Merge branch 'master' into ja_20190928_rationalize_search_param_extractor

azure-pipelines.yml

@@ -28,7 +28,12 @@ jobs:
           mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
       - script: bash <(curl https://codecov.io/bash) -t $(CODECOV_TOKEN)
         displayName: 'codecov'
-
+      - task: PublishCodeCoverageResults@1
+        inputs:
+          codeCoverageTool: 'JaCoCo'
+          summaryFileLocation: $(System.DefaultWorkingDirectory)/hapi-fhir-jacoco/target/site/jacoco-report/jacoco.xml
+          reportDirectory: $(System.DefaultWorkingDirectory)/hapi-fhir-jacoco/target/site/jacoco-report/
+          failIfCoverageEmpty: false
 
 # Potential Additional Maven3 Options:
 #publishJUnitResults: true
@@ -53,3 +58,5 @@ jobs:
 #checkStyleRunAnalysis: false # Optional
 #pmdRunAnalysis: false # Optional
 #findBugsRunAnalysis: false # Optional
+
+

examples/src/main/java/example/ConverterExamples.java

@@ -1,5 +1,6 @@
 package example;
 
+import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
 import org.hl7.fhir.convertors.*;
 import org.hl7.fhir.exceptions.FHIRException;
 

examples/src/main/java/example/ServerMetadataExamples.java

@@ -1,15 +1,13 @@
 package example;
 
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.rest.annotation.Search;
+import org.hl7.fhir.r4.model.InstantType;
+import org.hl7.fhir.r4.model.Patient;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.Tag;
-import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.rest.annotation.Search;
-
 public class ServerMetadataExamples {
 
    // START SNIPPET: serverMethod
@@ -21,33 +19,20 @@ public class ServerMetadataExamples {
       Patient patient = new Patient();
       retVal.add(patient);
       patient.setId("Patient/123");
-      patient.addName().addFamily("Smith").addGiven("John");
+      patient.addName().setFamily("Smith").addGiven("John");
       
-      // Create a tag list and add it to the resource
-      TagList tags = new TagList();
-      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag1.html", "Some tag");
-      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag2.html", "Another tag");
-      ResourceMetadataKeyEnum.TAG_LIST.put(patient, tags);
+      // Add tags
+		patient.getMeta().addTag()
+			.setSystem(Tag.HL7_ORG_FHIR_TAG)
+			.setCode("some_tag")
+			.setDisplay("Some tag");
+		patient.getMeta().addTag()
+			.setSystem(Tag.HL7_ORG_FHIR_TAG)
+			.setCode("another_tag")
+			.setDisplay("Another tag");
 
-      // Set some links (these can be provided as relative links or absolute)
-      // and the server will convert to absolute as appropriate
-      String linkAlternate = "Patient/7736";
-      ResourceMetadataKeyEnum.LINK_ALTERNATE.put(patient, linkAlternate);
-      String linkSearch = "Patient?name=smith&name=john";
-      ResourceMetadataKeyEnum.LINK_SEARCH.put(patient, linkSearch);
-      
-      // Set the published and updated dates
-      InstantDt pubDate = new InstantDt("2011-02-22");
-      ResourceMetadataKeyEnum.PUBLISHED.put(patient, pubDate);
-      InstantDt updatedDate = new InstantDt("2014-07-12T11:22:27Z");
-      ResourceMetadataKeyEnum.UPDATED.put(patient, updatedDate);
-      
-      // Set the resource title (note that if you are using HAPI's narrative
-      // generation capability, the narrative generator will often create
-      // useful titles automatically, and the server will create a default
-      // title if none is provided)
-      String title = "Patient John SMITH";
-      ResourceMetadataKeyEnum.TITLE.put(patient, title);
+      // Set the last updated date
+		patient.getMeta().setLastUpdatedElement(new InstantType("2011-02-22T11:22:00.0122Z"));
 
       return retVal;
    }

examples/src/main/java/example/ServerOperations.java

@@ -36,9 +36,12 @@ public class ServerOperations {
 	public void manualInputAndOutput(HttpServletRequest theServletRequest, HttpServletResponse theServletResponse) throws IOException {
 		String contentType = theServletRequest.getContentType();
 		byte[] bytes = IOUtils.toByteArray(theServletRequest.getInputStream());
-
 		ourLog.info("Received call with content type {} and {} bytes", contentType, bytes.length);
 
+		// In a real example we might do something more interesting with the received bytes,
+		// here we'll just replace them with hardcoded ones
+		bytes = new byte[] { 0, 1, 2, 3 };
+
 		theServletResponse.setContentType(contentType);
 		theServletResponse.getOutputStream().write(bytes);
 		theServletResponse.getOutputStream().close();

examples/src/main/java/example/ValidatorExamples.java

@@ -265,7 +265,7 @@ public class ValidatorExamples {
 			}
 
 			@Override
-			public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+			public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSet) {
 				// TODO: implement
 				return null;
 			}

hapi-fhir-base/pom.xml

@@ -100,10 +100,6 @@
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
 		</dependency>
-        <dependency>
-			<groupId>org.eclipse.jetty</groupId>
-			<artifactId>jetty-server</artifactId>
-		</dependency>
 
 		<!-- Logging -->
 		<dependency>
@@ -120,6 +116,11 @@
 			<optional>true</optional>
 		</dependency>
 
+		<dependency>
+			<groupId>org.awaitility</groupId>
+			<artifactId>awaitility</artifactId>
+			<scope>test</scope>
+		</dependency>
 
 	</dependencies>
 

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

@@ -20,25 +20,25 @@ package ca.uhn.fhir.context;
  * #L%
  */
 
-import java.lang.reflect.Constructor;
-import java.util.*;
 import ca.uhn.fhir.util.UrlUtil;
-
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBase;
 
+import java.lang.reflect.Constructor;
+import java.util.*;
+
 public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 
 	private static final Class<Void> VOID_CLASS = Void.class;
-	
+	private final Class<? extends T> myImplementingClass;
+	private final String myName;
+	private final boolean myStandardType;
 	private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<Class<?>, Constructor<T>>());
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
-	private final Class<? extends T> myImplementingClass;
-	private final String myName;
-	private final boolean myStandardType;
 	private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToExtension = new HashMap<String, RuntimeChildDeclaredExtensionDefinition>();
+	private BaseRuntimeElementDefinition<?> myRootParentDefinition;
 
 	public BaseRuntimeElementDefinition(String theName, Class<? extends T> theImplementingClass, boolean theStandardType) {
 		assert StringUtils.isNotBlank(theName);
@@ -168,9 +168,14 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 		}
 	}
 
+	public BaseRuntimeElementDefinition<?> getRootParentDefinition() {
+		return myRootParentDefinition;
+	}
+
 	/**
 	 * Invoked prior to use to perform any initialization and make object
 	 * mutable.
+	 *
 	 * @param theContext TODO
 	 */
 	void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
@@ -193,6 +198,16 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 		}
 
 		myExtensions = Collections.unmodifiableList(myExtensions);
+
+		Class parent = myImplementingClass;
+		do {
+			BaseRuntimeElementDefinition<?> parentDefinition = theClassToElementDefinitions.get(parent);
+			if (parentDefinition != null) {
+				myRootParentDefinition = parentDefinition;
+			}
+			parent = parent.getSuperclass();
+		} while (!parent.equals(Object.class));
+
 	}
 
 	@Override
@@ -210,15 +225,18 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 	}
 
 	public enum ChildTypeEnum {
-		COMPOSITE_DATATYPE, /**
+		COMPOSITE_DATATYPE,
+		/**
 		 * HL7.org structure style.
 		 */
-		CONTAINED_RESOURCE_LIST, /**
+		CONTAINED_RESOURCE_LIST,
+		/**
 		 * HAPI structure style.
 		 */
 		CONTAINED_RESOURCES, EXTENSION_DECLARED,
 		ID_DATATYPE,
-		PRIMITIVE_DATATYPE, /**
+		PRIMITIVE_DATATYPE,
+		/**
 		 * HAPI style.
 		 */
 		PRIMITIVE_XHTML,

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

@@ -20,6 +20,7 @@ import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.VersionUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.jena.riot.Lang;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
@@ -898,6 +899,11 @@ public class FhirContext {
 		}
 	}
 
+	@Override
+	public String toString() {
+		return "FhirContext[" + myVersion.getVersion().name() + "]";
+	}
+
 	/**
 	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2}
 	 */

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

@@ -29,6 +29,7 @@ import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.util.ReflectionUtil;
 import org.hl7.fhir.instance.model.api.*;
 
+import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.annotation.Annotation;
@@ -44,56 +45,47 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 class ModelScanner {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ModelScanner.class);
 
-	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinitions = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
+	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinitions = new HashMap<>();
 	private FhirContext myContext;
-	private Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = new HashMap<String, RuntimeResourceDefinition>();
-	private Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinitions = new HashMap<String, BaseRuntimeElementDefinition<?>>();
-	private Map<String, RuntimeResourceDefinition> myNameToResourceDefinitions = new HashMap<String, RuntimeResourceDefinition>();
-	private Map<String, Class<? extends IBaseResource>> myNameToResourceType = new HashMap<String, Class<? extends IBaseResource>>();
+	private Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = new HashMap<>();
+	private Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinitions = new HashMap<>();
+	private Map<String, RuntimeResourceDefinition> myNameToResourceDefinitions = new HashMap<>();
+	private Map<String, Class<? extends IBaseResource>> myNameToResourceType = new HashMap<>();
 	private RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
-	private Set<Class<? extends IBase>> myScanAlso = new HashSet<Class<? extends IBase>>();
+	private Set<Class<? extends IBase>> myScanAlso = new HashSet<>();
 	private FhirVersionEnum myVersion;
 
 	private Set<Class<? extends IBase>> myVersionTypes;
 
 	ModelScanner(FhirContext theContext, FhirVersionEnum theVersion, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theExistingDefinitions,
-					 Collection<Class<? extends IBase>> theResourceTypes) throws ConfigurationException {
+					 @Nonnull Collection<Class<? extends IBase>> theResourceTypes) throws ConfigurationException {
 		myContext = theContext;
 		myVersion = theVersion;
-		Set<Class<? extends IBase>> toScan;
-		if (theResourceTypes != null) {
-			toScan = new HashSet<Class<? extends IBase>>(theResourceTypes);
-		} else {
-			toScan = new HashSet<Class<? extends IBase>>();
-		}
+		Set<Class<? extends IBase>> toScan = new HashSet<>(theResourceTypes);
 		init(theExistingDefinitions, toScan);
 	}
 
-	public Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> getClassToElementDefinitions() {
+	Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> getClassToElementDefinitions() {
 		return myClassToElementDefinitions;
 	}
 
-	public Map<String, RuntimeResourceDefinition> getIdToResourceDefinition() {
+	Map<String, RuntimeResourceDefinition> getIdToResourceDefinition() {
 		return myIdToResourceDefinition;
 	}
 
-	public Map<String, BaseRuntimeElementDefinition<?>> getNameToElementDefinitions() {
+	Map<String, BaseRuntimeElementDefinition<?>> getNameToElementDefinitions() {
 		return myNameToElementDefinitions;
 	}
 
-	public Map<String, RuntimeResourceDefinition> getNameToResourceDefinition() {
+	Map<String, RuntimeResourceDefinition> getNameToResourceDefinition() {
 		return myNameToResourceDefinitions;
 	}
 
-	public Map<String, RuntimeResourceDefinition> getNameToResourceDefinitions() {
-		return (myNameToResourceDefinitions);
-	}
-
-	public Map<String, Class<? extends IBaseResource>> getNameToResourceType() {
+	Map<String, Class<? extends IBaseResource>> getNameToResourceType() {
 		return myNameToResourceType;
 	}
 
-	public RuntimeChildUndeclaredExtensionDefinition getRuntimeChildUndeclaredExtensionDefinition() {
+	RuntimeChildUndeclaredExtensionDefinition getRuntimeChildUndeclaredExtensionDefinition() {
 		return myRuntimeChildUndeclaredExtensionDefinition;
 	}
 
@@ -145,11 +137,10 @@ class ModelScanner {
 	}
 
 	private boolean isStandardType(Class<? extends IBase> theClass) {
-		boolean retVal = myVersionTypes.contains(theClass);
-		return retVal;
+		return myVersionTypes.contains(theClass);
 	}
 
-	private void scan(Class<? extends IBase> theClass) throws ConfigurationException {
+	void scan(Class<? extends IBase> theClass) throws ConfigurationException {
 		BaseRuntimeElementDefinition<?> existingDef = myClassToElementDefinitions.get(theClass);
 		if (existingDef != null) {
 			return;
@@ -204,9 +195,6 @@ class ModelScanner {
 		ourLog.debug("Scanning resource block class: {}", theClass.getName());
 
 		String resourceName = theClass.getCanonicalName();
-		if (isBlank(resourceName)) {
-			throw new ConfigurationException("Block type @" + Block.class.getSimpleName() + " annotation contains no name: " + theClass.getCanonicalName());
-		}
 
 		// Just in case someone messes up when upgrading from DSTU2
 		if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
@@ -341,14 +329,14 @@ class ModelScanner {
 
 	private void scanResourceForSearchParams(Class<? extends IBaseResource> theClass, RuntimeResourceDefinition theResourceDef) {
 
-		Map<String, RuntimeSearchParam> nameToParam = new HashMap<String, RuntimeSearchParam>();
-		Map<Field, SearchParamDefinition> compositeFields = new LinkedHashMap<Field, SearchParamDefinition>();
+		Map<String, RuntimeSearchParam> nameToParam = new HashMap<>();
+		Map<Field, SearchParamDefinition> compositeFields = new LinkedHashMap<>();
 
 		/*
 		 * Make sure we pick up fields in interfaces too.. This ensures that we
 		 * grab the _id field which generally gets picked up via interface
 		 */
-		Set<Field> fields = new HashSet<Field>(Arrays.asList(theClass.getFields()));
+		Set<Field> fields = new HashSet<>(Arrays.asList(theClass.getFields()));
 		Class<?> nextClass = theClass;
 		do {
 			for (Class<?> nextInterface : nextClass.getInterfaces()) {
@@ -400,12 +388,12 @@ class ModelScanner {
 		for (Entry<Field, SearchParamDefinition> nextEntry : compositeFields.entrySet()) {
 			SearchParamDefinition searchParam = nextEntry.getValue();
 
-			List<RuntimeSearchParam> compositeOf = new ArrayList<RuntimeSearchParam>();
+			List<RuntimeSearchParam> compositeOf = new ArrayList<>();
 			for (String nextName : searchParam.compositeOf()) {
 				RuntimeSearchParam param = nameToParam.get(nextName);
 				if (param == null) {
 					ourLog.warn("Search parameter {}.{} declares that it is a composite with compositeOf value '{}' but that is not a valid parametr name itself. Valid values are: {}",
-						new Object[]{theResourceDef.getName(), searchParam.name(), nextName, nameToParam.keySet()});
+						theResourceDef.getName(), searchParam.name(), nextName, nameToParam.keySet());
 					continue;
 				}
 				compositeOf.add(param);
@@ -417,7 +405,7 @@ class ModelScanner {
 	}
 
 	private Set<String> toTargetList(Class<? extends IBaseResource>[] theTarget) {
-		HashSet<String> retVal = new HashSet<String>();
+		HashSet<String> retVal = new HashSet<>();
 
 		for (Class<? extends IBaseResource> nextType : theTarget) {
 			ResourceDef resourceDef = nextType.getAnnotation(ResourceDef.class);
@@ -486,7 +474,7 @@ class ModelScanner {
 	}
 
 	static Set<Class<? extends IBase>> scanVersionPropertyFile(Set<Class<? extends IBase>> theDatatypes, Map<String, Class<? extends IBaseResource>> theResourceTypes, FhirVersionEnum theVersion, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theExistingElementDefinitions) {
-		Set<Class<? extends IBase>> retVal = new HashSet<Class<? extends IBase>>();
+		Set<Class<? extends IBase>> retVal = new HashSet<>();
 
 		try (InputStream str = theVersion.getVersionImplementation().getFhirVersionPropertiesFile()) {
 			Properties prop = new Properties();

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

@@ -1,100 +0,0 @@
-package ca.uhn.fhir.context;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
-import ca.uhn.fhir.model.api.annotation.ProvidesResources;
-
-/**
- * Scans a class tagged with {@code ProvidesResources} and adds any resources listed to its FhirContext's resource
- * definition list. This makes the profile generator find the classes.
- *
- * @see ca.uhn.fhir.model.api.annotation.ProvidesResources
- */
-public class ProvidedResourceScanner {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ProvidedResourceScanner.class);
-	private FhirContext myContext;
-
-	/**
-	 * Constructor
-	 * 
-	 * @param theContext
-	 *           - context whose resource definition list is to be updated by the scanner
-	 */
-	public ProvidedResourceScanner(FhirContext theContext) {
-		myContext = theContext;
-	}
-
-	/**
-	 * If {@code theProvider} is tagged with the {@code ProvidesResources} annotation, this method will add every
-	 * resource listed by the {@code resources} method.
-	 * <p>
-	 * Notes:
-	 * </p>
-	 * <ul>
-	 * <li>if {@code theProvider} isn't annotated with {@code resources} nothing is done; it's expected that most
-	 * RestfulServers and ResourceProviders won't be annotated.</li>
-	 * <li>any object listed in {@code resources} that doesn't implement {@code IResource} will generate a warning in the
-	 * log.</li>
-	 * </ul>
-	 *
-	 * @param theProvider
-	 *           - Normally, either a {@link ca.uhn.fhir.rest.server.RestfulServer} or a
-	 *           {@link ca.uhn.fhir.rest.server.IResourceProvider} that might be annotated with
-	 *           {@link ca.uhn.fhir.model.api.annotation.ProvidesResources}
-	 */
-	@SuppressWarnings("unchecked")
-	public void scanForProvidedResources(Object theProvider) {
-		ProvidesResources annotation = theProvider.getClass().getAnnotation(ProvidesResources.class);
-		if (annotation == null)
-			return;
-		for (Class<?> clazz : annotation.resources()) {
-			if (IBaseResource.class.isAssignableFrom(clazz)) {
-				myContext.getResourceDefinition((Class<? extends IBaseResource>) clazz);
-			} else {
-				ourLog.warn(clazz.getSimpleName() + "is not assignable from IResource");
-			}
-		}
-	}
-
-	/**
-	 * Remove any metadata that was added by any {@code ProvidesResources} annotation
-	 * present in {@code theProvider}. This method is callled from {@code RestfulService}
-	 * when it is unregistering a Resource Provider.
-	 *  
-	 * @param theProvider
-	 *           - Normally a {@link ca.uhn.fhir.rest.server.IResourceProvider} that might 
-	 *           be annotated with {@link ca.uhn.fhir.model.api.annotation.ProvidesResources}
-	 */
-	public void removeProvidedResources(Object theProvider) {
-		ProvidesResources annotation = theProvider.getClass().getAnnotation(ProvidesResources.class);
-		if (annotation == null)
-			return;
-		for (Class<?> clazz : annotation.resources()) {
-			if (IBaseResource.class.isAssignableFrom(clazz)) {
-				// TODO -- not currently used but should be finished for completeness
-			} else {
-				ourLog.warn(clazz.getSimpleName() + "is not assignable from IResource");
-			}
-		}
-	}
-}

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

@@ -102,6 +102,11 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
 	 */
 	boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
 
+	/**
+	 * Fetch the given ValueSet by URL
+	 */
+	IBaseResource fetchValueSet(FhirContext theContext, String theValueSetUrl);
+
 	/**
 	 * Validates that the given code exists and if possible returns a display
 	 * name. This method is called to check codes which are found in "example"
@@ -112,7 +117,7 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
 	 * @param theDisplay    The display name, if it should also be validated
 	 * @return Returns a validation result object
 	 */
-	CodeValidationResult<CDCT, IST> validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
+	CodeValidationResult<CDCT, IST> validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl);
 
 	/**
 	 * Look up a code using the system and code value

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

@@ -1,64 +0,0 @@
-package ca.uhn.fhir.model.api;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.util.ElementUtil;
-
-public class BaseBundle extends BaseElement /*implements IElement*/ {
-
-	private static final long serialVersionUID = 3349586533271409727L;
-	private StringDt myAuthorName;
-	private StringDt myAuthorUri;
-	private IdDt myId;
-
-	public StringDt getAuthorName() {
-		if (myAuthorName == null) {
-			myAuthorName = new StringDt();
-		}
-		return myAuthorName;
-	}
-
-	public StringDt getAuthorUri() {
-		if (myAuthorUri == null) {
-			myAuthorUri = new StringDt();
-		}
-		return myAuthorUri;
-	}
-
-	public IdDt getId() {
-		if (myId==null) {
-			myId=new IdDt();
-		}
-		return myId;
-	}
-
-	@Override
-	public boolean isEmpty() {
-		return ElementUtil.isEmpty(myAuthorName, myAuthorUri);
-	}
-
-	public void setId(IdDt theId) {
-		myId = theId;
-	}
-
-}

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

@@ -40,7 +40,7 @@ public interface IQueryParameterAnd<T extends IQueryParameterOr<?>> extends Seri
 	 * @param theContext TODO
 	 * @param theParamName TODO
 	 */
-	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, List<QualifiedParamList> theParameters) throws InvalidRequestException;
+	void setValuesAsQueryTokens(FhirContext theContext, String theParamName, List<QualifiedParamList> theParameters) throws InvalidRequestException;
 
 	/**
 	 * 
@@ -50,7 +50,7 @@ public interface IQueryParameterAnd<T extends IQueryParameterOr<?>> extends Seri
 	 *    for information on the <b>token</b> format
 	 * </p>
 	 */
-	public List<T> getValuesAsQueryTokens();
+	List<T> getValuesAsQueryTokens();
 
 	
 }

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

@@ -21,7 +21,6 @@ package ca.uhn.fhir.model.api;
  */
 
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@@ -29,7 +28,6 @@ import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.io.Serializable;
@@ -92,29 +90,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.setUserData(DELETED_AT.name(), theObject);
 		}
 	};
-	/**
-	 * Denotes the search score which a given resource should match in a transaction. See the FHIR transaction definition for information about this. Corresponds to the value in
-	 * <code>Bundle.entry.score</code> in a Bundle resource.
-	 * <p>
-	 * Note that search URL is only used in FHIR DSTU2 and later.
-	 * </p>
-	 * <p>
-	 * Values for this key are of type <b>{@link DecimalDt}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<DecimalDt> ENTRY_SCORE = new ResourceMetadataKeyEnum<DecimalDt>("ENTRY_SCORE") {
-		private static final long serialVersionUID = 1L;
 
