> patientPidsToExport = new HashSet<>(pidsOrThrowException);
 
 		if (myMdmEnabled) {
-			IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+			SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
+			IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), srd);
 			Long pidOrNull = myIdHelperService.getPidOrNull(group);
 			List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
 			goldenPidSourcePidTuple.forEach(tuple -> {
@@ -179,13 +180,12 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	 * @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
 	 */
 	private List<String> getMembers() {
-		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+		SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
+		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
 		List<IPrimitiveType> evaluate = myContext.newFhirPath().evaluate(group, "member.entity.reference", IPrimitiveType.class);
 		return  evaluate.stream().map(IPrimitiveType::getValueAsString).collect(Collectors.toList());
 	}
 
-
-
 	/**
 	 * Given the local myGroupId, perform an expansion to retrieve all resource IDs of member patients.
 	 * if myMdmEnabled is set to true, we also reach out to the IMdmLinkDao to attempt to also expand it into matched
@@ -195,7 +195,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	 */
 	private Set<String> expandAllPatientPidsFromGroup() {
 		Set<String> expandedIds = new HashSet<>();
-		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+		SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
+		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
 		Long pidOrNull = myIdHelperService.getPidOrNull(group);
 
 		//Attempt to perform MDM Expansion of membership

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupIdPresentValidator.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -26,7 +26,7 @@ import org.springframework.batch.core.JobParametersInvalidException;
 import org.springframework.batch.core.JobParametersValidator;
 
 
-import static ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig.*;
+import static ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig.*;
 import static org.slf4j.LoggerFactory.getLogger;
 
 public class GroupIdPresentValidator implements JobParametersValidator {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/PatientBulkItemReader.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -61,7 +61,7 @@ public class PatientBulkItemReader extends BaseBulkItemReader implements ItemRea
 	}
 
 	@Override
-	Iterator<ResourcePersistentId> getResourcePidIterator() {
+	protected Iterator<ResourcePersistentId> getResourcePidIterator() {
 		if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
 			String errorMessage = "You attempted to start a Patient Bulk Export, but the system has `Index Missing Fields` disabled. It must be enabled for Patient Bulk Export";
 			ourLog.error(errorMessage);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceToFileWriter.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -25,8 +25,9 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.batch.log.Logs;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.util.BinaryUtil;
@@ -100,7 +101,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 		IBaseBinary binary = BinaryUtil.newBinary(myFhirContext);
 		binary.setContentType(Constants.CT_FHIR_NDJSON);
 		binary.setContent(myOutputStream.toByteArray());
-		DaoMethodOutcome outcome = myBinaryDao.create(binary);
+		DaoMethodOutcome outcome = myBinaryDao.create(binary, new SystemRequestDetails());
 		return outcome.getResource().getIdElement();
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.job;
+package ca.uhn.fhir.jpa.bulk.export.job;
 
 /*-
  * #%L
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import org.slf4j.Logger;
 import org.springframework.batch.core.partition.support.Partitioner;
 import org.springframework.batch.item.ExecutionContext;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/model/BulkExportJobStatusEnum.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.model;
+package ca.uhn.fhir.jpa.bulk.export.model;
 
 /*-
  * #%L
@@ -20,7 +20,14 @@ package ca.uhn.fhir.jpa.bulk.model;
  * #L%
  */
 
-public enum BulkJobStatusEnum {
+import com.fasterxml.jackson.annotation.JsonFormat;
+
+@JsonFormat(shape = JsonFormat.Shape.STRING)
+public enum BulkExportJobStatusEnum {
+
+	/**
+	 * Sorting OK!
+	 */
 
 	SUBMITTED,
 	BUILDING,

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.model;
+package ca.uhn.fhir.jpa.bulk.export.model;
 
 /*-
  * #%L

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.provider;
+package ca.uhn.fhir.jpa.bulk.export.provider;
 
 /*-
  * #%L
@@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.bulk.provider;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
+import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
-import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
+import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
-import ca.uhn.fhir.jpa.bulk.model.BulkExportResponseJson;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.svc;
+package ca.uhn.fhir.jpa.bulk.export.svc;
 
