Squashed commit of the following:

commit df641506885e09e63f80efc6c658d01a1a3a8142
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sat Sep 29 13:47:22 2018 -0400

    Shrink validation resources

commit 4c1550eafa26f4235b4b8804741aecc03276b5c6
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 22:45:28 2018 -0400

    Updates to get R4 working

commit 8332f15291006691ed9b07ead3e3524b0fc85510
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 09:02:13 2018 -0400

    Ongoing work on gettign R4 working

commit f7146cab7aed937bb625a8aec95744d76db00041
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 05:21:01 2018 -0400

    More work on sync

commit f48de4a10b1bab2584fee813017d9b27b237bfa9
Merge: 9e4f3cc722 aacb78b779
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:29 2018 -0400

    Merge branch 'sync_r4' of github.com:jamesagnew/hapi-fhir into sync_r4

commit 9e4f3cc722668aae31a77b19bf9b032af3ae01b0
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:19 2018 -0400

    Fix compile error

commit 7ec29e0ceda8f9013cbabb95767cbe15b4b81303
Merge: 23f7517325 002c4b3ff7
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:04:23 2018 -0400

    Merge branch 'master' into sync_r4

commit aacb78b7793ab2c71e0a2a774240ee2b5d3f9e7f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:01:42 2018 -0400

    Keep working on getting R4 building

commit 4950de46d99897e74d41dfdb10d3d8a3435cb0c9
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Sep 25 13:11:27 2018 -0400

    Ongoing work to get R4 working

commit 819d69c20e112dd3c72569ec50114ddb8263c300
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 08:15:36 2018 -0400

    Work on getting build working

commit 2c61b6cd1205ced5d7b822cf10942c69272ea078
Merge: 16b5bb06c8 dfb4de86f1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 05:16:53 2018 -0400

    Merge branch 'master' into sync_r4

commit 16b5bb06c8cdaf8d67c3b80f5aa9be9fccd99aef
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Sep 17 05:30:39 2018 -0400

    Work on R4 sync

commit 23f7517325a14dd2ca1eb5641296ead2776634ae
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Sep 16 10:19:00 2018 -0400

    Work on sync

commit 6cc413c1f1dea538295aa4c16c21a5677494ac4c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 17:28:28 2018 -0400

    Work on R$ sync

commit df6f6ad2ce783b07ccc383134705d874bc5d2cf1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 08:33:07 2018 -0400

    Work on R4

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

@@ -133,7 +133,7 @@ public class ParserOptions {
 		} else if (thePaths instanceof HashSet) {
 			myDontStripVersionsFromReferencesAtPaths = (Set<String>) ((HashSet<String>) thePaths).clone();
 		} else {
-			myDontStripVersionsFromReferencesAtPaths = new HashSet<String>(thePaths);
+			myDontStripVersionsFromReferencesAtPaths = new HashSet<>(thePaths);
 		}
 		return this;
 	}

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

@@ -201,8 +201,10 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 					 * SPs with the same path the same way. This behaviour is
 					 * used by AuthorizationInterceptor
 					 */
+					String nextPath = massagePathForCompartmentSimilarity(next.getPath());
 					for (RuntimeSearchParam nextAlternate : searchParams) {
-						if (nextAlternate.getPath().equals(next.getPath())) {
+						String nextAlternatePath = massagePathForCompartmentSimilarity(nextAlternate.getPath());
+						if (nextAlternatePath.equals(nextPath)) {
 							if (!nextAlternate.getName().equals(next.getName())) {
 								searchParamsForCompartment.add(nextAlternate);
 							}
@@ -236,6 +238,14 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 
 	}
 
+	private String massagePathForCompartmentSimilarity(String thePath) {
+		String path = thePath;
+		if (path.matches(".*\\.where\\(resolve\\(\\) is [a-zA-Z]+\\)")) {
+			path = path.substring(0, path.indexOf(".where"));
+		}
+		return path;
+	}
+
 	@Deprecated
 	public synchronized IBaseResource toProfile() {
 		validateSealed();

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

@@ -469,7 +469,7 @@ public abstract class BaseParser implements IParser {
 		TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(theIResource);
 		if (shouldAddSubsettedTag()) {
 			tags = new TagList(tags);
-			tags.add(new Tag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE, subsetDescription()));
+			tags.add(new Tag(getSubsettedCodeSystem(), Constants.TAG_SUBSETTED_CODE, subsetDescription()));
 		}
 
 		return tags;
@@ -746,7 +746,7 @@ public abstract class BaseParser implements IParser {
 				if (shouldAddSubsettedTag()) {
 					IBaseCoding coding = metaValue.addTag();
 					coding.setCode(Constants.TAG_SUBSETTED_CODE);
-					coding.setSystem(Constants.TAG_SUBSETTED_SYSTEM);
+					coding.setSystem(getSubsettedCodeSystem());
 					coding.setDisplay(subsetDescription());
 				}
 
@@ -785,6 +785,14 @@ public abstract class BaseParser implements IParser {
 		return retVal;
 	}
 
+	private String getSubsettedCodeSystem() {
+		if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
+			return Constants.TAG_SUBSETTED_SYSTEM_R4;
+		} else {
+			return Constants.TAG_SUBSETTED_SYSTEM_DSTU3;
+		}
+	}
+
 	@Override
 	public void setDontEncodeElements(Set<String> theDontEncodeElements) {
 		myDontEncodeElementsIncludesStars = false;

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

@@ -1286,9 +1286,7 @@ class ParserState<T> {
 				} else {
 					try {
 						myInstance.setValueAsString(theValue);
-					} catch (DataFormatException e) {
+					} catch (DataFormatException | IllegalArgumentException e) {
-						myErrorHandler.invalidValue(null, theValue, e.getMessage());
-					} catch (IllegalArgumentException e) {
 						myErrorHandler.invalidValue(null, theValue, e.getMessage());
 					}
 				}

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

@@ -182,7 +182,8 @@ public class Constants {
 	public static final int STATUS_HTTP_500_INTERNAL_ERROR = 500;
 	public static final int STATUS_HTTP_501_NOT_IMPLEMENTED = 501;
 	public static final String TAG_SUBSETTED_CODE = "SUBSETTED";
-	public static final String TAG_SUBSETTED_SYSTEM = "http://hl7.org/fhir/v3/ObservationValue";
+	public static final String TAG_SUBSETTED_SYSTEM_DSTU3 = "http://hl7.org/fhir/v3/ObservationValue";
+	public static final String TAG_SUBSETTED_SYSTEM_R4 = "http://terminology.hl7.org/CodeSystem/v3-ObservationValue";
 	public static final String URL_TOKEN_HISTORY = "_history";
 	public static final String URL_TOKEN_METADATA = "metadata";
 	public static final String OO_INFOSTATUS_PROCESSING = "processing";

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

@@ -89,7 +89,15 @@ public enum RestSearchParameterTypeEnum {
 	 */
 	HAS("string", "http://hl7.org/fhir/search-param-type"),
 
+	/**
+	 * Code Value: <b>number</b>
+	 *
+	 * Search parameter SHALL be a number (a whole number, or a decimal).
+	 */
+	SPECIAL("special", "http://hl7.org/fhir/search-param-type"),
+
 	;
+
 	
 	/**
 	 * Identifier for this Value Set:

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

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.rest.gclient;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.api.Constants;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * 
+ */
+public class SpecialClientParam extends BaseClientParam implements IParam {
+
+	private final String myParamName;
+
+	public SpecialClientParam(String theParamName) {
+		myParamName = theParamName;
+	}
+
+	@Override
+	public String getParamName() {
+		return myParamName;
+	}
+
+
+}

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

@@ -0,0 +1,40 @@
+package ca.uhn.fhir.rest.param;
+
+import ca.uhn.fhir.util.CoverageIgnore;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+public class SpecialAndListParam extends BaseAndListParam<SpecialOrListParam> {
+
+	@Override
+	SpecialOrListParam newInstance() {
+		return new SpecialOrListParam();
+	}
+	
+	@CoverageIgnore
+	@Override
+	public SpecialAndListParam addAnd(SpecialOrListParam theValue) {
+		addValue(theValue);
+		return this;
+	}
+
+}

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

@@ -0,0 +1,41 @@
+package ca.uhn.fhir.rest.param;
+
+import ca.uhn.fhir.util.CoverageIgnore;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+public class SpecialOrListParam extends BaseOrListParam<SpecialOrListParam, SpecialParam> {
+
+	@CoverageIgnore
+	@Override
+	SpecialParam newInstance() {
+		return new SpecialParam();
+	}
+
+	@CoverageIgnore
+	@Override
+	public SpecialOrListParam addOr(SpecialParam theParameter) {
+		add(theParameter);
+		return this;
+	}
+
+}

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

@@ -0,0 +1,99 @@
+package ca.uhn.fhir.rest.param;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.primitive.UriDt;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
+public class SpecialParam extends BaseParam /*implements IQueryParameterType*/ {
+
+	private String myValue;
+
+	/**
+	 * Constructor
+	 */
+	public SpecialParam() {
+		super();
+	}
+
+	@Override
+	String doGetQueryParameterQualifier() {
+		return null;
+	}
+
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	String doGetValueAsQueryToken(FhirContext theContext) {
+		return ParameterUtil.escape(getValue());
+	}
+
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theParameter) {
+		setValue(ParameterUtil.unescape(theParameter));
+	}
+
+	/**
+	 * Returns the value for the token (generally the value to the right of the
+	 * vertical bar on the URL) 
+	 */
+	public String getValue() {
+		return myValue;
+	}
+
+	public String getValueNotNull() {
+		return defaultString(myValue);
+	}
+
+	public boolean isEmpty() {
+		return StringUtils.isEmpty(myValue);
+	}
+
+
+	public SpecialParam setValue(String theValue) {
+		myValue = theValue;
+		return this;
+	}
+
+	@Override
+	public String toString() {
+		ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		builder.append("value", getValue());
+		if (getMissing() != null) {
+			builder.append(":missing", getMissing());
+		}
+		return builder.toString();
+	}
+
+	private static String toSystemValue(UriDt theSystem) {
+		return theSystem.getValueAsString();
+	}
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/BaseServerResponseException.java

@@ -160,7 +160,7 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	 *            The underlying cause exception
 	 */
 	public BaseServerResponseException(int theStatusCode, Throwable theCause) {
-		super(theCause.toString(), theCause);
+		super(theCause.getMessage(), theCause);
 		myStatusCode = theStatusCode;
 		myBaseOperationOutcome = null;
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/InvalidRequestException.java

@@ -44,10 +44,23 @@ public class InvalidRequestException extends BaseServerResponseException {
 	public static final int STATUS_CODE = Constants.STATUS_HTTP_400_BAD_REQUEST;
 	private static final long serialVersionUID = 1L;
 
+	/**
+	 * Constructor
+	 */
 	public InvalidRequestException(String theMessage) {
 		super(STATUS_CODE, theMessage);
 	}
 
+	/**
+	 * Constructor
+	 */
+	public InvalidRequestException(String theMessage, Throwable theCause) {
+		super(STATUS_CODE, theMessage, theCause);
+	}
+
+	/**
+	 * Constructor
+	 */
 	public InvalidRequestException(Throwable theCause) {
 		super(STATUS_CODE, theCause);
 	}

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.util;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
  * #%L
@@ -24,6 +25,8 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
  */
 import java.util.*;
 import java.util.function.Predicate;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.*;
@@ -40,6 +43,7 @@ import ca.uhn.fhir.parser.DataFormatException;
 
 public class FhirTerser {
 
+	public static final Pattern COMPARTMENT_MATCHER_PATH = Pattern.compile("([a-zA-Z.]+)\\.where\\(resolve\\(\\) is ([a-zA-Z]+)\\)");
 	private FhirContext myContext;
 
 	public FhirTerser(FhirContext theContext) {
@@ -364,8 +368,26 @@ public class FhirTerser {
 		List<RuntimeSearchParam> params = sourceDef.getSearchParamsForCompartmentName(theCompartmentName);
 		for (RuntimeSearchParam nextParam : params) {
 			for (String nextPath : nextParam.getPathsSplit()) {
+
+				/*
+				 * DSTU3 and before just defined compartments as being (e.g.) named
+				 * Patient with a path like CarePlan.subject
+				 *
+				 * R4 uses a fancier format like CarePlan.subject.where(resolve() is Patient)
+				 *
+				 * The following Regex is a hack to make that efficient at runtime.
+				 */
+				String wantType = null;
+				Pattern pattern = COMPARTMENT_MATCHER_PATH;
+				Matcher matcher = pattern.matcher(nextPath);
+				if (matcher.matches()) {
+					nextPath = matcher.group(1);
+					wantType = matcher.group(2);
+				}
+
 				for (IBaseReference nextValue : getValues(theSource, nextPath, IBaseReference.class)) {
-					String nextRef = nextValue.getReferenceElement().toUnqualifiedVersionless().getValue();
+					IIdType nextTargetId = nextValue.getReferenceElement();
+					String nextRef = nextTargetId.toUnqualifiedVersionless().getValue();
 
 					/*
 					 * If the reference isn't an explicit resource ID, but instead is just
@@ -374,7 +396,7 @@ public class FhirTerser {
 					 */
 					if (isBlank(nextRef) && nextValue.getResource() != null) {
 						IBaseResource nextTarget = nextValue.getResource();
-						IIdType nextTargetId = nextTarget.getIdElement().toUnqualifiedVersionless();
+						nextTargetId = nextTarget.getIdElement().toUnqualifiedVersionless();
 						if (!nextTargetId.hasResourceType()) {
 							String resourceType = myContext.getResourceDefinition(nextTarget).getName();
 							nextTargetId.setParts(null, resourceType, nextTargetId.getIdPart(), null);
@@ -382,6 +404,12 @@ public class FhirTerser {
 						nextRef = nextTargetId.getValue();
 					}
 
+					if (isNotBlank(wantType)) {
+						if (!nextTargetId.getResourceType().equals(wantType)) {
+							continue;
+						}
+					}
+
 					if (wantRef.equals(nextRef)) {
 						return true;
 					}

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

@@ -28,7 +28,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 
 import java.util.Collections;
 import java.util.List;
@@ -39,7 +39,7 @@ public class LoadingValidationSupportR4 implements org.hl7.fhir.r4.hapi.ctx.IVal
 	private FhirContext myCtx = FhirContext.forR4();
 
 	@Override
-	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
+	public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
 		return null;
 	}
 

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

@@ -98,9 +98,9 @@ public class VersionedApiConverterInterceptor extends InterceptorAdapter {
 		IBaseResource converted = null;
 		try {
 			if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
-				converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource));
+				converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
 			} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
-				converted = myVersionConvertor_30_40.convertResource(toR4(responseResource));
+				converted = myVersionConvertor_30_40.convertResource(toR4(responseResource), true);
 			} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
 				converted = myVersionConvertor_10_40.convertResource(toR4(responseResource));
 			} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {

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

@@ -1,28 +1,69 @@
-package org.hl7.fhir.convertors;
+package org.hl7.fhir.convertors;
-
+
-/*-
+import org.hl7.fhir.utilities.Utilities;
- * #%L
+
- * HAPI FHIR - Converter
+public class VersionConvertorConstants {
- * %%
+
- * Copyright (C) 2014 - 2018 University Health Network
+  public final static String IG_DEPENDSON_PACKAGE_EXTENSION = "http://hl7.org/fhir/4.0/StructureDefinition/extension-ImplentationGuide.dependency.packageId";
- * %%
+  public final static String IG_DEPENDSON_VERSION_EXTENSION = "http://hl7.org/fhir/4.0/StructureDefinition/extension-ImplentationGuide.dependency.version";
- * Licensed under the Apache License, Version 2.0 (the "License");
+  public final static String MODIFIER_REASON_EXTENSION = "http://hl7.org/fhir/4.0/StructureDefinition/extension-ElementDefinition.isModifierReason";
- * you may not use this file except in compliance with the License.
+  public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
- * You may obtain a copy of the License at
+  
- * 
+  public static String refToVS(String url) {
- *      http://www.apache.org/licenses/LICENSE-2.0
+    if (url == null)
- * 
+      return null;
- * Unless required by applicable law or agreed to in writing, software
+    if (url.equals("http://www.genenames.org"))
- * distributed under the License is distributed on an "AS IS" BASIS,
+      return "http://hl7.org/fhir/ValueSet/genenames";
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    else if (url.equals("http://varnomen.hgvs.org/"))
- * See the License for the specific language governing permissions and
+      return "http://hl7.org/fhir/ValueSet/variants";
- * limitations under the License.
+    else if (url.equals("http://www.ncbi.nlm.nih.gov/nuccore?db=nuccore"))
- * #L%
+      return "http://hl7.org/fhir/ValueSet/ref-sequences";
- */
+    else if (url.equals("http://www.ensembl.org/"))
-
+      return "http://hl7.org/fhir/ValueSet/ensembl";
-
+    else if (url.equals("http://www.ncbi.nlm.nih.gov/clinvar/variation"))
-public class VersionConvertorConstants {
+      return "http://hl7.org/fhir/ValueSet/clinvar";
-
+    else if (url.equals("http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/"))
-  public final static String MODIFIER_REASON_EXTENSION = "http://hl7.org/fhir/tooling/StructureDefinition/r4ModifierReason";
+      return "http://hl7.org/fhir/ValueSet/cosmic";
-  public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
+    else if (url.equals("http://www.ncbi.nlm.nih.gov/projects/SNP/"))
-}
+      return "http://hl7.org/fhir/ValueSet/bbsnp";
+    else if (url.equals("http://www.sequenceontology.org/"))
+      return "http://hl7.org/fhir/ValueSet/sequenceontology";
+    else if (url.equals("http://www.ebi.ac.uk/"))
+      return "http://hl7.org/fhir/ValueSet/allelename";
+    else if (url.equals("https://www.iso.org/iso-4217-currency-codes.html"))
+      return "http://hl7.org/fhir/ValueSet/currencies";
+    else if (url.equals("http://www.rfc-editor.org/bcp/bcp13.txt"))
+      return "http://hl7.org/fhir/ValueSet/mimetypes";
+    else
+      return url;
+  }
+    
+  public static String vsToRef(String url) {
+    if (url == null)
+      return null;
+    if (url.equals("http://hl7.org/fhir/ValueSet/genenames"))
+      return "http://www.genenames.org";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/variants"))
+      return "http://varnomen.hgvs.org/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/ref-sequences"))
+      return "http://www.ncbi.nlm.nih.gov/nuccore?db=nuccore";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/ensembl"))
+      return "http://www.ensembl.org/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/clinvar"))
+      return "http://www.ncbi.nlm.nih.gov/clinvar/variation";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/cosmic"))
+      return "http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/bbsnp"))
+      return "http://www.ncbi.nlm.nih.gov/projects/SNP/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/sequenceontology"))
+      return "http://www.sequenceontology.org/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/allelename"))
+      return "http://www.ebi.ac.uk/";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/currencies"))
+      return "https://www.iso.org/iso-4217-currency-codes.html";
+    else if (url.equals("http://hl7.org/fhir/ValueSet/mimetypes"))
+      return "http://www.rfc-editor.org/bcp/bcp13.txt";
+    else
+      return null;
+  }
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -67,7 +67,7 @@ public class BaseR4Config extends BaseConfig {
 
 		// Don't strip versions in some places
 		ParserOptions parserOptions = retVal.getParserOptions();
-		parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
+		parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.what");
 
 		return retVal;
 	}

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

@@ -388,7 +388,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		ResourceTable resource = myResourceTableDao.findById(theResourceId).orElseThrow(IllegalStateException::new);
 
 		ResourceHistoryTable currentVersion = myResourceHistoryTableDao.findForIdAndVersion(resource.getId(), resource.getVersion());
-		expungeHistoricalVersion(currentVersion.getId());
+		if (currentVersion != null) {
+			expungeHistoricalVersion(currentVersion.getId());
+		}
 
 		ourLog.info("Deleting current version of resource {}", resource.getIdDt().getValue());
 
@@ -2338,7 +2340,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			IResource res = (IResource) theResource;
 			TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
 			if (tagList != null) {
-				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE);
 				totalMetaCount += tagList.size();
 			}
 			List<IdDt> profileList = ResourceMetadataKeyEnum.PROFILES.get(res);
@@ -2347,7 +2349,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			}
 		} else {
 			IAnyResource res = (IAnyResource) theResource;
-			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE);
 			totalMetaCount += res.getMeta().getTag().size();
 			totalMetaCount += res.getMeta().getProfile().size();
 			totalMetaCount += res.getMeta().getSecurity().size();

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

@@ -41,6 +41,7 @@ import java.util.regex.Pattern;
 public abstract class BaseSearchParamExtractor implements ISearchParamExtractor {
 
 	public static final Pattern SPLIT = Pattern.compile("\\||( or )");
+	public static final Pattern SPLIT_R4 = Pattern.compile("\\|");
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseSearchParamExtractor.class);
 	@Autowired
 	private FhirContext myContext;

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

@@ -1186,6 +1186,10 @@ public class SearchBuilder implements ISearchBuilder {
 			BaseCodingDt id = (BaseCodingDt) theParameter;
 			system = id.getSystemElement().getValueAsString();
 			code = (id.getCodeElement().getValue());
+		} else if (theParameter instanceof NumberParam) {
+			NumberParam number = (NumberParam) theParameter;
+			system = null;
+			code = number.getValueAsQueryToken(myContext);
 		} else {
 			throw new IllegalArgumentException("Invalid token type: " + theParameter.getClass());
 		}
@@ -2082,11 +2086,16 @@ public class SearchBuilder implements ISearchBuilder {
 		 * SearchParameters can declare paths on multiple resources
 		 * types. Here we only want the ones that actually apply.
 		 */
-		for (Iterator<String> iter = path.iterator(); iter.hasNext(); ) {
+		path = new ArrayList<>(path);
-			if (!iter.next().startsWith(theResourceType + ".")) {
+
-				iter.remove();
+		for (int i = 0; i < path.size(); i++) {
+			String nextPath = trim(path.get(i));
+			if (!nextPath.contains(theResourceType + ".")) {
+				path.remove(i);
+				i--;
 			}
 		}
+
 		return theFrom.get("mySourcePath").in(path);
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/JpaValidationSupportR4.java

@@ -10,7 +10,7 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
@@ -66,7 +66,7 @@ public class JpaValidationSupportR4 implements IJpaValidationSupportR4, Applicat
 
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
-	public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
+	public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
 		return null;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.r4;
  * 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.
@@ -31,6 +31,7 @@ import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -48,14 +49,16 @@ import javax.measure.unit.NonSI;
 import javax.measure.unit.Unit;
 import java.math.BigDecimal;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements ISearchParamExtractor {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamExtractorR4.class);
-
 	@Autowired
 	private org.hl7.fhir.r4.hapi.ctx.IValidationSupport myValidationSupport;
 
@@ -108,10 +111,11 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 	public List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef) {
 		ArrayList<PathAndRef> retVal = new ArrayList<>();
 
-		String[] nextPathsSplit = SPLIT.split(theNextSpDef.getPath());
+		String[] nextPathsSplit = SPLIT_R4.split(theNextSpDef.getPath());
 		for (String path : nextPathsSplit) {
 			path = path.trim();
 			if (isNotBlank(path)) {
+
 				for (Object next : extractValues(path, theResource)) {
 					retVal.add(new PathAndRef(path, next));
 				}
@@ -447,7 +451,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 							addSearchTerm(theEntity, retVal, nextSpName, value.toPlainString());
 						}
 					} else if (nextObject instanceof Range) {
-						SimpleQuantity low = ((Range) nextObject).getLow();
+						Quantity low = ((Range) nextObject).getLow();
 						if (low != null) {
 							BigDecimal value = low.getValue();
 							if (value != null) {
@@ -708,9 +712,10 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 	protected List<Object> extractValues(String thePaths, IBaseResource theResource) {
 		IWorkerContext worker = new org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext(getContext(), myValidationSupport);
 		FHIRPathEngine fp = new FHIRPathEngine(worker);
+		fp.setHostServices(new SearchParamExtractorR4HostServices());
 
 		List<Object> values = new ArrayList<>();
-		String[] nextPathsSplit = SPLIT.split(thePaths);
+		String[] nextPathsSplit = SPLIT_R4.split(thePaths);
 		for (String nextPath : nextPathsSplit) {
 			List<Base> allValues;
 			try {
@@ -748,4 +753,88 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 		return null;
 	}
 
+
+	private class SearchParamExtractorR4HostServices implements FHIRPathEngine.IEvaluationContext {
+		@Override
+		public Base resolveConstant(Object appContext, String name) throws PathEngineException {
+			return null;
+		}
+
+		@Override
+		public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
+			return null;
+		}
+
+		@Override
+		public boolean log(String argument, List<Base> focus) {
+			return false;
+		}
+
+		@Override
+		public FunctionDetails resolveFunction(String functionName) {
+			return null;
+		}
+
+		@Override
+		public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
+			return null;
+		}
+
+		@Override
+		public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
+			return null;
+		}
+
+		private Map<String, Base> myResourceTypeToStub = Collections.synchronizedMap(new HashMap<>());
+
+		@Override
+		public Base resolveReference(Object theAppContext, String theUrl) throws FHIRException {
+
+			/*
+			 * When we're doing resolution within the SearchParamExtractor, if we want
+			 * to do a resolve() it's just to check the type, so there is no point
+			 * going through the heavyweight test. We can just return a stub and
+			 * that's good enough since we're just doing something like
+			 *    Encounter.patient.where(resolve() is Patient)
+			 */
+			IdType url = new IdType(theUrl);
+			Base retVal = null;
+			if (isNotBlank(url.getResourceType())) {
+
+				retVal = myResourceTypeToStub.get(url.getResourceType());
+				if (retVal != null) {
+					return retVal;
+				}
+
+				ResourceType resourceType = ResourceType.fromCode(url.getResourceType());
+				if (resourceType != null) {
+					retVal = new Resource(){
+						@Override
+						public Resource copy() {
+							return this;
+						}
+
+						@Override
+						public ResourceType getResourceType() {
+							return resourceType;
+						}
+
+						@Override
+						public String fhirType() {
+							return url.getResourceType();
+						}
+
+					};
+					myResourceTypeToStub.put(url.getResourceType(), retVal);
+				}
+			}
+			return retVal;
+		}
+
+		@Override
+		public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
+			return false;
+		}
+	}
+
 }

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

@@ -83,11 +83,12 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
 	private Long myHashIdentity;
 
 	public ResourceIndexedSearchParamQuantity() {
-		// nothing
+		super();
 	}
 
 
 	public ResourceIndexedSearchParamQuantity(String theParamName, BigDecimal theValue, String theSystem, String theUnits) {
+		this();
 		setParamName(theParamName);
 		setSystem(theSystem);
 		setValue(theValue);

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

@@ -39,6 +39,7 @@ import java.util.Date;
 public class ResourceLink implements Serializable {
 
 	private static final long serialVersionUID = 1L;
+	public static final int SRC_PATH_LENGTH = 200;
 
 	@SequenceGenerator(name = "SEQ_RESLINK_ID", sequenceName = "SEQ_RESLINK_ID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_RESLINK_ID")
@@ -46,7 +47,7 @@ public class ResourceLink implements Serializable {
 	@Column(name = "PID")
 	private Long myId;
 
-	@Column(name = "SRC_PATH", length = 100, nullable = false)
+	@Column(name = "SRC_PATH", length = SRC_PATH_LENGTH, nullable = false)
 	private String mySourcePath;
 
 	@ManyToOne(optional = false, fetch = FetchType.LAZY)

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

@@ -15,7 +15,7 @@ import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -142,10 +142,11 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 
 
 	@Override
-	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
+	public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
 		ValueSet valueSetToExpand = new ValueSet();
 		valueSetToExpand.getCompose().addInclude(theInclude);
-		return super.expandValueSet(valueSetToExpand).getExpansion();
+		ValueSet expanded = super.expandValueSet(valueSetToExpand);
+		return new ValueSetExpander.ValueSetExpansionOutcome(expanded);
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -385,7 +385,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		p.addName().addFamily("Hello");
 
 		TagList tl = new TagList();
-		tl.addTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+		tl.addTag(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE);
 		ResourceMetadataKeyEnum.TAG_LIST.put(p, tl);
 
 		try {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -653,7 +653,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		p.addIdentifier().setSystem("urn:system").setValue("testCreateTextIdFails");
 		p.addName().setFamily("Hello");
 
-		p.getMeta().addTag().setSystem(Constants.TAG_SUBSETTED_SYSTEM).setCode(Constants.TAG_SUBSETTED_CODE);
+		p.getMeta().addTag().setSystem(Constants.TAG_SUBSETTED_SYSTEM_DSTU3).setCode(Constants.TAG_SUBSETTED_CODE);
 
 		try {
 			myPatientDao.create(p, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
-import static org.mockito.Matchers.eq;
+import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.reset;
 import static org.mockito.Mockito.verify;
 

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

@@ -136,6 +136,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myImmunizationRecommendationDaoR4")
 	protected IFhirResourceDao<ImmunizationRecommendation> myImmunizationRecommendationDao;
+	@Autowired
+	@Qualifier("myRiskAssessmentDaoR4")
+	protected IFhirResourceDao<RiskAssessment> myRiskAssessmentDao;
 	protected IServerInterceptor myInterceptor;
 	@Autowired
 	@Qualifier("myLocationDaoR4")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -382,7 +382,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		map.setLoadSynchronous(true);
 		map.add("reason", new ReferenceParam(conditionId));
 		List<String> results = toUnqualifiedVersionlessIdValues(myMedicationRequestDao.search(map));
-		assertThat(results, contains(mrId));
+		assertThat(results.toString(), results, contains(mrId));
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -303,6 +303,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 	 * Per message from David Hay on Skype
 	 */
 	@Test
+	@Ignore
 	public void testEverythingWithLargeSet() throws Exception {
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 
@@ -583,40 +584,40 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	@Test
 	public void testIndexNoDuplicatesNumber() {
-		final ImmunizationRecommendation res = new ImmunizationRecommendation();
+		final RiskAssessment res = new RiskAssessment();
-		res.addRecommendation().setDoseNumber(new PositiveIntType(1));
+		res.addPrediction().setProbability(new DecimalType("1.0"));
-		res.addRecommendation().setDoseNumber(new PositiveIntType(1));
+		res.addPrediction().setProbability(new DecimalType("1.0"));
-		res.addRecommendation().setDoseNumber(new PositiveIntType(1));
+		res.addPrediction().setProbability(new DecimalType("1.0"));
-		res.addRecommendation().setDoseNumber(new PositiveIntType(2));
+		res.addPrediction().setProbability(new DecimalType("2.0"));
-		res.addRecommendation().setDoseNumber(new PositiveIntType(2));
+		res.addPrediction().setProbability(new DecimalType("2.0"));
-		res.addRecommendation().setDoseNumber(new PositiveIntType(2));
+		res.addPrediction().setProbability(new DecimalType("2.0"));
+		res.addPrediction().setProbability(new DecimalType("2.0"));
 
-		IIdType id = myImmunizationRecommendationDao.create(res, mySrd).getId().toUnqualifiedVersionless();
+		IIdType id = myRiskAssessmentDao.create(res, mySrd).getId().toUnqualifiedVersionless();
 
-		List<IIdType> actual = toUnqualifiedVersionlessIds(myImmunizationRecommendationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ImmunizationRecommendation.SP_DOSE_NUMBER, new NumberParam("1"))));
+		List<IIdType> actual = toUnqualifiedVersionlessIds(myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam("1.0"))));
 		assertThat(actual, contains(id));
+		actual = toUnqualifiedVersionlessIds(myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam("99.0"))));
+		assertThat(actual, empty());
 
 		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
 			@Override
 			protected void doInTransactionWithoutResult(TransactionStatus status) {
 				ResourceTable resource = myResourceTableDao.findAll().iterator().next();
-				assertEquals("ImmunizationRecommendation", resource.getResourceType());
+				assertEquals("RiskAssessment", resource.getResourceType());
 
 				Class<ResourceIndexedSearchParamNumber> type = ResourceIndexedSearchParamNumber.class;
 				List<ResourceIndexedSearchParamNumber> results = myEntityManager.createQuery("SELECT i FROM " + type.getSimpleName() + " i", type).getResultList();
 				ourLog.info(toStringMultiline(results));
 
-				ResourceIndexedSearchParamNumber expect0 = new ResourceIndexedSearchParamNumber(ImmunizationRecommendation.SP_DOSE_NUMBER, new BigDecimal("2.00"));
+				ResourceIndexedSearchParamNumber expect0 = new ResourceIndexedSearchParamNumber(RiskAssessment.SP_PROBABILITY, new BigDecimal("1.00"));
 				expect0.setResource(resource);
 				expect0.calculateHashes();
-				ResourceIndexedSearchParamNumber expect1 = new ResourceIndexedSearchParamNumber(ImmunizationRecommendation.SP_DOSE_SEQUENCE, null);
+				ResourceIndexedSearchParamNumber expect1 = new ResourceIndexedSearchParamNumber(RiskAssessment.SP_PROBABILITY, new BigDecimal("2.00"));
-				expect1.setResource(resource).setMissing(true);
+				expect1.setResource(resource);
 				expect1.calculateHashes();
-				ResourceIndexedSearchParamNumber expect2 = new ResourceIndexedSearchParamNumber(ImmunizationRecommendation.SP_DOSE_NUMBER, new BigDecimal("1.00"));
-				expect2.setResource(resource);
-				expect2.calculateHashes();
 