-		@Override
-		public DecimalDt get(IResource theResource) {
-			return getDecimalFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_SCORE);
-		}
-
-		@Override
-		public void put(IResource theResource, DecimalDt theObject) {
-			theResource.getResourceMetadata().put(ENTRY_SCORE, theObject);
-		}
-	};
 	/**
 	 * If present and populated with a {@link BundleEntrySearchModeEnum}, contains the "bundle entry search mode", which is the value of the status field in the Bundle entry containing this resource.
 	 * The value for this key corresponds to field <code>Bundle.entry.search.mode</code>. This value can be set to provide a status value of "include" for included resources being returned by a
@@ -187,67 +163,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 		}
 
 	};
-	/**
-	 * If present and populated with a string, provides the "alternate link" (the link element in the bundle entry with <code>rel="alternate"</code>). Server implementations may populate this with a
-	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient/1243") in which case the server will convert this to
-	 * an absolute URL at runtime.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> LINK_ALTERNATE = new ResourceMetadataKeyEnum<String>("LINK_ALTERNATE") {
-		private static final long serialVersionUID = 1L;
 
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_ALTERNATE);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(LINK_ALTERNATE, theObject);
-		}
-	};
-	/**
-	 * If present and populated with a string, provides the "search link" (the link element in the bundle entry with <code>rel="search"</code>). Server implementations may populate this with a
-	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient?name=tester") in which case the server will convert
-	 * this to an absolute URL at runtime.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> LINK_SEARCH = new ResourceMetadataKeyEnum<String>("LINK_SEARCH") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_SEARCH);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(LINK_SEARCH, theObject);
-		}
-	};
-	/**
-	 * The value for this key represents a previous ID used to identify this resource. This key is currently only used internally during transaction method processing.
-	 * <p>
-	 * Values for this key are of type <b>{@link IdDt}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<IdDt> PREVIOUS_ID = new ResourceMetadataKeyEnum<IdDt>("PREVIOUS_ID") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public IdDt get(IResource theResource) {
-			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PREVIOUS_ID);
-		}
-
-		@Override
-		public void put(IResource theResource, IdDt theObject) {
-			theResource.getResourceMetadata().put(PREVIOUS_ID, theObject);
-		}
-	};
 	/**
 	 * The value for this key represents a {@link List} of profile IDs that this resource claims to conform to.
 	 * <p>
@@ -301,18 +217,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			if (obj == null) {
 				return null;
 			}
-			try {
-				@SuppressWarnings("unchecked")
-				List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) obj;
-				if (securityLabels.isEmpty()) {
-					return null;
-				}
-				return securityLabels;
-			} catch (ClassCastException e) {
-				throw new InternalErrorException("Found an object of type '" + obj.getClass().getCanonicalName() + "' in resource metadata for key SECURITY_LABELS - Expected "
-					+ BaseCodingDt.class.getCanonicalName());
-			}
-
+			//noinspection unchecked
+			return (List<BaseCodingDt>) obj;
 		}
 
 		@Override
@@ -337,14 +243,9 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			Object retValObj = theResource.getResourceMetadata().get(TAG_LIST);
 			if (retValObj == null) {
 				return null;
-			} else if (retValObj instanceof TagList) {
-				if (((TagList) retValObj).isEmpty()) {
-					return null;
-				}
+			} else {
 				return (TagList) retValObj;
 			}
-			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + TAG_LIST.name() + " - Expected "
-				+ TagList.class.getCanonicalName());
 		}
 
 		@Override
@@ -352,25 +253,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(TAG_LIST, theObject);
 		}
 	};
-	/**
-	 * If present and populated with a string (as an instance of {@link String}), this value contains the title for this resource, as supplied in any bundles containing the resource.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> TITLE = new ResourceMetadataKeyEnum<String>("TITLE") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), TITLE);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(TITLE, theObject);
-		}
-	};
 	/**
 	 * The value for this key is the bundle entry <b>Updated</b> time. This is defined by FHIR as "Last Updated for resource". This value is also used for populating the "Last-Modified" header in the
 	 * case of methods that return a single resource (read, vread, etc.)
@@ -398,7 +280,10 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 * <p>
 	 * Values for this key are of type <b>{@link String}</b>
 	 * </p>
+	 *
+	 * @deprecated The {@link IResource#getId()} resource ID will now be populated with the version ID via the {@link IdDt#getVersionIdPart()} method
 	 */
+	@Deprecated
 	public static final ResourceMetadataKeyEnum<String> VERSION = new ResourceMetadataKeyEnum<String>("VERSION") {
 		private static final long serialVersionUID = 1L;
 
@@ -426,7 +311,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
 		@Override
 		public IdDt get(IResource theResource) {
-			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION_ID);
+			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata());
 		}
 
 		@Override
@@ -474,32 +359,45 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
 	public abstract void put(IResource theResource, T theObject);
 
-	@Override
-	public String toString() {
-		return myValue;
+	public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
+
+		private static final long serialVersionUID = 1L;
+
+		public ResourceMetadataKeySupportingAnyResource(String theValue) {
+			super(theValue);
 		}
 
-	private static DecimalDt getDecimalFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<DecimalDt> theKey) {
-		Object retValObj = theResourceMetadata.get(theKey);
+		public abstract T2 get(IAnyResource theResource);
+
+		public abstract void put(IAnyResource theResource, T2 theObject);
+
+	}
+
+	public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
+		public ExtensionResourceMetadataKey(String theUrl) {
+			super(theUrl);
+		}
+
+		@Override
+		public ExtensionDt get(IResource theResource) {
+			Object retValObj = theResource.getResourceMetadata().get(this);
 			if (retValObj == null) {
 				return null;
-		} else if (retValObj instanceof DecimalDt) {
-			if (((DecimalDt) retValObj).isEmpty()) {
-				return null;
+			} else if (retValObj instanceof ExtensionDt) {
+				return (ExtensionDt) retValObj;
 			}
-			return (DecimalDt) retValObj;
-		} else if (retValObj instanceof String) {
-			if (StringUtils.isBlank((String) retValObj)) {
-				return null;
+			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+				+ "' in resource metadata for key " + this.name() + " - Expected "
+				+ ExtensionDt.class.getCanonicalName());
 		}
-			return new DecimalDt((String) retValObj);
-		} else if (retValObj instanceof Double) {
-			return new DecimalDt((Double) retValObj);
+
+		@Override
+		public void put(IResource theResource, ExtensionDt theObject) {
+			theResource.getResourceMetadata().put(this, theObject);
 		}
-		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-			+ InstantDt.class.getCanonicalName());
 	}
 
+
 	@SuppressWarnings("unchecked")
 	private static <T extends Enum<?>> T getEnumFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<T> theKey, Class<T> theEnumType,
 																								IValueSetEnumBinder<T> theBinder) {
@@ -515,8 +413,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			+ InstantDt.class.getCanonicalName());
 	}
 
-	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
-		return toId(theKey, theResourceMetadata.get(theKey));
+	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata) {
+		return toId(ResourceMetadataKeyEnum.VERSION_ID, theResourceMetadata.get(ResourceMetadataKeyEnum.VERSION_ID));
 	}
 
 	private static List<IdDt> getIdListFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
@@ -586,49 +484,11 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			}
 			return (IdDt) retValObj;
 		} else if (retValObj instanceof Number) {
-			return new IdDt(((Number) retValObj).toString());
+			return new IdDt(retValObj.toString());
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
 			+ IdDt.class.getCanonicalName());
 	}
 
-	public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
-
-		private static final long serialVersionUID = 1L;
-
-		public ResourceMetadataKeySupportingAnyResource(String theValue) {
-			super(theValue);
-		}
-
-		public abstract T2 get(IAnyResource theResource);
-
-		public abstract void put(IAnyResource theResource, T2 theObject);
-
-	}
-
-	public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
-		public ExtensionResourceMetadataKey(String url) {
-			super(url);
-		}
-
-		@Override
-		public ExtensionDt get(IResource theResource) {
-			Object retValObj = theResource.getResourceMetadata().get(this);
-			if (retValObj == null) {
-				return null;
-			} else if (retValObj instanceof ExtensionDt) {
-				return (ExtensionDt) retValObj;
-			}
-			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
-				+ "' in resource metadata for key " + this.name() + " - Expected "
-				+ ExtensionDt.class.getCanonicalName());
-		}
-
-		@Override
-		public void put(IResource theResource, ExtensionDt theObject) {
-			theResource.getResourceMetadata().put(this, theObject);
-		}
-	}
-
 
 }

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

@@ -168,18 +168,6 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
 		return this;
 	}
 
-	public String toHeaderValue() {
-		StringBuilder b = new StringBuilder();
-		b.append(this.getTerm());
-		if (isNotBlank(this.getLabel())) {
-			b.append("; label=\"").append(this.getLabel()).append('"');
-		}
-		if (isNotBlank(this.getScheme())) {
-			b.append("; scheme=\"").append(this.getScheme()).append('"');
-		}
-		return b.toString();
-	}
-
 	@Override
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);

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

@@ -1,43 +0,0 @@
-package ca.uhn.fhir.model.api.annotation;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-
-/**
- * IResourceProvider and RestfulServer subclasses can use this annotation to designate which custom resources they can provide.
- * These resources will automatically be added to the resource list used for profile generation.
- * <pre>
- * Examples:
- * {@literal @}ProvidesResources(resource=CustomObservation.class)
- * class CustomObservationResourceProvider implements IResourceProvider{...}
- *
- * {@literal @}ProvidesResources(resource={CustomPatient.class,CustomObservation.class}){...}
- * class FhirServer extends RestfulServer
- * }
- * </pre>
- * Note that you needn't annotate both the IResourceProvider and the RestfulServer for a given resource; either one will suffice.
- */
-@Retention(RetentionPolicy.RUNTIME)
-public @interface ProvidesResources {
-    Class<?>[] resources();
-}

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

@@ -36,5 +36,7 @@ import java.lang.annotation.Target;
 @Retention(RetentionPolicy.RUNTIME)
 @Target(value=ElementType.METHOD)
 public @interface Metadata {
-	// nothing for now
+
+	long cacheMillis() default 60 * 1000L;
+
 }

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

@@ -26,7 +26,9 @@ import java.util.*;
 
 public class Constants {
 
+	public static final String CT_TEXT_CSV = "text/csv";
 	public static final String HEADER_REQUEST_ID = "X-Request-ID";
+	public static final String HEADER_REQUEST_SOURCE = "X-Request-Source";
 	public static final String CACHE_CONTROL_MAX_RESULTS = "max-results";
 	public static final String CACHE_CONTROL_NO_CACHE = "no-cache";
 	public static final String CACHE_CONTROL_NO_STORE = "no-store";
@@ -241,6 +243,15 @@ public class Constants {
 	 * Operation name for the $lastn operation
 	 */
 	public static final String OPERATION_LASTN = "$lastn";
+	/**
+	 * <p>
+	 * This extension represents the equivalent of the
+	 * <code>Resource.meta.source</code> field within R4+ resources, and is for
+	 * use in DSTU3 resources. It should contain a value of type <code>uri</code>
+	 * and will be located on the Resource.meta
+	 * </p>
+	 */
+	public static final String EXT_META_SOURCE = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-source";
 
 	static {
 		CHARSET_UTF8 = StandardCharsets.UTF_8;

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

@@ -1,5 +1,12 @@
 package ca.uhn.fhir.rest.api;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 /*
@@ -22,13 +29,6 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
  * #L%
  */
 
-import java.util.ArrayList;
-import java.util.StringTokenizer;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IQueryParameterOr;
-import ca.uhn.fhir.model.api.IQueryParameterType;
-
 public class QualifiedParamList extends ArrayList<String> {
 
 	private static final long serialVersionUID = 1L;
@@ -108,6 +108,13 @@ public class QualifiedParamList extends ArrayList<String> {
 
 		}
 
+		// If no value was found, at least add that empty string as a value. It should get ignored later, but at
+		// least this lets us give a sensible error message if the parameter name was bad. See
+		// ResourceProviderR4Test#testParameterWithNoValueThrowsError_InvalidChainOnCustomSearch for an example
+		if (retVal.size() == 0) {
+			retVal.add("");
+		}
+
 		return retVal;
 	}
 

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

@@ -33,12 +33,6 @@ import java.util.Map;
  */
 public interface IHttpResponse {
 
-	/**
-	 * @deprecated This method was deprecated in HAPI FHIR 2.2 because its name has a typo. Use {@link #bufferEntity()} instead.
-	 */
-	@Deprecated
-	void bufferEntitity() throws IOException;
-
 	/**
 	 * Buffer the message entity data.
 	 * <p>

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

@@ -248,26 +248,30 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
 
 	@Override
 	public boolean equals(Object theO) {
-		if (this == theO) return true;
+		if (this == theO) {
+			return true;
+		}
 
-		if (theO == null || getClass() != theO.getClass()) return false;
+		if (theO == null || getClass() != theO.getClass()) {
+			return false;
+		}
 
 		TokenParam that = (TokenParam) theO;
 
-		return new EqualsBuilder()
-			.append(myModifier, that.myModifier)
-			.append(mySystem, that.mySystem)
-			.append(myValue, that.myValue)
-			.isEquals();
+		EqualsBuilder b = new EqualsBuilder();
+		b.append(myModifier, that.myModifier);
+		b.append(mySystem, that.mySystem);
+		b.append(myValue, that.myValue);
+		return b.isEquals();
 	}
 
 	@Override
 	public int hashCode() {
-		return new HashCodeBuilder(17, 37)
-			.append(myModifier)
-			.append(mySystem)
-			.append(myValue)
-			.toHashCode();
+		HashCodeBuilder b = new HashCodeBuilder(17, 37);
+		b.append(myModifier);
+		b.append(mySystem);
+		b.append(myValue);
+		return b.toHashCode();
 	}
 
 	private static String toSystemValue(UriDt theSystem) {

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

@@ -0,0 +1,74 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
+
+public class AsyncUtil {
+	private static final Logger ourLog = LoggerFactory.getLogger(AsyncUtil.class);
+
+	/**
+	 * Non instantiable
+	 */
+	private AsyncUtil() {
+	}
+
+	/**
+	 * Calls Thread.sleep and if an InterruptedException occurs, logs a warning but otherwise continues
+	 *
+	 * @param theMillis The number of millis to sleep
+	 * @return Did we sleep the whole amount
+	 */
+	public static boolean sleep(long theMillis) {
+		try {
+			Thread.sleep(theMillis);
+			return true;
+		} catch (InterruptedException theE) {
+			Thread.currentThread().interrupt();
+			ourLog.warn("Sleep for {}ms was interrupted", theMillis);
+			return false;
+		}
+	}
+
+	public static boolean awaitLatchAndThrowInternalErrorExceptionOnInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
+		try {
+			return theInitialCollectionLatch.await(theTime, theTimeUnit);
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new InternalErrorException(e);
+		}
+	}
+
+	public static boolean awaitLatchAndIgnoreInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
+		try {
+			return theInitialCollectionLatch.await(theTime, theTimeUnit);
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			ourLog.warn("Interrupted while waiting for latch");
+			return false;
+		}
+	}
+}

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

@@ -20,9 +20,8 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.*;
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -35,12 +34,10 @@ public class AttachmentUtil {
 	 * Fetches the base64Binary value of Attachment.data, creating it if it does not
 	 * already exist.
 	 */
-	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<byte[]> getOrCreateData(FhirContext theContext, ICompositeType theAttachment) {
 		return getOrCreateChild(theContext, theAttachment, "data", "base64Binary");
 	}
 
-	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<String> getOrCreateContentType(FhirContext theContext, ICompositeType theAttachment) {
 		return getOrCreateChild(theContext, theAttachment, "contentType", "string");
 	}
@@ -64,6 +61,16 @@ public class AttachmentUtil {
 			});
 	}
 
+	public static void setUrl(FhirContext theContext, ICompositeType theAttachment, String theUrl) {
+		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "url");
+		assert entryChild != null : "Version " + theContext + " has no child " + "url";
+		String typeName = "uri";
+		if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
+			typeName = "url";
+		}
+		entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, typeName, theUrl));
+	}
+
 	public static void setContentType(FhirContext theContext, ICompositeType theAttachment, String theContentType) {
 		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "contentType");
 		entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, "code", theContentType));
@@ -88,7 +95,9 @@ public class AttachmentUtil {
 	 */
 	@SuppressWarnings("unchecked")
 	static <T> IPrimitiveType<T> newPrimitive(FhirContext theContext, String theType, T theValue) {
-		IPrimitiveType<T> primitive = (IPrimitiveType<T>) theContext.getElementDefinition(theType).newInstance();
+		BaseRuntimeElementDefinition<?> elementDefinition = theContext.getElementDefinition(theType);
+		Validate.notNull(elementDefinition, "Unknown type %s for %s", theType, theContext);
+		IPrimitiveType<T> primitive = (IPrimitiveType<T>) elementDefinition.newInstance();
 		primitive.setValue(theValue);
 		return primitive;
 	}
@@ -100,4 +109,8 @@ public class AttachmentUtil {
 		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theElement.getClass());
 		return def.getChildByName(theName);
 	}
+
+	public static ICompositeType newInstance(FhirContext theFhirCtx) {
+		return (ICompositeType) theFhirCtx.getElementDefinition("Attachment").newInstance();
+	}
 }

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

@@ -1,19 +1,20 @@
 package ca.uhn.fhir.util;
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.bundle.BundleEntryMutator;
+import ca.uhn.fhir.util.bundle.BundleEntryParts;
+import ca.uhn.fhir.util.bundle.EntryListAccumulator;
+import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
 import org.apache.commons.lang3.tuple.Pair;
-import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.instance.model.api.*;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
+import java.util.function.Consumer;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
@@ -42,37 +43,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  */
 public class BundleUtil {
 
-	public static class BundleEntryParts {
-		private final RequestTypeEnum myRequestType;
-		private final IBaseResource myResource;
-		private final String myUrl;
-		private final String myConditionalUrl;
-
-		BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
-			super();
-			myRequestType = theRequestType;
-			myUrl = theUrl;
-			myResource = theResource;
-			myConditionalUrl = theConditionalUrl;
-		}
-
-		public RequestTypeEnum getRequestType() {
-			return myRequestType;
-		}
-
-		public IBaseResource getResource() {
-			return myResource;
-		}
-
-		public String getConditionalUrl() {
-			return myConditionalUrl;
-		}
-
-		public String getUrl() {
-			return myUrl;
-		}
-	}
-
 	/**
 	 * @return Returns <code>null</code> if the link isn't found or has no value
 	 */
@@ -185,20 +155,25 @@ public class BundleUtil {
 	 * Extract all of the resources from a given bundle
 	 */
 	public static List<BundleEntryParts> toListOfEntries(FhirContext theContext, IBaseBundle theBundle) {
-		List<BundleEntryParts> retVal = new ArrayList<>();
+		EntryListAccumulator entryListAccumulator = new EntryListAccumulator();
+		processEntries(theContext, theBundle, entryListAccumulator);
+		return entryListAccumulator.getList();
+	}
 
-		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
-		BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
-		List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
 
-		BaseRuntimeElementCompositeDefinition<?> entryChildElem = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
+	public static void processEntries(FhirContext theContext, IBaseBundle theBundle, Consumer<ModifiableBundleEntry> theProcessor) {
+		RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
+		BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
+		List<IBase> entries = entryChildDef.getAccessor().getValues(theBundle);
 
-		BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
-		BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
-		BaseRuntimeElementCompositeDefinition<?> requestElem = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
-		BaseRuntimeChildDefinition requestUrlChild = requestElem.getChildByName("url");
-		BaseRuntimeChildDefinition requestIfNoneExistChild = requestElem.getChildByName("ifNoneExist");
-		BaseRuntimeChildDefinition methodChild = requestElem.getChildByName("method");
+		BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
+
+		BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
+		BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
+		BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
+		BaseRuntimeChildDefinition requestUrlChildDef = requestChildContentsDef.getChildByName("url");
+		BaseRuntimeChildDefinition requestIfNoneExistChildDef = requestChildContentsDef.getChildByName("ifNoneExist");
+		BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
 
 		for (IBase nextEntry : entries) {
 			IBaseResource resource = null;
@@ -206,15 +181,15 @@ public class BundleUtil {
 			RequestTypeEnum requestType = null;
 			String conditionalUrl = null;
 
-			for (IBase next : resourceChild.getAccessor().getValues(nextEntry)) {
-				resource = (IBaseResource) next;
+			for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
+				resource = (IBaseResource) nextResource;
 			}
-			for (IBase nextRequest : requestChild.getAccessor().getValues(nextEntry)) {
-				for (IBase nextUrl : requestUrlChild.getAccessor().getValues(nextRequest)) {
+			for (IBase nextRequest : requestChildDef.getAccessor().getValues(nextEntry)) {
+				for (IBase nextUrl : requestUrlChildDef.getAccessor().getValues(nextRequest)) {
 					url = ((IPrimitiveType<?>) nextUrl).getValueAsString();
 				}
-				for (IBase nextUrl : methodChild.getAccessor().getValues(nextRequest)) {
-					String methodString = ((IPrimitiveType<?>) nextUrl).getValueAsString();
+				for (IBase nextMethod : methodChildDef.getAccessor().getValues(nextRequest)) {
+					String methodString = ((IPrimitiveType<?>) nextMethod).getValueAsString();
 					if (isNotBlank(methodString)) {
 						requestType = RequestTypeEnum.valueOf(methodString);
 					}
@@ -227,7 +202,7 @@ public class BundleUtil {
 							conditionalUrl = url != null && url.contains("?") ? url : null;
 							break;
 						case POST:
-							List<IBase> ifNoneExistReps = requestIfNoneExistChild.getAccessor().getValues(nextRequest);
+							List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
 							if (ifNoneExistReps.size() > 0) {
 								IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
 								conditionalUrl = ifNoneExist.getValueAsString();
@@ -241,11 +216,10 @@ public class BundleUtil {
 			 * All 3 might be null - That's ok because we still want to know the
 			 * order in the original bundle.
 			 */
-			retVal.add(new BundleEntryParts(requestType, url, resource, conditionalUrl));
+			BundleEntryMutator mutator = new BundleEntryMutator(nextEntry, requestChildDef, requestChildContentsDef);
+			ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(requestType, url, resource, conditionalUrl), mutator);
+			theProcessor.accept(entry);
 		}
-
-
-		return retVal;
 	}
 