 /*-
  * #%L
@@ -23,16 +23,15 @@ package ca.uhn.fhir.jpa.bulk.svc;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
-import ca.uhn.fhir.fhirpath.IFhirPath;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
-import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
+import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
-import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
+import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
-import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@@ -43,16 +42,13 @@ import ca.uhn.fhir.jpa.model.sched.HapiJob;
 import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.UrlUtil;
-import com.google.common.collect.Sets;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hl7.fhir.instance.model.api.IBase;
 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.JobExecutionContext;
@@ -78,9 +74,9 @@ import java.util.Set;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
-import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.GROUP;
+import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.GROUP;
-import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.PATIENT;
+import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.PATIENT;
-import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.SYSTEM;
+import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.SYSTEM;
 import static ca.uhn.fhir.util.UrlUtil.escapeUrlParam;
 import static ca.uhn.fhir.util.UrlUtil.escapeUrlParams;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -136,7 +132,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 		Optional<BulkExportJobEntity> jobToProcessOpt = myTxTemplate.execute(t -> {
 			Pageable page = PageRequest.of(0, 1);
-			Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByStatus(page, BulkJobStatusEnum.SUBMITTED);
+			Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByStatus(page, BulkExportJobStatusEnum.SUBMITTED);
 			if (submittedJobs.isEmpty()) {
 				return Optional.empty();
 			}
@@ -158,7 +154,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 				Optional<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByJobId(jobUuid);
 				if (submittedJobs.isPresent()) {
 					BulkExportJobEntity jobEntity = submittedJobs.get();
-					jobEntity.setStatus(BulkJobStatusEnum.ERROR);
+					jobEntity.setStatus(BulkExportJobStatusEnum.ERROR);
 					jobEntity.setStatusMessage(e.getMessage());
 					myBulkExportJobDao.save(jobEntity);
 				}
@@ -208,8 +204,8 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 					for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
 
 						ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
-						getBinaryDao().delete(toId(nextFile.getResourceId()));
+						getBinaryDao().delete(toId(nextFile.getResourceId()), new SystemRequestDetails());
-						getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), null);
+						getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), new SystemRequestDetails());
 						myBulkExportCollectionFileDao.deleteByPid(nextFile.getId());
 
 					}
@@ -344,7 +340,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		if (useCache) {
 			Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis);
 			Pageable page = PageRequest.of(0, 10);
-			Slice<BulkExportJobEntity> existing = myBulkExportJobDao.findExistingJob(page, request, cutoff, BulkJobStatusEnum.ERROR);
+			Slice<BulkExportJobEntity> existing = myBulkExportJobDao.findExistingJob(page, request, cutoff, BulkExportJobStatusEnum.ERROR);
 			if (!existing.isEmpty()) {
 				return toSubmittedJobInfo(existing.iterator().next());
 			}
@@ -373,7 +369,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 		BulkExportJobEntity job = new BulkExportJobEntity();
 		job.setJobId(UUID.randomUUID().toString());
-		job.setStatus(BulkJobStatusEnum.SUBMITTED);
+		job.setStatus(BulkExportJobStatusEnum.SUBMITTED);
 		job.setSince(since);
 		job.setCreated(new Date());
 		job.setRequest(request);
@@ -445,7 +441,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		retVal.setStatusMessage(job.getStatusMessage());
 		retVal.setRequest(job.getRequest());
 
-		if (job.getStatus() == BulkJobStatusEnum.COMPLETE) {
+		if (job.getStatus() == BulkExportJobStatusEnum.COMPLETE) {
 			for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
 				for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
 					retVal.addFile()

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportCollectionFileDaoSvc.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.svc;
+package ca.uhn.fhir.jpa.bulk.export.svc;
 
 /*-
  * #%L

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportDaoSvc.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.bulk.svc;
+package ca.uhn.fhir.jpa.bulk.export.svc;
 
 /*-
  * #%L
@@ -20,9 +20,7 @@ package ca.uhn.fhir.jpa.bulk.svc;
  * #L%
  */
 
-import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
-import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@@ -84,12 +82,12 @@ public class BulkExportDaoSvc {
 	}
 
 	@Transactional
-	public void setJobToStatus(String theJobUUID, BulkJobStatusEnum theStatus) {
+	public void setJobToStatus(String theJobUUID, BulkExportJobStatusEnum theStatus) {
 		setJobToStatus(theJobUUID, theStatus, null);
 	}
 