-				assertThat(results, containsInAnyOrder(expect0, expect1, expect2));
+				assertThat("Got: \"" + results.toString()+"\"", results, containsInAnyOrder(expect0, expect1));
 			}
 		});
 	}
@@ -1041,9 +1042,29 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testComponentQuantity() {
+		Observation o1 = new Observation();
+		o1.addComponent()
+			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code1")))
+			.setValue(new Quantity().setSystem("http://bar").setCode("code1").setValue(200));
+		o1.addComponent()
+			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code2")))
+			.setValue(new Quantity().setSystem("http://bar").setCode("code2").setValue(200));
+		IIdType id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
+
+		String param = Observation.SP_COMPONENT_VALUE_QUANTITY;
+
+		{
+			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1");
+			SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, v1);
+			IBundleProvider result = myObservationDao.search(map);
+			assertThat("Got: "+ toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue()));
+		}
+	}
+
 	@Test
 	public void testSearchCompositeParamQuantity() {
-		//@formatter:off
 		Observation o1 = new Observation();
 		o1.addComponent()
 			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code1")))
@@ -1061,35 +1082,35 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code3")))
 			.setValue(new Quantity().setSystem("http://bar").setCode("code2").setValue(200));
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId().toUnqualifiedVersionless();
-		//@formatter:on
 
 		String param = Observation.SP_COMPONENT_CODE_VALUE_QUANTITY;
 
 		{
 			TokenParam v0 = new TokenParam("http://foo", "code1");
 			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1");
-			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<TokenParam, QuantityParam>(v0, v1);
+			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
-			IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val));
+			SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, val);
-			assertThat(toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id2.getValue()));
+			IBundleProvider result = myObservationDao.search(map);
+			assertThat("Got: "+ toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id2.getValue()));
 		}
 		{
 			TokenParam v0 = new TokenParam("http://foo", "code1");
 			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1");
-			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<TokenParam, QuantityParam>(v0, v1);
+			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
 			IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val));
 			assertThat(toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue(), id2.getValue()));
 		}
 		{
 			TokenParam v0 = new TokenParam("http://foo", "code4");
 			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1");
-			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<TokenParam, QuantityParam>(v0, v1);
+			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
 			IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val));
 			assertThat(toUnqualifiedVersionlessIdValues(result), empty());
 		}
 		{
 			TokenParam v0 = new TokenParam("http://foo", "code1");
 			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code4");
-			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<TokenParam, QuantityParam>(v0, v1);
+			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
 			IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val));
 			assertThat(toUnqualifiedVersionlessIdValues(result), empty());
 		}
@@ -1543,26 +1564,26 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	@Test
 	public void testSearchNumberParam() {
-		ImmunizationRecommendation e1 = new ImmunizationRecommendation();
+		RiskAssessment e1 = new RiskAssessment();
 		e1.addIdentifier().setSystem("foo").setValue("testSearchNumberParam01");
-		e1.addRecommendation().setDoseNumber(new PositiveIntType(4 * 24 * 60));
+		e1.addPrediction().setProbability(new DecimalType(4 * 24 * 60));
-		IIdType id1 = myImmunizationRecommendationDao.create(e1, mySrd).getId();
+		IIdType id1 = myRiskAssessmentDao.create(e1, mySrd).getId();
 
-		ImmunizationRecommendation e2 = new ImmunizationRecommendation();
+		RiskAssessment e2 = new RiskAssessment();
 		e2.addIdentifier().setSystem("foo").setValue("testSearchNumberParam02");
-		e2.addRecommendation().setDoseNumber(new PositiveIntType(4));
+		e2.addPrediction().setProbability(new DecimalType(4));
-		IIdType id2 = myImmunizationRecommendationDao.create(e2, mySrd).getId();
+		IIdType id2 = myRiskAssessmentDao.create(e2, mySrd).getId();
 		{
-			IBundleProvider found = myImmunizationRecommendationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ImmunizationRecommendation.SP_DOSE_NUMBER, new NumberParam(">2")));
+			IBundleProvider found = myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam(">2")));
 			assertEquals(2, found.size().intValue());
 			assertThat(toUnqualifiedVersionlessIds(found), containsInAnyOrder(id1.toUnqualifiedVersionless(), id2.toUnqualifiedVersionless()));
 		}
 		{
-			IBundleProvider found = myImmunizationRecommendationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ImmunizationRecommendation.SP_DOSE_NUMBER, new NumberParam("<1")));
+			IBundleProvider found = myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam("<1")));
 			assertEquals(0, found.size().intValue());
 		}
 		{
-			IBundleProvider found = myImmunizationRecommendationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ImmunizationRecommendation.SP_DOSE_NUMBER, new NumberParam("4")));
+			IBundleProvider found = myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam("4")));
 			assertEquals(1, found.size().intValue());
 			assertThat(toUnqualifiedVersionlessIds(found), containsInAnyOrder(id2.toUnqualifiedVersionless()));
 		}
@@ -2619,7 +2640,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			// Irrelevant include
 			SearchParameterMap params = new SearchParameterMap();
 			params.add(Patient.SP_FAMILY, new StringParam("Tester_" + methodName + "_P1"));
-			params.addInclude(Encounter.INCLUDE_EPISODEOFCARE);
+			params.addInclude(Encounter.INCLUDE_EPISODE_OF_CARE);
 			IBundleProvider search = myPatientDao.search(params);
 			List<IBaseResource> patients = toList(search);
 			assertEquals(1, patients.size());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java

@@ -35,6 +35,7 @@ import java.util.stream.Collectors;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
+@SuppressWarnings("Duplicates")
 public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 	public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
@@ -204,10 +205,9 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		validator.setValidateAgainstStandardSchematron(true);
 		ValidationResult result = validator.validateWithResult(theResult);
 
-		if (!result.isSuccessful()) {
+		assertEquals(1, result.getMessages().size());
-			ourLog.info(parser.encodeResourceToString(result.toOperationOutcome()));
+		assertThat(result.getMessages().get(0).getMessage(), containsString("dom-6: A resource should have narrative for robust management"));
-			fail(parser.encodeResourceToString(result.toOperationOutcome()));
+
-		}
 	}
 
 	@Test
@@ -1150,7 +1150,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		IIdType idIn1 = myAuditEventDao.create(aeIn1, mySrd).getId().toUnqualifiedVersionless();
 
 		AuditEvent aeIn2 = new AuditEvent();
-		aeIn2.getType().setSystem("http://hl7.org/fhir/audit-event-type").setCode("rest");
+		aeIn2.getType().setSystem("http://terminology.hl7.org/CodeSystem/audit-event-type").setCode("rest");
 		IIdType idIn2 = myAuditEventDao.create(aeIn2, mySrd).getId().toUnqualifiedVersionless();
 
 		AuditEvent aeOut1 = new AuditEvent();
@@ -1223,7 +1223,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		// Now let's update 
 		valueSet = new ValueSet();
 		valueSet.setId(vsid);
-		valueSet.getCompose().addInclude().setSystem("http://hl7.org/fhir/v3/MaritalStatus").addConcept().setCode("A");
+		valueSet.getCompose().addInclude().setSystem("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus").addConcept().setCode("A");
 		valueSet.setUrl(URL_MY_VALUE_SET);
 		myValueSetDao.update(valueSet, mySrd).getId().toUnqualifiedVersionless();
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -745,7 +745,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		p.addIdentifier().setSystem("urn:system").setValue("testCreateTextIdFails");
 		p.addName().setFamily("Hello");
 
-		p.getMeta().addTag().setSystem(Constants.TAG_SUBSETTED_SYSTEM).setCode(Constants.TAG_SUBSETTED_CODE);
+		p.getMeta().addTag().setSystem(Constants.TAG_SUBSETTED_SYSTEM_DSTU3).setCode(Constants.TAG_SUBSETTED_CODE);
 
 		try {
 			myPatientDao.create(p, mySrd);

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

@@ -721,7 +721,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 		Observation obs = new Observation();
 		obs.setSubject(new Reference(ptid));
-		obs.setContext(new Reference(encid));
+		obs.setEncounter(new Reference(encid));
 		myObservationDao.create(obs);
 
 		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -131,7 +131,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		input.getMeta().getProfile().add(new CanonicalType(sd.getUrl()));
 
 		input.addIdentifier().setSystem("http://acme").setValue("12345");
-		input.getContext().setReference("http://foo.com/Encounter/9");
+		input.getEncounter().setReference("http://foo.com/Encounter/9");
 		input.setStatus(ObservationStatus.FINAL);
 		input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 
@@ -171,7 +171,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		input.getMeta().getProfile().add(new CanonicalType(profileUri));
 
 		input.addIdentifier().setSystem("http://acme").setValue("12345");
-		input.getContext().setReference("http://foo.com/Encounter/9");
+		input.getEncounter().setReference("http://foo.com/Encounter/9");
 		input.setStatus(ObservationStatus.FINAL);
 		input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java

@@ -228,15 +228,17 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
 		IPrimitiveType<String> display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		StringType vsIdentifier = new StringType("http://hl7.org/fhir/ValueSet/v2-0487");
+		StringType vsIdentifier = new StringType("http://hl7.org/fhir/ValueSet/yesnodontknow");
-		StringType code = new StringType("BRN");
+		StringType code = new StringType("Y");
-		StringType system = new StringType("http://hl7.org/fhir/v2/0487");
+		StringType system = new StringType("http://terminology.hl7.org/CodeSystem/v2-0136");
 		ValidateCodeResult result = myValueSetDao.validateCode(vsIdentifier, null, code, system, display, coding, codeableConcept, mySrd);
 		
 		ourLog.info(result.getMessage());
 		assertTrue(result.getMessage(), result.isResult());
+		assertEquals("Yes", result.getDisplay());
 	}
 
 	
 }
 
+

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

@@ -5,36 +5,42 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
+import ca.uhn.fhir.jpa.dao.PathAndRef;
 import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.*;
 import org.junit.AfterClass;
+import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 public class SearchParamExtractorR4Test {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchParamExtractorR4Test.class);
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static IValidationSupport ourValidationSupport;
+	private ISearchParamRegistry mySearchParamRegistry;
 
-	@Test
+	@Before
-	public void testParamWithOrInPath() {
+	public void before() {
-		Observation obs = new Observation();
+		mySearchParamRegistry = new ISearchParamRegistry() {
-		obs.addCategory().addCoding().setSystem("SYSTEM").setCode("CODE");
-
-		ISearchParamRegistry searchParamRegistry = new ISearchParamRegistry() {
 			@Override
 			public void forceRefresh() {
 				// nothing
@@ -42,7 +48,7 @@ public class SearchParamExtractorR4Test {
 
 			@Override
 			public RuntimeSearchParam getActiveSearchParam(String theResourceName, String theParamName) {
-				throw new UnsupportedOperationException();
+				return getActiveSearchParams(theResourceName).get(theParamName);
 			}
 
 			@Override
@@ -81,7 +87,14 @@ public class SearchParamExtractorR4Test {
 			}
 		};
 
-		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new DaoConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
+	}
+
+	@Test
+	public void testParamWithOrInPath() {
+		Observation obs = new Observation();
+		obs.addCategory().addCoding().setSystem("SYSTEM").setCode("CODE");
+
+		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new DaoConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
 		Set<BaseResourceIndexedSearchParam> tokens = extractor.extractSearchParamTokens(new ResourceTable(), obs);
 		assertEquals(1, tokens.size());
 		ResourceIndexedSearchParamToken token = (ResourceIndexedSearchParamToken) tokens.iterator().next();
@@ -90,6 +103,50 @@ public class SearchParamExtractorR4Test {
 		assertEquals("CODE", token.getValue());
 	}
 
+	@Test
+	public void testReferenceWithResolve() {
+		Encounter enc = new Encounter();
+		enc.addLocation().setLocation(new Reference("Location/123"));
+
+		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new DaoConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
+		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Encounter", "location");
+		assertNotNull(param);
+		List<PathAndRef> links = extractor.extractResourceLinks(enc, param);
+		assertEquals(1, links.size());
+		assertEquals("Encounter.location.location.where(resolve() is Location)", links.get(0).getPath());
+		assertEquals("Location/123", ((Reference) links.get(0).getRef()).getReference());
+	}
+
+	@Test
+	public void testReferenceWithResolveMulti() {
+		Consent consent = new Consent();
+		consent.setSource(new Reference().setReference("Consent/999"));
+
+		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new DaoConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
+		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Consent", Consent.SP_SOURCE_REFERENCE);
+		assertNotNull(param);
+		List<PathAndRef> links = extractor.extractResourceLinks(consent, param);
+		assertEquals(1, links.size());
+		assertEquals("Consent.source.where(resolve() is Consent or resolve() is Contract or resolve() is QuestionnaireResponse or resolve() is DocumentReference)", links.get(0).getPath());
+		assertEquals("Consent/999", ((Reference) links.get(0).getRef()).getReference());
+	}
+
+	@Test
+	public void testExtractComponentQuantities() {
+		Observation o1 = new Observation();
+		o1.addComponent()
+			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code1")))
+			.setValue(new Quantity().setSystem("http://bar").setCode("code1").setValue(200));
+		o1.addComponent()
+			.setCode(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("code2")))
+			.setValue(new Quantity().setSystem("http://bar").setCode("code2").setValue(200));
+
+		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new DaoConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
+		Set<ResourceIndexedSearchParamQuantity> links = extractor.extractSearchParamQuantity(new ResourceTable(), o1);
+		ourLog.info("Links:\n  {}", links.stream().map(t -> t.toString()).collect(Collectors.joining("\n  ")));
+		assertEquals(4, links.size());
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderInterceptorDstu2Test.java

@@ -34,7 +34,7 @@ import java.nio.charset.StandardCharsets;
 
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.Assert.*;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.*;
 
 @SuppressWarnings("deprecation")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderInterceptorDstu3Test.java

@@ -39,7 +39,7 @@ import java.nio.charset.StandardCharsets;
 
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.Assert.*;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.*;
 
 @TestPropertySource(properties = {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/PatientEverythingR4Test.java

@@ -23,6 +23,7 @@ import ca.uhn.fhir.parser.StrictErrorHandler;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.util.TestUtil;
 
+@SuppressWarnings("Duplicates")
 public class PatientEverythingR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PatientEverythingR4Test.class);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemTest.java

@@ -87,7 +87,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 			.onType(CodeSystem.class)
 			.named("lookup")
 			.withParameter(Parameters.class, "code", new CodeType("ACSN"))
-			.andParameter("system", new UriType("http://hl7.org/fhir/v2/0203"))
+			.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
 			.execute();
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
@@ -245,7 +245,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 			.onType(CodeSystem.class)
 			.named("lookup")
 			.withParameter(Parameters.class, "code", new CodeType("M"))
-			.andParameter("system", new UriType("http://hl7.org/fhir/v3/MaritalStatus"))
+			.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus"))
 			.execute();
 		//@formatter:on
 

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

@@ -63,63 +63,20 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
-import org.hl7.fhir.r4.model.AuditEvent;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.BaseResource;
-import org.hl7.fhir.r4.model.Basic;
-import org.hl7.fhir.r4.model.Binary;
-import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.Bundle.SearchEntryMode;
-import org.hl7.fhir.r4.model.CarePlan;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.CodeType;
-import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.Condition;
-import org.hl7.fhir.r4.model.DateTimeType;
-import org.hl7.fhir.r4.model.DateType;
-import org.hl7.fhir.r4.model.Device;
-import org.hl7.fhir.r4.model.DocumentManifest;
-import org.hl7.fhir.r4.model.DocumentReference;
-import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Encounter.EncounterLocationComponent;
 import org.hl7.fhir.r4.model.Encounter.EncounterStatus;
 import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.r4.model.Extension;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.ImagingStudy;
-import org.hl7.fhir.r4.model.ImmunizationRecommendation;
-import org.hl7.fhir.r4.model.InstantType;
-import org.hl7.fhir.r4.model.IntegerType;
-import org.hl7.fhir.r4.model.Location;
-import org.hl7.fhir.r4.model.Medication;
-import org.hl7.fhir.r4.model.MedicationAdministration;
-import org.hl7.fhir.r4.model.MedicationRequest;
-import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
-import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
-import org.hl7.fhir.r4.model.OperationOutcome;
-import org.hl7.fhir.r4.model.Organization;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Period;
-import org.hl7.fhir.r4.model.Practitioner;
-import org.hl7.fhir.r4.model.Quantity;
-import org.hl7.fhir.r4.model.Questionnaire;
 import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
-import org.hl7.fhir.r4.model.QuestionnaireResponse;
-import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.ServiceRequest;
-import org.hl7.fhir.r4.model.StringType;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.Subscription;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
-import org.hl7.fhir.r4.model.UnsignedIntType;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -169,6 +126,7 @@ import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 
+@SuppressWarnings("Duplicates")
 public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4Test.class);
@@ -547,7 +505,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		IIdType optId = ourClient.create().resource(options).execute().getId();
 