 	/**
@@ -278,4 +252,25 @@ public class BundleUtil {
 		}
 		return retVal;
 	}
+
+	/**
+	 * DSTU3 did not allow the PATCH verb for transaction bundles- so instead we infer that a bundle
+	 * is a patch if the payload is a binary resource containing a patch. This method
+	 * tests whether a resource (which should have come from
+	 * <code>Bundle.entry.resource</code> is a Binary resource with a patch
+	 * payload type.
+	 */
+	public static boolean isDstu3TransactionPatch(IBaseResource thePayloadResource) {
+		boolean isPatch = false;
+		if (thePayloadResource instanceof IBaseBinary) {
+			String contentType = ((IBaseBinary) thePayloadResource).getContentType();
+			 try {
+				 PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentType);
+				 isPatch = true;
+			 } catch (InvalidRequestException e) {
+				 // ignore
+			 }
+		}
+		return isPatch;
+	}
 }

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

@@ -735,25 +735,15 @@ public class FhirTerser {
 									valueType = (Class<? extends IBase>) valueType.getSuperclass();
 								}
 
-								if (childElementDef == null) {
-									StringBuilder b = new StringBuilder();
-									b.append("Found value of type[");
-									b.append(nextValue.getClass().getSimpleName());
-									b.append("] which is not valid for field[");
-									b.append(nextChild.getElementName());
-									b.append("] in ");
-									b.append(childDef.getName());
-									b.append(" - Valid types: ");
-									for (Iterator<String> iter = new TreeSet<>(nextChild.getValidChildNames()).iterator(); iter.hasNext(); ) {
-										BaseRuntimeElementDefinition<?> childByName = nextChild.getChildByName(iter.next());
-										b.append(childByName.getImplementingClass().getSimpleName());
-										if (iter.hasNext()) {
-											b.append(", ");
-										}
-									}
-									throw new DataFormatException(b.toString());
+								Class<? extends IBase> typeClass = nextValue.getClass();
+								while (childElementDef == null && IBase.class.isAssignableFrom(typeClass)) {
+									//noinspection unchecked
+									typeClass = (Class<? extends IBase>) typeClass.getSuperclass();
+									childElementDef = nextChild.getChildElementDefinitionByDatatype(typeClass);
 								}
 
+								Validate.notNull(childElementDef, "Found value of type[%s] which is not valid for field[%s] in %s", nextValue.getClass(), nextChild.getElementName(), childDef.getName());
+
 								visit(nextValue, nextChild, childElementDef, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
 							}
 						}

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

@@ -0,0 +1,38 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.text.DecimalFormat;
+
+public class FileUtil {
+	// Use "bytes" instead of just "b" because it reads easier in logs
+	private static final String[] UNITS = new String[]{"Bytes", "kB", "MB", "GB", "TB"};
+
+	public static String formatFileSize(long theBytes) {
+		if (theBytes <= 0) {
+			return "0 " + UNITS[0];
+		}
+		int digitGroups = (int) (Math.log10(theBytes) / Math.log10(1024));
+		digitGroups = Math.min(digitGroups, UNITS.length - 1);
+		return new DecimalFormat("###0.#").format(theBytes / Math.pow(1024, digitGroups)) + " " + UNITS[digitGroups];
+	}
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/IModelVisitor2.java

@@ -45,7 +45,7 @@ public interface IModelVisitor2 {
 	/**
 	 *
 	 */
-	boolean acceptUndeclaredExtension(IBaseExtension<?, ?> theNextExt, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath);
+	default boolean acceptUndeclaredExtension(IBaseExtension<?, ?> theNextExt, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) { return true; }
 
 
 }

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

@@ -23,9 +23,9 @@ package ca.uhn.fhir.util;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.FhirContext;
-import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseMetaType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.rest.api.Constants;
+import org.hl7.fhir.instance.model.api.*;
 
 import java.util.List;
 
@@ -46,6 +46,29 @@ public class MetaUtil {
 		return retVal;
 	}
 
+	/**
+	 * Sets the value for <code>Resource.meta.source</code> for R4+ resources, and places the value in
+	 * an extension on <code>Resource.meta</code>
+	 * with the URL <code>http://hapifhir.io/fhir/StructureDefinition/resource-meta-source</code> for DSTU3.
+	 *
+	 * @param theContext  The FhirContext object
+	 * @param theResource The resource to modify
+	 * @param theValue    The source URI
+	 * @see <a href="http://hl7.org/fhir/resource-definitions.html#Resource.meta">Meta.source</a>
+	 */
+	@SuppressWarnings("unchecked")
+	public static void setSource(FhirContext theContext, IBaseResource theResource, String theValue) {
+		if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
+			MetaUtil.setSource(theContext, theResource.getMeta(), theValue);
+		} else if (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
+			IBaseExtension<?, ?> sourceExtension = ((IBaseHasExtensions) theResource.getMeta()).addExtension();
+			sourceExtension.setUrl(Constants.EXT_META_SOURCE);
+			IPrimitiveType<String> value = (IPrimitiveType<String>) theContext.getElementDefinition("uri").newInstance();
+			value.setValue(theValue);
+			sourceExtension.setValue(value);
+		}
+	}
+
 	public static void setSource(FhirContext theContext, IBaseMetaType theMeta, String theValue) {
 		BaseRuntimeElementCompositeDefinition<?> elementDef = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theMeta.getClass());
 		BaseRuntimeChildDefinition sourceChild = elementDef.getChildByName("source");

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

@@ -19,22 +19,17 @@ package ca.uhn.fhir.util;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.util.List;
 
+import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * Utilities for dealing with OperationOutcome resources across various model versions
@@ -43,20 +38,17 @@ public class OperationOutcomeUtil {
 
 	/**
 	 * Add an issue to an OperationOutcome
-	 * 
-	 * @param theCtx
-	 *           The fhir context
-	 * @param theOperationOutcome
-	 *           The OO resource to add to
-	 * @param theSeverity
-	 *           The severity (fatal | error | warning | information)
-	 * @param theDetails
-	 *           The details string
+	 *  @param theCtx              The fhir context
+	 * @param theOperationOutcome The OO resource to add to
+	 * @param theSeverity         The severity (fatal | error | warning | information)
+	 * @param theDetails          The details string
 	 * @param theCode
+	 * @return Returns the newly added issue
 	 */
-	public static void addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode) {
+	public static IBase addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode) {
 		IBase issue = createIssue(theCtx, theOperationOutcome);
 		populateDetails(theCtx, issue, theSeverity, theDetails, theLocation, theCode);
+		return issue;
 	}
 
 	private static IBase createIssue(FhirContext theCtx, IBaseResource theOutcome) {
@@ -140,7 +132,6 @@ public class OperationOutcomeUtil {
 
 		BaseRuntimeElementDefinition<?> stringDef = detailsChild.getChildByName(detailsChild.getElementName());
 		BaseRuntimeChildDefinition severityChild = issueElement.getChildByName("severity");
-		BaseRuntimeChildDefinition locationChild = issueElement.getChildByName("location");
 
 		IPrimitiveType<?> severityElem = (IPrimitiveType<?>) severityChild.getChildByName("severity").newInstance(severityChild.getInstanceConstructorArguments());
 		severityElem.setValueAsString(theSeverity);
@@ -150,7 +141,13 @@ public class OperationOutcomeUtil {
 		string.setValueAsString(theDetails);
 		detailsChild.getMutator().setValue(theIssue, string);
 
+		addLocationToIssue(theCtx, theIssue, theLocation);
+	}
+
+	public static void addLocationToIssue(FhirContext theContext, IBase theIssue, String theLocation) {
 		if (isNotBlank(theLocation)) {
+			BaseRuntimeElementCompositeDefinition<?> issueElement = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theIssue.getClass());
+			BaseRuntimeChildDefinition locationChild = issueElement.getChildByName("location");
 			IPrimitiveType<?> locationElem = (IPrimitiveType<?>) locationChild.getChildByName("location").newInstance(locationChild.getInstanceConstructorArguments());
 			locationElem.setValueAsString(theLocation);
 			locationChild.getMutator().addValue(theIssue, locationElem);

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

@@ -72,6 +72,8 @@ public class ParametersUtil {
 	}
 
 	private static void addClientParameter(FhirContext theContext, Object theValue, IBaseResource theTargetResource, BaseRuntimeChildDefinition paramChild, BaseRuntimeElementCompositeDefinition<?> paramChildElem, String theName) {
+		Validate.notNull(theValue, "theValue must not be null");
+
 		if (theValue instanceof IBaseResource) {
 			IBase parameter = createParameterRepetition(theContext, theTargetResource, paramChild, paramChildElem, theName);
 			paramChildElem.getChildByName("resource").getMutator().addValue(parameter, (IBaseResource) theValue);
@@ -162,7 +164,6 @@ public class ParametersUtil {
 		IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theCtx.getElementDefinition("boolean").newInstance();
 		value.setValue(theValue);
 		addParameterToParameters(theCtx, theParameters, theName, value);
-
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -51,16 +51,8 @@ public class ReflectionUtil {
 	}
 
 	public static Class<?> getGenericCollectionTypeOfField(Field next) {
-		Class<?> type;
 		ParameterizedType collectionType = (ParameterizedType) next.getGenericType();
-		Type firstArg = collectionType.getActualTypeArguments()[0];
-		if (ParameterizedType.class.isAssignableFrom(firstArg.getClass())) {
-			ParameterizedType pt = ((ParameterizedType) firstArg);
-			type = (Class<?>) pt.getRawType();
-		} else {
-			type = (Class<?>) firstArg;
-		}
-		return type;
+		return getGenericCollectionTypeOf(collectionType.getActualTypeArguments()[0]);
 	}
 
 	/**
@@ -84,42 +76,37 @@ public class ReflectionUtil {
 	}
 
 	public static Class<?> getGenericCollectionTypeOfMethodParameter(Method theMethod, int theParamIndex) {
-		Class<?> type;
 		Type genericParameterType = theMethod.getGenericParameterTypes()[theParamIndex];
 		if (Class.class.equals(genericParameterType) || Class.class.equals(genericParameterType.getClass())) {
 			return null;
 		}
 		ParameterizedType collectionType = (ParameterizedType) genericParameterType;
-		Type firstArg = collectionType.getActualTypeArguments()[0];
-		if (ParameterizedType.class.isAssignableFrom(firstArg.getClass())) {
-			ParameterizedType pt = ((ParameterizedType) firstArg);
-			type = (Class<?>) pt.getRawType();
-		} else {
-			type = (Class<?>) firstArg;
-		}
-		return type;
+		return getGenericCollectionTypeOf(collectionType.getActualTypeArguments()[0]);
 	}
 
-	@SuppressWarnings({ "rawtypes" })
 	public static Class<?> getGenericCollectionTypeOfMethodReturnType(Method theMethod) {
-		Class<?> type;
 		Type genericReturnType = theMethod.getGenericReturnType();
 		if (!(genericReturnType instanceof ParameterizedType)) {
 			return null;
 		}
 		ParameterizedType collectionType = (ParameterizedType) genericReturnType;
-		Type firstArg = collectionType.getActualTypeArguments()[0];
-		if (ParameterizedType.class.isAssignableFrom(firstArg.getClass())) {
-			ParameterizedType pt = ((ParameterizedType) firstArg);
+		return getGenericCollectionTypeOf(collectionType.getActualTypeArguments()[0]);
+	}
+
+	@SuppressWarnings({ "rawtypes" })
+	private static Class<?> getGenericCollectionTypeOf(Type theType) {
+		Class<?> type;
+		if (ParameterizedType.class.isAssignableFrom(theType.getClass())) {
+			ParameterizedType pt = ((ParameterizedType) theType);
 			type = (Class<?>) pt.getRawType();
-		} else if (firstArg instanceof TypeVariable<?>) {
-			Type decl = ((TypeVariable) firstArg).getBounds()[0];
+		} else if (theType instanceof TypeVariable<?>) {
+			Type decl = ((TypeVariable) theType).getBounds()[0];
 			return (Class<?>) decl;
-		} else if (firstArg instanceof WildcardType) {
-			Type decl = ((WildcardType) firstArg).getUpperBounds()[0];
+		} else if (theType instanceof WildcardType) {
+			Type decl = ((WildcardType) theType).getUpperBounds()[0];
 			return (Class<?>) decl;
 		} else {
-			type = (Class<?>) firstArg;
+			type = (Class<?>) theType;
 		}
 		return type;
 	}
@@ -154,8 +141,7 @@ public class ReflectionUtil {
 	public static Object newInstanceOfFhirServerType(String theType) {
 		String errorMessage = "Unable to instantiate server framework. Please make sure that hapi-fhir-server library is on your classpath!";
 		String wantedType = "ca.uhn.fhir.rest.api.server.IFhirVersionServer";
-		Object fhirServerVersion = newInstanceOfType(theType, errorMessage, wantedType);
-		return fhirServerVersion;
+		return newInstanceOfType(theType, errorMessage, wantedType);
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.util;
 
 import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
 
 import java.text.DecimalFormat;
@@ -9,8 +10,6 @@ import java.util.Date;
 import java.util.LinkedList;
 import java.util.concurrent.TimeUnit;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -48,12 +47,14 @@ public class StopWatch {
 	private long myStarted = now();
 	private TaskTiming myCurrentTask;
 	private LinkedList<TaskTiming> myTasks;
+
 	/**
 	 * Constructor
 	 */
 	public StopWatch() {
 		super();
 	}
+
 	/**
 	 * Constructor
 	 *
@@ -63,7 +64,13 @@ public class StopWatch {
 		myStarted = theStart.getTime();
 	}
 
-	public StopWatch(long theL) {
+	/**
+	 * Constructor
+	 *
+	 * @param theStart The time that the stopwatch was started
+	 */
+	public StopWatch(long theStart) {
+		myStarted = theStart;
 	}
 
 	private void addNewlineIfContentExists(StringBuilder theB) {
@@ -120,6 +127,8 @@ public class StopWatch {
 				b.append(": ");
 				b.append(formatMillis(delta));
 			}
+		} else {
+			b.append("No tasks");
 		}
 
 		TaskTiming last = null;
@@ -257,13 +266,12 @@ public class StopWatch {
 	 */
 	public void startTask(String theTaskName) {
 		endCurrentTask();
-		if (isNotBlank(theTaskName)) {
+		Validate.notBlank(theTaskName, "Task name must not be blank");
 		myCurrentTask = new TaskTiming()
 			.setTaskName(theTaskName)
 			.setStart(now());
 		myTasks.add(myCurrentTask);
 	}
-	}
 
 	/**
 	 * Formats value in an appropriate format. See {@link #formatMillis(long)}}
@@ -331,18 +339,18 @@ public class StopWatch {
 	/**
 	 * Append a right-aligned and zero-padded numeric value to a `StringBuilder`.
 	 */
-	static private void append(StringBuilder tgt, String pfx, int dgt, long val) {
-		tgt.append(pfx);
-		if (dgt > 1) {
-			int pad = (dgt - 1);
-			for (long xa = val; xa > 9 && pad > 0; xa /= 10) {
+	static void appendRightAlignedNumber(StringBuilder theStringBuilder, String thePrefix, int theNumberOfDigits, long theValueToAppend) {
+		theStringBuilder.append(thePrefix);
+		if (theNumberOfDigits > 1) {
+			int pad = (theNumberOfDigits - 1);
+			for (long xa = theValueToAppend; xa > 9 && pad > 0; xa /= 10) {
 				pad--;
 			}
 			for (int xa = 0; xa < pad; xa++) {
-				tgt.append('0');
+				theStringBuilder.append('0');
 			}
 		}
-		tgt.append(val);
+		theStringBuilder.append(theValueToAppend);
 	}
 
 	/**
@@ -399,11 +407,11 @@ public class StopWatch {
 			}
 		} else {
 			long millisAsLong = (long) theMillis;
-			append(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
-			append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
-			append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
+			appendRightAlignedNumber(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
+			appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
+			appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
 			if (theMillis <= DateUtils.MILLIS_PER_MINUTE) {
-				append(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
+				appendRightAlignedNumber(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
 			}
 		}
 		return buf.toString();

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

@@ -8,6 +8,8 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import com.google.common.escape.Escaper;
 import com.google.common.net.PercentEscaper;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.utils.URLEncodedUtils;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.io.UnsupportedEncodingException;
@@ -457,4 +459,23 @@ public class UrlUtil {
 		return theString;
 	}
 
+	public static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
+		List<NameValuePair> parameters;
+		String matchUrl = theMatchUrl;
+		int questionMarkIndex = matchUrl.indexOf('?');
+		if (questionMarkIndex != -1) {
+			matchUrl = matchUrl.substring(questionMarkIndex + 1);
+		}
+		matchUrl = matchUrl.replace("|", "%7C");
+		matchUrl = matchUrl.replace("=>=", "=%3E%3D");
+		matchUrl = matchUrl.replace("=<=", "=%3C%3D");
+		matchUrl = matchUrl.replace("=>", "=%3E");
+		matchUrl = matchUrl.replace("=<", "=%3C");
+		if (matchUrl.contains(" ")) {
+			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - URL is invalid (must not contain spaces)");
+		}
+
+		parameters = URLEncodedUtils.parse((matchUrl), Constants.CHARSET_UTF8, '&');
+		return parameters;
+	}
 }

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

@@ -30,7 +30,13 @@ import com.ctc.wstx.stax.WstxOutputFactory;
 import org.apache.commons.text.StringEscapeUtils;
 import org.codehaus.stax2.XMLOutputFactory2;
 import org.codehaus.stax2.io.EscapingWriterFactory;
+import org.w3c.dom.Document;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.stream.*;
 import javax.xml.stream.events.XMLEvent;
 import java.io.*;
@@ -40,7 +46,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 
 /**
  * Utility methods for working with the StAX API.
- * 
+ * <p>
  * This class contains code adapted from the Apache Axiom project.
  */
 public class XmlUtil {
@@ -1507,6 +1513,73 @@ public class XmlUtil {
 		VALID_ENTITY_NAMES = Collections.unmodifiableMap(validEntityNames);
 	}
 
+	/** Non-instantiable */
+	private XmlUtil() {}
+
+	private static final class ExtendedEntityReplacingXmlResolver implements XMLResolver {
+		@Override
+		public Object resolveEntity(String thePublicID, String theSystemID, String theBaseURI, String theNamespace) {
+			if (thePublicID == null && theSystemID == null) {
+				if (theNamespace != null && VALID_ENTITY_NAMES.containsKey(theNamespace)) {
+					return new String(Character.toChars(VALID_ENTITY_NAMES.get(theNamespace)));
+				}
+			}
+
+			return null;
+		}
+	}
+
+	public static class MyEscaper implements EscapingWriterFactory {
+
+		@Override
+		public Writer createEscapingWriterFor(OutputStream theOut, String theEnc) throws UnsupportedEncodingException {
+			return createEscapingWriterFor(new OutputStreamWriter(theOut, theEnc), theEnc);
+		}
+
+		@Override
+		public Writer createEscapingWriterFor(final Writer theW, String theEnc) {
+			return new Writer() {
+
+				@Override
+				public void close() throws IOException {
+					theW.close();
+				}
+
+				@Override
+				public void flush() throws IOException {
+					theW.flush();
+				}
+
+				@Override
+				public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
+					boolean hasEscapable = false;
+					for (int i = 0; i < theLen && !hasEscapable; i++) {
+						char nextChar = theCbuf[i + theOff];
+						switch (nextChar) {
+							case '<':
+							case '>':
+							case '"':
+							case '&':
+								hasEscapable = true;
+								break;
+							default:
+								break;
+						}
+					}
+
+					if (!hasEscapable) {
+						theW.write(theCbuf, theOff, theLen);
+						return;
+					}
+
+					String escaped = StringEscapeUtils.escapeXml10(new String(theCbuf, theOff, theLen));
+					theW.write(escaped.toCharArray());
+				}
+			};
+		}
+
+	}
+
 	private static XMLOutputFactory createOutputFactory() throws FactoryConfigurationError {
 		try {
 			// Detect if we're running with the Android lib, and force repackaged Woodstox to be used
@@ -1637,15 +1710,11 @@ public class XmlUtil {
 			try {
 				Class.forName("com.ctc.wstx.stax.WstxInputFactory");
 				boolean isWoodstox = inputFactory instanceof com.ctc.wstx.stax.WstxInputFactory;
-				if ( !isWoodstox )
-				{
+				if (!isWoodstox) {
 					// Check if implementation is woodstox by property since instanceof check does not work if running in JBoss
-					try
-					{
+					try {
 						isWoodstox = inputFactory.getProperty("org.codehaus.stax2.implVersion") != null;
-					}
-					catch ( Exception e )
-					{
+					} catch (Exception e) {
 						// ignore
 					}
 				}
@@ -1673,7 +1742,6 @@ public class XmlUtil {
 		return ourOutputFactory;
 	}
 
-
 	private static void logStaxImplementation(Class<?> theClass) {
 		IDependencyLog logger = DependencyLogFactory.createJarLogger();
 		if (logger != null) {
@@ -1682,7 +1750,6 @@ public class XmlUtil {
 		ourHaveLoggedStaxImplementation = true;
 	}
 
-	
 	static XMLInputFactory newInputFactory() throws FactoryConfigurationError {
 		XMLInputFactory inputFactory;
 		try {
@@ -1767,68 +1834,30 @@ public class XmlUtil {
 		}
 	}
 
-	private static final class ExtendedEntityReplacingXmlResolver implements XMLResolver {
-		@Override
-		public Object resolveEntity(String thePublicID, String theSystemID, String theBaseURI, String theNamespace) {
-			if (thePublicID == null && theSystemID == null) {
-				if (theNamespace != null && VALID_ENTITY_NAMES.containsKey(theNamespace)) {
-					return new String(Character.toChars(VALID_ENTITY_NAMES.get(theNamespace)));
-				}
+	public static Document parseDocument(String theInput) throws IOException, SAXException {
+		DocumentBuilder builder = null;
+		try {
+			DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
+			docBuilderFactory.setNamespaceAware(true);
+			docBuilderFactory.setXIncludeAware(false);
+			docBuilderFactory.setExpandEntityReferences(false);
+			try {
+				docBuilderFactory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
+				docBuilderFactory.setFeature("http://xml.org/sax/features/external-general-entities", false);
+				docBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
+				docBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
+				docBuilderFactory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
+				throwUnitTestExceptionIfConfiguredToDoSo();
+			} catch (Exception e) {
+				ourLog.warn("Failed to set feature on XML parser: " + e.toString());
 			}
 
-			return null;
-		}
+			builder = docBuilderFactory.newDocumentBuilder();
+		} catch (ParserConfigurationException e) {
+			throw new ConfigurationException(e);
 		}
 