 	@Transactional
-	public void setJobToStatus(String theJobUUID, BulkJobStatusEnum theStatus, String theStatusMessage) {
+	public void setJobToStatus(String theJobUUID, BulkExportJobStatusEnum theStatus, String theStatusMessage) {
 		Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(theJobUUID);
 		if (!oJob.isPresent()) {
 			ourLog.error("Job with UUID {} doesn't exist!", theJobUUID);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/api/IBulkDataImportSvc.java

@@ -0,0 +1,93 @@
+package ca.uhn.fhir.jpa.bulk.imprt.api;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.bulk.imprt.model.BulkImportJobFileJson;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
+
+import javax.annotation.Nonnull;
+import java.util.List;
+
+public interface IBulkDataImportSvc {
+
+	/**
+	 * Create a new job in {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING} state (meaning it won't yet be worked on and can be added to)
+	 */
+	String createNewJob(BulkImportJobJson theJobDescription, @Nonnull List<BulkImportJobFileJson> theInitialFiles);
+
+	/**
+	 * Add more files to a job in {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING} state
+	 *
+	 * @param theJobId The job ID
+	 * @param theFiles The files to add to the job
+	 */
+	void addFilesToJob(String theJobId, List<BulkImportJobFileJson> theFiles);
+
+	/**
+	 * Move a job from {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING}
+	 * state to {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#READY READY}
+	 * state, meaning that is is a candidate to be picked up for processing
+	 *
+	 * @param theJobId The job ID
+	 */
+	void markJobAsReadyForActivation(String theJobId);
+
+	/**
+	 * This method is intended to be called from the job scheduler, and will begin execution on
+	 * the next job in status {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#READY READY}
+	 *
+	 * @return Returns {@literal true} if a job was activated
+	 */
+	boolean activateNextReadyJob();
+
+	/**
+	 * Updates the job status for the given job
+	 */
+	void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus);
+
+	/**
+	 * Updates the job status for the given job
+	 */
+	void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage);
+
+	/**
+	 * Gets the number of files available for a given Job ID
+	 *
+	 * @param theJobId The job ID
+	 * @return The file count
+	 */
+	BulkImportJobJson fetchJob(String theJobId);
+
+	/**
+	 * Fetch a given file by job ID
+	 *
+	 * @param theJobId     The job ID
+	 * @param theFileIndex The index of the file within the job
+	 * @return The file
+	 */
+	BulkImportJobFileJson fetchFile(String theJobId, int theFileIndex);
+
+	/**
+	 * Delete all input files associated with a particular job
+	 */
+	void deleteJobFiles(String theJobId);
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.jpa.bulk.imprt.job;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.bulk.export.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
+import org.springframework.batch.core.ExitStatus;
+import org.springframework.batch.core.StepExecution;
+import org.springframework.batch.core.StepExecutionListener;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Will run before and after a job to set the status to whatever is appropriate.
+ */
+public class ActivateBulkImportEntityStepListener implements StepExecutionListener {
+
+	@Autowired
+	private IBulkDataImportSvc myBulkImportDaoSvc;
+
+	@Override
+	public void beforeStep(StepExecution theStepExecution) {
+		String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
+		if (jobUuid != null) {
+			myBulkImportDaoSvc.setJobToStatus(jobUuid, BulkImportJobStatusEnum.RUNNING);
+		}
+	}
+
+	@Override
+	public ExitStatus afterStep(StepExecution theStepExecution) {
+		return ExitStatus.EXECUTING;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java

@@ -0,0 +1,76 @@
+package ca.uhn.fhir.jpa.bulk.imprt.job;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.batch.log.Logs;
+import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
+import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
+import ca.uhn.fhir.util.IoUtil;
+import com.google.common.io.LineReader;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.batch.item.ItemReader;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+
+import java.io.StringReader;
+
+@SuppressWarnings("UnstableApiUsage")
+public class BulkImportFileReader implements ItemReader<ParsedBulkImportRecord> {
+
+	@Autowired
+	private IBulkDataImportSvc myBulkDataImportSvc;
+	@Autowired
+	private FhirContext myFhirContext;
+	@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+	private String myJobUuid;
+	@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
+	private int myFileIndex;
+
+	private StringReader myReader;
+	private LineReader myLineReader;
+	private int myLineIndex;
+	private String myTenantName;
+
+	@Override
+	public ParsedBulkImportRecord read() throws Exception {
+
+		if (myReader == null) {
+			BulkImportJobFileJson file = myBulkDataImportSvc.fetchFile(myJobUuid, myFileIndex);
+			myTenantName = file.getTenantName();
+			myReader = new StringReader(file.getContents());
+			myLineReader = new LineReader(myReader);
+		}
+
+		String nextLine = myLineReader.readLine();
+		if (nextLine == null) {
+			IoUtil.closeQuietly(myReader);
+			return null;
+		}
+
+		Logs.getBatchTroubleshootingLog().debug("Reading line {} file index {} for job: {}", myLineIndex++, myFileIndex, myJobUuid);
+
+		IBaseResource parsed = myFhirContext.newJsonParser().parseResource(nextLine);
+		return new ParsedBulkImportRecord(myTenantName, parsed);
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java