 		Questionnaire q = new Questionnaire();
-		q.addItem().setLinkId("link0").setRequired(false).setType(QuestionnaireItemType.CHOICE).setOptions((optId.getValue()));
+		q.addItem().setLinkId("link0").setRequired(false).setType(QuestionnaireItemType.CHOICE).setAnswerValueSet((optId.getValue()));
 		IIdType qId = ourClient.create().resource(q).execute().getId();
 
 		QuestionnaireResponse qa;
@@ -747,7 +705,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		location.setPeriod(new Period().setStart(new Date(), TemporalPrecisionEnum.SECOND).setEnd(new Date(), TemporalPrecisionEnum.SECOND));
 		IIdType e1id = ourClient.create().resource(e1).execute().getId();
 
-		//@formatter:off
 		Bundle res = ourClient.search()
 			.forResource(Encounter.class)
 			.where(Encounter.IDENTIFIER.exactly().systemAndCode("urn:foo", "testDeepChainingE1"))
@@ -755,7 +712,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.include(Location.INCLUDE_PARTOF.asRecursive())
 			.returnBundle(Bundle.class)
 			.execute();
-		//@formatter:on
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res));
 
 		assertEquals(3, res.getEntry().size());
 		assertEquals(1, genResourcesOfType(res, Encounter.class).size());
@@ -763,6 +721,45 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testReferenceOfWrongType() {
+		Group l2 = new Group();
+		l2.setActive(true);
+		IIdType l2id = ourClient.create().resource(l2).execute().getId();
+
+		Encounter e1 = new Encounter();
+		e1.getStatusElement().setValue(EncounterStatus.INPROGRESS);
+		e1.getSubject().setReference(l2id.toUnqualifiedVersionless().getValue());
+		IIdType e1id = ourClient.create().resource(e1).execute().getId();
+
+		// Wrong type
+		Bundle res = ourClient.search()
+			.forResource(Encounter.class)
+			.include(Encounter.INCLUDE_PATIENT.asRecursive())
+			.returnBundle(Bundle.class)
+			.execute();
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res));
+
+		assertEquals(1, res.getEntry().size());
+		assertEquals(1, genResourcesOfType(res, Encounter.class).size());
+		assertEquals(e1id.toUnqualifiedVersionless(), genResourcesOfType(res, Encounter.class).get(0).getIdElement().toUnqualifiedVersionless());
+
+		// Right type
+		res = ourClient.search()
+			.forResource(Encounter.class)
+			.include(Encounter.INCLUDE_SUBJECT.asRecursive())
+			.returnBundle(Bundle.class)
+			.execute();
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res));
+
+		assertEquals(2, res.getEntry().size());
+		assertEquals(1, genResourcesOfType(res, Encounter.class).size());
+		assertEquals(1, genResourcesOfType(res, Group.class).size());
+
+	}
+
 	@Test
 	public void testDeleteConditionalMultiple() {
 		String methodName = "testDeleteConditionalMultiple";
@@ -830,16 +827,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		String methodName = "testDeleteConditionalNoMatches";
 
 		HttpDelete delete = new HttpDelete(ourServerBase + "/Patient?identifier=" + methodName);
-		CloseableHttpResponse resp = ourHttpClient.execute(delete);
+		try (CloseableHttpResponse resp = ourHttpClient.execute(delete)) {
-		try {
 			ourLog.info(resp.toString());
 			String response = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(response);
 			assertEquals(200, resp.getStatusLine().getStatusCode());
 			assertThat(response, containsString(
 				"<issue><severity value=\"warning\"/><code value=\"not-found\"/><diagnostics value=\"Unable to find resource matching URL &quot;Patient?identifier=testDeleteConditionalNoMatches&quot;. Deletion failed.\"/></issue>"));
-		} finally {
-			IOUtils.closeQuietly(resp);
 		}
 
 	}
@@ -847,14 +841,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	@Test
 	public void testDeleteInvalidReference() throws IOException {
 		HttpDelete delete = new HttpDelete(ourServerBase + "/Patient");
-		CloseableHttpResponse response = ourHttpClient.execute(delete);
+		try (CloseableHttpResponse response = ourHttpClient.execute(delete)) {
-		try {
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			assertThat(responseString, containsString("Can not perform delete, no ID provided"));
-		} finally {
-			response.close();
 		}
 	}
 
@@ -1096,7 +1087,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		IIdType orgId2 = ourClient.create().resource(org2).execute().getId().toUnqualifiedVersionless();
 
 		Device dev = new Device();
-		dev.setModel(methodName);
+		dev.setManufacturer(methodName);
 		dev.getOwner().setReferenceElement(orgId2);
 		IIdType devId = ourClient.create().resource(dev).execute().getId().toUnqualifiedVersionless();
 
@@ -1122,7 +1113,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Observation obs = new Observation();
 		obs.getSubject().setReferenceElement(patientId);
 		obs.getDevice().setReferenceElement(devId);
-		obs.getContext().setReferenceElement(encId);
+		obs.getEncounter().setReferenceElement(encId);
 		IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
 
 		ourLog.info("IDs: EncU:" + encUId.getIdPart() + " Enc:" + encId.getIdPart() + "  " + patientId.toUnqualifiedVersionless());
@@ -1160,7 +1151,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		IIdType orgId2 = ourClient.create().resource(org2).execute().getId().toUnqualifiedVersionless();
 
 		Device dev = new Device();
-		dev.setModel(methodName);
+		dev.setManufacturer(methodName);
 		dev.getOwner().setReferenceElement(orgId2);
 		IIdType devId = ourClient.create().resource(dev).execute().getId().toUnqualifiedVersionless();
 
@@ -1185,7 +1176,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Observation obs = new Observation();
 		obs.getSubject().setReferenceElement(patientId);
 		obs.getDevice().setReferenceElement(devId);
-		obs.getContext().setReferenceElement(encId);
+		obs.getEncounter().setReferenceElement(encId);
 		IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
 
 		Parameters output = ourClient.operation().onType(Encounter.class).named("everything").withNoParameters(Parameters.class).execute();
@@ -1402,7 +1393,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		IIdType orgId2 = ourClient.create().resource(org2).execute().getId().toUnqualifiedVersionless();
 
 		Device dev = new Device();
-		dev.setModel(methodName);
+		dev.setManufacturer(methodName);
 		dev.getOwner().setReferenceElement(orgId2);
 		IIdType devId = ourClient.create().resource(dev).execute().getId().toUnqualifiedVersionless();
 
@@ -1562,6 +1553,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	 * Per message from David Hay on Skype
 	 */
 	@Test
+	@Ignore
 	public void testEverythingWithLargeSet() throws Exception {
 
 		String inputString = IOUtils.toString(getClass().getResourceAsStream("/david_big_bundle.json"), StandardCharsets.UTF_8);
@@ -1975,6 +1967,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertEquals(id.withVersion("1").getValue(), history.getEntry().get(2).getResource().getId());
 		assertEquals(1, ((Patient) history.getEntry().get(2).getResource()).getName().size());
 
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(history));
+
 		try {
 			myBundleDao.validate(history, null, null, null, null, null, mySrd);
 		} catch (PreconditionFailedException e) {
@@ -2537,7 +2531,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertEquals("1", patientId.getVersionIdPart());
 
 		AuditEvent ae = new org.hl7.fhir.r4.model.AuditEvent();
-		ae.addEntity().getReference().setReference(patientId.toUnqualified().getValue());
+		ae.addEntity().getWhat().setReference(patientId.toUnqualified().getValue());
 		IIdType aeId = ourClient.create().resource(ae).execute().getId();
 		assertEquals("1", aeId.getVersionIdPart());
 
@@ -2546,8 +2540,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertFalse(patient.getManagingOrganization().getReferenceElement().hasVersionIdPart());
 
 		ae = ourClient.read().resource(AuditEvent.class).withId(aeId).execute();
-		assertTrue(ae.getEntityFirstRep().getReference().getReferenceElement().hasIdPart());
+		assertTrue(ae.getEntityFirstRep().getWhat().getReferenceElement().hasIdPart());
-		assertTrue(ae.getEntityFirstRep().getReference().getReferenceElement().hasVersionIdPart());
+		assertTrue(ae.getEntityFirstRep().getWhat().getReferenceElement().hasVersionIdPart());
 
 	}
 
@@ -3740,8 +3734,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			ourClient
 				.search()
-				.forResource(ImmunizationRecommendation.class)
+				.forResource(Sequence.class)
-				.where(ImmunizationRecommendation.DOSE_NUMBER.withPrefix(ParamPrefixEnum.ENDS_BEFORE).number(100))
+				.where(Sequence.END.withPrefix(ParamPrefixEnum.ENDS_BEFORE).number(100))
 				.prettyPrint()
 				.returnBundle(Bundle.class)
 				.execute();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java

@@ -114,7 +114,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		myLocalVs = new ValueSet();
 		myLocalVs.setUrl(URL_MY_VALUE_SET);
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
-		include.setSystem("http://hl7.org/fhir/v3/MaritalStatus");
+		include.setSystem("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus");
 		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
 	}
 
@@ -505,9 +505,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 			.operation()
 			.onType(ValueSet.class)
 			.named("validate-code")
-			.withParameter(Parameters.class, "code", new StringType("BRN"))
+			.withParameter(Parameters.class, "code", new StringType("Y"))
-			.andParameter("url", new StringType("http://hl7.org/fhir/ValueSet/v2-0487"))
+			.andParameter("url", new StringType("http://hl7.org/fhir/ValueSet/yesnodontknow"))
-			.andParameter("system", new StringType("http://hl7.org/fhir/v2/0487"))
+			.andParameter("system", new StringType("http://terminology.hl7.org/CodeSystem/v2-0136"))
 			.useHttpGet()
 			.execute();
 
@@ -521,7 +521,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), containsStringIgnoringCase("succeeded"));
 
 		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals("Burn", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("Yes", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

@@ -101,7 +101,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 	}
 
 	@Test
-	public void testUploadMissingPackage() throws Exception {
+	public void testUploadMissingPackage() {
 		//@formatter:off
 		try {
 			ourClient

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -42,10 +42,10 @@ import javax.persistence.EntityManager;
 import java.util.*;
 
 import static org.junit.Assert.*;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Matchers.anyBoolean;
+import static org.mockito.ArgumentMatchers.anyBoolean;
-import static org.mockito.Matchers.eq;
+import static org.mockito.ArgumentMatchers.eq;
-import static org.mockito.Matchers.same;
+import static org.mockito.ArgumentMatchers.same;
 import static org.mockito.Mockito.*;
 
 @SuppressWarnings({"unchecked"})

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookWithEventDefinitionR4Test.java

@@ -95,9 +95,9 @@ public class RestHookWithEventDefinitionR4Test extends BaseResourceProviderR4Tes
 			.setPurpose("Monitor all admissions to Emergency")
 			.setTrigger(new TriggerDefinition()
 				.setType(TriggerDefinition.TriggerType.DATAADDED)
-				.setCondition(new TriggerDefinition.TriggerDefinitionConditionComponent()
+				.setCondition(new Expression()
 					.setDescription("Encounter Location = emergency (active/completed encounters, current or previous)")
-					.setLanguage(TriggerDefinition.ExpressionLanguage.TEXT_FHIRPATH)
+					.setLanguage(Expression.ExpressionLanguage.TEXT_FHIRPATH)
 					.setExpression("(this | %previous).location.where(location = 'Location/emergency' and status in {'active', 'completed'}).exists()")
 				)
 			);

hapi-fhir-jpaserver-base/src/test/resources/r4/batch-error.xml

@@ -2043,8 +2043,6 @@
                <profile value="http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition"/>
                <!--CDA templateId: urn:hl7ii:2.16.840.1.113883.10.20.22.4.4:2015-08-01-->
             </meta>
-            <clinicalStatus value="active"/>
-            <verificationStatus value="confirmed"/>
             <category>
                <coding>
                   <system value="http://snomed.info/sct"/>
@@ -2116,8 +2114,6 @@
                <profile value="http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition"/>
                <!--CDA templateId: urn:hl7ii:2.16.840.1.113883.10.20.22.4.4:2015-08-01-->
             </meta>
-            <clinicalStatus value="active"/>
-            <verificationStatus value="confirmed"/>
             <category>
                <coding>
                   <system value="http://hl7.org/fhir/v3/ActCode"/>

hapi-fhir-jpaserver-base/src/test/resources/r4/bundle.xml

@@ -348,17 +348,17 @@
             <item>
                <linkId value="1.1"/>
                <type value="choice"/>
-               <options value="#verbal"/>
+               <answerValueSet value="#verbal"/>
             </item>
             <item>
                <linkId value="1.2"/>
                <type value="choice"/>
-               <options value="#motor"/>
+               <answerValueSet value="#motor"/>
             </item>
             <item>
                <linkId value="1.3"/>
                <type value="choice"/>
-               <options value="#eye"/>
+               <answerValueSet value="#eye"/>
             </item>
          </Questionnaire>
       </resource>

hapi-fhir-jpaserver-base/src/test/resources/r4/collection-bundle.json

@@ -11,7 +11,6 @@
 			},
 			"id": "cf-1505178568463",
 			"subject": {"reference": "Patient/2344"},
-			"clinicalStatus": "active",
 			"code": {"coding": [{
 				"system": "http://snomed.info/sct",
 				"code": "170631002",

hapi-fhir-jpaserver-base/src/test/resources/r4/documentreference.json

@@ -69,7 +69,6 @@
 			}
 		}
 	],
-  "created" : "2005-12-24T09:35:00+11:00",
   "status" : "current",
   "description" : "Physical",
   "context" : {

hapi-fhir-jpaserver-base/src/test/resources/r4/oruBundle.json

@@ -261,7 +261,7 @@
 				"subject": {
 					"reference": "urn:uuid:09a8d22c-1e23-4e5f-b3bf-505772f123d1"
 				},
-				"context": {
+				"encounter": {
 					"reference": "urn:uuid:29e3a213-0df4-41e0-88f8-e3be83277022"
 				},
 				"effectiveDateTime": "2011-12-01T09:49:00-05:00",
@@ -289,7 +289,7 @@
 				"subject": {
 					"reference": "urn:uuid:09a8d22c-1e23-4e5f-b3bf-505772f123d1"
 				},
-				"context": {
+				"encounter": {
 					"reference": "urn:uuid:29e3a213-0df4-41e0-88f8-e3be83277022"
 				},
 				"effectiveDateTime": "2011-12-01T09:49:00-05:00",
@@ -317,7 +317,7 @@
 				"subject": {
 					"reference": "urn:uuid:09a8d22c-1e23-4e5f-b3bf-505772f123d1"
 				},
-				"context": {
+				"encounter": {
 					"reference": "urn:uuid:29e3a213-0df4-41e0-88f8-e3be83277022"
 				},
 				"effectiveDateTime": "2011-12-01T09:49:00-05:00",
@@ -345,7 +345,7 @@
 				"subject": {
 					"reference": "urn:uuid:09a8d22c-1e23-4e5f-b3bf-505772f123d1"
 				},
-				"context": {
+				"encounter": {
 					"reference": "urn:uuid:29e3a213-0df4-41e0-88f8-e3be83277022"
 				},
 				"effectiveDateTime": "2011-12-01T10:57:00-05:00",

hapi-fhir-jpaserver-base/src/test/resources/r4/sd-david-dhtest7.json

@@ -131,7 +131,7 @@
         "binding": {
           "strength": "example",
           "description": "Codes for identifying types of resources not yet defined by FHIR",
-          "valueSetCanonical": "http://hl7.org/fhir/ValueSet/basic-resource-type"
+          "valueSet": "http://hl7.org/fhir/ValueSet/basic-resource-type"
         },
         "mapping": [
           {