-	public static class MyEscaper implements EscapingWriterFactory {
-
-		@Override
-		public Writer createEscapingWriterFor(OutputStream theOut, String theEnc) throws UnsupportedEncodingException {
-			return createEscapingWriterFor(new OutputStreamWriter(theOut, theEnc), theEnc);
-		}
-
-		@Override
-		public Writer createEscapingWriterFor(final Writer theW, String theEnc) {
-			return new Writer() {
-
-				@Override
-				public void close() throws IOException {
-					theW.close();
-				}
-
-				@Override
-				public void flush() throws IOException {
-					theW.flush();
-				}
-
-				@Override
-				public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
-					boolean hasEscapable = false;
-					for (int i = 0; i < theLen && !hasEscapable; i++) {
-						char nextChar = theCbuf[i + theOff];
-						switch (nextChar) {
-						case '<':
-						case '>':
-						case '"':
-						case '&':
-							hasEscapable = true;
-							break;
-						default:
-							break;
+		InputSource src = new InputSource(new StringReader(theInput));
+		return builder.parse(src);
 	}
 }
-
-					if (!hasEscapable) {
-						theW.write(theCbuf, theOff, theLen);
-						return;
-					}
-
-					String escaped = StringEscapeUtils.escapeXml10(new String(theCbuf, theOff, theLen));
-					theW.write(escaped.toCharArray());
-				}
-			};
-		}
-
-	}
-
-}

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

@@ -0,0 +1,48 @@
+package ca.uhn.fhir.util.bundle;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.ParametersUtil;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+public class BundleEntryMutator {
+	private final IBase myEntry;
+	private final BaseRuntimeChildDefinition myRequestChildDef;
+	private final BaseRuntimeElementCompositeDefinition<?> myRequestChildContentsDef;
+
+	public BundleEntryMutator(IBase theEntry, BaseRuntimeChildDefinition theRequestChildDef, BaseRuntimeElementCompositeDefinition<?> theRequestChildContentsDef) {
+		myEntry = theEntry;
+		myRequestChildDef = theRequestChildDef;
+		myRequestChildContentsDef = theRequestChildContentsDef;
+	}
+
+	void setRequestUrl(FhirContext theFhirContext, String theRequestUrl) {
+		BaseRuntimeChildDefinition requestUrlChildDef = myRequestChildContentsDef.getChildByName("url");
+		IPrimitiveType<?> url = ParametersUtil.createUri(theFhirContext, theRequestUrl);
+		for (IBase nextRequest : myRequestChildDef.getAccessor().getValues(myEntry)) {
+			requestUrlChildDef.getMutator().addValue(nextRequest, url);
+		}
+	}
+}

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

@@ -0,0 +1,55 @@
+package ca.uhn.fhir.util.bundle;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public class BundleEntryParts {
+	private final RequestTypeEnum myRequestType;
+	private final IBaseResource myResource;
+	private final String myUrl;
+	private final String myConditionalUrl;
+
+	public BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
+		super();
+		myRequestType = theRequestType;
+		myUrl = theUrl;
+		myResource = theResource;
+		myConditionalUrl = theConditionalUrl;
+	}
+
+	public RequestTypeEnum getRequestType() {
+		return myRequestType;
+	}
+
+	public IBaseResource getResource() {
+		return myResource;
+	}
+
+	public String getConditionalUrl() {
+		return myConditionalUrl;
+	}
+
+	public String getUrl() {
+		return myUrl;
+	}
+}

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

@@ -0,0 +1,38 @@
+package ca.uhn.fhir.util.bundle;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.Consumer;
+
+public class EntryListAccumulator implements Consumer<ModifiableBundleEntry> {
+	private final List<BundleEntryParts> myList = new ArrayList<>();
+
+	@Override
+	public void accept(ModifiableBundleEntry theModifiableBundleEntry) {
+		myList.add(theModifiableBundleEntry.getBundleEntryParts());
+	}
+
+	public List<BundleEntryParts> getList() {
+		return myList;
+	}
+}

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

@@ -0,0 +1,45 @@
+package ca.uhn.fhir.util.bundle;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+
+public class ModifiableBundleEntry {
+	private final BundleEntryParts myBundleEntryParts;
+	private final BundleEntryMutator myBundleEntryMutator;
+
+	public ModifiableBundleEntry(BundleEntryParts theBundleEntryParts, BundleEntryMutator theBundleEntryMutator) {
+		myBundleEntryParts = theBundleEntryParts;
+		myBundleEntryMutator = theBundleEntryMutator;
+	}
+
+	BundleEntryParts getBundleEntryParts() {
+		return myBundleEntryParts;
+	}
+
+	public void setRequestUrl(FhirContext theFhirContext, String theRequestUrl) {
+		myBundleEntryMutator.setRequestUrl(theFhirContext, theRequestUrl);
+	}
+
+	public String getRequestUrl() {
+		return myBundleEntryParts.getUrl();
+	}
+}

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

@@ -1,6 +1,6 @@
-package ca.uhn.fhir.model.primitive;
+package ca.uhn.fhir.validation;
 
-/*
+/*-
  * #%L
  * HAPI FHIR - Core Library
  * %%
@@ -20,19 +20,13 @@ package ca.uhn.fhir.model.primitive;
  * #L%
  */
 
-import ca.uhn.fhir.model.api.IElement;
-import ca.uhn.fhir.model.api.annotation.DatatypeDef;
+/**
+ * This interface marks a {@link IValidatorModule validator module} that uses the FHIR
+ * FhirInstanceValidator as the underlying engine (i.e. it performs
+ * profile validation)
+ */
+public interface IInstanceValidatorModule extends IValidatorModule {
 
-@DatatypeDef(name = "idref")
-public class IdrefDt extends StringDt {
+	// nothing extra yet
 
-	private IElement myTarget;
-
-	public IElement getTarget() {
-		return myTarget;
-	}
-
-	public void setTarget(IElement theTarget) {
-		myTarget = theTarget;
-	}
 }

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

@@ -19,26 +19,32 @@ package ca.uhn.fhir.validation;
  * limitations under the License.
  * #L%
  */
-import java.io.*;
-import java.nio.charset.Charset;
-import java.util.*;
-
-import javax.xml.XMLConstants;
-import javax.xml.transform.Source;
-import javax.xml.transform.stream.StreamSource;
-import javax.xml.validation.*;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.io.input.BOMInputStream;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.w3c.dom.ls.LSInput;
-import org.w3c.dom.ls.LSResourceResolver;
-import org.xml.sax.*;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.BOMInputStream;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.w3c.dom.ls.LSInput;
+import org.w3c.dom.ls.LSResourceResolver;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXNotRecognizedException;
+import org.xml.sax.SAXParseException;
+
+import javax.xml.XMLConstants;
+import javax.xml.transform.Source;
+import javax.xml.transform.stream.StreamSource;
+import javax.xml.validation.Schema;
+import javax.xml.validation.SchemaFactory;
+import javax.xml.validation.Validator;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
+import java.util.*;
 
 public class SchemaBaseValidator implements IValidatorModule {
 	public static final String RESOURCES_JAR_NOTE = "Note that as of HAPI FHIR 1.2, DSTU2 validation files are kept in a separate JAR (hapi-fhir-validation-resources-XXX.jar) which must be added to your classpath. See the HAPI FHIR download page for more information.";
@@ -47,7 +53,7 @@ public class SchemaBaseValidator implements IValidatorModule {
 	private static final Set<String> SCHEMA_NAMES;
 
 	static {
-		HashSet<String> sn = new HashSet<String>();
+		HashSet<String> sn = new HashSet<>();
 		sn.add("xml.xsd");
 		sn.add("xhtml1-strict.xsd");
 		sn.add("fhir-single.xsd");
@@ -59,15 +65,15 @@ public class SchemaBaseValidator implements IValidatorModule {
 		SCHEMA_NAMES = Collections.unmodifiableSet(sn);
 	}
 
-	private Map<String, Schema> myKeyToSchema = new HashMap<String, Schema>();
+	private final Map<String, Schema> myKeyToSchema = new HashMap<>();
 	private FhirContext myCtx;
 
 	public SchemaBaseValidator(FhirContext theContext) {
 		myCtx = theContext;
 	}
 
-	private void doValidate(IValidationContext<?> theContext, String schemaName) {
-		Schema schema = loadSchema("dstu", schemaName);
+	private void doValidate(IValidationContext<?> theContext) {
+		Schema schema = loadSchema();
 
 		try {
 			Validator validator = schema.newValidator();
@@ -99,17 +105,14 @@ public class SchemaBaseValidator implements IValidatorModule {
 			message.setMessage(e.getLocalizedMessage());
 			message.setSeverity(ResultSeverityEnum.FATAL);
 			theContext.addValidationMessage(message);
-		} catch (SAXException e) {
-			// Catch all
-			throw new ConfigurationException("Could not load/parse schema file", e);
-		} catch (IOException e) {
+		} catch (SAXException | IOException e) {
 			// Catch all
 			throw new ConfigurationException("Could not load/parse schema file", e);
 		}
 	}
 
-	private Schema loadSchema(String theVersion, String theSchemaName) {
-		String key = theVersion + "-" + theSchemaName;
+	private Schema loadSchema() {
+		String key = "fhir-single.xsd";
 
 		synchronized (myKeyToSchema) {
 			Schema schema = myKeyToSchema.get(key);
@@ -117,7 +120,7 @@ public class SchemaBaseValidator implements IValidatorModule {
 				return schema;
 			}
 
-			Source baseSource = loadXml(null, theSchemaName);
+			Source baseSource = loadXml("fhir-single.xsd");
 
 			SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
 			schemaFactory.setResourceResolver(new MyResourceResolver());
@@ -129,69 +132,40 @@ public class SchemaBaseValidator implements IValidatorModule {
 					 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
 					 */
 					schemaFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
-				}catch (SAXNotRecognizedException snex){
-					ourLog.warn("Jaxp 1.5 Support not found.",snex);
+				} catch (SAXNotRecognizedException e) {
+					ourLog.warn("Jaxp 1.5 Support not found.", e);
 				}
 				schema = schemaFactory.newSchema(new Source[]{baseSource});
 			} catch (SAXException e) {
-				throw new ConfigurationException("Could not load/parse schema file: " + theSchemaName, e);
+				throw new ConfigurationException("Could not load/parse schema file: " + "fhir-single.xsd", e);
 			}
 			myKeyToSchema.put(key, schema);
 			return schema;
 		}
 	}
 
-	private Source loadXml(String theSystemId, String theSchemaName) {
+	Source loadXml(String theSchemaName) {
 		String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theSchemaName;
 		ourLog.debug("Going to load resource: {}", pathToBase);
-		InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
+		try (InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase)) {
 			if (baseIs == null) {
 				throw new InternalErrorException("Schema not found. " + RESOURCES_JAR_NOTE);
 			}
-		baseIs = new BOMInputStream(baseIs, false);
-		InputStreamReader baseReader = new InputStreamReader(baseIs, Charset.forName("UTF-8"));
-		Source baseSource = new StreamSource(baseReader, theSystemId);
-		//FIXME resource leak
-		return baseSource;
+			try (BOMInputStream bomInputStream = new BOMInputStream(baseIs, false)) {
+				try (InputStreamReader baseReader = new InputStreamReader(bomInputStream, StandardCharsets.UTF_8)) {
+					// Buffer so that we can close the input stream
+					String contents = IOUtils.toString(baseReader);
+					return new StreamSource(new StringReader(contents), null);
+				}
+			}
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
+		}
 	}
 
 	@Override
 	public void validateResource(IValidationContext<IBaseResource> theContext) {
-		doValidate(theContext, "fhir-single.xsd");
-	}
-
-	private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
-
-		private IValidationContext<?> myContext;
-
-		public MyErrorHandler(IValidationContext<?> theContext) {
-			myContext = theContext;
-		}
-
-		private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
-			SingleValidationMessage message = new SingleValidationMessage();
-			message.setLocationLine(theException.getLineNumber());
-			message.setLocationCol(theException.getColumnNumber());
-			message.setMessage(theException.getLocalizedMessage());
-			message.setSeverity(theSeverity);
-			myContext.addValidationMessage(message);
-		}
-
-		@Override
-		public void error(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.ERROR);
-		}
-
-		@Override
-		public void fatalError(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.FATAL);
-		}
-
-		@Override
-		public void warning(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.WARNING);
-		}
-
+		doValidate(theContext);
 	}
 
 	private final class MyResourceResolver implements LSResourceResolver {
@@ -225,4 +199,38 @@ public class SchemaBaseValidator implements IValidatorModule {
 		}
 	}
 
+	private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
+
+		private IValidationContext<?> myContext;
+
+		MyErrorHandler(IValidationContext<?> theContext) {
+			myContext = theContext;
+		}
+
+		private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
+			SingleValidationMessage message = new SingleValidationMessage();
+			message.setLocationLine(theException.getLineNumber());
+			message.setLocationCol(theException.getColumnNumber());
+			message.setMessage(theException.getLocalizedMessage());
+			message.setSeverity(theSeverity);
+			myContext.addValidationMessage(message);
+		}
+
+		@Override
+		public void error(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.ERROR);
+		}
+
+		@Override
+		public void fatalError(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.FATAL);
+		}
+
+		@Override
+		public void warning(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.WARNING);
+		}
+
+	}
+
 }

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

@@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import java.util.Collections;
 import java.util.List;
 
+import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -120,7 +121,19 @@ public class ValidationResult {
 				location = null;
 			}
 			String severity = next.getSeverity() != null ? next.getSeverity().getCode() : null;
-			OperationOutcomeUtil.addIssue(myCtx, theOperationOutcome, severity, next.getMessage(), location, Constants.OO_INFOSTATUS_PROCESSING);
+			IBase issue = OperationOutcomeUtil.addIssue(myCtx, theOperationOutcome, severity, next.getMessage(), location, Constants.OO_INFOSTATUS_PROCESSING);
+			
+			if (next.getLocationLine() != null || next.getLocationCol() != null) {
+				String line = "(unknown)";
+				if (next.getLocationLine() != null) {
+					line = next.getLocationLine().toString();
+				}
+				String col = "(unknown)";
+				if (next.getLocationCol() != null) {
+					col = next.getLocationCol().toString();
+				}
+				OperationOutcomeUtil.addLocationToIssue(myCtx, issue, "Line " + line + ", Col " + col);
+			}
 		}
 
 		if (myMessages.isEmpty()) {

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

@@ -50,14 +50,12 @@ public interface IAnyResource extends IBaseResource {
 
 	String getId();
 
-	@Override
 	IIdType getIdElement();
 
 	IPrimitiveType<String> getLanguageElement();
 
 	Object getUserData(String name);
 
-	@Override
 	IAnyResource setId(String theId);
 
 	void setUserData(String name, Object value);

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

@@ -25,6 +25,8 @@ public interface IBaseBinary extends IBaseResource {
 
 	byte[] getContent();
 
+	IPrimitiveType<byte[]> getContentElement();
+
 	String getContentAsBase64();
 
 	String getContentType();

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

@@ -44,6 +44,6 @@ public interface IBaseEnumFactory<T extends Enum<?>> extends Serializable {
 	/**
 	 * Get the system for a given enum value
 	 */
-	String toSystem(T theValue);
+	default String toSystem(T theValue) { return null; }
 
 }

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

@@ -66,7 +66,7 @@ ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFail
 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.
 
-ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.externalizedBinaryStorageExtensionFoundInRequestBody=Illegal extension found in request payload: {0}
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.externalizedBinaryStorageExtensionFoundInRequestBody=Illegal extension found in request payload - URL "{0}" and value "{1}"
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
@@ -125,9 +125,9 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownPath=Unable to find content
 ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of type {0} at path {1} is not appropriate for binary storage: {2}
 
 
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 
 ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnumTest.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.model.api;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class ResourceMetadataKeyEnumTest {
+
+	@Test
+	public void testHashCode() {
+		assertEquals(-60968467, ResourceMetadataKeyEnum.PUBLISHED.hashCode());
+	}
+
+	@Test
+	public void testEquals() {
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, null);
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, "");
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PUBLISHED);
+		assertEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PROFILES);
+	}
+
+
+	@Test
+	public void testExtensionResourceEquals() {
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://bar"));
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), null);
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), "");
+		assertEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"));
+
+		ResourceMetadataKeyEnum.ExtensionResourceMetadataKey foo = new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo");
+		assertEquals(foo, foo);
+	}
+
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagTest.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.model.api;
+
+import org.junit.Test;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import static org.junit.Assert.*;
+
+public class TagTest {
+
+	@Test
+	public void testEquals() {
+		Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		Tag tag2 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		Tag tag3 = new Tag().setScheme("scheme2").setTerm("term").setLabel("label");
+		Tag tag4 = new Tag().setScheme("scheme").setTerm("term2").setLabel("label");
+
+		assertEquals(tag1, tag1);
+		assertEquals(tag1, tag2);
+		assertNotEquals(tag1, tag3);
+		assertNotEquals(tag1, tag4);
+		assertNotEquals(tag1, null);
+		assertNotEquals(tag1, "");
+	}
+
+	@Test
+	public void testHashCode() {
+		Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		assertEquals(1920714536, tag1.hashCode());
+	}
+
+	@Test
+	public void testConstructors() throws URISyntaxException {
+		assertTrue(new Tag().isEmpty());
+		assertFalse(new Tag("http://foo").isEmpty());
+		assertFalse(new Tag("http://foo", "http://bar").isEmpty());
+		assertFalse(new Tag(new URI("http://foo"), new URI("http://bar"), "Label").isEmpty());
+		assertTrue(new Tag((URI)null, null, "Label").isEmpty());
+
+		assertEquals("http://foo", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getSystem());
+		assertEquals("http://bar", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getCode());
+		assertEquals("Label", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getDisplay());
+	}
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/ConstantsTest.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.rest.api;
+
+import org.junit.Test;
+
+public class ConstantsTest {
+
+	@Test
+	public void testConstants() {
+		new Constants();
+	}
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java

@@ -2,13 +2,34 @@ package ca.uhn.fhir.rest.param;
 
 import org.junit.Test;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 
 public class TokenParamTest {
 	@Test
 	public void testEquals() {
 		TokenParam tokenParam1 = new TokenParam("foo", "bar");
 		TokenParam tokenParam2 = new TokenParam("foo", "bar");
+		TokenParam tokenParam3 = new TokenParam("foo", "baz");
+		assertEquals(tokenParam1, tokenParam1);
 		assertEquals(tokenParam1, tokenParam2);
+		assertNotEquals(tokenParam1, tokenParam3);
+		assertNotEquals(tokenParam1, null);
+		assertNotEquals(tokenParam1, "");
 	}
+
+	@Test
+	public void testHashCode() {
+		TokenParam tokenParam1 = new TokenParam("foo", "bar");
+		assertEquals(4716638, tokenParam1.hashCode());
+	}
+
+
+	@Test
+	public void testIsEmpty() {
+		assertFalse(new TokenParam("foo", "bar").isEmpty());
+		assertTrue(new TokenParam("", "").isEmpty());
+		assertTrue(new TokenParam().isEmpty());
+		assertEquals("", new TokenParam().getValueNotNull());
+	}
+
 }

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

@@ -0,0 +1,62 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.junit.Test;
+
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import static org.awaitility.Awaitility.await;
+
+public class AsyncUtilTest {
+
+	@Test
+	public void testSleep() {
+		AsyncUtil.sleep(10);
+	}
+
+	@Test
+	public void testSleepWithInterrupt() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(true);
+		Thread thread = new Thread(() -> {
+			boolean outcome = AsyncUtil.sleep(10000);
+			outcomeHolder.set(outcome);
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get() == false);
+	}
+
+	@Test
+	public void testAwaitLatchAndThrowInternalErrorException() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(false);
+
+		CountDownLatch latch = new CountDownLatch(1);
+		Thread thread = new Thread(() -> {
+			try {
+				AsyncUtil.awaitLatchAndThrowInternalErrorExceptionOnInterrupt(latch, 10, TimeUnit.SECONDS);
+			} catch (InternalErrorException e) {
+				outcomeHolder.set(true);
+			}
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get());
+	}
+
+	@Test
+	public void testAwaitLatchIgnoreInterruption() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(true);
+
+		CountDownLatch latch = new CountDownLatch(1);
+		Thread thread = new Thread(() -> {
+			boolean outcome = AsyncUtil.awaitLatchAndIgnoreInterrupt(latch, 10, TimeUnit.SECONDS);
+			outcomeHolder.set(outcome);
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get() == false);
+	}
+
+}

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

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.util;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class FileUtilTest {
+
+	@Test
+	public void formatFileSize() {
+		assertEquals("0 Bytes", FileUtil.formatFileSize(0).replace(",", "."));
+		assertEquals("1 Bytes", FileUtil.formatFileSize(1).replace(",", "."));
+		assertEquals("1.2 kB", FileUtil.formatFileSize(1234).replace(",", "."));
+		assertEquals("12.1 kB", FileUtil.formatFileSize(12345).replace(",", "."));
+		assertEquals("11.8 MB", FileUtil.formatFileSize(12345678).replace(",", "."));
+		assertEquals("103.5 GB", FileUtil.formatFileSize(111111111111L).replace(",", "."));
+		assertEquals("101.1 TB", FileUtil.formatFileSize(111111111111111L).replace(",", "."));
+		assertEquals("10105.5 TB", FileUtil.formatFileSize(11111111111111111L).replace(",", "."));
+	}
+}

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

@@ -128,6 +128,56 @@ public class StopWatchTest {
 		assertEquals("TASK1: 500ms\nTASK2: 100ms", taskDurations);
 	}
 
+	@Test
+	public void testFormatTaskDurationsDelayBetweenTasks() {
+		StopWatch sw = new StopWatch();
+
+		StopWatch.setNowForUnitTestForUnitTest(1000L);
+		sw.startTask("TASK1");
+
+		StopWatch.setNowForUnitTestForUnitTest(1500L);
+		sw.endCurrentTask();
+
+		StopWatch.setNowForUnitTestForUnitTest(2000L);
+		sw.startTask("TASK2");
+
+		StopWatch.setNowForUnitTestForUnitTest(2100L);
+		sw.endCurrentTask();
+
+		StopWatch.setNowForUnitTestForUnitTest(2200L);
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("TASK1: 500ms\n" +
+			"Between: 500ms\n" +
+			"TASK2: 100ms\n" +
+			"After last task: 100ms", taskDurations);
+	}
+
+	@Test
+	public void testFormatTaskDurationsLongDelayBeforeStart() {
+		StopWatch sw = new StopWatch(0);
+
+		StopWatch.setNowForUnitTestForUnitTest(1000L);
+		sw.startTask("TASK1");
+
+		StopWatch.setNowForUnitTestForUnitTest(1500L);
+		sw.startTask("TASK2");
+
+		StopWatch.setNowForUnitTestForUnitTest(1600L);
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("Before first task: 1000ms\nTASK1: 500ms\nTASK2: 100ms", taskDurations);
+	}
+
+	@Test
+	public void testFormatTaskDurationsNoTasks() {
+		StopWatch sw = new StopWatch(0);
+
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("No tasks", taskDurations);
+	}
+
 	@Test
 	public void testFormatThroughput60Ops4Min() {
 		StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
@@ -210,4 +260,34 @@ public class StopWatchTest {
 		assertThat(string, matchesPattern("^[0-9]{3,4}ms$"));
 	}
 