@@ -0,0 +1,74 @@
+package ca.uhn.fhir.jpa.bulk.imprt.job;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
+import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.batch.item.ItemWriter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+
+import java.util.List;
+
+public class BulkImportFileWriter implements ItemWriter<ParsedBulkImportRecord> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileWriter.class);
+	@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+	private String myJobUuid;
+	@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
+	private int myFileIndex;
+	@Value("#{stepExecutionContext['" + BulkImportPartitioner.ROW_PROCESSING_MODE + "']}")
+	private JobFileRowProcessingModeEnum myRowProcessingMode;
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	@SuppressWarnings({"SwitchStatementWithTooFewBranches", "rawtypes", "unchecked"})
+	@Override
+	public void write(List<? extends ParsedBulkImportRecord> theItemLists) throws Exception {
+		ourLog.info("Beginning bulk import write {} chunks Job[{}] FileIndex[{}]", theItemLists.size(), myJobUuid, myFileIndex);
+
+		for (ParsedBulkImportRecord nextItem : theItemLists) {
+
+			SystemRequestDetails requestDetails = new SystemRequestDetails();
+			requestDetails.setTenantId(nextItem.getTenantName());
+
+			// Yeah this is a lame switch - We'll add more later I swear
+			switch (myRowProcessingMode) {
+				default:
+				case FHIR_TRANSACTION:
+					IFhirSystemDao systemDao = myDaoRegistry.getSystemDao();
+					IBaseResource inputBundle = nextItem.getRowContent();
+					systemDao.transactionNested(requestDetails, inputBundle);
+					break;
+			}
+
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java

@@ -0,0 +1,57 @@
+package ca.uhn.fhir.jpa.bulk.imprt.job;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.bulk.export.job.BulkExportJobConfig;
+import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
+import org.springframework.batch.core.BatchStatus;
+import org.springframework.batch.core.StepContribution;
+import org.springframework.batch.core.scope.context.ChunkContext;
+import org.springframework.batch.core.step.tasklet.Tasklet;
+import org.springframework.batch.repeat.RepeatStatus;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+
+/**
+ * Will run before and after a job to set the status to whatever is appropriate.
+ */
+public class BulkImportJobCloser implements Tasklet {
+
+	@Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+	private String myJobUUID;
+
+	@Autowired
+	private IBulkDataImportSvc myBulkDataImportSvc;
+
+	@Override
+	public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) {
+		BatchStatus executionStatus = theChunkContext.getStepContext().getStepExecution().getJobExecution().getStatus();
+		if (executionStatus == BatchStatus.STARTED) {
+			myBulkDataImportSvc.setJobToStatus(myJobUUID, BulkImportJobStatusEnum.COMPLETE);
+			myBulkDataImportSvc.deleteJobFiles(myJobUUID);
+		} else {
+			myBulkDataImportSvc.setJobToStatus(myJobUUID, BulkImportJobStatusEnum.ERROR, "Found job in status: " + executionStatus);
+			myBulkDataImportSvc.deleteJobFiles(myJobUUID);
+		}
+		return RepeatStatus.FINISHED;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java