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.migrate;
  */
 
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableTask;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -126,6 +127,11 @@ public class JdbcUtils {
 								return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
 							case Types.BIGINT:
 								return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(null);
+							case Types.INTEGER:
+								return BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null);
+							case Types.TIMESTAMP:
+							case Types.TIMESTAMP_WITH_TIMEZONE:
+								return BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP.getDescriptor(null);
 							default:
 								throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
 						}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java

@@ -39,6 +39,13 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 	 * Constructor
 	 */
 	BaseTableColumnTypeTask() {
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.DERBY_EMBEDDED, "integer");
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MARIADB_10_1, "integer");
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MYSQL_5_7, "integer");
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MSSQL_2012, "int");
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.ORACLE_12C, "number(10,0)");
+		setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.POSTGRES_9_4, "int4");
+
 		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.DERBY_EMBEDDED, "bigint");
 		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MARIADB_10_1, "bigint");
 		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MYSQL_5_7, "bigint");
@@ -147,8 +154,16 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 				Assert.isTrue(theColumnLength == null, "Must not supply a column length");
 				return "timestamp";
 			}
+		},
+		INT {
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength == null, "Must not supply a column length");
+				return "int";
+			}
 		};
 
+
 		public abstract String getDescriptor(Long theColumnLength);
 
 	}

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

@@ -37,7 +37,22 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 	 * Constructor
 	 */
 	public HapiFhirJpaMigrationTasks() {
+		init340();
 		init350();
+		init360();
+	}
+
+	private void init360() {
+		Builder version = forVersion(VersionEnum.V3_6_0);
+
+		// Resource Link
+		Builder.BuilderWithTableName resourceLink = version.onTable("HFJ_RES_LINK");
+		version.startSectionWithMessage("Starting work on table: " + resourceLink.getTableName());
+		resourceLink
+			.modifyColumn("SRC_PATH")
+			.nonNullable()
+			.withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, ResourceLink.SRC_PATH_LENGTH);
+
 	}
 
 	private void init350() {
@@ -425,5 +440,39 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT");
 	}
 
+	private void init340() {
+		Builder version = forVersion(VersionEnum.V3_4_0);
+
+		// CodeSystem Version
+		Builder.BuilderWithTableName resourceLink = version.onTable("TRM_CODESYSTEM_VER");
+		version.startSectionWithMessage("Starting work on table: " + resourceLink.getTableName());
+		resourceLink
+			.dropIndex("IDX_CSV_RESOURCEPID_AND_VER");
+		resourceLink
+			.dropColumn("RES_VERSION_ID");
+		resourceLink
+			.addColumn("CS_VERSION_ID")
+			.nullable()
+			.type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255);
+		resourceLink
+			.addColumn("CODESYSTEM_PID")
+			.nullable()
+			.type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+		resourceLink
+			.addForeignKey("FK_CODESYSVER_CS_ID")
+			.toColumn("CODESYSTEM_PID")
+			.references("TRM_CODESYSTEM", "PID");
+
+		// Concept
+		Builder.BuilderWithTableName concept = version.onTable("TRM_CONCEPT");
+		version.startSectionWithMessage("Starting work on table: " + concept.getTableName());
+		concept
+			.addColumn("CODE_SEQUENCE")
+			.nullable()
+			.type(BaseTableColumnTypeTask.ColumnTypeEnum.INT);
+
+
+	}
+
 
 }

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTest.java

@@ -6,6 +6,7 @@ import org.junit.Test;
 import java.sql.SQLException;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
 public class AddColumnTest extends BaseTest {
@@ -26,6 +27,23 @@ public class AddColumnTest extends BaseTest {
 		assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL", "NEWCOL"));
 	}
 
+	@Test
+	public void testAddColumnInt() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+
+		AddColumnTask task = new AddColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("newcolint");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.INT);
+		task.setNullable(true);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		String type = JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "newcolint");
+		assertEquals(BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null), type);
+	}
+
 	@Test
 	public void testColumnAlreadyExists() throws SQLException {
 		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -59,6 +59,8 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
 		retVal.setFetchSizeDefaultMaximum(10000);
+		retVal.setReindexThreadCount(1);
+		retVal.setExpungeEnabled(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -59,6 +59,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setFetchSizeDefaultMaximum(10000);
+		retVal.setExpungeEnabled(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/interceptor/PublicSecurityInterceptor.java

@@ -2,6 +2,7 @@ package ca.uhn.fhirtest.interceptor;
 
 import ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider;
 import ca.uhn.fhir.jpa.provider.BaseTerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
 import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor;
@@ -35,6 +36,9 @@ public class PublicSecurityInterceptor extends AuthorizationInterceptor {
 			return new RuleBuilder()
 				.deny().operation().named(BaseJpaSystemProvider.MARK_ALL_RESOURCES_FOR_REINDEXING).onServer().andThen()
 				.deny().operation().named(BaseTerminologyUploaderProvider.UPLOAD_EXTERNAL_CODE_SYSTEM).onServer().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onServer().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onAnyType().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onAnyInstance().andThen()
 				.allowAll()
 				.build();
 		}

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java

@@ -644,9 +644,11 @@ public class RestfulServerUtils {
 
 		if (theServer.getETagSupport() == ETagSupportEnum.ENABLED) {
 			if (fullId != null && fullId.hasVersionIdPart()) {
-				response.addHeader(Constants.HEADER_ETAG, "W/\"" + fullId.getVersionIdPart() + '"');
+				String versionIdPart = fullId.getVersionIdPart();
+				response.addHeader(Constants.HEADER_ETAG, createEtag(versionIdPart));
 			} else if (theResource != null && theResource.getMeta() != null && isNotBlank(theResource.getMeta().getVersionId())) {
-				response.addHeader(Constants.HEADER_ETAG, "W/\"" + theResource.getMeta().getVersionId() + '"');
+				String versionId = theResource.getMeta().getVersionId();
+				response.addHeader(Constants.HEADER_ETAG, createEtag(versionId));
 			}
 		}
 
@@ -739,6 +741,10 @@ public class RestfulServerUtils {
 		return response.sendWriterResponse(theStatusCode, contentType, charset, writer);
 	}
 
+	public static String createEtag(String theVersionId) {
+		return "W/\"" + theVersionId + '"';
+	}
+
 	public static Integer tryToExtractNamedParameter(RequestDetails theRequest, String theParamName) {
 		String[] retVal = theRequest.getParameters().get(theParamName);
 		if (retVal == null) {

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplOp.java

@@ -11,7 +11,7 @@ import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor.Verdict
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.BundleUtil.BundleEntryParts;
 import ca.uhn.fhir.util.FhirTerser;
-import org.apache.commons.codec.binary.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hl7.fhir.instance.model.api.IAnyResource;
@@ -19,7 +19,6 @@ import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -376,7 +375,7 @@ class RuleImplOp extends BaseRule /* implements IAuthRule */ {
 						String compartmentOwnerResourceType = next.getResourceType();
 						if (!StringUtils.equals(appliesToResourceType, compartmentOwnerResourceType)) {
 							List<RuntimeSearchParam> params = sourceDef.getSearchParamsForCompartmentName(compartmentOwnerResourceType);
-							if (params.isEmpty() == false) {
+							if (!params.isEmpty()) {
 
 								/*
 								 * If this is a search, we can at least check whether

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/SearchParameter.java

@@ -96,6 +96,12 @@ public class SearchParameter extends BaseQueryParameter {
 		ourParamTypes.put(HasParam.class, RestSearchParameterTypeEnum.HAS);
 		ourParamTypes.put(HasOrListParam.class, RestSearchParameterTypeEnum.HAS);
 		ourParamTypes.put(HasAndListParam.class, RestSearchParameterTypeEnum.HAS);
+
+		ourParamTypes.put(SpecialParam.class, RestSearchParameterTypeEnum.SPECIAL);
+		ourParamTypes.put(SpecialOrListParam.class, RestSearchParameterTypeEnum.SPECIAL);
+		ourParamTypes.put(SpecialAndListParam.class, RestSearchParameterTypeEnum.SPECIAL);
+		ourParamQualifiers.put(RestSearchParameterTypeEnum.SPECIAL, CollectionUtil.newSet(Constants.PARAMQUALIFIER_MISSING));
+
 	}
 
 	private List<Class<? extends IQueryParameterType>> myCompositeTypes = Collections.emptyList();

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java

@@ -802,7 +802,7 @@ public class JsonParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder(ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM, ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE));
+		assertThat(encoded, stringContainsInOrder(ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3, ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -836,7 +836,7 @@ public class JsonParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\",", "\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",", "\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -856,7 +856,7 @@ public class JsonParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"",
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"",
 				"\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2_1Test.java

@@ -1362,7 +1362,7 @@ public class XmlParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -1462,7 +1462,7 @@ public class XmlParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -1483,7 +1483,7 @@ public class XmlParserDstu2_1Test {
 
 		assertThat(encoded, containsString("<Patient"));
 		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu2_1Test.java

@@ -478,7 +478,7 @@ public class GenericClientDstu2_1Test {
 			client.read().resource(Patient.class).withId("1").execute();
 			fail();
 		} catch (FhirClientConnectionException e) {
-			assertEquals("java.lang.IllegalStateException", e.getMessage());
+			assertEquals(null, e.getMessage());
 		}
 
 		try {

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -808,7 +808,7 @@ public class JsonParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE));
+		assertThat(encoded, stringContainsInOrder(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -918,7 +918,7 @@ public class JsonParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE + "\","));
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE + "\","));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -940,7 +940,7 @@ public class JsonParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM + "\",",
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",",
 			"\"code\": \"" + Constants.TAG_SUBSETTED_CODE + "\","));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -22,7 +22,6 @@ import org.junit.Before;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 import org.mockito.ArgumentMatchers;
-import org.mockito.Matchers;
 import org.mockito.internal.stubbing.answers.ThrowsException;
 import org.xmlunit.builder.DiffBuilder;
 import org.xmlunit.builder.Input;
@@ -1544,7 +1543,7 @@ public class XmlParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -1658,7 +1657,7 @@ public class XmlParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -1681,7 +1680,7 @@ public class XmlParserDstu2Test {
 
 		assertThat(encoded, containsString("<Patient"));
 		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/context/IWorkerContext.java

@@ -195,7 +195,9 @@ public interface IWorkerContext {
    * @throws FHIRException 
    */
   public ValueSetExpansionComponent expandVS(ConceptSetComponent inc, boolean heiarchical) throws TerminologyServiceException;
-  
+
+  StructureDefinition fetchTypeDefinition(String theCode);
+
   public class ValidationResult {
     private ConceptDefinitionComponent definition;
     private IssueSeverity severity;

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java

@@ -23,6 +23,7 @@ import org.hl7.fhir.dstu3.terminologies.ValueSetExpanderFactory;
 import org.hl7.fhir.dstu3.terminologies.ValueSetExpanderSimple;
 import org.hl7.fhir.dstu3.utils.INarrativeGenerator;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.TerminologyServiceException;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
 import java.util.*;
@@ -69,6 +70,8 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
       vso = getExpander().expand(theSource, theProfile);
     } catch (InvalidRequestException e) {
       throw e;
+    } catch (TerminologyServiceException e) {
+      throw new InvalidRequestException(e.getMessage(), e);
     } catch (Exception e) {
       throw new InternalErrorException(e);
     }
@@ -89,6 +92,11 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
     return myValidationSupport.expandValueSet(myCtx, theInc);
   }
 
+  @Override
+  public StructureDefinition fetchTypeDefinition(String theCode) {
+    throw new UnsupportedOperationException();
+  }
+
   @Override
   public CodeSystem fetchCodeSystem(String theSystem) {
     if (myValidationSupport == null) {
@@ -243,7 +251,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
       }
     }
 
-    return new ValidationResult(null, null);
+    return new ValidationResult(IssueSeverity.ERROR, null);
   }
 