+
+	@Test
+	public void testAppendRightAlignedNumber() {
+		StringBuilder b= new StringBuilder();
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 0, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 1, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 2, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 3, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 4, 100);
+		assertEquals("PFX0100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 10, 100);
+		assertEquals("PFX0000000100", b.toString());
+	}
+
 }

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

@@ -248,6 +248,13 @@
 			<artifactId>jansi</artifactId>
 		</dependency>
 
+		<!-- Test Deps -->
+		<dependency>
+			<groupId>org.awaitility</groupId>
+			<artifactId>awaitility</artifactId>
+			<scope>test</scope>
+		</dependency>
+
 	</dependencies>
 
 	<build>

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

@@ -398,7 +398,7 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 	}
 
 	protected IGenericClient newClientWithBaseUrl(CommandLine theCommandLine, String theBaseUrl, String theBasicAuthOptionName, String theBearerTokenOptionName) throws ParseException {
-		myFhirCtx.getRestfulClientFactory().setSocketTimeout(10 * 60 * 1000);
+		myFhirCtx.getRestfulClientFactory().setSocketTimeout((int) DateUtils.MILLIS_PER_HOUR);
 		IGenericClient retVal = myFhirCtx.newRestfulGenericClient(theBaseUrl);
 
 		String basicAuthHeaderValue = getAndParseOptionBasicAuthHeader(theCommandLine, theBasicAuthOptionName);

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

@@ -55,6 +55,7 @@ import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
@@ -79,7 +80,7 @@ public class ExampleDataUploader extends BaseCommand {
 		}
 	}
 
-	private Bundle getBundleFromFileDstu2(Integer limit, File inputFile, FhirContext ctx) throws IOException, UnsupportedEncodingException {
+	private Bundle getBundleFromFileDstu2(Integer limit, File inputFile, FhirContext ctx) throws IOException {
 
 		Bundle bundle = new Bundle();
 
@@ -98,13 +99,13 @@ public class ExampleDataUploader extends BaseCommand {
 				break;
 			}
 
-			int len = 0;
+			int len;
 			ByteArrayOutputStream bos = new ByteArrayOutputStream();
 			while ((len = zis.read(buffer)) > 0) {
 				bos.write(buffer, 0, len);
 			}
 			byte[] exampleBytes = bos.toByteArray();
-			String exampleString = new String(exampleBytes, "UTF-8");
+			String exampleString = new String(exampleBytes, StandardCharsets.UTF_8);
 
 			if (ourLog.isTraceEnabled()) {
 				ourLog.trace("Next example: " + exampleString);
@@ -145,7 +146,7 @@ public class ExampleDataUploader extends BaseCommand {
 	}
 
 	@SuppressWarnings("unchecked")
-	private org.hl7.fhir.dstu3.model.Bundle getBundleFromFileDstu3(Integer limit, File inputFile, FhirContext ctx) throws IOException, UnsupportedEncodingException {
+	private org.hl7.fhir.dstu3.model.Bundle getBundleFromFileDstu3(Integer limit, File inputFile, FhirContext ctx) throws IOException {
 
 		org.hl7.fhir.dstu3.model.Bundle bundle = new org.hl7.fhir.dstu3.model.Bundle();
 		bundle.setType(BundleType.TRANSACTION);
@@ -168,13 +169,13 @@ public class ExampleDataUploader extends BaseCommand {
 				break;
 			}
 
-			int len = 0;
+			int len;
 			ByteArrayOutputStream bos = new ByteArrayOutputStream();
 			while ((len = zis.read(buffer)) > 0) {
 				bos.write(buffer, 0, len);
 			}
 			byte[] exampleBytes = bos.toByteArray();
-			String exampleString = new String(exampleBytes, "UTF-8");
+			String exampleString = new String(exampleBytes, StandardCharsets.UTF_8);
 
 			if (ourLog.isTraceEnabled()) {
 				ourLog.trace("Next example: " + exampleString);
@@ -229,7 +230,7 @@ public class ExampleDataUploader extends BaseCommand {
 	}
 
 	@SuppressWarnings("unchecked")
-	private org.hl7.fhir.r4.model.Bundle getBundleFromFileR4(Integer limit, File inputFile, FhirContext ctx) throws IOException, UnsupportedEncodingException {
+	private org.hl7.fhir.r4.model.Bundle getBundleFromFileR4(Integer limit, File inputFile, FhirContext ctx) throws IOException {
 
 		org.hl7.fhir.r4.model.Bundle bundle = new org.hl7.fhir.r4.model.Bundle();
 		bundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);
@@ -252,13 +253,13 @@ public class ExampleDataUploader extends BaseCommand {
 				break;
 			}
 
-			int len = 0;
+			int len;
 			ByteArrayOutputStream bos = new ByteArrayOutputStream();
 			while ((len = zis.read(buffer)) > 0) {
 				bos.write(buffer, 0, len);
 			}
 			byte[] exampleBytes = bos.toByteArray();
-			String exampleString = new String(exampleBytes, "UTF-8");
+			String exampleString = new String(exampleBytes, StandardCharsets.UTF_8);
 
 			if (ourLog.isTraceEnabled()) {
 				ourLog.trace("Next example: " + exampleString);
@@ -369,8 +370,7 @@ public class ExampleDataUploader extends BaseCommand {
 
 	private void processBundleDstu2(FhirContext ctx, Bundle bundle) {
 
-		Map<String, Integer> ids = new HashMap<String, Integer>();
-		Set<String> fullIds = new HashSet<String>();
+		Set<String> fullIds = new HashSet<>();
 
 		for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
 			Entry next = iterator.next();
@@ -397,13 +397,14 @@ public class ExampleDataUploader extends BaseCommand {
 				}
 			}
 		}
-		Set<String> qualIds = new TreeSet<String>();
-		for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
-			Entry next = iterator.next();
+		Set<String> qualIds = new TreeSet<>();
+
+		for (Entry next : bundle.getEntry()) {
 			if (next.getResource().getId().getIdPart() != null) {
 				String nextId = next.getResource().getId().getValue();
 				next.getRequest().setMethod(HTTPVerbEnum.PUT);
 				next.getRequest().setUrl(nextId);
+				qualIds.add(nextId);
 			}
 		}
 
@@ -449,15 +450,14 @@ public class ExampleDataUploader extends BaseCommand {
 
 	private void processBundleDstu3(FhirContext ctx, org.hl7.fhir.dstu3.model.Bundle bundle) {
 
-		Map<String, Integer> ids = new HashMap<String, Integer>();
-		Set<String> fullIds = new HashSet<String>();
+		Set<String> fullIds = new HashSet<>();
 
 		for (Iterator<BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
 			BundleEntryComponent next = iterator.next();
 
 			// DataElement have giant IDs that seem invalid, need to investigate this..
-			if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType())
-				|| "OperationOutcome".equals(next.getResource().getResourceType()) || "OperationDefinition".equals(next.getResource().getResourceType())) {
+			if ("Subscription".equals(next.getResource().getResourceType().name()) || "DataElement".equals(next.getResource().getResourceType().name())
+				|| "OperationOutcome".equals(next.getResource().getResourceType().name()) || "OperationDefinition".equals(next.getResource().getResourceType().name())) {
 				ourLog.info("Skipping " + next.getResource().getResourceType() + " example");
 				iterator.remove();
 			} else {
@@ -477,13 +477,13 @@ public class ExampleDataUploader extends BaseCommand {
 				}
 			}
 		}
-		Set<String> qualIds = new TreeSet<String>();
-		for (Iterator<BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
-			BundleEntryComponent next = iterator.next();
+		Set<String> qualIds = new TreeSet<>();
+		for (BundleEntryComponent next : bundle.getEntry()) {
 			if (next.getResource().getIdElement().getIdPart() != null) {
 				String nextId = next.getResource().getIdElement().getValue();
 				next.getRequest().setMethod(HTTPVerb.PUT);
 				next.getRequest().setUrl(nextId);
+				qualIds.add(nextId);
 			}
 		}
 
@@ -529,15 +529,14 @@ public class ExampleDataUploader extends BaseCommand {
 
 	private void processBundleR4(FhirContext ctx, org.hl7.fhir.r4.model.Bundle bundle) {
 
-		Map<String, Integer> ids = new HashMap<String, Integer>();
-		Set<String> fullIds = new HashSet<String>();
+		Set<String> fullIds = new HashSet<>();
 
 		for (Iterator<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
 			org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next = iterator.next();
 
 			// DataElement have giant IDs that seem invalid, need to investigate this..
-			if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType())
-				|| "OperationOutcome".equals(next.getResource().getResourceType()) || "OperationDefinition".equals(next.getResource().getResourceType())) {
+			if ("Subscription".equals(next.getResource().getResourceType().name()) || "DataElement".equals(next.getResource().getResourceType().name())
+				|| "OperationOutcome".equals(next.getResource().getResourceType().name()) || "OperationDefinition".equals(next.getResource().getResourceType().name())) {
 				ourLog.info("Skipping " + next.getResource().getResourceType() + " example");
 				iterator.remove();
 			} else {
@@ -557,13 +556,13 @@ public class ExampleDataUploader extends BaseCommand {
 				}
 			}
 		}
-		Set<String> qualIds = new TreeSet<String>();
-		for (Iterator<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
-			org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next = iterator.next();
+		Set<String> qualIds = new TreeSet<>();
+		for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next : bundle.getEntry()) {
 			if (next.getResource().getIdElement().getIdPart() != null) {
 				String nextId = next.getResource().getIdElement().getValue();
 				next.getRequest().setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT);
 				next.getRequest().setUrl(nextId);
+				qualIds.add(nextId);
 			}
 		}
 
@@ -635,7 +634,7 @@ public class ExampleDataUploader extends BaseCommand {
 
 		boolean cacheFile = theCommandLine.hasOption('c');
 
-		Collection<File> inputFiles = null;
+		Collection<File> inputFiles;
 		try {
 			inputFiles = loadFile(specUrl, filepath, cacheFile);
 			for (File inputFile : inputFiles) {
@@ -694,13 +693,11 @@ public class ExampleDataUploader extends BaseCommand {
 						continue;
 					}
 
-					boolean found = false;
 					for (int j = 0; j < resources.size(); j++) {
 						String candidateTarget = resources.get(j).getIdElement().getValue();
 						if (isNotBlank(nextTarget) && nextTarget.equals(candidateTarget)) {
 							ourLog.info("Reflexively adding resource {} to bundle as it is a reference target", nextTarget);
 							subResourceList.add(resources.remove(j));
-							found = true;
 							break;
 						}
 					}

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

@@ -123,16 +123,13 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 	private void convertConceptMapToCsv(ConceptMap theConceptMap) {
 		Path path = Paths.get(file);
 		ourLog.info("Exporting ConceptMap to CSV: {}", path);
-		try (
-			Writer writer = Files.newBufferedWriter(path);
-			CSVPrinter csvPrinter = new CSVPrinter(
-				writer,
-				CSVFormat
-					.DEFAULT
+		try (Writer writer = Files.newBufferedWriter(path)) {
+
+			CSVFormat format = CSVFormat.DEFAULT
 				.withRecordSeparator("\n")
 				.withHeader(Header.class)
-					.withQuoteMode(QuoteMode.ALL));
-		) {
+				.withQuoteMode(QuoteMode.ALL);
+			try (CSVPrinter csvPrinter = new CSVPrinter(writer, format)) {
 				for (ConceptMapGroupComponent group : theConceptMap.getGroup()) {
 					for (SourceElementComponent element : group.getElement()) {
 						for (ConceptMap.TargetElementComponent target : element.getTarget()) {
@@ -153,6 +150,8 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 						}
 					}
 				}
+				csvPrinter.flush();
+			}
 		} catch (IOException ioe) {
 			throw new InternalErrorException(ioe);
 		}

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java

@@ -91,7 +91,7 @@ public class LoadingValidationSupportDstu3 implements IValidationSupport {
 	}
 
 	@Override
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
 		return null;
 	}
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportR4.java

@@ -98,7 +98,7 @@ public class LoadingValidationSupportR4 implements org.hl7.fhir.r4.hapi.ctx.IVal
 	}
 
 	@Override
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSet) {
 		return null;
 	}
 

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

@@ -20,7 +20,7 @@ package ca.uhn.fhir.cli;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -44,7 +44,7 @@ public class ToggleSearchParametersCommand extends BaseCommand {
 		Options options = new Options();
 		addFhirVersionOption(options);
 		addBaseUrlOption(options);
-		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
+		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
 		addBasicAuthOption(options);
 		return options;
 	}

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

@@ -20,30 +20,48 @@ package ca.uhn.fhir.cli;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.util.AttachmentUtil;
+import ca.uhn.fhir.util.FileUtil;
 import ca.uhn.fhir.util.ParametersUtil;
+import com.google.common.annotations.VisibleForTesting;
+import com.google.common.base.Charsets;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.CountingInputStream;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.ICompositeType;
+import org.hl7.fhir.r4.model.CodeSystem;
+
+import java.io.*;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class UploadTerminologyCommand extends BaseCommand {
-	// TODO: Don't use qualified names for loggers in HAPI CLI.
+	static final String UPLOAD_TERMINOLOGY = "upload-terminology";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
-	private static final String UPLOAD_EXTERNAL_CODE_SYSTEM = "upload-external-code-system";
+	private static final long DEFAULT_TRANSFER_SIZE_LIMIT = 10 * FileUtils.ONE_MB;
+	private static long ourTransferSizeLimit = DEFAULT_TRANSFER_SIZE_LIMIT;
 
 	@Override
 	public String getCommandDescription() {
-		return "Uploads a terminology package (e.g. a SNOMED CT ZIP file) to a server, using the $" + UPLOAD_EXTERNAL_CODE_SYSTEM + " operation.";
+		return "Uploads a terminology package (e.g. a SNOMED CT ZIP file or a custom terminology bundle) to a server, using the appropriate operation.";
 	}
 
 	@Override
 	public String getCommandName() {
-		return "upload-terminology";
+		return UPLOAD_TERMINOLOGY;
 	}
 
 	@Override
@@ -52,9 +70,9 @@ public class UploadTerminologyCommand extends BaseCommand {
 
 		addFhirVersionOption(options);
 		addBaseUrlOption(options);
-		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
+		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
 		addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
-		addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
+		addOptionalOption(options, "m", "mode", true, "The upload mode: SNAPSHOT (default), ADD, REMOVE");
 		addBasicAuthOption(options);
 		addVerboseLoggingOption(options);
 
@@ -65,6 +83,14 @@ public class UploadTerminologyCommand extends BaseCommand {
 	public void run(CommandLine theCommandLine) throws ParseException {
 		parseFhirContext(theCommandLine);
 
+		ModeEnum mode;
+		String modeString = theCommandLine.getOptionValue("m", "SNAPSHOT");
+		try {
+			mode = ModeEnum.valueOf(modeString);
+		} catch (IllegalArgumentException e) {
+			throw new ParseException("Invalid mode: " + modeString);
+		}
+
 		String termUrl = theCommandLine.getOptionValue("u");
 		if (isBlank(termUrl)) {
 			throw new ParseException("No URL provided");
@@ -77,29 +103,166 @@ public class UploadTerminologyCommand extends BaseCommand {
 
 		IGenericClient client = super.newClient(theCommandLine);
 		IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
-		ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, "url", termUrl);
-		for (String next : datafile) {
-			ParametersUtil.addParameterToParametersString(myFhirCtx, inputParameters, "localfile", next);
-		}
-		if (theCommandLine.hasOption("custom")) {
-			ParametersUtil.addParameterToParametersCode(myFhirCtx, inputParameters, "contentMode", "custom");
-		}
 
 		if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {
 			client.registerInterceptor(new LoggingInterceptor(true));
 		}
 
+		switch (mode) {
+			case SNAPSHOT:
+				invokeOperation(termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM);
+				break;
+			case ADD:
+				invokeOperation(termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD);
+				break;
+			case REMOVE:
+				invokeOperation(termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE);
+				break;
+		}
+
+	}
+
+	private void invokeOperation(String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName) throws ParseException {
+		ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
+
+		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+		ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
+		int compressedSourceBytesCount = 0;
+		int compressedFileCount = 0;
+		boolean haveCompressedContents = false;
+		try {
+			for (String nextDataFile : theDatafile) {
+
+				try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
+					if (nextDataFile.endsWith(".csv")) {
+
+						ourLog.info("Compressing and adding file: {}", nextDataFile);
+						ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
+						zipOutputStream.putNextEntry(nextEntry);
+
+						CountingInputStream countingInputStream = new CountingInputStream(fileInputStream);
+						IOUtils.copy(countingInputStream, zipOutputStream);
+						haveCompressedContents = true;
+						compressedSourceBytesCount += countingInputStream.getCount();
+
+						zipOutputStream.flush();
+						ourLog.info("Finished compressing {}", nextDataFile);
+
+					} else if (nextDataFile.endsWith(".zip")) {
+
+						ourLog.info("Adding ZIP file: {}", nextDataFile);
+						String fileName = "file:" + nextDataFile;
+						addFileToRequestBundle(theInputParameters, fileName, IOUtils.toByteArray(fileInputStream));
+
+					} else if (nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml")) {
+
+						ourLog.info("Adding CodeSystem resource file: {}", nextDataFile);
+
+						String contents = IOUtils.toString(fileInputStream, Charsets.UTF_8);
+						EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(contents);
+						if (encoding == null) {
+							throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
+						}
+
+						CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
+						ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
+
+					} else {
+
+						throw new ParseException("Don't know how to handle file: " + nextDataFile);
+
+					}
+				}
+
+			}
+			zipOutputStream.flush();
+			zipOutputStream.close();
+		} catch (IOException e) {
+			throw new ParseException(e.toString());
+		}
+
+		if (haveCompressedContents) {
+			byte[] compressedBytes = byteArrayOutputStream.toByteArray();
+			ourLog.info("Compressed {} bytes in {} file(s) into {} bytes", FileUtil.formatFileSize(compressedSourceBytesCount), compressedFileCount, FileUtil.formatFileSize(compressedBytes.length));
+
+			addFileToRequestBundle(theInputParameters, "file:/files.zip", compressedBytes);
+		}
+
 		ourLog.info("Beginning upload - This may take a while...");
 
-		IBaseParameters response = client
+		if (ourLog.isDebugEnabled() || "true".equals(System.getProperty("test"))) {
+			ourLog.info("Submitting parameters: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theInputParameters));
+		}
+
+		IBaseParameters response;
+		try {
+			response = theClient
 				.operation()
 				.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
-			.named(UPLOAD_EXTERNAL_CODE_SYSTEM)
-			.withParameters(inputParameters)
+				.named(theOperationName)
+				.withParameters(theInputParameters)
 				.execute();
+		} catch (BaseServerResponseException e) {
+			if (e.getOperationOutcome() != null) {
+				ourLog.error("Received the following response:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+			}
+			throw e;
+		}
+
 
 		ourLog.info("Upload complete!");
 		ourLog.info("Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
 	}
 
+	private void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
+
+		byte[] bytes = theBytes;
+		String fileName = theFileName;
+
+		if (bytes.length > ourTransferSizeLimit) {
+			ourLog.info("File size is greater than {} - Going to use a local file reference instead of a direct HTTP transfer. Note that this will only work when executing this command on the same server as the FHIR server itself.", FileUtil.formatFileSize(ourTransferSizeLimit));
+
+			String suffix = fileName.substring(fileName.lastIndexOf("."));
+			try {
+				File tempFile = File.createTempFile("hapi-fhir-cli", suffix);
+				tempFile.deleteOnExit();
+				try (OutputStream fileOutputStream = new FileOutputStream(tempFile, false)) {
+					fileOutputStream.write(bytes);
+					bytes = null;
+					fileName = "localfile:" + tempFile.getAbsolutePath();
+				}
+			} catch (IOException e) {
+				throw new CommandFailureException(e);
+			}
+		}
+
+		ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
+		AttachmentUtil.setUrl(myFhirCtx, attachment, fileName);
+		if (bytes != null) {
+			AttachmentUtil.setData(myFhirCtx, attachment, bytes);
+		}
+		ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
+	}
+
+	private enum ModeEnum {
+		SNAPSHOT, ADD, REMOVE
+	}
+
+	@VisibleForTesting
+	static void setTransferSizeLimitForUnitTest(long theTransferSizeLimit) {
+		if (theTransferSizeLimit <= 0) {
+			ourTransferSizeLimit = DEFAULT_TRANSFER_SIZE_LIMIT;
+		}else {
+			ourTransferSizeLimit = theTransferSizeLimit;
+		}
+	}
+
+	static String stripPath(String thePath) {
+		String retVal = thePath;
+		if (retVal.contains("/")) {
+			retVal = retVal.substring(retVal.lastIndexOf("/"));
+		}
+		return retVal;
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml

@@ -34,7 +34,13 @@
 	<!--
 	It's useful to have this log when uploading big terminologies
 	-->
-	<logger name="ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl" additivity="false" level="info">
+	<logger name="ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+	<logger name="ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
+	<logger name="ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl" additivity="false" level="info">
 		<appender-ref ref="STDOUT" />
 	</logger>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandDstu3Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
+import ca.uhn.fhir.test.utilities.JettyUtil;
 import ca.uhn.fhir.test.utilities.LoggingRule;
 import ca.uhn.fhir.util.TestUtil;
 import com.google.common.base.Charsets;
@@ -24,10 +25,9 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 
+import static org.awaitility.Awaitility.await;
 import static org.junit.Assert.assertEquals;
 
-import ca.uhn.fhir.test.utilities.JettyUtil;
-
 public class ExportConceptMapToCsvCommandDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandDstu3Test.class);
 	private static final String CM_URL = "http://example.com/conceptmap";
@@ -36,7 +36,7 @@ public class ExportConceptMapToCsvCommandDstu3Test {
 	private static final String CS_URL_1 = "http://example.com/codesystem/1";
 	private static final String CS_URL_2 = "http://example.com/codesystem/2";
 	private static final String CS_URL_3 = "http://example.com/codesystem/3";
-	private static final String FILE = "./target/output.csv";
+	private static final String FILE = "./target/output_dstu3.csv";
 
 	private static String ourBase;
 	private static IGenericClient ourClient;
@@ -44,13 +44,47 @@ public class ExportConceptMapToCsvCommandDstu3Test {
 	private static int ourPort;
 	private static Server ourServer;
 	private static String ourVersion = "dstu3";
-	@Rule
-	public LoggingRule myLoggingRule = new LoggingRule();
 
 	static {
 		System.setProperty("test", "true");
 	}
 
+	@Rule
+	public LoggingRule myLoggingRule = new LoggingRule();
+
+	@Test
+	public void testExportConceptMapToCsvCommand() throws IOException {
+		ourLog.debug("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
+
+		App.main(new String[]{"export-conceptmap-to-csv",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", CM_URL,
+			"-f", FILE,
+			"-l"});
+		await().until(() -> new File(FILE).exists());
+
+		String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
+
+		ourLog.info("Going to read file: {}", FILE);
+		String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
+		assertEquals(expected, result);
+
+		FileUtils.deleteQuietly(new File(FILE));
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
 		JettyUtil.closeServer(ourServer);
@@ -81,38 +115,6 @@ public class ExportConceptMapToCsvCommandDstu3Test {
 		ourClient.create().resource(createConceptMap()).execute();
 	}
 