@@ -0,0 +1,169 @@
+package ca.uhn.fhir.jpa.bulk.imprt.job;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.batch.BatchConstants;
+import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.JobParametersValidator;
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
+import org.springframework.batch.core.configuration.annotation.JobScope;
+import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
+import org.springframework.batch.core.configuration.annotation.StepScope;
+import org.springframework.batch.core.partition.PartitionHandler;
+import org.springframework.batch.core.partition.support.TaskExecutorPartitionHandler;
+import org.springframework.batch.item.ItemWriter;
+import org.springframework.batch.repeat.CompletionPolicy;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.core.task.TaskExecutor;
+
+import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.BULK_IMPORT_JOB_NAME;
+
+/**
+ * Spring batch Job configuration file. Contains all necessary plumbing to run a
+ * Bulk Export job.
+ */
+@Configuration
+public class BulkImportJobConfig {
+
+	public static final String JOB_PARAM_COMMIT_INTERVAL = "commitInterval";
+
+	@Autowired
+	private StepBuilderFactory myStepBuilderFactory;
+
+	@Autowired
+	private JobBuilderFactory myJobBuilderFactory;
+
+	@Autowired
+	@Qualifier(BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
+	private TaskExecutor myTaskExecutor;
+
+	@Bean(name = BULK_IMPORT_JOB_NAME)
+	@Lazy
+	public Job bulkImportJob() throws Exception {
+		return myJobBuilderFactory.get(BULK_IMPORT_JOB_NAME)
+			.validator(bulkImportJobParameterValidator())
+			.start(bulkImportPartitionStep())
+			.next(bulkImportCloseJobStep())
+			.build();
+	}
+
+	@Bean
+	public JobParametersValidator bulkImportJobParameterValidator() {
+		return new BulkImportJobParameterValidator();
+	}
+
+	@Bean
+	public CreateBulkImportEntityTasklet createBulkImportEntityTasklet() {
+		return new CreateBulkImportEntityTasklet();
+	}
+
+	@Bean
+	@JobScope
+	public ActivateBulkImportEntityStepListener activateBulkImportEntityStepListener() {
+		return new ActivateBulkImportEntityStepListener();
+	}
+
+	@Bean
+	public Step bulkImportPartitionStep() throws Exception {
+		return myStepBuilderFactory.get("bulkImportPartitionStep")
+			.partitioner("bulkImportPartitionStep", bulkImportPartitioner())
+			.partitionHandler(partitionHandler())
+			.listener(activateBulkImportEntityStepListener())
+			.gridSize(10)
+			.build();
+	}
+
+	private PartitionHandler partitionHandler() throws Exception {
+		assert myTaskExecutor != null;
+
+		TaskExecutorPartitionHandler retVal = new TaskExecutorPartitionHandler();
+		retVal.setStep(bulkImportProcessFilesStep());
+		retVal.setTaskExecutor(myTaskExecutor);
+		retVal.afterPropertiesSet();
+		return retVal;
+	}
+
+	@Bean
+	public Step bulkImportCloseJobStep() {
+		return myStepBuilderFactory.get("bulkImportCloseJobStep")
+			.tasklet(bulkImportJobCloser())
+			.build();
+	}
+
+	@Bean
+	@JobScope
+	public BulkImportJobCloser bulkImportJobCloser() {
+		return new BulkImportJobCloser();
+	}
+
+	@Bean
+	@JobScope
+	public BulkImportPartitioner bulkImportPartitioner() {
+		return new BulkImportPartitioner();
+	}
+
+
+	@Bean
+	public Step bulkImportProcessFilesStep() {
+		CompletionPolicy completionPolicy = completionPolicy();
+
+		return myStepBuilderFactory.get("bulkImportProcessFilesStep")
+			.<ParsedBulkImportRecord, ParsedBulkImportRecord>chunk(completionPolicy)
+			.reader(bulkImportFileReader())
+			.writer(bulkImportFileWriter())
+			.listener(bulkImportStepListener())
+			.listener(completionPolicy)
+			.build();
+	}
+
+	@Bean
+	@StepScope
+	public CompletionPolicy completionPolicy() {
+		return new BulkImportProcessStepCompletionPolicy();
+	}
+
+	@Bean
+	@StepScope
+	public ItemWriter<ParsedBulkImportRecord> bulkImportFileWriter() {
+		return new BulkImportFileWriter();
+	}
+
+
+	@Bean
+	@StepScope
+	public BulkImportFileReader bulkImportFileReader() {
+		return new BulkImportFileReader();
+	}
+
+	@Bean
+	@StepScope
+	public BulkImportStepListener bulkImportStepListener() {
+		return new BulkImportStepListener();
+	}
+
+
+}