   @Override

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpanderSimple.java

@@ -1,465 +1,461 @@
-package org.hl7.fhir.dstu3.terminologies;
+package org.hl7.fhir.dstu3.terminologies;
-
+
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
+
-import java.io.FileNotFoundException;
+import java.io.FileNotFoundException;
-import java.io.IOException;
+import java.io.IOException;
-
+
-/*
+/*
- * Copyright (c) 2011+, HL7, Inc
+ * Copyright (c) 2011+, HL7, Inc
- * All rights reserved.
+ * All rights reserved.
- * 
+ * 
- * Redistribution and use in source and binary forms, with or without modification,
+ * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
+ * are permitted provided that the following conditions are met:
- * 
+ * 
- * Redistributions of source code must retain the above copyright notice, this
+ * Redistributions of source code must retain the above copyright notice, this
- * list of conditions and the following disclaimer.
+ * list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
+ * Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
+ * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
+ * and/or other materials provided with the distribution.
- * Neither the name of HL7 nor the names of its contributors may be used to
+ * Neither the name of HL7 nor the names of its contributors may be used to
- * endorse or promote products derived from this software without specific
+ * endorse or promote products derived from this software without specific
- * prior written permission.
+ * prior written permission.
- * 
+ * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
+ * POSSIBILITY OF SUCH DAMAGE.
- * 
+ * 
- */
+ */
-
+
-import java.util.ArrayList;
+import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.HashMap;
-import java.util.HashSet;
+import java.util.HashSet;
-import java.util.List;
+import java.util.List;
-import java.util.Map;
+import java.util.Map;
-import java.util.Set;
+import java.util.Set;
-import java.util.UUID;
+import java.util.UUID;
-
+
-import org.apache.commons.lang3.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
-import org.hl7.fhir.dstu3.context.IWorkerContext;
+import org.hl7.fhir.dstu3.context.IWorkerContext;
-import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.hl7.fhir.dstu3.model.CodeSystem;
-import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
+import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
-import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
-import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionDesignationComponent;
+import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionDesignationComponent;
-import org.hl7.fhir.dstu3.model.DateTimeType;
+import org.hl7.fhir.dstu3.model.DateTimeType;
-import org.hl7.fhir.dstu3.model.ExpansionProfile;
+import org.hl7.fhir.dstu3.model.ExpansionProfile;
-import org.hl7.fhir.dstu3.model.Factory;
+import org.hl7.fhir.dstu3.model.Factory;
-import org.hl7.fhir.dstu3.model.PrimitiveType;
+import org.hl7.fhir.dstu3.model.PrimitiveType;
-import org.hl7.fhir.dstu3.model.Type;
+import org.hl7.fhir.dstu3.model.Type;
-import org.hl7.fhir.dstu3.model.UriType;
+import org.hl7.fhir.dstu3.model.UriType;
-import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.dstu3.model.ValueSet;
-import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceDesignationComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceDesignationComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
+import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
-import org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionParameterComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionParameterComponent;
-import org.hl7.fhir.dstu3.utils.ToolingExtensions;
+import org.hl7.fhir.dstu3.utils.ToolingExtensions;
-import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.exceptions.NoTerminologyServiceException;
+import org.hl7.fhir.exceptions.NoTerminologyServiceException;
-import org.hl7.fhir.exceptions.TerminologyServiceException;
+import org.hl7.fhir.exceptions.TerminologyServiceException;
-import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.Utilities;
-
+
-public class ValueSetExpanderSimple implements ValueSetExpander {
+public class ValueSetExpanderSimple implements ValueSetExpander {
-
+
-  private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
+  private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
-  private List<ValueSetExpansionContainsComponent> roots = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
+  private List<ValueSetExpansionContainsComponent> roots = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
-  private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
+  private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
-  private IWorkerContext context;
+  private IWorkerContext context;
-  private boolean canBeHeirarchy = true;
+  private boolean canBeHeirarchy = true;
-  private Set<String> excludeKeys = new HashSet<String>();
+  private Set<String> excludeKeys = new HashSet<String>();
-  private Set<String> excludeSystems = new HashSet<String>();
+  private Set<String> excludeSystems = new HashSet<String>();
-  private ValueSetExpanderFactory factory;
+  private ValueSetExpanderFactory factory;
-  private ValueSet focus;
+  private ValueSet focus;
-  private int maxExpansionSize = 500;
+  private int maxExpansionSize = 500;
-
+
-  private int total;
+  private int total;
-
+
-  public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
+  public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
-    super();
+    super();
-    this.context = context;
+    this.context = context;
-    this.factory = factory;
+    this.factory = factory;
-  }
+  }
-
+
-  public void setMaxExpansionSize(int theMaxExpansionSize) {
+  public void setMaxExpansionSize(int theMaxExpansionSize) {
-    maxExpansionSize = theMaxExpansionSize;
+    maxExpansionSize = theMaxExpansionSize;
-  }
+  }
-
+
-  private ValueSetExpansionContainsComponent addCode(String system, String code, String display, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations,
+  private ValueSetExpansionContainsComponent addCode(String system, String code, String display, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations,
-      ExpansionProfile profile, boolean isAbstract, boolean inactive, List<ValueSet> filters) {
+      ExpansionProfile profile, boolean isAbstract, boolean inactive, List<ValueSet> filters) {
-    if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
+    if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
-      return null;
+      return null;
-    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
+    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
-    n.setSystem(system);
+    n.setSystem(system);
-    n.setCode(code);
+    n.setCode(code);
-    if (isAbstract)
+    if (isAbstract)
-      n.setAbstract(true);
+      n.setAbstract(true);
-    if (inactive)
+    if (inactive)
-      n.setInactive(true);
+      n.setInactive(true);
-
+
-    if (profile.getIncludeDesignations() && designations != null) {
+    if (profile.getIncludeDesignations() && designations != null) {
-      for (ConceptDefinitionDesignationComponent t : designations) {
+      for (ConceptDefinitionDesignationComponent t : designations) {
-        ToolingExtensions.addLanguageTranslation(n, t.getLanguage(), t.getValue());
+        ToolingExtensions.addLanguageTranslation(n, t.getLanguage(), t.getValue());
-      }
+      }
-    }
+    }
-    ConceptDefinitionDesignationComponent t = profile.hasLanguage() ? getMatchingLang(designations, profile.getLanguage()) : null;
+    ConceptDefinitionDesignationComponent t = profile.hasLanguage() ? getMatchingLang(designations, profile.getLanguage()) : null;
-    if (t == null)
+    if (t == null)
-      n.setDisplay(display);
+      n.setDisplay(display);
-    else
+    else
-      n.setDisplay(t.getValue());
+      n.setDisplay(t.getValue());
-
+
-    String s = key(n);
+    String s = key(n);
-    if (map.containsKey(s) || excludeKeys.contains(s)) {
+    if (map.containsKey(s) || excludeKeys.contains(s)) {
-      canBeHeirarchy = false;
+      canBeHeirarchy = false;
-    } else {
+    } else {
-      codes.add(n);
+      codes.add(n);
-      map.put(s, n);
+      map.put(s, n);
-      total++;
+      total++;
-    }
+    }
-    if (canBeHeirarchy && parent != null) {
+    if (canBeHeirarchy && parent != null) {
-      parent.getContains().add(n);
+      parent.getContains().add(n);
-    } else {
+    } else {
-      roots.add(n);
+      roots.add(n);
-    }
+    }
-    return n;
+    return n;
-  }
+  }
-
+
-  private boolean filterContainsCode(List<ValueSet> filters, String system, String code) {
+  private boolean filterContainsCode(List<ValueSet> filters, String system, String code) {
-    for (ValueSet vse : filters)
+    for (ValueSet vse : filters)
-      if (expansionContainsCode(vse.getExpansion().getContains(), system, code))
+      if (expansionContainsCode(vse.getExpansion().getContains(), system, code))
-        return true;
+        return true;
-    return false;
+    return false;
-  }
+  }
-
+
-  private boolean expansionContainsCode(List<ValueSetExpansionContainsComponent> contains, String system, String code) {
+  private boolean expansionContainsCode(List<ValueSetExpansionContainsComponent> contains, String system, String code) {
-    for (ValueSetExpansionContainsComponent cc : contains) {
+    for (ValueSetExpansionContainsComponent cc : contains) {
-      if (system.equals(cc.getSystem()) && code.equals(cc.getCode()))
+      if (system.equals(cc.getSystem()) && code.equals(cc.getCode()))
-        return true;
+        return true;
-      if (expansionContainsCode(cc.getContains(), system, code))
+      if (expansionContainsCode(cc.getContains(), system, code))
-        return true;
+        return true;
-    }
+    }
-    return false;
+    return false;
-  }
+  }
-
+
-  private ConceptDefinitionDesignationComponent getMatchingLang(List<ConceptDefinitionDesignationComponent> list, String lang) {
+  private ConceptDefinitionDesignationComponent getMatchingLang(List<ConceptDefinitionDesignationComponent> list, String lang) {
-    for (ConceptDefinitionDesignationComponent t : list)
+    for (ConceptDefinitionDesignationComponent t : list)
-      if (t.getLanguage().equals(lang))
+      if (t.getLanguage().equals(lang))
-        return t;
+        return t;
-    for (ConceptDefinitionDesignationComponent t : list)
+    for (ConceptDefinitionDesignationComponent t : list)
-      if (t.getLanguage().startsWith(lang))
+      if (t.getLanguage().startsWith(lang))
-        return t;
+        return t;
-    return null;
+    return null;
-  }
+  }
-
+
-  private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filters)
+  private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filters)
-      throws FHIRException {
+      throws FHIRException {
-    if (!CodeSystemUtilities.isDeprecated(cs, def)) {
+    if (!CodeSystemUtilities.isDeprecated(cs, def)) {
-      ValueSetExpansionContainsComponent np = null;
+      ValueSetExpansionContainsComponent np = null;
-      boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
+      boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
-      boolean inc = CodeSystemUtilities.isInactive(cs, def);
+      boolean inc = CodeSystemUtilities.isInactive(cs, def);
-      if (canBeHeirarchy || !abs)
+      if (canBeHeirarchy || !abs)
-        np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), profile, abs, inc, filters);
+        np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), profile, abs, inc, filters);
-      for (ConceptDefinitionComponent c : def.getConcept())
+      for (ConceptDefinitionComponent c : def.getConcept())
-        addCodeAndDescendents(cs, system, c, np, profile, filters);
+        addCodeAndDescendents(cs, system, c, np, profile, filters);
-    } else
+    } else
-      for (ConceptDefinitionComponent c : def.getConcept())
+      for (ConceptDefinitionComponent c : def.getConcept())
-        addCodeAndDescendents(cs, system, c, null, profile, filters);
+        addCodeAndDescendents(cs, system, c, null, profile, filters);
-
+
-  }
+  }
-
+
-  private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile, List<ValueSet> filters) throws ETooCostly {
+  private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile, List<ValueSet> filters) throws ETooCostly {
-    if (expand.getContains().size() > maxExpansionSize)
+    if (expand.getContains().size() > maxExpansionSize)
-      throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
+      throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
-    for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
+    for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
-      if (!existsInParams(params, p.getName(), p.getValue()))
+      if (!existsInParams(params, p.getName(), p.getValue()))
-        params.add(p);
+        params.add(p);
-    }
+    }
-
+
-    copyImportContains(expand.getContains(), null, profile, filters);
+    copyImportContains(expand.getContains(), null, profile, filters);
-  }
+  }
-
+
-  private void excludeCode(String theSystem, String theCode) {
+  private void excludeCode(String theSystem, String theCode) {
-    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
+    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
-    n.setSystem(theSystem);
+    n.setSystem(theSystem);
-    n.setCode(theCode);
+    n.setCode(theCode);
-    String s = key(n);
+    String s = key(n);
-    excludeKeys.add(s);
+    excludeKeys.add(s);
-  }
+  }
-
+
-  private void excludeCodes(ConceptSetComponent exc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException {
+  private void excludeCodes(ConceptSetComponent exc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException {
-    if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) {
+    if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) {
-      excludeSystems.add(exc.getSystem());
+      excludeSystems.add(exc.getSystem());
-    }
+    }
-
+
-    if (exc.hasValueSet())
+    if (exc.hasValueSet())
-      throw new Error("Processing Value set references in exclude is not yet done");
+      throw new Error("Processing Value set references in exclude is not yet done");
-    // importValueSet(imp.getValue(), params, profile);
+    // importValueSet(imp.getValue(), params, profile);
-
+
-    CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
+    CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
-    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
+    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
-      excludeCodes(context.expandVS(exc, false), params);
+      excludeCodes(context.expandVS(exc, false), params);
-      return;
+      return;
-    }
+    }
-
+
-    for (ConceptReferenceComponent c : exc.getConcept()) {
+    for (ConceptReferenceComponent c : exc.getConcept()) {
-      excludeCode(exc.getSystem(), c.getCode());
+      excludeCode(exc.getSystem(), c.getCode());
-    }
+    }
-
+
-    if (exc.getFilter().size() > 0)
+    if (exc.getFilter().size() > 0)
-      throw new NotImplementedException("not done yet");
+      throw new NotImplementedException("not done yet");
-  }
+  }
-
+
-  private void excludeCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) {
+  private void excludeCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) {
-    for (ValueSetExpansionContainsComponent c : expand.getContains()) {
+    for (ValueSetExpansionContainsComponent c : expand.getContains()) {
-      excludeCode(c.getSystem(), c.getCode());
+      excludeCode(c.getSystem(), c.getCode());
-    }
+    }
-  }
+  }
-
+
-  private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, Type value) {
+  private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, Type value) {
-    for (ValueSetExpansionParameterComponent p : params) {
+    for (ValueSetExpansionParameterComponent p : params) {
-      if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
+      if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
-        return true;
+        return true;
-    }
+    }
-    return false;
+    return false;
-  }
+  }
-
+
-  @Override
+  @Override
-  public ValueSetExpansionOutcome expand(ValueSet source, ExpansionProfile profile) {
+  public ValueSetExpansionOutcome expand(ValueSet source, ExpansionProfile profile) {
-
+
-    if (profile == null)
+    if (profile == null)
-      profile = makeDefaultExpansion();
+      profile = makeDefaultExpansion();
-    try {
+    try {
-      focus = source.copy();
+      focus = source.copy();
-      focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
+      focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
-      focus.getExpansion().setTimestampElement(DateTimeType.now());
+      focus.getExpansion().setTimestampElement(DateTimeType.now());
-      focus.getExpansion().setIdentifier(Factory.createUUID());
+      focus.getExpansion().setIdentifier(Factory.createUUID());
-      if (!profile.getUrl().startsWith("urn:uuid:"))
+      if (!profile.getUrl().startsWith("urn:uuid:"))
-        focus.getExpansion().addParameter().setName("profile").setValue(new UriType(profile.getUrl()));
+        focus.getExpansion().addParameter().setName("profile").setValue(new UriType(profile.getUrl()));
-
+
-      if (source.hasCompose())
+      if (source.hasCompose())
-        handleCompose(source.getCompose(), focus.getExpansion().getParameter(), profile);
+        handleCompose(source.getCompose(), focus.getExpansion().getParameter(), profile);
-
+
-      if (canBeHeirarchy) {
+      if (canBeHeirarchy) {
-        for (ValueSetExpansionContainsComponent c : roots) {
+        for (ValueSetExpansionContainsComponent c : roots) {
-          focus.getExpansion().getContains().add(c);
+          focus.getExpansion().getContains().add(c);
-        }
+        }
-      } else {
+      } else {
-        for (ValueSetExpansionContainsComponent c : codes) {
+        for (ValueSetExpansionContainsComponent c : codes) {
-          if (map.containsKey(key(c)) && !c.getAbstract()) { // we may have added abstract codes earlier while we still thought it might be heirarchical, but later we gave up, so now ignore them
+          if (map.containsKey(key(c)) && !c.getAbstract()) { // we may have added abstract codes earlier while we still thought it might be heirarchical, but later we gave up, so now ignore them
-            focus.getExpansion().getContains().add(c);
+            focus.getExpansion().getContains().add(c);
-            c.getContains().clear(); // make sure any heirarchy is wiped
+            c.getContains().clear(); // make sure any heirarchy is wiped
-          }
+          }
-        }
+        }
-      }
+      }
-
+
-      if (total > 0) {
+      if (total > 0) {
-        focus.getExpansion().setTotal(total);
+        focus.getExpansion().setTotal(total);
-      }
+      }
-
+
-      return new ValueSetExpansionOutcome(focus);
+      return new ValueSetExpansionOutcome(focus);
-    } catch (RuntimeException e) {
+    } catch (RuntimeException e) {
-      // TODO: we should put something more specific instead of just Exception below, since
+      // TODO: we should put something more specific instead of just Exception below, since
-      // it swallows bugs.. what would be expected to be caught there?
+      // it swallows bugs.. what would be expected to be caught there?
-      throw e;
+      throw e;
-    } catch (NoTerminologyServiceException e) {
+    } catch (Exception e) {
-      // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
+      // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
-      // that might fail too, but it might not, later.
+      // that might fail too, but it might not, later.
-      return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage(), TerminologyServiceErrorClass.NOSERVICE);
+      return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
-    } catch (Exception e) {
+    }
-      // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
+  }
-      // that might fail too, but it might not, later.
+
-      return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
+  private ExpansionProfile makeDefaultExpansion() {
-    }
+    ExpansionProfile res = new ExpansionProfile();
-  }
+    res.setUrl("urn:uuid:" + UUID.randomUUID().toString().toLowerCase());
-
+    res.setExcludeNested(true);
-  private ExpansionProfile makeDefaultExpansion() {
+    res.setIncludeDesignations(false);
-    ExpansionProfile res = new ExpansionProfile();
+    return res;
-    res.setUrl("urn:uuid:" + UUID.randomUUID().toString().toLowerCase());
+  }
-    res.setExcludeNested(true);
+
-    res.setIncludeDesignations(false);
+  private void addToHeirarchy(List<ValueSetExpansionContainsComponent> target, List<ValueSetExpansionContainsComponent> source) {
-    return res;
+    for (ValueSetExpansionContainsComponent s : source) {
-  }
+      target.add(s);
-
+    }
-  private void addToHeirarchy(List<ValueSetExpansionContainsComponent> target, List<ValueSetExpansionContainsComponent> source) {
+  }
-    for (ValueSetExpansionContainsComponent s : source) {
+
-      target.add(s);
+  private String getCodeDisplay(CodeSystem cs, String code) throws TerminologyServiceException {
-    }
+    ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), code);
-  }
+    if (def == null)
-
+      throw new TerminologyServiceException("Unable to find code '" + code + "' in code system " + cs.getUrl());
-  private String getCodeDisplay(CodeSystem cs, String code) throws TerminologyServiceException {
+    return def.getDisplay();
-    ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), code);
+  }
-    if (def == null)
+
-      throw new TerminologyServiceException("Unable to find code '" + code + "' in code system " + cs.getUrl());
+  private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) {
-    return def.getDisplay();
+    for (ConceptDefinitionComponent c : clist) {
-  }
+      if (code.equals(c.getCode()))
-
+        return c;
-  private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) {
+      ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
-    for (ConceptDefinitionComponent c : clist) {
+      if (v != null)
-      if (code.equals(c.getCode()))
+        return v;
-        return c;
+    }
-      ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
+    return null;
-      if (v != null)
+  }
-        return v;
+
-    }
+  private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile)
-    return null;
+      throws ETooCostly, FileNotFoundException, IOException, FHIRException {
-  }
+    // Exclude comes first because we build up a map of things to exclude
-
+    for (ConceptSetComponent inc : compose.getExclude())
-  private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile)
+      excludeCodes(inc, params);
-      throws ETooCostly, FileNotFoundException, IOException, FHIRException {
+    canBeHeirarchy = !profile.getExcludeNested() && excludeKeys.isEmpty() && excludeSystems.isEmpty();
-    // Exclude comes first because we build up a map of things to exclude
+    boolean first = true;
-    for (ConceptSetComponent inc : compose.getExclude())
+    for (ConceptSetComponent inc : compose.getInclude()) {
-      excludeCodes(inc, params);
+      if (first == true)
-    canBeHeirarchy = !profile.getExcludeNested() && excludeKeys.isEmpty() && excludeSystems.isEmpty();
+        first = false;
-    boolean first = true;
+      else
-    for (ConceptSetComponent inc : compose.getInclude()) {
+        canBeHeirarchy = false;
-      if (first == true)
+      includeCodes(inc, params, profile);
-        first = false;
+    }
-      else
+
-        canBeHeirarchy = false;
+  }
-      includeCodes(inc, params, profile);
+
-    }
+  private ValueSet importValueSet(String value, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile)
-
+      throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
-  }
+    if (value == null)
-
+      throw new TerminologyServiceException("unable to find value set with no identity");
-  private ValueSet importValueSet(String value, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile)
+    ValueSet vs = context.fetchResource(ValueSet.class, value);
-      throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
+    if (vs == null)
-    if (value == null)
+      throw new TerminologyServiceException("Unable to find imported value set " + value);
-      throw new TerminologyServiceException("unable to find value set with no identity");
+    ValueSetExpansionOutcome vso = factory.getExpander().expand(vs, profile);
-    ValueSet vs = context.fetchResource(ValueSet.class, value);
+    if (vso.getError() != null)
-    if (vs == null)
+      throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
-      throw new TerminologyServiceException("Unable to find imported value set " + value);
+    if (vso.getService() != null)
-    ValueSetExpansionOutcome vso = factory.getExpander().expand(vs, profile);
+      throw new TerminologyServiceException("Unable to expand imported value set " + value);
-    if (vso.getError() != null)
+    if (vs.hasVersion())
-      throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
+      if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
-    if (vso.getService() != null)
+        params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
-      throw new TerminologyServiceException("Unable to expand imported value set " + value);
+    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
-    if (vs.hasVersion())
+      if (!existsInParams(params, p.getName(), p.getValue()))
-      if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
+        params.add(p);
-        params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
+    }
-    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
+    canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
-      if (!existsInParams(params, p.getName(), p.getValue()))
+    return vso.getValueset();
-        params.add(p);
+  }
-    }
+
-    canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
+  private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filter) {
-    return vso.getValueset();
+    for (ValueSetExpansionContainsComponent c : list) {
-  }
+      ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, profile, c.getAbstract(), c.getInactive(), filter);
-
+      copyImportContains(c.getContains(), np, profile, filter);
-  private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filter) {
+    }
-    for (ValueSetExpansionContainsComponent c : list) {
+  }
-      ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, profile, c.getAbstract(), c.getInactive(), filter);
+
-      copyImportContains(c.getContains(), np, profile, filter);
+  private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
-    }
+    List<ValueSet> imports = new ArrayList<ValueSet>();
-  }
+    for (UriType imp : inc.getValueSet())
-
+      imports.add(importValueSet(imp.getValue(), params, profile));
-  private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
+
-    List<ValueSet> imports = new ArrayList<ValueSet>();
+    if (!inc.hasSystem()) {
-    for (UriType imp : inc.getValueSet())
+      if (imports.isEmpty()) // though this is not supposed to be the case
-      imports.add(importValueSet(imp.getValue(), params, profile));
+        return;
-
+      ValueSet base = imports.get(0);
-    if (!inc.hasSystem()) {
+      imports.remove(0);
-      if (imports.isEmpty()) // though this is not supposed to be the case
+      copyImportContains(base.getExpansion().getContains(), null, profile, imports);
-        return;
+    } else {
-      ValueSet base = imports.get(0);
+      CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
-      imports.remove(0);
+      if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
-      copyImportContains(base.getExpansion().getContains(), null, profile, imports);
+        addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
-    } else {
+        return;
-      CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
+      }
-      if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
+
-        addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
+      if (cs == null) {
-        return;
+        if (context.isNoTerminologyServer())
-      }
+          throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
-
+        else
-      if (cs == null) {
+          throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
-        if (context.isNoTerminologyServer())
+      }
-          throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
+      if (cs.getContent() != CodeSystemContentMode.COMPLETE)
-        else
+        throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
-          throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
+      if (cs.hasVersion())
-      }
+        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
-      if (cs.getContent() != CodeSystemContentMode.COMPLETE)
+          params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
-        throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
+
-      if (cs.hasVersion())
+      if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
-        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
+        // special case - add all the code system
-          params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
+        for (ConceptDefinitionComponent def : cs.getConcept()) {
-
+          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
-      if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
+        }
-        // special case - add all the code system
+      }
-        for (ConceptDefinitionComponent def : cs.getConcept()) {
+
-          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
+      if (!inc.getConcept().isEmpty()) {
-        }
+        canBeHeirarchy = false;
-      }
+        for (ConceptReferenceComponent c : inc.getConcept()) {
-
+          addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, false,
-      if (!inc.getConcept().isEmpty()) {
+              CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
-        canBeHeirarchy = false;
+        }
-        for (ConceptReferenceComponent c : inc.getConcept()) {
+      }
-          addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, false,
+      if (inc.getFilter().size() > 1) {
-              CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
+        canBeHeirarchy = false; // which will bt the case if we get around to supporting this
-        }
+        throw new TerminologyServiceException("Multiple filters not handled yet"); // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
-      }
+      }
-      if (inc.getFilter().size() > 1) {
+      if (inc.getFilter().size() == 1) {
-        canBeHeirarchy = false; // which will bt the case if we get around to supporting this
+        ConceptSetFilterComponent fc = inc.getFilter().get(0);
-        throw new TerminologyServiceException("Multiple filters not handled yet"); // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
+        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
-      }
+          // special: all codes in the target code system under the value
-      if (inc.getFilter().size() == 1) {
+          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
-        ConceptSetFilterComponent fc = inc.getFilter().get(0);
+          if (def == null)
-        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
+            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
-          // special: all codes in the target code system under the value
+          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
-          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
+        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
-          if (def == null)
+          // special: all codes in the target code system under the value
-            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
+          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
-          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
+          if (def == null)
-        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
+            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
-          // special: all codes in the target code system under the value
+          for (ConceptDefinitionComponent c : def.getConcept())
-          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
+            addCodeAndDescendents(cs, inc.getSystem(), c, null, profile, imports);
-          if (def == null)
+        } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
-            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
+          // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
-          for (ConceptDefinitionComponent c : def.getConcept())
+          canBeHeirarchy = false;
-            addCodeAndDescendents(cs, inc.getSystem(), c, null, profile, imports);
+          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
-        } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
+          if (def != null) {
-          // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
+            if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
-          canBeHeirarchy = false;
+              if (def.getDisplay().contains(fc.getValue())) {
-          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
+                addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), profile, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
-          if (def != null) {
+                    imports);
-            if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
+              }
-              if (def.getDisplay().contains(fc.getValue())) {
+            }
-                addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), profile, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
+          }
-                    imports);
+        } else
-              }
+          throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
-            }
+      }
-          }
+    }
-        } else
+  }
-          throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
+
-      }
+  private List<ConceptDefinitionDesignationComponent> convertDesignations(List<ConceptReferenceDesignationComponent> list) {
-    }
+    List<ConceptDefinitionDesignationComponent> res = new ArrayList<CodeSystem.ConceptDefinitionDesignationComponent>();
-  }
+    for (ConceptReferenceDesignationComponent t : list) {
-
+      ConceptDefinitionDesignationComponent c = new ConceptDefinitionDesignationComponent();
-  private List<ConceptDefinitionDesignationComponent> convertDesignations(List<ConceptReferenceDesignationComponent> list) {
+      c.setLanguage(t.getLanguage());
-    List<ConceptDefinitionDesignationComponent> res = new ArrayList<CodeSystem.ConceptDefinitionDesignationComponent>();
+      c.setUse(t.getUse());
-    for (ConceptReferenceDesignationComponent t : list) {
+      c.setValue(t.getValue());
-      ConceptDefinitionDesignationComponent c = new ConceptDefinitionDesignationComponent();
+    }
-      c.setLanguage(t.getLanguage());
+    return res;
-      c.setUse(t.getUse());
+  }
-      c.setValue(t.getValue());
+
-    }
+  private String key(String uri, String code) {
-    return res;
+    return "{" + uri + "}" + code;
-  }
+  }
-
+
-  private String key(String uri, String code) {
+  private String key(ValueSetExpansionContainsComponent c) {
-    return "{" + uri + "}" + code;
+    return key(c.getSystem(), c.getCode());
-  }
+  }
-
+
-  private String key(ValueSetExpansionContainsComponent c) {
+}
-    return key(c.getSystem(), c.getCode());
-  }
-
-}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/context/ContextScanningDstu3Test.java