-	@Test
-	public void testExportConceptMapToCsvCommand() throws IOException {
-		ourLog.debug("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
-
-		App.main(new String[] {"export-conceptmap-to-csv",
-			"-v", ourVersion,
-			"-t", ourBase,
-			"-u", CM_URL,
-			"-f", FILE,
-			"-l"});
-
-		String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
-
-		ourLog.info("Going to read file: {}", FILE);
-		String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
-		assertEquals(expected, result);
-
-		FileUtils.deleteQuietly(new File(FILE));
-	}
-
 	static ConceptMap createConceptMap() {
 		ConceptMap conceptMap = new ConceptMap();
 		conceptMap

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandR4Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
+import ca.uhn.fhir.test.utilities.JettyUtil;
 import ca.uhn.fhir.util.TestUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.FileUtils;
@@ -22,10 +23,9 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 
+import static org.awaitility.Awaitility.await;
 import static org.junit.Assert.assertEquals;
 
-import ca.uhn.fhir.test.utilities.JettyUtil;
-
 public class ExportConceptMapToCsvCommandR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandR4Test.class);
 	private static final String CM_URL = "http://example.com/conceptmap";
@@ -34,7 +34,7 @@ public class ExportConceptMapToCsvCommandR4Test {
 	private static final String CS_URL_1 = "http://example.com/codesystem/1";
 	private static final String CS_URL_2 = "http://example.com/codesystem/2";
 	private static final String CS_URL_3 = "http://example.com/codesystem/3";
-	private static final String FILE = new File("./target/output.csv").getAbsolutePath();
+	private static final String FILE = new File("./target/output_r4.csv").getAbsolutePath();
 
 	private static String ourBase;
 	private static IGenericClient ourClient;
@@ -47,6 +47,37 @@ public class ExportConceptMapToCsvCommandR4Test {
 		System.setProperty("test", "true");
 	}
 
+	@Test
+	public void testExportConceptMapToCsvCommand() throws IOException {
+		ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
+
+		App.main(new String[]{"export-conceptmap-to-csv",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", CM_URL,
+			"-f", FILE,
+			"-l"});
+		await().until(() -> new File(FILE).exists());
+
+		String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
+		String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
+		assertEquals(expected, result);
+
+		FileUtils.deleteQuietly(new File(FILE));
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
 		JettyUtil.closeServer(ourServer);
@@ -77,36 +108,6 @@ public class ExportConceptMapToCsvCommandR4Test {
 		ourClient.create().resource(createConceptMap()).execute();
 	}
 
-	@Test
-	public void testExportConceptMapToCsvCommand() throws IOException {
-		ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
-
-		App.main(new String[] {"export-conceptmap-to-csv",
-			"-v", ourVersion,
-			"-t", ourBase,
-			"-u", CM_URL,
-			"-f", FILE,
-			"-l"});
-
-		String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
-			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
-		String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
-		assertEquals(expected, result);
-
-		FileUtils.deleteQuietly(new File(FILE));
-	}
-
 	static ConceptMap createConceptMap() {
 		ConceptMap conceptMap = new ConceptMap();
 		conceptMap

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java

@@ -0,0 +1,367 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.test.BaseTest;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.term.UploadStatistics;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hamcrest.Matchers;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.io.*;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.matchesPattern;
+import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.*;
+
+@RunWith(MockitoJUnitRunner.class)
+public class UploadTerminologyCommandTest extends BaseTest {
+
+	static {
+		System.setProperty("test", "true");
+	}
+
+	private Server myServer;
+	private FhirContext myCtx = FhirContext.forR4();
+	@Mock
+	private ITermLoaderSvc myTermLoaderSvc;
+	@Captor
+	private ArgumentCaptor<List<ITermLoaderSvc.FileDescriptor>> myDescriptorListCaptor;
+
+	private int myPort;
+	private String myConceptsFileName = "target/concepts.csv";
+	private File myConceptsFile = new File(myConceptsFileName);
+	private String myHierarchyFileName = "target/hierarchy.csv";
+	private File myHierarchyFile = new File(myHierarchyFileName);
+	private String myCodeSystemFileName = "target/codesystem.json";
+	private File myCodeSystemFile = new File(myCodeSystemFileName);
+	private String myTextFileName = "target/hello.txt";
+	private File myTextFile = new File(myTextFileName);
+	private File myArchiveFile;
+	private String myArchiveFileName;
+
+	@Test
+	public void testDeltaAdd() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "ADD",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
+
+	@Test
+	public void testDeltaAddUsingCodeSystemResource() throws IOException {
+
+		try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+			CodeSystem cs = new CodeSystem();
+			cs.addConcept().setCode("CODE").setDisplay("Display");
+			myCtx.newJsonParser().encodeResourceToWriter(cs, w);
+		}
+
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "ADD",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myCodeSystemFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("concepts.csv", listOfDescriptors.get(0).getFilename());
+		String uploadFile = IOUtils.toString(listOfDescriptors.get(0).getInputStream(), Charsets.UTF_8);
+		assertThat(uploadFile, containsString("CODE,Display"));
+	}
+
+	@Test
+	public void testDeltaAddInvalidResource() throws IOException {
+
+		try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+			Patient patient = new Patient();
+			patient.setActive(true);
+			myCtx.newJsonParser().encodeResourceToWriter(patient, w);
+		}
+
+		try {
+			App.main(new String[]{
+				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+				"-v", "r4",
+				"-m", "ADD",
+				"-t", "http://localhost:" + myPort,
+				"-u", "http://foo",
+				"-d", myCodeSystemFileName
+			});
+			fail();
+		} catch (Error e) {
+			assertThat(e.toString(), containsString("Incorrect resource type found, expected \"CodeSystem\" but found \"Patient\""));
+		}
+	}
+
+	@Test
+	public void testDeltaAddInvalidFileType() throws IOException {
+
+		try (FileWriter w = new FileWriter(myTextFileName, false)) {
+			w.append("Help I'm a Bug");
+		}
+
+		try {
+			App.main(new String[]{
+				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+				"-v", "r4",
+				"-m", "ADD",
+				"-t", "http://localhost:" + myPort,
+				"-u", "http://foo",
+				"-d", myTextFileName
+			});
+			fail();
+		} catch (Error e) {
+			assertThat(e.toString(), containsString("Don't know how to handle file:"));
+		}
+	}
+
+	@Test
+	public void testDeltaAddUsingCompressedFile() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+		writeArchiveFile(myConceptsFile, myHierarchyFile);
+
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "ADD",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myArchiveFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern("^file:.*temp.*\\.zip$"));
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
+
+	@Test
+	public void testDeltaAddInvalidFileName() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+
+		try {
+			App.main(new String[]{
+				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+				"-v", "r4",
+				"-m", "ADD",
+				"-t", "http://localhost:" + myPort,
+				"-u", "http://foo",
+				"-d", myConceptsFileName + "/foo.csv",
+				"-d", myHierarchyFileName
+			});
+		} catch (Error e) {
+			assertThat(e.toString(), Matchers.containsString("FileNotFoundException: target/concepts.csv/foo.csv"));
+		}
+	}
+
+	@Test
+	public void testDeltaRemove() throws IOException {
+		writeConceptAndHierarchyFiles();
+
+		when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "REMOVE",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadDeltaRemove(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+
+	}
+
+	@Test
+	public void testSnapshot() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+
+		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "SNAPSHOT",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadCustom(any(), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
+
+	/**
+	 * When transferring large files, we use a local file to store the binary instead of
+	 * using HTTP to transfer a giant base 64 encoded attachment. Hopefully we can
+	 * replace this with a bulk data import at some point when that gets implemented.
+	 */
+	@Test
+	public void testSnapshotLargeFile() throws IOException {
+		UploadTerminologyCommand.setTransferSizeLimitForUnitTest(10);
+
+		writeConceptAndHierarchyFiles();
+
+		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "SNAPSHOT",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadCustom(any(), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern(".*\\.zip$"));
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
+
+	private void writeArchiveFile(File... theFiles) throws IOException {
+		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+		ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
+
+		for (File next : theFiles) {
+			ZipEntry nextEntry = new ZipEntry(UploadTerminologyCommand.stripPath(next.getAbsolutePath()));
+			zipOutputStream.putNextEntry(nextEntry);
+
+			try (FileInputStream fileInputStream = new FileInputStream(next)) {
+				IOUtils.copy(fileInputStream, zipOutputStream);
+			}
+
+		}
+
+		zipOutputStream.flush();
+		zipOutputStream.close();
+
+		myArchiveFile = File.createTempFile("temp", ".zip");
+		myArchiveFile.deleteOnExit();
+		myArchiveFileName = myArchiveFile.getAbsolutePath();
+		try (FileOutputStream fos = new FileOutputStream(myArchiveFile, false)) {
+			fos.write(byteArrayOutputStream.toByteArray());
+		}
+	}
+
+
+	private void writeConceptAndHierarchyFiles() throws IOException {
+		try (FileWriter w = new FileWriter(myConceptsFile, false)) {
+			w.append("CODE,DISPLAY\n");
+			w.append("ANIMALS,Animals\n");
+			w.append("CATS,Cats\n");
+			w.append("DOGS,Dogs\n");
+		}
+
+		try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
+			w.append("PARENT,CHILD\n");
+			w.append("ANIMALS,CATS\n");
+			w.append("ANIMALS,DOGS\n");
+		}
+	}
+
+
+	@After
+	public void after() throws Exception {
+		JettyUtil.closeServer(myServer);
+
+		FileUtils.deleteQuietly(myConceptsFile);
+		FileUtils.deleteQuietly(myHierarchyFile);
+		FileUtils.deleteQuietly(myArchiveFile);
+		FileUtils.deleteQuietly(myCodeSystemFile);
+		FileUtils.deleteQuietly(myTextFile);
+
+		UploadTerminologyCommand.setTransferSizeLimitForUnitTest(-1);
+	}
+
+	@Before
+	public void before() throws Exception {
+		myServer = new Server(0);
+
+		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(myCtx);
+		servlet.registerProvider(provider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		myServer.setHandler(proxyHandler);
+		JettyUtil.startServer(myServer);
+		myPort = JettyUtil.getPortForStartedServer(myServer);
+
+	}
+
+
+}

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

@@ -51,17 +51,12 @@ public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResp
 		this.myResponse = theResponse;
 	}
 
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if (myEntityBuffered) {
 			return;
 		}
-		InputStream responseEntity = readEntity();
+		try (InputStream responseEntity = readEntity()) {
 			if (responseEntity != null) {
 				myEntityBuffered = true;
 				try {
@@ -71,6 +66,7 @@ public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResp
 				}
 			}
 		}
+	}
 
 	@Override
 	public void close() {

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

@@ -87,11 +87,13 @@ public class ApacheHttpClient extends BaseHttpClient implements IHttpClient {
 	}
 
 
+	@Override
 	protected IHttpRequest createHttpRequest() {
 		IHttpRequest retVal = createHttpRequest((HttpEntity)null);
 		return retVal;
 	}
 
+	@Override
 	protected IHttpRequest createHttpRequest(byte[] content) {
 		/*
 		 * Note: Be careful about changing which constructor we use for
@@ -109,6 +111,7 @@ public class ApacheHttpClient extends BaseHttpClient implements IHttpClient {
 		return result;
 	}
 
+	@Override
 	protected IHttpRequest createHttpRequest(Map<String, List<String>> theParams) {
 		List<NameValuePair> parameters = new ArrayList<NameValuePair>();
 		for (Entry<String, List<String>> nextParam : theParams.entrySet()) {
@@ -124,6 +127,7 @@ public class ApacheHttpClient extends BaseHttpClient implements IHttpClient {
 	}
 
 
+	@Override
 	protected IHttpRequest createHttpRequest(String theContents) {
 		/*
 		 * We aren't using a StringEntity here because the constructors

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.rest.client.apache;
  */
 import java.io.*;
 import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 
 import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
@@ -53,28 +54,22 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 		this.myResponse = theResponse;
 	}
 
-	@Deprecated // override deprecated method
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if (myEntityBuffered) {
 			return;
 		}
-		InputStream respEntity = readEntity();
+		try (InputStream respEntity = readEntity()) {
 			if (respEntity != null) {
 				this.myEntityBuffered = true;
 				try {
 					this.myEntityBytes = IOUtils.toByteArray(respEntity);
 				} catch (IllegalStateException e) {
-				// FIXME resouce leak
 					throw new InternalErrorException(e);
 				}
 			}
 		}
+	}
 
 	@Override
 	public void close() {
@@ -103,7 +98,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 			if (Constants.STATUS_HTTP_204_NO_CONTENT != myResponse.getStatusLine().getStatusCode()) {
 				ourLog.debug("Response did not specify a charset, defaulting to utf-8");
 			}
-			charset = Charset.forName("UTF-8");
+			charset = StandardCharsets.UTF_8;
 		}
 
 		return new InputStreamReader(readEntity(), charset);
@@ -115,11 +110,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 		if (myResponse.getAllHeaders() != null) {
 			for (Header next : myResponse.getAllHeaders()) {
 				String name = next.getName().toLowerCase();
-				List<String> list = headers.get(name);
-				if (list == null) {
-					list = new ArrayList<>();
-					headers.put(name, list);
-				}
+				List<String> list = headers.computeIfAbsent(name, k -> new ArrayList<>());
 				list.add(next.getValue());
 			}
 

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

@@ -71,18 +71,18 @@ public class ApacheRestfulClientFactory extends RestfulClientFactory {
 	}
 
 	@Override
-	protected ApacheHttpClient getHttpClient(String theServerBase) {
+	protected synchronized ApacheHttpClient getHttpClient(String theServerBase) {
 		return new ApacheHttpClient(getNativeHttpClient(), new StringBuilder(theServerBase), null, null, null, null);
 	}
 
 	@Override
-	public IHttpClient getHttpClient(StringBuilder theUrl, Map<String, List<String>> theIfNoneExistParams,
+	public synchronized IHttpClient getHttpClient(StringBuilder theUrl, Map<String, List<String>> theIfNoneExistParams,
 			String theIfNoneExistString, RequestTypeEnum theRequestType, List<Header> theHeaders) {
 		return new ApacheHttpClient(getNativeHttpClient(), theUrl, theIfNoneExistParams, theIfNoneExistString, theRequestType,
 				theHeaders);
 	}
 
-	public synchronized HttpClient getNativeHttpClient() {
+	public HttpClient getNativeHttpClient() {
 		if (myHttpClient == null) {
 
 			//FIXME potential resoource leak

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

@@ -71,52 +71,52 @@ public abstract class RestfulClientFactory implements IRestfulClientFactory {
 	}
 
 	@Override
-	public int getConnectionRequestTimeout() {
+	public synchronized int getConnectionRequestTimeout() {
 		return myConnectionRequestTimeout;
 	}
 
 	@Override
-	public int getConnectTimeout() {
+	public synchronized int getConnectTimeout() {
 		return myConnectTimeout;
 	}
 
 	/**
 	 * Return the proxy username to authenticate with the HTTP proxy
 	 */
-	protected String getProxyUsername() {
+	protected synchronized String getProxyUsername() {
 		return myProxyUsername;
 	}
 
 	/**
 	 * Return the proxy password to authenticate with the HTTP proxy
 	 */
-	protected String getProxyPassword() {
+	protected synchronized String getProxyPassword() {
 		return myProxyPassword;
 	}
 
 	@Override
-	public void setProxyCredentials(String theUsername, String thePassword) {
+	public synchronized void setProxyCredentials(String theUsername, String thePassword) {
 		myProxyUsername = theUsername;
 		myProxyPassword = thePassword;
 	}
 
 	@Override
-	public ServerValidationModeEnum getServerValidationMode() {
+	public synchronized ServerValidationModeEnum getServerValidationMode() {
 		return myServerValidationMode;
 	}
 
 	@Override
-	public int getSocketTimeout() {
+	public synchronized int getSocketTimeout() {
 		return mySocketTimeout;
 	}
 
 	@Override
-	public int getPoolMaxTotal() {
+	public synchronized int getPoolMaxTotal() {
 		return myPoolMaxTotal;
 	}
 
 	@Override
-	public int getPoolMaxPerRoute() {
+	public synchronized int getPoolMaxPerRoute() {
 		return myPoolMaxPerRoute;
 	}
 
@@ -217,7 +217,7 @@ public abstract class RestfulClientFactory implements IRestfulClientFactory {
 	}
 
 	@Override
-	public void setServerValidationMode(ServerValidationModeEnum theServerValidationMode) {
+	public synchronized void setServerValidationMode(ServerValidationModeEnum theServerValidationMode) {
 		Validate.notNull(theServerValidationMode, "theServerValidationMode may not be null");
 		myServerValidationMode = theServerValidationMode;
 	}
@@ -242,13 +242,13 @@ public abstract class RestfulClientFactory implements IRestfulClientFactory {
 
 	@Deprecated // override deprecated method
 	@Override
-	public ServerValidationModeEnum getServerValidationModeEnum() {
+	public synchronized ServerValidationModeEnum getServerValidationModeEnum() {
 		return getServerValidationMode();
 	}
 
 	@Deprecated // override deprecated method
 	@Override
-	public void setServerValidationModeEnum(ServerValidationModeEnum theServerValidationMode) {
+	public synchronized void setServerValidationModeEnum(ServerValidationModeEnum theServerValidationMode) {
 		setServerValidationMode(theServerValidationMode);
 	}
 

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.rest.client.interceptor;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -76,6 +77,7 @@ public class LoggingInterceptor implements IClientInterceptor {
 		}
 	}
 
+	@Override
 	@Hook(Pointcut.CLIENT_REQUEST)
 	public void interceptRequest(IHttpRequest theRequest) {
 		if (myLogRequestSummary) {
@@ -93,14 +95,13 @@ public class LoggingInterceptor implements IClientInterceptor {
 				if (content != null) {
 					myLog.info("Client request body:\n{}", content);
 				}
-			} catch (IllegalStateException e) {
-				myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
-			} catch (IOException e) {
+			} catch (IllegalStateException | IOException e) {
 				myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
 			}
 		}
 	}
 
+	@Override
 	@Hook(Pointcut.CLIENT_RESPONSE)
 	public void interceptResponse(IHttpResponse theResponse) throws IOException {
 		if (myLogResponseSummary) {
@@ -145,11 +146,8 @@ public class LoggingInterceptor implements IClientInterceptor {
 		}
 
 		if (myLogResponseBody) {
-			//TODO: Use of a deprecated method should be resolved.
-			theResponse.bufferEntitity();
-			InputStream respEntity = null;
-			try  {
-				respEntity = theResponse.readEntity();
+			theResponse.bufferEntity();
+			try (InputStream respEntity = theResponse.readEntity()) {
 				if (respEntity != null) {
 					final byte[] bytes;
 					try {
@@ -157,12 +155,10 @@ public class LoggingInterceptor implements IClientInterceptor {
 					} catch (IllegalStateException e) {
 						throw new InternalErrorException(e);
 					}
-					myLog.info("Client response body:\n{}", new String(bytes, "UTF-8"));
+					myLog.info("Client response body:\n{}", new String(bytes, StandardCharsets.UTF_8));
 				} else {
 					myLog.info("Client response body: (none)");
 				}
-			} finally {
-				IOUtils.closeQuietly(respEntity);
 			}
 		}
 	}
@@ -176,7 +172,9 @@ public class LoggingInterceptor implements IClientInterceptor {
 				Iterator<String> values = theHeaders.get(key).iterator();
 				while(values.hasNext()) {
 					String value = values.next();
-						b.append(key + ": " + value);
+						b.append(key);
+						b.append(": ");
+						b.append(value);
 						if (nameEntries.hasNext() || values.hasNext()) {
 							b.append('\n');
 						}

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

@@ -22,7 +22,6 @@ package ca.uhn.fhir.rest.client.method;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.Reader;
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.*;

hapi-fhir-converter/pom.xml

@@ -10,8 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-converter</artifactId>
-	<!-- TODO: BND changed to jar temporarily -->
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<dependencies>
 		<dependency>
@@ -152,10 +151,6 @@
 			</resource>
 		</resources>
 		<plugins>
-			<!--
-			TODO: BND
-			With this enabled, JAR file contains a bunch of .class files that
-			seem to get copied in from org.hl7.fhir.convertors
 			<plugin>
 				<groupId>org.apache.felix</groupId>
 				<artifactId>maven-bundle-plugin</artifactId>
@@ -170,7 +165,6 @@
 					</instructions>
 				</configuration>
 			</plugin>
-			-->
 		</plugins>
 	</build>
 </project>

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

@@ -29,6 +29,8 @@ import ca.uhn.fhir.rest.api.server.ResponseDetails;
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
+import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
+import org.hl7.fhir.converter.NullVersionConverterAdvisor40;
 import org.hl7.fhir.convertors.*;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;

hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor30.java

@@ -1,4 +1,4 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.converter;
 
 /*
  * #%L
@@ -20,6 +20,7 @@ package org.hl7.fhir.convertors;
  * #L%
  */
 
+import org.hl7.fhir.convertors.VersionConvertorAdvisor30;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.ValueSet;

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

@@ -1,4 +1,4 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.converter;
 
 /*
  * #%L
@@ -20,6 +20,7 @@ package org.hl7.fhir.convertors;
  * #L%
  */
 
+import org.hl7.fhir.convertors.VersionConvertorAdvisor40;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;

hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor50.java

@@ -1,4 +1,4 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.converter;
 
 /*
  * #%L
@@ -20,6 +20,7 @@ package org.hl7.fhir.convertors;
  * #L%
  */
 
+import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
 import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.model.Bundle;

hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_10_30Test.java

@@ -1,7 +1,8 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.converter;
 
 import static org.junit.Assert.assertEquals;
 
+import org.hl7.fhir.convertors.VersionConvertor_10_30;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.dstu2.model.Resource;

hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_14_30Test.java

@@ -1,7 +1,8 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.converter;
 
 import static org.junit.Assert.assertEquals;
 
+import org.hl7.fhir.convertors.VersionConvertor_14_30;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.junit.Test;
 

hapi-fhir-docs/pom.xml

@@ -87,6 +87,12 @@
 			<artifactId>slf4j-simple</artifactId>
 			<version>1.7.28</version>
 		</dependency>
+		<!-- Needed for JEE/Servlet support -->
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
 	</dependencies>
 
 	<build>

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

@@ -20,7 +20,7 @@ package ca.uhn.hapi.fhir.docs;
  * #L%
  */
 
-import org.hl7.fhir.convertors.NullVersionConverterAdvisor30;
+import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
 import org.hl7.fhir.convertors.VersionConvertor_10_30;
 import org.hl7.fhir.convertors.VersionConvertor_14_30;
 import org.hl7.fhir.exceptions.FHIRException;

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

@@ -290,7 +290,7 @@ public class ValidatorExamples {
 			}
 
 			@Override
-			public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+			public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
 				// TODO: implement (or return null if your implementation does not support this function)
 				return null;
 			}

hapi-fhir-igpacks/src/main/java/ca/uhn/fhir/igpacks/parser/IgPackParserDstu2.java

@@ -35,10 +35,12 @@ public class IgPackParserDstu2 extends BaseIgPackParser<IValidationSupport> {
 		super(massage(theCtx));
 	}
 
+	@Override
 	protected IValidationSupport createValidationSupport(Map<IIdType, IBaseResource> theIgResources) {
 		return new IgPackValidationSupportDstu2(theIgResources);
 	}
 
+	@Override
 	protected FhirVersionEnum provideExpectedVersion() {
 		return FhirVersionEnum.DSTU2_HL7ORG;
 	}

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

@@ -37,10 +37,12 @@ public class IgPackParserDstu3 extends BaseIgPackParser<IValidationSupport> {
 		super(theCtx);
 	}
 
+	@Override
 	protected IValidationSupport createValidationSupport(Map<IIdType, IBaseResource> theIgResources) {
 		return new IgPackValidationSupportDstu3(theIgResources);
 	}
 
+	@Override
 	protected FhirVersionEnum provideExpectedVersion() {
 		return FhirVersionEnum.DSTU3;
 	}

hapi-fhir-igpacks/src/main/java/ca/uhn/fhir/igpacks/parser/IgPackValidationSupportDstu3.java

@@ -123,7 +123,7 @@ public class IgPackValidationSupportDstu3 implements IValidationSupport {
 	}
 
 	@Override
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
 		return null;
 	}
 

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

@@ -51,11 +51,6 @@ public class JaxRsHttpResponse extends BaseHttpResponse implements IHttpResponse
 		this.myResponse = theResponse;
 	}
 
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if(!myBufferedEntity && myResponse.hasEntity()) {

hapi-fhir-jaxrsserver-example/pom.xml

@@ -120,5 +120,4 @@
 			</plugin>
 		</plugins>
 	</build>
-
 </project>

hapi-fhir-jpaserver-base/pom.xml

@@ -46,7 +46,6 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-csv</artifactId>
-			<version>1.3</version>
 		</dependency>
 
 		<dependency>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/BaseBinaryStorageSvcImpl.java

@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
@@ -34,6 +33,8 @@ import javax.annotation.Nonnull;
 import java.io.InputStream;
 import java.security.SecureRandom;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
 	private final SecureRandom myRandom;
 	private final String CHARS = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
@@ -66,7 +67,8 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
 		myMinimumBinarySize = theMinimumBinarySize;
 	}
 
-	String newRandomId() {
+	@Override
+	public String newBlobId() {
 		StringBuilder b = new StringBuilder();
 		for (int i = 0; i < ID_LENGTH; i++) {
 			int nextInt = Math.abs(myRandom.nextInt());
@@ -89,13 +91,13 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
 
 	@Nonnull
 	CountingInputStream createCountingInputStream(InputStream theInputStream) {
-		InputStream is = ByteStreams.limit(theInputStream, myMaximumBinarySize + 1L);
+		InputStream is = ByteStreams.limit(theInputStream, getMaximumBinarySize() + 1L);
 		return new CountingInputStream(is) {
 			@Override
 			public int getCount() {
 				int retVal = super.getCount();
-				if (retVal > myMaximumBinarySize) {
-					throw new PayloadTooLargeException("Binary size exceeds maximum: " + myMaximumBinarySize);
+				if (retVal > getMaximumBinarySize()) {
+					throw new PayloadTooLargeException("Binary size exceeds maximum: " + getMaximumBinarySize());
 				}
 				return retVal;
 			}
@@ -103,4 +105,11 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
 	}
 
 
+	String provideIdForNewBlob(String theBlobIdOrNull) {
+		String id = theBlobIdOrNull;
+		if (isBlank(theBlobIdOrNull)) {
+			id = newBlobId();
+		}
+		return id;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/BinaryAccessProvider.java

@@ -86,20 +86,13 @@ public class BinaryAccessProvider {
 
 		IBinaryTarget target = findAttachmentForRequest(resource, path, theRequestDetails);
 
-		Optional<? extends IBaseExtension<?, ?>> attachmentId = target
-			.getTarget()
-			.getExtension()
-			.stream()
-			.filter(t -> JpaConstants.EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()))
-			.findFirst();
-
+		Optional<String> attachmentId = target.getAttachmentId();
 		if (attachmentId.isPresent()) {
 
 			@SuppressWarnings("unchecked")
-			IPrimitiveType<String> value = (IPrimitiveType<String>) attachmentId.get().getValue();
-			String blobId = value.getValueAsString();
+			String blobId = attachmentId.get();
 
-			IBinaryStorageSvc.StoredDetails blobDetails = myBinaryStorageSvc.fetchBlobDetails(theResourceId, blobId);
+			StoredDetails blobDetails = myBinaryStorageSvc.fetchBlobDetails(theResourceId, blobId);
 			if (blobDetails == null) {
 				String msg = myCtx.getLocalizer().getMessage(BinaryAccessProvider.class, "unknownBlobId");
 				throw new InvalidRequestException(msg);
@@ -179,7 +172,7 @@ public class BinaryAccessProvider {
 		if (size > 0) {
 			if (myBinaryStorageSvc != null) {
 				if (myBinaryStorageSvc.shouldStoreBlob(size, theResourceId, requestContentType)) {
-					IBinaryStorageSvc.StoredDetails storedDetails = myBinaryStorageSvc.storeBlob(theResourceId, requestContentType, theRequestDetails.getInputStream());
+					StoredDetails storedDetails = myBinaryStorageSvc.storeBlob(theResourceId, null, requestContentType, theRequestDetails.getInputStream());
 					size = storedDetails.getBytes();
 					blobId = storedDetails.getBlobId();
 					Validate.notBlank(blobId, "BinaryStorageSvc returned a null blob ID"); // should not happen
@@ -192,19 +185,7 @@ public class BinaryAccessProvider {
 			size = bytes.length;
 			target.setData(bytes);
 		} else {
-
-			target
-				.getTarget()
-				.getExtension()
-				.removeIf(t -> JpaConstants.EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()));
-			target.setData(null);
-
-			IBaseExtension<?, ?> ext = target.getTarget().addExtension();
-			ext.setUrl(JpaConstants.EXT_EXTERNALIZED_BINARY_ID);
-			ext.setUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED, Boolean.TRUE);
-			IPrimitiveType<String> blobIdString = (IPrimitiveType<String>) myCtx.getElementDefinition("string").newInstance();
-			blobIdString.setValueAsString(blobId);
-			ext.setValue(blobIdString);
+			replaceDataWithExtension(target, blobId);
 		}
 
 		target.setContentType(requestContentType);
@@ -217,52 +198,81 @@ public class BinaryAccessProvider {
 		return outcome.getResource();
 	}
 
-	@Nonnull
-	private IBinaryTarget findAttachmentForRequest(IBaseResource theResource, String thePath, ServletRequestDetails theRequestDetails) {
-		FhirContext ctx = theRequestDetails.getFhirContext();
+	public void replaceDataWithExtension(IBinaryTarget theTarget, String theBlobId) {
+		theTarget
+			.getTarget()
+			.getExtension()
+			.removeIf(t -> JpaConstants.EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()));
+		theTarget.setData(null);
 
-		Optional<IBase> type = ctx.newFluentPath().evaluateFirst(theResource, thePath, IBase.class);
-		String resType = myCtx.getResourceDefinition(theResource).getName();
-		if (!type.isPresent()) {
-			String msg = myCtx.getLocalizer().getMessageSanitized(BinaryAccessProvider.class, "unknownPath", resType, thePath);
-			throw new InvalidRequestException(msg);
+		IBaseExtension<?, ?> ext = theTarget.getTarget().addExtension();
+		ext.setUrl(JpaConstants.EXT_EXTERNALIZED_BINARY_ID);
+		ext.setUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED, Boolean.TRUE);
+		IPrimitiveType<String> blobIdString = (IPrimitiveType<String>) myCtx.getElementDefinition("string").newInstance();
+		blobIdString.setValueAsString(theBlobId);
+		ext.setValue(blobIdString);
 	}
 
+	@Nonnull
+	private IBinaryTarget findAttachmentForRequest(IBaseResource theResource, String thePath, ServletRequestDetails theRequestDetails) {
+		Optional<IBase> type = myCtx.newFluentPath().evaluateFirst(theResource, thePath, IBase.class);
+		String resType = this.myCtx.getResourceDefinition(theResource).getName();
+		if (!type.isPresent()) {
+			String msg = this.myCtx.getLocalizer().getMessageSanitized(BinaryAccessProvider.class, "unknownPath", resType, thePath);
+			throw new InvalidRequestException(msg);
+		}
+		IBase element = type.get();
+
+		Optional<IBinaryTarget> binaryTarget = toBinaryTarget(element);
+
+		if (binaryTarget.isPresent() == false) {
+			BaseRuntimeElementDefinition<?> def2 = myCtx.getElementDefinition(element.getClass());
+			String msg = this.myCtx.getLocalizer().getMessageSanitized(BinaryAccessProvider.class, "unknownType", resType, thePath, def2.getName());
+			throw new InvalidRequestException(msg);
+		} else {
+			return binaryTarget.get();
+		}
+
+	}
+
+	public Optional<IBinaryTarget> toBinaryTarget(IBase theElement) {
+		IBinaryTarget binaryTarget = null;
+
 		// Path is attachment
-		BaseRuntimeElementDefinition<?> def = ctx.getElementDefinition(type.get().getClass());
+		BaseRuntimeElementDefinition<?> def = myCtx.getElementDefinition(theElement.getClass());
 		if (def.getName().equals("Attachment")) {
-			ICompositeType attachment = (ICompositeType) type.get();
-			return new IBinaryTarget() {
+			ICompositeType attachment = (ICompositeType) theElement;
+			binaryTarget = new IBinaryTarget() {
 				@Override
 				public void setSize(Integer theSize) {
-					AttachmentUtil.setSize(myCtx, attachment, theSize);
+					AttachmentUtil.setSize(BinaryAccessProvider.this.myCtx, attachment, theSize);
 				}
 
 				@Override
 				public String getContentType() {
-					return AttachmentUtil.getOrCreateContentType(myCtx, attachment).getValueAsString();
+					return AttachmentUtil.getOrCreateContentType(BinaryAccessProvider.this.myCtx, attachment).getValueAsString();
 				}
 
 				@Override
 				public byte[] getData() {
-					IPrimitiveType<byte[]> dataDt = AttachmentUtil.getOrCreateData(theRequestDetails.getFhirContext(), attachment);
+					IPrimitiveType<byte[]> dataDt = AttachmentUtil.getOrCreateData(myCtx, attachment);
 					return dataDt.getValue();
 				}
 
 				@Override
 				public IBaseHasExtensions getTarget() {
-					return (IBaseHasExtensions) AttachmentUtil.getOrCreateData(theRequestDetails.getFhirContext(), attachment);
+					return (IBaseHasExtensions) AttachmentUtil.getOrCreateData(myCtx, attachment);
 				}
 
 				@Override
 				public void setContentType(String theContentType) {
-					AttachmentUtil.setContentType(myCtx, attachment, theContentType);
+					AttachmentUtil.setContentType(BinaryAccessProvider.this.myCtx, attachment, theContentType);
 				}
 
 
 				@Override
 				public void setData(byte[] theBytes) {
-					AttachmentUtil.setData(theRequestDetails.getFhirContext(), attachment, theBytes);
+					AttachmentUtil.setData(myCtx, attachment, theBytes);
 				}
 
 
@@ -271,8 +281,8 @@ public class BinaryAccessProvider {
 
 		// Path is Binary
 		if (def.getName().equals("Binary")) {
-			IBaseBinary binary = (IBaseBinary) type.get();
-			return new IBinaryTarget() {
+			IBaseBinary binary = (IBaseBinary) theElement;
+			binaryTarget = new IBinaryTarget() {
 				@Override
 				public void setSize(Integer theSize) {
 					// ignore
@@ -290,7 +300,7 @@ public class BinaryAccessProvider {
 
 				@Override
 				public IBaseHasExtensions getTarget() {
-					return (IBaseHasExtensions) BinaryUtil.getOrCreateData(myCtx, binary);
+					return (IBaseHasExtensions) BinaryUtil.getOrCreateData(BinaryAccessProvider.this.myCtx, binary);
 				}
 
 				@Override
@@ -308,9 +318,7 @@ public class BinaryAccessProvider {
 			};
 		}
 
-		String msg = myCtx.getLocalizer().getMessageSanitized(BinaryAccessProvider.class, "unknownType", resType, thePath, def.getName());
-		throw new InvalidRequestException(msg);
-
+		return Optional.ofNullable(binaryTarget);
 	}
 
 	private String validateResourceTypeAndPath(@IdParam IIdType theResourceId, @OperationParam(name = "path", min = 1, max = 1) IPrimitiveType<String> thePath) {
@@ -340,25 +348,5 @@ public class BinaryAccessProvider {
 		return dao;
 	}
 
-	/**
-	 * Wraps an Attachment datatype or Binary resource, since they both
-	 * hold binary content but don't look entirely similar
-	 */
-	private interface IBinaryTarget {
-
-		void setSize(Integer theSize);
-
-		String getContentType();
-
-		void setContentType(String theContentType);
-
-		byte[] getData();
-
-		void setData(byte[] theBytes);
-
-		IBaseHasExtensions getTarget();
-
-	}
-
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/BinaryStorageInterceptor.java

@@ -20,23 +20,37 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.Hook;
 import ca.uhn.fhir.interceptor.api.Interceptor;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.IModelVisitor2;
+import org.apache.commons.io.FileUtils;
+import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.r4.model.IdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import java.util.List;
+import javax.annotation.Nonnull;
+import javax.annotation.PostConstruct;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.*;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.jpa.model.util.JpaConstants.EXT_EXTERNALIZED_BINARY_ID;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 @Interceptor
 public class BinaryStorageInterceptor {
 
@@ -45,12 +59,39 @@ public class BinaryStorageInterceptor {
 	private IBinaryStorageSvc myBinaryStorageSvc;
 	@Autowired
 	private FhirContext myCtx;
+	@Autowired
+	private BinaryAccessProvider myBinaryAccessProvider;
+	private Class<? extends IPrimitiveType<byte[]>> myBinaryType;
+	private String myDeferredListKey;
+	private long myAutoDeExternalizeMaximumBytes = 10 * FileUtils.ONE_MB;
+
+	/**
+	 * Any externalized binaries will be rehydrated if their size is below this thhreshold when
+	 * reading the resource back. Default is 10MB.
+	 */
+	public long getAutoDeExternalizeMaximumBytes() {
+		return myAutoDeExternalizeMaximumBytes;
+	}
+
+	/**
+	 * Any externalized binaries will be rehydrated if their size is below this thhreshold when
+	 * reading the resource back. Default is 10MB.
+	 */
+	public void setAutoDeExternalizeMaximumBytes(long theAutoDeExternalizeMaximumBytes) {
+		myAutoDeExternalizeMaximumBytes = theAutoDeExternalizeMaximumBytes;
+	}
+
+	@SuppressWarnings("unchecked")
+	@PostConstruct
+	public void start() {
+		myBinaryType = (Class<? extends IPrimitiveType<byte[]>>) myCtx.getElementDefinition("base64Binary").getImplementingClass();
+		myDeferredListKey = getClass().getName() + "_" + hashCode() + "_DEFERRED_LIST";
+	}
 
 	@Hook(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE)
 	public void expungeResource(AtomicInteger theCounter, IBaseResource theResource) {
 
-		Class<? extends IBase> binaryType = myCtx.getElementDefinition("base64Binary").getImplementingClass();
-		List<? extends IBase> binaryElements = myCtx.newTerser().getAllPopulatedChildElementsOfType(theResource, binaryType);
+		List<? extends IBase> binaryElements = myCtx.newTerser().getAllPopulatedChildElementsOfType(theResource, myBinaryType);
 
 		List<String> attachmentIds = binaryElements
 			.stream()
@@ -67,4 +108,215 @@ public class BinaryStorageInterceptor {
 		}
 
 	}
+
+	@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED)
+	public void extractLargeBinariesBeforeCreate(ServletRequestDetails theRequestDetails, IBaseResource theResource, Pointcut thePointcut) throws IOException {
+		extractLargeBinaries(theRequestDetails, theResource, thePointcut);
+	}
+
+	@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED)
+	public void extractLargeBinariesBeforeUpdate(ServletRequestDetails theRequestDetails, IBaseResource thePreviousResource, IBaseResource theResource, Pointcut thePointcut) throws IOException {
+		blockIllegalExternalBinaryIds(thePreviousResource, theResource);
+		extractLargeBinaries(theRequestDetails, theResource, thePointcut);
+	}
+
+	/**
+	 * Don't allow clients to submit resources with binary storage attachments declared unless the ID was already in the
+	 * resource. In other words, only HAPI itself may add a binary storage ID extension to a resource unless that
+	 * extension was already present.
+	 */
+	private void blockIllegalExternalBinaryIds(IBaseResource thePreviousResource, IBaseResource theResource) {
+		Set<String> existingBinaryIds = new HashSet<>();
+		if (thePreviousResource != null) {
+			List<? extends IPrimitiveType<byte[]>> base64fields = myCtx.newTerser().getAllPopulatedChildElementsOfType(thePreviousResource, myBinaryType);
+			for (IPrimitiveType<byte[]> nextBase64 : base64fields) {
+				if (nextBase64 instanceof IBaseHasExtensions) {
+					((IBaseHasExtensions) nextBase64)
+						.getExtension()
+						.stream()
+						.filter(t -> t.getUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED) == null)
+						.filter(t -> EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()))
+						.map(t -> (IPrimitiveType) t.getValue())
+						.map(t -> t.getValueAsString())
+						.filter(t -> isNotBlank(t))
+						.forEach(t -> existingBinaryIds.add(t));
+				}
+			}
+		}
+
+		List<? extends IPrimitiveType<byte[]>> base64fields = myCtx.newTerser().getAllPopulatedChildElementsOfType(theResource, myBinaryType);
+		for (IPrimitiveType<byte[]> nextBase64 : base64fields) {
+			if (nextBase64 instanceof IBaseHasExtensions) {
+				Optional<String> hasExternalizedBinaryReference = ((IBaseHasExtensions) nextBase64)
+					.getExtension()
+					.stream()
+					.filter(t -> t.getUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED) == null)
+					.filter(t -> t.getUrl().equals(EXT_EXTERNALIZED_BINARY_ID))
+					.map(t->(IPrimitiveType) t.getValue())
+					.map(t->t.getValueAsString())
+					.filter(t->isNotBlank(t))
+					.filter(t->{
+						return !existingBinaryIds.contains(t);
+					}).findFirst();
+
+				if (hasExternalizedBinaryReference.isPresent()) {
+					String msg = myCtx.getLocalizer().getMessage(BaseHapiFhirDao.class, "externalizedBinaryStorageExtensionFoundInRequestBody", EXT_EXTERNALIZED_BINARY_ID, hasExternalizedBinaryReference.get());
+					throw new InvalidRequestException(msg);
+				}
+			}
+		}
+
+	}
+
+	private void extractLargeBinaries(ServletRequestDetails theRequestDetails, IBaseResource theResource, Pointcut thePointcut) throws IOException {
+		if (theRequestDetails == null) {
+			// RequestDetails will only be null for internal HAPI events.  If externalization is required for them it will need to be done in a different way.
+			return;
+		}
+		IIdType resourceId = theResource.getIdElement();
+		if (!resourceId.hasResourceType() && resourceId.hasIdPart()) {
+			String resourceType = myCtx.getResourceDefinition(theResource).getName();
+			resourceId = new IdType(resourceType + "/" + resourceId.getIdPart());
+		}
+
+		List<IBinaryTarget> attachments = recursivelyScanResourceForBinaryData(theResource);
+		for (IBinaryTarget nextTarget : attachments) {
+			byte[] data = nextTarget.getData();
+			if (data != null && data.length > 0) {
+
+				long nextPayloadLength = data.length;
+				String nextContentType = nextTarget.getContentType();
+				boolean shouldStoreBlob = myBinaryStorageSvc.shouldStoreBlob(nextPayloadLength, resourceId, nextContentType);
+				if (shouldStoreBlob) {
+
+					String newBlobId;
+					if (resourceId.hasIdPart()) {
+						ByteArrayInputStream inputStream = new ByteArrayInputStream(data);
+						StoredDetails storedDetails = myBinaryStorageSvc.storeBlob(resourceId, null, nextContentType, inputStream);
+						newBlobId = storedDetails.getBlobId();
+					} else {
+						assert thePointcut == Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED : thePointcut.name();
+						newBlobId = myBinaryStorageSvc.newBlobId();
+						List<DeferredBinaryTarget> deferredBinaryTargets = getOrCreateDeferredBinaryStorageMap(theRequestDetails);
+						DeferredBinaryTarget newDeferredBinaryTarget = new DeferredBinaryTarget(newBlobId, nextTarget, data);
+						deferredBinaryTargets.add(newDeferredBinaryTarget);
+					}
+
+					myBinaryAccessProvider.replaceDataWithExtension(nextTarget, newBlobId);
+				}
+			}
+
+		}
+	}
+
+	@Nonnull
+	@SuppressWarnings("unchecked")
+	private List<DeferredBinaryTarget> getOrCreateDeferredBinaryStorageMap(ServletRequestDetails theRequestDetails) {
+		List<DeferredBinaryTarget> deferredBinaryTargets = (List<DeferredBinaryTarget>) theRequestDetails.getUserData().get(getDeferredListKey());
+		if (deferredBinaryTargets == null) {
+			deferredBinaryTargets = new ArrayList<>();
+			theRequestDetails.getUserData().put(getDeferredListKey(), deferredBinaryTargets);
+		}
+		return deferredBinaryTargets;
+	}
+
+	@SuppressWarnings("unchecked")
+	@Hook(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED)
+	public void storeLargeBinariesBeforeCreatePersistence(ServletRequestDetails theRequestDetails, IBaseResource theResource, Pointcut thePoincut) throws IOException {
+		if (theRequestDetails == null) {
+			return;
+		}
+		List<DeferredBinaryTarget> deferredBinaryTargets = (List<DeferredBinaryTarget>) theRequestDetails.getUserData().get(getDeferredListKey());
+		if (deferredBinaryTargets != null) {
+			IIdType resourceId = theResource.getIdElement();
+			for (DeferredBinaryTarget next : deferredBinaryTargets) {
+				String blobId = next.getBlobId();
+				IBinaryTarget target = next.getBinaryTarget();
+				InputStream dataStream = next.getDataStream();
+				String contentType = target.getContentType();
+				myBinaryStorageSvc.storeBlob(resourceId, blobId, contentType, dataStream);
+			}
+		}
+	}
+
+	private String getDeferredListKey() {
+		return myDeferredListKey;
+	}
+
+	@Hook(Pointcut.STORAGE_PRESHOW_RESOURCES)
+	public void preShow(IPreResourceShowDetails theDetails) throws IOException {
+		long unmarshalledByteCount = 0;
+
+		for (IBaseResource nextResource : theDetails) {
+
+			IIdType resourceId = nextResource.getIdElement();
+			List<IBinaryTarget> attachments = recursivelyScanResourceForBinaryData(nextResource);
+
+			for (IBinaryTarget nextTarget : attachments) {
+				Optional<String> attachmentId = nextTarget.getAttachmentId();
+				if (attachmentId.isPresent()) {
+
+					StoredDetails blobDetails = myBinaryStorageSvc.fetchBlobDetails(resourceId, attachmentId.get());
+					if (blobDetails == null) {
+						String msg = myCtx.getLocalizer().getMessage(BinaryAccessProvider.class, "unknownBlobId");
+						throw new InvalidRequestException(msg);
+					}
+
+					if ((unmarshalledByteCount + blobDetails.getBytes()) < myAutoDeExternalizeMaximumBytes) {
+
+						byte[] bytes = myBinaryStorageSvc.fetchBlob(resourceId, attachmentId.get());
+						nextTarget.setData(bytes);
+						unmarshalledByteCount += blobDetails.getBytes();
+					}
+				}
+			}
+
+		}
+	}
+
+	@Nonnull
+	private List<IBinaryTarget> recursivelyScanResourceForBinaryData(IBaseResource theResource) {
+		List<IBinaryTarget> binaryTargets = new ArrayList<>();
+		myCtx.newTerser().visit(theResource, new IModelVisitor2() {
+			@Override
+			public boolean acceptElement(IBase theElement, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
+
+				if (theElement.getClass().equals(myBinaryType)) {
+					IBase parent = theContainingElementPath.get(theContainingElementPath.size() - 2);
+					Optional<IBinaryTarget> binaryTarget = myBinaryAccessProvider.toBinaryTarget(parent);
+					if (binaryTarget.isPresent()) {
+						binaryTargets.add(binaryTarget.get());
+					}
+				}
+				return true;
+			}
+		});
+		return binaryTargets;
+	}
+
+	private static class DeferredBinaryTarget {
+		private final String myBlobId;
+		private final IBinaryTarget myBinaryTarget;
+		private final InputStream myDataStream;
+
+		private DeferredBinaryTarget(String theBlobId, IBinaryTarget theBinaryTarget, byte[] theData) {
+			myBlobId = theBlobId;
+			myBinaryTarget = theBinaryTarget;
+			myDataStream = new ByteArrayInputStream(theData);
+		}
+
+		String getBlobId() {
+			return myBlobId;
+		}
+
+		IBinaryTarget getBinaryTarget() {
+			return myBinaryTarget;
+		}
+
+		InputStream getDataStream() {
+			return myDataStream;
+		}
+	}
+
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/DatabaseBlobBinaryStorageSvcImpl.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.binstore;
 