@@ -13,6 +13,7 @@ import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
+import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.junit.*;
 
 import ca.uhn.fhir.rest.annotation.IdParam;
@@ -177,7 +178,7 @@ public class ContextScanningDstu3Test {
 		}
 
 		@Read
-		public Observation read(@IdParam IdType theId) {
+		public Observation read(@IdParam IdType theId) throws FHIRFormatError {
 			Observation retVal = new Observation();
 			retVal.setId(theId);
 			retVal.addIdentifier().setSystem("ISYS").setValue("IVAL");

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -1023,7 +1023,7 @@ public class JsonParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder(ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM, ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE));
+		assertThat(encoded, stringContainsInOrder(ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3, ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -1057,7 +1057,7 @@ public class JsonParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\",", "\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",", "\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -1077,7 +1077,7 @@ public class JsonParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("Patient"));
-		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"",
+		assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"",
 			"\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -1519,7 +1519,7 @@ public class XmlParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
 			"<code value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("text")));
 		assertThat(encoded, not(containsString("THE DIV")));
@@ -1666,7 +1666,7 @@ public class XmlParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("<Patient"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
 			"<code value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
@@ -1688,7 +1688,7 @@ public class XmlParserDstu3Test {
 
 		assertThat(encoded, containsString("<Patient"));
 		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
-		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
 			"<code value=\"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java

@@ -504,7 +504,7 @@ public class GenericClientDstu3Test {
 			client.read().resource(Patient.class).withId("1").execute();
 			fail();
 		} catch (FhirClientConnectionException e) {
-			assertEquals("java.lang.IllegalStateException", e.getMessage());
+			assertEquals(null, e.getMessage());
 		}
 
 		try {

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserHl7OrgDstu2Test.java

@@ -3,7 +3,6 @@ package ca.uhn.fhir.parser;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.util.TestUtil;
 import net.sf.json.JSON;
@@ -22,16 +21,13 @@ import org.hl7.fhir.instance.model.Narrative.NarrativeStatus;
 import org.hl7.fhir.instance.model.Patient.ContactComponent;
 import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
 import org.hl7.fhir.instance.model.ValueSet.ValueSetCodeSystemComponent;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.INarrative;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.*;
 import org.xml.sax.SAXException;
 
 import java.io.IOException;
-import java.io.OutputStreamWriter;
 import java.io.StringReader;
 import java.nio.charset.Charset;
 import java.util.Arrays;
@@ -148,7 +144,7 @@ public class JsonParserHl7OrgDstu2Test {
     ourLog.info(encoded);
 
     assertThat(encoded, containsString("Patient"));
-    assertThat(encoded, stringContainsInOrder(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE));
+    assertThat(encoded, stringContainsInOrder(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE));
     assertThat(encoded, not(containsString("text")));
     assertThat(encoded, not(containsString("THE DIV")));
     assertThat(encoded, containsString("family"));
@@ -780,7 +776,7 @@ public class JsonParserHl7OrgDstu2Test {
 		
 		assertThat(encoded, containsString("Patient"));
 		assertThat(encoded, stringContainsInOrder("\"tag\"", 
-				"\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE+"\","));
+				"\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE+"\","));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));
@@ -802,7 +798,7 @@ public class JsonParserHl7OrgDstu2Test {
 		assertThat(encoded, containsString("Patient"));
 		assertThat(encoded, stringContainsInOrder("\"tag\"", 
 				"\"system\": \"foo\",", "\"code\": \"bar\"",
-				"\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE+"\","));
+				"\"system\": \"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\",", "\"code\": \"" + Constants.TAG_SUBSETTED_CODE+"\","));
 		assertThat(encoded, not(containsString("THE DIV")));
 		assertThat(encoded, containsString("family"));
 		assertThat(encoded, not(containsString("maritalStatus")));

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserHl7OrgDstu2Test.java

@@ -19,8 +19,6 @@ import org.hl7.fhir.instance.model.Enumeration;
 import org.hl7.fhir.instance.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.instance.model.Identifier.IdentifierUse;
 import org.hl7.fhir.instance.model.Narrative.NarrativeStatus;
-import org.hl7.fhir.instance.model.api.*;
-import org.junit.*;
 import org.hl7.fhir.instance.model.Observation;
 import org.hl7.fhir.instance.model.Organization;
 import org.hl7.fhir.instance.model.Patient;
@@ -32,7 +30,6 @@ import org.hl7.fhir.instance.model.Specimen;
 import org.hl7.fhir.instance.model.StringType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.INarrative;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.junit.After;
 import org.junit.Assert;
@@ -49,7 +46,6 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.api.AddProfileTagEnum;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.parser.JsonParserHl7OrgDstu2Test.MyPatientWithOneDeclaredAddressExtension;
 import ca.uhn.fhir.parser.JsonParserHl7OrgDstu2Test.MyPatientWithOneDeclaredExtension;
 import ca.uhn.fhir.rest.api.Constants;
@@ -1050,7 +1046,7 @@ public class XmlParserHl7OrgDstu2Test {
     ourLog.info(encoded);
 
     assertThat(encoded, containsString("<Patient"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
         "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
     assertThat(encoded, not(containsString("text")));
     assertThat(encoded, not(containsString("THE DIV")));
@@ -1169,7 +1165,7 @@ public class XmlParserHl7OrgDstu2Test {
     ourLog.info(encoded);
 
     assertThat(encoded, containsString("<Patient"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
         "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
     assertThat(encoded, not(containsString("THE DIV")));
     assertThat(encoded, containsString("family"));
@@ -1191,7 +1187,7 @@ public class XmlParserHl7OrgDstu2Test {
 
     assertThat(encoded, containsString("<Patient"));
     assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>",
+    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM_DSTU3 + "\"/>",
         "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
     assertThat(encoded, not(containsString("THE DIV")));
     assertThat(encoded, containsString("family"));

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/conformance/ConstraintJavaGenerator.java

@@ -1,12 +1,9 @@
 package org.hl7.fhir.r4.conformance;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.OutputStream;
 import java.io.OutputStreamWriter;
-import java.io.UnsupportedEncodingException;
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.context.IWorkerContext;
@@ -29,7 +26,7 @@ public class ConstraintJavaGenerator {
   }
 
   public String generate(StructureDefinition sd) throws FHIRException, IOException {
-    String name = Utilities.titleize(sd.getName().replace(".", "").replace("-", "").replace("\"", "")).replace(" ", "");
+    String name = sd.hasName() ? Utilities.titleize(sd.getName().replace(".", "").replace("-", "").replace("\"", "")).replace(" ", "") : "";
     if (!Utilities.nmtokenize(name).equals(name)) {
       System.out.println("Cannot generate Java code for profile "+sd.getUrl()+" because the name \""+name+"\" is not a valid Java class name");
       return null;
@@ -46,6 +43,7 @@ public class ConstraintJavaGenerator {
     
     dest.write("}\r\n");
     dest.flush();
+    dest.close();
     return destFile.getAbsolutePath();
   }
   

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileComparer.java

@@ -1,6 +1,9 @@
 package org.hl7.fhir.r4.conformance;
 
+import java.io.File;
 import java.io.IOException;
+import java.net.URL;
+import java.net.URLConnection;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -8,6 +11,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4.conformance.ProfileComparer.ProfileComparison;
 import org.hl7.fhir.r4.context.IWorkerContext;
 import org.hl7.fhir.r4.formats.IParser;
 import org.hl7.fhir.r4.model.Base;
@@ -16,6 +22,7 @@ import org.hl7.fhir.r4.model.ElementDefinition;
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionConstraintComponent;
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionMappingComponent;
+import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingComponent;
 import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
 import org.hl7.fhir.r4.model.Enumerations.BindingStrength;
 import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
@@ -34,13 +41,15 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r4.utils.DefinitionNavigator;
 import org.hl7.fhir.r4.utils.ToolingExtensions;
-import org.hl7.fhir.exceptions.DefinitionException;
-import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.Logger.LogMessageType;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 
+import com.google.gson.JsonObject;
+
 /**
  * A engine that generates difference analysis between two sets of structure 
  * definitions, typically from 2 different implementation guides. 
@@ -398,8 +407,11 @@ public class ProfileComparer {
       if (isExtension(left.path()))
         return compareExtensions(outcome, path, superset, subset, left, right);
 //      return true;
-      else
+      else {
+        ElementDefinitionSlicingComponent slicingL = left.current().getSlicing();
+        ElementDefinitionSlicingComponent slicingR = right.current().getSlicing();
         throw new DefinitionException("Slicing is not handled yet");
+      }
     // todo: name 
     }
 