 import ca.uhn.fhir.jpa.dao.data.IBinaryStorageEntityDao;
 import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import com.google.common.hash.HashingInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.CountingInputStream;
@@ -57,13 +58,13 @@ public class DatabaseBlobBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 
 	@Override
 	@Transactional(Transactional.TxType.SUPPORTS)
-	public StoredDetails storeBlob(IIdType theResourceId, String theContentType, InputStream theInputStream) {
+	public StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) {
 		Date publishedDate = new Date();
 
 		HashingInputStream hashingInputStream = createHashingInputStream(theInputStream);
 		CountingInputStream countingInputStream = createCountingInputStream(hashingInputStream);
 
-		String id = newRandomId();
+		String id = super.provideIdForNewBlob(theBlobIdOrNull);
 
 		BinaryStorageEntity entity = new BinaryStorageEntity();
 		entity.setResourceId(theResourceId.toUnqualifiedVersionless().getValue());
@@ -126,12 +127,7 @@ public class DatabaseBlobBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 			return false;
 		}
 
-		try {
-			InputStream inputStream = entityOpt.get().getBlob().getBinaryStream();
-			IOUtils.copy(inputStream, theOutputStream);
-		} catch (SQLException e) {
-			throw new IOException(e);
-		}
+		copyBlobToOutputStream(theOutputStream, entityOpt.get());
 
 		return true;
 	}
@@ -139,6 +135,32 @@ public class DatabaseBlobBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 	@Override
 	public void expungeBlob(IIdType theResourceId, String theBlobId) {
 		Optional<BinaryStorageEntity> entityOpt = myBinaryStorageEntityDao.findByIdAndResourceId(theBlobId, theResourceId.toUnqualifiedVersionless().getValue());
-		entityOpt.ifPresent(theBinaryStorageEntity -> myBinaryStorageEntityDao.delete(theBinaryStorageEntity));
+		entityOpt.ifPresent(theBinaryStorageEntity -> myBinaryStorageEntityDao.deleteByPid(theBinaryStorageEntity.getBlobId()));
+	}
+
+	@Override
+	public byte[] fetchBlob(IIdType theResourceId, String theBlobId) throws IOException {
+		BinaryStorageEntity entityOpt = myBinaryStorageEntityDao
+			.findByIdAndResourceId(theBlobId, theResourceId.toUnqualifiedVersionless().getValue())
+			.orElseThrow(() -> new ResourceNotFoundException("Unknown blob ID: " + theBlobId + " for resource ID " + theResourceId));
+
+		return copyBlobToByteArray(entityOpt);
+	}
+
+	void copyBlobToOutputStream(OutputStream theOutputStream, BinaryStorageEntity theEntity) throws IOException {
+		try (InputStream inputStream = theEntity.getBlob().getBinaryStream()) {
+			IOUtils.copy(inputStream, theOutputStream);
+		} catch (SQLException e) {
+			throw new IOException(e);
+		}
+	}
+
+	byte[] copyBlobToByteArray(BinaryStorageEntity theEntity) throws IOException {
+		int size = theEntity.getSize();
+		try {
+			return IOUtils.toByteArray(theEntity.getBlob().getBinaryStream(), size);
+		} catch (SQLException e) {
+			throw new IOException(e);
+		}
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/FilesystemBinaryStorageSvcImpl.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.binstore;
  */
 
 import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
@@ -31,6 +32,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.CountingInputStream;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.jetbrains.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -63,8 +65,8 @@ public class FilesystemBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 	}
 
 	@Override
-	public StoredDetails storeBlob(IIdType theResourceId, String theContentType, InputStream theInputStream) throws IOException {
-		String id = newRandomId();
+	public StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) throws IOException {
+		String id = super.provideIdForNewBlob(theBlobIdOrNull);
 		File storagePath = getStoragePath(id, true);
 
 		// Write binary file
@@ -111,17 +113,31 @@ public class FilesystemBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 
 	@Override
 	public boolean writeBlob(IIdType theResourceId, String theBlobId, OutputStream theOutputStream) throws IOException {
+		InputStream inputStream = getInputStream(theResourceId, theBlobId);
+
+		if (inputStream != null) {
+			try {
+				IOUtils.copy(inputStream, theOutputStream);
+				theOutputStream.close();
+			} finally {
+				inputStream.close();
+			}
+		}
+
+		return false;
+	}
+
+	@Nullable
+	private InputStream getInputStream(IIdType theResourceId, String theBlobId) throws FileNotFoundException {
 		File storagePath = getStoragePath(theBlobId, false);
+		InputStream inputStream = null;
 		if (storagePath != null) {
 			File file = getStorageFilename(storagePath, theResourceId, theBlobId);
 			if (file.exists()) {
-				try (InputStream inputStream = new FileInputStream(file)) {
-					IOUtils.copy(inputStream, theOutputStream);
-					theOutputStream.close();
+				inputStream = new FileInputStream(file);
 			}
 		}
-		}
-		return false;
+		return inputStream;
 	}
 
 	@Override
@@ -139,6 +155,20 @@ public class FilesystemBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 		}
 	}
 
+	@Override
+	public byte[] fetchBlob(IIdType theResourceId, String theBlobId) throws IOException {
+		StoredDetails details = fetchBlobDetails(theResourceId, theBlobId);
+		try (InputStream inputStream = getInputStream(theResourceId, theBlobId)) {
+
+			if (inputStream != null) {
+				return IOUtils.toByteArray(inputStream, details.getBytes());
+			}
+
+		}
+
+		throw new ResourceNotFoundException("Unknown blob ID: " + theBlobId + " for resource ID " + theResourceId);
+	}
+
 	private void delete(File theStorageFile, String theBlobId) {
 		Validate.isTrue(theStorageFile.delete(), "Failed to delete file for blob %s", theBlobId);
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

@@ -20,22 +20,12 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.util.JsonDateDeserializer;
-import ca.uhn.fhir.jpa.util.JsonDateSerializer;
-import com.fasterxml.jackson.annotation.JsonAutoDetect;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
-import com.fasterxml.jackson.databind.annotation.JsonSerialize;
-import com.google.common.hash.HashingInputStream;
-import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.hl7.fhir.instance.model.api.IIdType;
 
 import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.util.Date;
 
 public interface IBinaryStorageSvc {
 
@@ -77,15 +67,22 @@ public interface IBinaryStorageSvc {
 	 */
 	boolean shouldStoreBlob(long theSize, IIdType theResourceId, String theContentType);
 
+	/**
+	 * Generate a new blob ID that will be passed to {@link #storeBlob(IIdType, String, String, InputStream)} later
+	 */
+	String newBlobId();
+
 	/**
 	 * Store a new binary blob
 	 *
 	 * @param theResourceId   The resource ID that owns this blob. Note that it should not be possible to retrieve a blob without both the resource ID and the blob ID being correct.
+	 * @param theBlobIdOrNull If set, forces
 	 * @param theContentType  The content type to associate with this blob
 	 * @param theInputStream  An InputStream to read from. This method should close the stream when it has been fully consumed.
 	 * @return Returns details about the stored data
 	 */
-	StoredDetails storeBlob(IIdType theResourceId, String theContentType, InputStream theInputStream) throws IOException;
+	@Nonnull
+	StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) throws IOException;
 
 	StoredDetails fetchBlobDetails(IIdType theResourceId, String theBlobId) throws IOException;
 
@@ -96,100 +93,12 @@ public interface IBinaryStorageSvc {
 
 	void expungeBlob(IIdType theResourceId, String theBlobId);
 
-
-	@JsonInclude(JsonInclude.Include.NON_NULL)
-	@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
-	class StoredDetails {
-
-		@JsonProperty("blobId")
-		private String myBlobId;
-		@JsonProperty("bytes")
-		private long myBytes;
-		@JsonProperty("contentType")
-		private String myContentType;
-		@JsonProperty("hash")
-		private String myHash;
-		@JsonProperty("published")
-		@JsonSerialize(using = JsonDateSerializer.class)
-		@JsonDeserialize(using = JsonDateDeserializer.class)
-		private Date myPublished;
-
 	/**
-		 * Constructor
+	 * Fetch the contents of the given blob
+	 *
+	 * @param theResourceId The resource ID
+	 * @param theBlobId     The blob ID
+	 * @return The payload as a byte array
 	 */
-		@SuppressWarnings("unused")
-		public StoredDetails() {
-			super();
-		}
-
-		/**
-		 * Constructor
-		 */
-		public StoredDetails(@Nonnull String theBlobId, long theBytes, @Nonnull String theContentType, HashingInputStream theIs, Date thePublished) {
-			myBlobId = theBlobId;
-			myBytes = theBytes;
-			myContentType = theContentType;
-			myHash = theIs.hash().toString();
-			myPublished = thePublished;
-		}
-
-		@Override
-		public String toString() {
-			return new ToStringBuilder(this)
-				.append("blobId", myBlobId)
-				.append("bytes", myBytes)
-				.append("contentType", myContentType)
-				.append("hash", myHash)
-				.append("published", myPublished)
-				.toString();
-		}
-
-		public String getHash() {
-			return myHash;
-		}
-
-		public StoredDetails setHash(String theHash) {
-			myHash = theHash;
-			return this;
-		}
-
-		public Date getPublished() {
-			return myPublished;
-		}
-
-		public StoredDetails setPublished(Date thePublished) {
-			myPublished = thePublished;
-			return this;
-		}
-
-		@Nonnull
-		public String getContentType() {
-			return myContentType;
-		}
-
-		public StoredDetails setContentType(String theContentType) {
-			myContentType = theContentType;
-			return this;
-		}
-
-		@Nonnull
-		public String getBlobId() {
-			return myBlobId;
-		}
-
-		public StoredDetails setBlobId(String theBlobId) {
-			myBlobId = theBlobId;
-			return this;
-		}
-
-		public long getBytes() {
-			return myBytes;
-		}
-
-		public StoredDetails setBytes(long theBytes) {
-			myBytes = theBytes;
-			return this;
-		}
-
-	}
+	byte[] fetchBlob(IIdType theResourceId, String theBlobId) throws IOException;
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryTarget.java

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.jpa.binstore;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.util.Optional;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+/**
+ * Wraps an Attachment datatype or Binary resource, since they both
+ * hold binary content but don't look entirely similar
+ */
+interface IBinaryTarget {
+
+	void setSize(Integer theSize);
+
+	String getContentType();
+
+	void setContentType(String theContentType);
+
+	byte[] getData();
+
+	void setData(byte[] theBytes);
+
+	IBaseHasExtensions getTarget();
+
+	@SuppressWarnings("unchecked")
+	default Optional<String> getAttachmentId() {
+		return getTarget()
+			.getExtension()
+			.stream()
+			.filter(t -> JpaConstants.EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()))
+			.filter(t -> t.getValue() instanceof IPrimitiveType)
+			.map(t -> (IPrimitiveType<String>) t.getValue())
+			.map(t -> t.getValue())
+			.filter(t -> isNotBlank(t))
+			.findFirst();
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/MemoryBinaryStorageSvcImpl.java

@@ -49,8 +49,8 @@ public class MemoryBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl impleme
 	}
 
 	@Override
-	public StoredDetails storeBlob(IIdType theResourceId, String theContentType, InputStream theInputStream) throws IOException {
-		String id = newRandomId();
+	public StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) throws IOException {
+		String id = super.provideIdForNewBlob(theBlobIdOrNull);
 		String key = toKey(theResourceId, id);
 
 		HashingInputStream hashingIs = createHashingInputStream(theInputStream);
@@ -88,8 +88,18 @@ public class MemoryBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl impleme
 		myDetailsMap.remove(key);
 	}
 
+	@Override
+	public byte[] fetchBlob(IIdType theResourceId, String theBlobId) {
+		String key = toKey(theResourceId, theBlobId);
+		return myDataMap.get(key);
+	}
+
 	private String toKey(IIdType theResourceId, String theBlobId) {
 		return theBlobId + '-' + theResourceId.toUnqualifiedVersionless().getValue();
 	}
 
+	public void clear() {
+		myDetailsMap.clear();
+		myDataMap.clear();
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

@@ -53,7 +53,12 @@ public class NullBinaryStorageSvcImpl implements IBinaryStorageSvc {
 	}
 
 	@Override
-	public StoredDetails storeBlob(IIdType theResourceId, String theContentType, InputStream theInputStream) {
+	public String newBlobId() {
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) {
 		throw new UnsupportedOperationException();
 	}
 
@@ -71,4 +76,9 @@ public class NullBinaryStorageSvcImpl implements IBinaryStorageSvc {
 	public void expungeBlob(IIdType theIdElement, String theBlobId) {
 		throw new UnsupportedOperationException();
 	}
+
+	@Override
+	public byte[] fetchBlob(IIdType theResourceId, String theBlobId) {
+		throw new UnsupportedOperationException();
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/StoredDetails.java

@@ -0,0 +1,130 @@
+package ca.uhn.fhir.jpa.binstore;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.util.JsonDateDeserializer;
+import ca.uhn.fhir.jpa.util.JsonDateSerializer;
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import com.google.common.hash.HashingInputStream;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+
+import javax.annotation.Nonnull;
+import java.util.Date;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
+public class StoredDetails {
+
+	@JsonProperty("blobId")
+	private String myBlobId;
+	@JsonProperty("bytes")
+	private long myBytes;
+	@JsonProperty("contentType")
+	private String myContentType;
+	@JsonProperty("hash")
+	private String myHash;
+	@JsonProperty("published")
+	@JsonSerialize(using = JsonDateSerializer.class)
+	@JsonDeserialize(using = JsonDateDeserializer.class)
+	private Date myPublished;
+
+	/**
+	 * Constructor
+	 */
+	@SuppressWarnings("unused")
+	public StoredDetails() {
+		super();
+	}
+
+	/**
+	 * Constructor
+	 */
+	public StoredDetails(@Nonnull String theBlobId, long theBytes, @Nonnull String theContentType, HashingInputStream theIs, Date thePublished) {
+		myBlobId = theBlobId;
+		myBytes = theBytes;
+		myContentType = theContentType;
+		myHash = theIs.hash().toString();
+		myPublished = thePublished;
+	}
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this)
+			.append("blobId", myBlobId)
+			.append("bytes", myBytes)
+			.append("contentType", myContentType)
+			.append("hash", myHash)
+			.append("published", myPublished)
+			.toString();
+	}
+
+	public String getHash() {
+		return myHash;
+	}
+
+	public StoredDetails setHash(String theHash) {
+		myHash = theHash;
+		return this;
+	}
+
+	public Date getPublished() {
+		return myPublished;
+	}
+
+	public StoredDetails setPublished(Date thePublished) {
+		myPublished = thePublished;
+		return this;
+	}
+
+	@Nonnull
+	public String getContentType() {
+		return myContentType;
+	}
+
+	public StoredDetails setContentType(String theContentType) {
+		myContentType = theContentType;
+		return this;
+	}
+
+	@Nonnull
+	public String getBlobId() {
+		return myBlobId;
+	}
+
+	public StoredDetails setBlobId(String theBlobId) {
+		myBlobId = theBlobId;
+		return this;
+	}
+
+	public long getBytes() {
+		return myBytes;
+	}
+
+	public StoredDetails setBytes(long theBytes) {
+		myBytes = theBytes;
+		return this;
+	}
+
+}

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

@@ -165,7 +165,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 		if (jobToDelete.isPresent()) {
 
-			ourLog.info("Deleting bulk export job: {}", jobToDelete.get().getJobId());
+			ourLog.info("Deleting bulk export job: {}", jobToDelete.get());
 
 			myTxTemplate.execute(t -> {
 
@@ -176,17 +176,20 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 						ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
 						getBinaryDao().delete(toId(nextFile.getResourceId()));
 						getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), null);
-						myBulkExportCollectionFileDao.delete(nextFile);
+						myBulkExportCollectionFileDao.deleteByPid(nextFile.getId());
 
 					}
 
-					myBulkExportCollectionDao.delete(nextCollection);
+					myBulkExportCollectionDao.deleteByPid(nextCollection.getId());
 				}
 
-				myBulkExportJobDao.delete(job);
+				ourLog.info("*** ABOUT TO DELETE");
+				myBulkExportJobDao.deleteByPid(job.getId());
 				return null;
 			});
 
+			ourLog.info("Finished deleting bulk export job: {}", jobToDelete.get());
+
 		}
 
 	}
@@ -452,11 +455,17 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 	}
 
 	@Override
-	@Transactional
+	@Transactional(Transactional.TxType.NEVER)
 	public synchronized void cancelAndPurgeAllJobs() {
-		myBulkExportCollectionFileDao.deleteAll();
-		myBulkExportCollectionDao.deleteAll();
-		myBulkExportJobDao.deleteAll();
+		myTxTemplate.execute(t -> {
+			ourLog.info("Deleting all files");
+			myBulkExportCollectionFileDao.deleteAllFiles();
+			ourLog.info("Deleting all collections");
+			myBulkExportCollectionDao.deleteAllFiles();
+			ourLog.info("Deleting all jobs");
+			myBulkExportJobDao.deleteAllFiles();
+			return null;
+		});
 	}
 
 	@DisallowConcurrentExecution

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

@@ -6,8 +6,8 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
 import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
-import ca.uhn.fhir.jpa.bulk.BulkDataExportSvcImpl;
 import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.bulk.BulkDataExportSvcImpl;
 import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
@@ -28,10 +28,17 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
 import ca.uhn.fhir.jpa.subscription.dbmatcher.CompositeInMemoryDaoSubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.dbmatcher.DaoSubscriptionMatcher;
-import ca.uhn.fhir.jpa.subscription.module.cache.ISubscribableChannelFactory;
 import ca.uhn.fhir.jpa.subscription.module.cache.LinkedBlockingQueueSubscribableChannelFactory;
+import ca.uhn.fhir.jpa.subscription.module.channel.ISubscribableChannelFactory;
 import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
+import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -256,7 +263,6 @@ public abstract class BaseConfig {
 	}
 
 
-
 	public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
 		theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
 		theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java

@@ -0,0 +1,54 @@
+package ca.uhn.fhir.jpa.config;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public abstract class BaseConfigDstu3Plus extends BaseConfig {
+
+	@Bean
+	public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
+		return new TermCodeSystemStorageSvcImpl();
+	}
+
+	@Bean
+	public ITermDeferredStorageSvc termDeferredStorageSvc() {
+		return new TermDeferredStorageSvcImpl();
+	}
+
+	@Bean
+	public ITermReindexingSvc termReindexingSvc() {
+		return new TermReindexingSvcImpl();
+	}
+
+	@Bean
+	public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
+
+}