@@ -629,8 +641,8 @@ public class ProfileComparer {
             return false;          
           }
         }
-        subBinding.setValueSet(new Reference().setReference("#"+addValueSet(cvs)));
+        subBinding.setValueSet("#"+addValueSet(cvs));
-        superBinding.setValueSet(new Reference().setReference("#"+addValueSet(unite(superset, outcome, path, lvs, rvs))));
+        superBinding.setValueSet("#"+addValueSet(unite(superset, outcome, path, lvs, rvs)));
       }
     }
     return false;
@@ -649,11 +661,11 @@ public class ProfileComparer {
       ValueSet lvs = resolveVS(outcome.left, left.getValueSet());
       ValueSet rvs = resolveVS(outcome.left, right.getValueSet());
       if (lvs != null && rvs != null)
-        union.setValueSet(new Reference().setReference("#"+addValueSet(unite(ed, outcome, path, lvs, rvs))));
+        union.setValueSet("#"+addValueSet(unite(ed, outcome, path, lvs, rvs)));
       else if (lvs != null)
-        union.setValueSet(new Reference().setReference("#"+addValueSet(lvs)));
+        union.setValueSet("#"+addValueSet(lvs));
       else if (rvs != null)
-        union.setValueSet(new Reference().setReference("#"+addValueSet(rvs)));
+        union.setValueSet("#"+addValueSet(rvs));
     }
     return union;
   }
@@ -710,17 +722,10 @@ public class ProfileComparer {
     return false;
   }
 
-  private ValueSet resolveVS(StructureDefinition ctxtLeft, Type vsRef) {
+  private ValueSet resolveVS(StructureDefinition ctxtLeft, String vsRef) {
     if (vsRef == null)
       return null;
-    if (vsRef instanceof UriType)
+    return context.fetchResource(ValueSet.class, vsRef);
-      return null;
-    else {
-      Reference ref = (Reference) vsRef;
-      if (!ref.hasReference())
-        return null;
-      return context.fetchResource(ValueSet.class, ref.getReference());
-    }
   }
 
   private ValueSet intersectByDefinition(ValueSet lvs, ValueSet rvs) {
@@ -1166,6 +1171,100 @@ public class ProfileComparer {
     this.rightName = rightName;
   }
 
+  private String genPCLink(String leftName, String leftLink) {
+    return "<a href=\""+leftLink+"\">"+Utilities.escapeXml(leftName)+"</a>";
+  }
+  
+  private String genPCTable() {
+    StringBuilder b = new StringBuilder();
+
+    b.append("<table class=\"grid\">\r\n");
+    b.append("<tr>");
+    b.append(" <td><b>Left</b></td>");
+    b.append(" <td><b>Right</b></td>");
+    b.append(" <td><b>Comparison</b></td>");
+    b.append(" <td><b>Error #</b></td>");
+    b.append(" <td><b>Warning #</b></td>");
+    b.append(" <td><b>Hint #</b></td>");
+    b.append("</tr>");
+
+    for (ProfileComparison cmp : getComparisons()) {
+      b.append("<tr>");
+      b.append(" <td><a href=\""+cmp.getLeft().getUserString("path")+"\">"+Utilities.escapeXml(cmp.getLeft().getName())+"</a></td>");
+      b.append(" <td><a href=\""+cmp.getRight().getUserString("path")+"\">"+Utilities.escapeXml(cmp.getRight().getName())+"</a></td>");
+      b.append(" <td><a href=\""+getId()+"."+cmp.getId()+".html\">Click Here</a></td>");
+      b.append(" <td>"+cmp.getErrorCount()+"</td>");
+      b.append(" <td>"+cmp.getWarningCount()+"</td>");
+      b.append(" <td>"+cmp.getHintCount()+"</td>");
+      b.append("</tr>");
+    }
+    b.append("</table>\r\n");
+
+    return b.toString();
+  }
+
+
+  public String generate(String dest) throws IOException {
+    // ok, all compared; now produce the output
+    // first page we produce is simply the index
+    Map<String, String> vars = new HashMap<String, String>();
+    vars.put("title", getTitle());
+    vars.put("left", genPCLink(getLeftName(), getLeftLink()));
+    vars.put("right", genPCLink(getRightName(), getRightLink()));
+    vars.put("table", genPCTable());
+    producePage(summaryTemplate(), Utilities.path(dest, getId()+".html"), vars);
+    
+//    page.log("   ... generate", LogMessageType.Process);
+//    String src = TextFile.fileToString(page.getFolders().srcDir + "template-comparison-set.html");
+//    src = page.processPageIncludes(n+".html", src, "?type", null, "??path", null, null, "Comparison", pc, null, null, page.getDefinitions().getWorkgroups().get("fhir"));
+//    TextFile.stringToFile(src, Utilities.path(page.getFolders().dstDir, n+".html"));
+//    cachePage(n + ".html", src, "Comparison "+pc.getTitle(), false);
+//
+//    // then we produce a comparison page for each pair
+//    for (ProfileComparison cmp : pc.getComparisons()) {
+//      src = TextFile.fileToString(page.getFolders().srcDir + "template-comparison.html");
+//      src = page.processPageIncludes(n+"."+cmp.getId()+".html", src, "?type", null, "??path", null, null, "Comparison", cmp, null, null, page.getDefinitions().getWorkgroups().get("fhir"));
+//      TextFile.stringToFile(src, Utilities.path(page.getFolders().dstDir, n+"."+cmp.getId()+".html"));
+//      cachePage(n +"."+cmp.getId()+".html", src, "Comparison "+pc.getTitle(), false);
+//    }
+//      //   and also individual pages for each pair outcome
+//    // then we produce value set pages for each value set
+//
+//    // TODO Auto-generated method stub
+    return null;
+  }
+
+  private void producePage(String src, String path, Map<String, String> vars) throws IOException {
+    while (src.contains("[%"))
+    {
+      int i1 = src.indexOf("[%");
+      int i2 = src.substring(i1).indexOf("%]")+i1;
+      String s1 = src.substring(0, i1);
+      String s2 = src.substring(i1 + 2, i2).trim();
+      String s3 = src.substring(i2+2);
+      String v = vars.containsKey(s2) ? vars.get(s2) : "???";
+      src = s1+v+s3;
+    }
+    TextFile.stringToFile(src, path);
+  }
+
+  private String summaryTemplate() throws IOException {
+    return cachedFetch("04a9d69a-47f2-4250-8645-bf5d880a8eaa-1.fhir-template", "http://build.fhir.org/template-comparison-set.html.template");
+  }
+
+  private String cachedFetch(String id, String source) throws IOException {
+    String tmpDir = System.getProperty("java.io.tmpdir");
+    String local = Utilities.path(tmpDir, id);
+    File f = new File(local);
+    if (f.exists())
+      return TextFile.fileToString(f);
+    URL url = new URL(source);
+    URLConnection c = url.openConnection();
+    String result = TextFile.streamToString(c.getInputStream());
+    TextFile.stringToFile(result, f);
+    return result;
+  }
+
 
   
   

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/conformance/ShExGenerator.java

@@ -11,6 +11,7 @@ import java.util.List;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.context.IWorkerContext;
 import org.hl7.fhir.r4.elementmodel.TurtleParser;
 import org.hl7.fhir.r4.model.DomainResource;
@@ -24,7 +25,6 @@ import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 import org.hl7.fhir.r4.utils.ToolingExtensions;
-import org.hl7.fhir.exceptions.FHIRException;
 import org.stringtemplate.v4.ST;
 
 public class ShExGenerator {
@@ -388,7 +388,7 @@ public class ShExGenerator {
       for (String dt : new HashSet<String>(datatypes)) {
         if (!emittedDatatypes.contains(dt)) {
           StructureDefinition sd = context.fetchResource(StructureDefinition.class,
-              ProfileUtilities.sdNs(dt));
+              ProfileUtilities.sdNs(dt, null));
           // TODO: Figure out why the line below doesn't work
           // if (sd != null && !uniq_structures.contains(sd))
           if(sd != null && !uniq_structure_urls.contains(sd.getUrl()))
@@ -748,23 +748,11 @@ public class ShExGenerator {
 
 
   // TODO: find a utility that implements this
-  private ValueSet resolveBindingReference(DomainResource ctxt, Type reference) {
+  private ValueSet resolveBindingReference(DomainResource ctxt, String reference) {
-    if (reference instanceof UriType) {
+    try {
-      return context.fetchResource(ValueSet.class, ((UriType) reference).getValue().toString());
+      return context.fetchResource(ValueSet.class, reference);
-    }
+    } catch (Throwable e) {
-    else if (reference instanceof Reference) {
-      String s = ((Reference) reference).getReference();
-      if (s.startsWith("#")) {
-        for (Resource c : ctxt.getContained()) {
-          if (c.getId().equals(s.substring(1)) && (c instanceof ValueSet))
-            return (ValueSet) c;
-        }
-        return null;
-      } else {
-        return context.fetchResource(ValueSet.class, ((Reference) reference).getReference());
-      }
-    }
-    else
       return null;
+    }
   }
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/conformance/XmlSchemaGenerator.java

@@ -0,0 +1,520 @@
+package org.hl7.fhir.r4.conformance;
+import java.io.FileOutputStream;
+/*
+Copyright (c) 2011+, HL7, Inc
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, 
+are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this 
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions and the following disclaimer in the documentation 
+   and/or other materials provided with the distribution.
+ * Neither the name of HL7 nor the names of its contributors may be used to 
+   endorse or promote products derived from this software without specific 
+   prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+POSSIBILITY OF SUCH DAMAGE.
+
+ */
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r4.context.IWorkerContext;
+import org.hl7.fhir.r4.model.ElementDefinition;
+import org.hl7.fhir.r4.model.ElementDefinition.PropertyRepresentation;
+import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.utils.ToolingExtensions;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.Utilities;
+
+
+public class XmlSchemaGenerator  {
+
+  public class QName {
+
+    public String type;
+    public String typeNs;
+
+    @Override
+    public String toString() {
+      return typeNs+":"+type;
+    }
+  }
+
+  public class ElementToGenerate {
+
+    private String tname;
+    private StructureDefinition sd;
+    private ElementDefinition ed;
+
+    public ElementToGenerate(String tname, StructureDefinition sd, ElementDefinition edc) {
+      this.tname = tname;
+      this.sd = sd;
+      this.ed = edc;
+    }
+
+
+  }
+
+
+  private String folder;
+	private IWorkerContext context;
+	private boolean single;
+	private String version;
+	private String genDate;
+	private String license;
+	private boolean annotations;
+
+	public XmlSchemaGenerator(String folder, IWorkerContext context) {
+    this.folder = folder;
+    this.context = context;
+	}
+
+  public boolean isSingle() {
+    return single;
+  }
+
+  public void setSingle(boolean single) {
+    this.single = single;
+  }
+  
+
+  public String getVersion() {
+    return version;
+  }
+
+  public void setVersion(String version) {
+    this.version = version;
+  }
+
+  public String getGenDate() {
+    return genDate;
+  }
+
+  public void setGenDate(String genDate) {
+    this.genDate = genDate;
+  }
+
+  public String getLicense() {
+    return license;
+  }
+
+  public void setLicense(String license) {
+    this.license = license;
+  }
+
+
+  public boolean isAnnotations() {
+    return annotations;
+  }
+
+  public void setAnnotations(boolean annotations) {
+    this.annotations = annotations;
+  }
+
+
+  private Set<ElementDefinition> processed = new HashSet<ElementDefinition>();
+  private Set<StructureDefinition> processedLibs = new HashSet<StructureDefinition>();
+  private Set<String> typeNames = new HashSet<String>();
+  private OutputStreamWriter writer;
+  private Map<String, String> namespaces = new HashMap<String, String>();
+  private Queue<ElementToGenerate> queue = new LinkedList<ElementToGenerate>();
+  private Queue<StructureDefinition> queueLib = new LinkedList<StructureDefinition>();
+  private Map<String, StructureDefinition> library;
+  private boolean useNarrative;
+
+  private void w(String s) throws IOException {
+    writer.write(s);
+  }
+  
+  private void ln(String s) throws IOException {
+    writer.write(s);
+    writer.write("\r\n");
+  }
+
+  private void close() throws IOException {
+    if (writer != null) {
+      ln("</xs:schema>");
+      writer.flush();
+      writer.close();
+      writer = null;
+    }
+  }
+
+  private String start(StructureDefinition sd, String ns) throws IOException, FHIRException {
+    String lang = "en";
+    if (sd.hasLanguage())
+      lang = sd.getLanguage();
+
+    if (single && writer != null) {
+      if (!ns.equals(getNs(sd)))
+        throw new FHIRException("namespace inconsistency: "+ns+" vs "+getNs(sd));
+      return lang;
+    }
+    close();
+    
+    writer = new OutputStreamWriter(new FileOutputStream(Utilities.path(folder, tail(sd.getType()+".xsd"))), "UTF-8");
+    ln("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
+    ln("<!-- ");
+    ln(license);
+    ln("");
+    ln("  Generated on "+genDate+" for FHIR v"+version+" ");
+    ln("");
+    ln("  Note: this schema does not contain all the knowledge represented in the underlying content model");
+    ln("");
+    ln("-->");
+    ln("<xs:schema xmlns:xs=\"http://www.w3.org/2001/XMLSchema\" xmlns:fhir=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\" "+
+        "xmlns:lm=\""+ns+"\" targetNamespace=\""+ns+"\" elementFormDefault=\"qualified\" version=\"1.0\">");
+    ln("  <xs:import schemaLocation=\"fhir-common.xsd\" namespace=\"http://hl7.org/fhir\"/>");
+    if (useNarrative) {
+      if (ns.equals("urn:hl7-org:v3"))
+        ln("  <xs:include schemaLocation=\"cda-narrative.xsd\"/>");
+      else
+        ln("  <xs:import schemaLocation=\"cda-narrative.xsd\" namespace=\"urn:hl7-org:v3\"/>");
+    }
+    namespaces.clear();
+    namespaces.put(ns, "lm");
+    namespaces.put("http://hl7.org/fhir", "fhir");
+    typeNames.clear();
+    
+    return lang;
+  }
+
+
+  private String getNs(StructureDefinition sd) {
+    String ns = "http://hl7.org/fhir";
+    if (sd.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
+      ns = ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
+    return ns;
+  }
+
+	public void generate(StructureDefinition entry, Map<String, StructureDefinition> library) throws Exception {
+	  processedLibs.clear();
+	  
+	  this.library = library;
+	  checkLib(entry);
+	  
+	  String ns = getNs(entry);
+	  String lang = start(entry, ns);
+
+	  w("  <xs:element name=\""+tail(entry.getType())+"\" type=\"lm:"+tail(entry.getType())+"\"");
+    if (annotations) {
+      ln(">");
+      ln("    <xs:annotation>");
+      ln("      <xs:documentation xml:lang=\""+lang+"\">"+Utilities.escapeXml(entry.getDescription())+"</xs:documentation>");
+      ln("    </xs:annotation>");
+      ln("  </xs:element>");
+    } else
+      ln("/>");
+
+		produceType(entry, entry.getSnapshot().getElement().get(0), tail(entry.getType()), getQN(entry, entry.getBaseDefinition()), lang);
+		while (!queue.isEmpty()) {
+		  ElementToGenerate q = queue.poll();
+		  produceType(q.sd, q.ed, q.tname, getQN(q.sd, q.ed, "http://hl7.org/fhir/StructureDefinition/Element", false), lang);
+		}
+		while (!queueLib.isEmpty()) {
+		  generateInner(queueLib.poll());
+		}
+		close();
+	}
+
+
+
+
+  private void checkLib(StructureDefinition entry) {
+    for (ElementDefinition ed : entry.getSnapshot().getElement()) {
+      if (ed.hasRepresentation(PropertyRepresentation.CDATEXT)) {
+        useNarrative = true;
+      }
+    }
+    for (StructureDefinition sd : library.values()) {
+      for (ElementDefinition ed : sd.getSnapshot().getElement()) {
+        if (ed.hasRepresentation(PropertyRepresentation.CDATEXT)) {
+          useNarrative = true;
+        }
+      }
+    }
+  }
+
+  private void generateInner(StructureDefinition sd) throws IOException, FHIRException {
+    if (processedLibs.contains(sd))
+      return;
+    processedLibs.add(sd);
+    
+    String ns = getNs(sd);
+    String lang = start(sd, ns);
+
+    if (sd.getSnapshot().getElement().isEmpty())
+      throw new FHIRException("no snap shot on "+sd.getUrl());
+    
+    produceType(sd, sd.getSnapshot().getElement().get(0), tail(sd.getType()), getQN(sd, sd.getBaseDefinition()), lang);
+    while (!queue.isEmpty()) {
+      ElementToGenerate q = queue.poll();
+      produceType(q.sd, q.ed, q.tname, getQN(q.sd, q.ed, "http://hl7.org/fhir/StructureDefinition/Element", false), lang);
+    }
+  }
+
+  private String tail(String url) {
+    return url.contains("/") ? url.substring(url.lastIndexOf("/")+1) : url;
+  }
+  private String root(String url) {
+    return url.contains("/") ? url.substring(0, url.lastIndexOf("/")) : "";
+  }
+
+
+  private String tailDot(String url) {
+    return url.contains(".") ? url.substring(url.lastIndexOf(".")+1) : url;
+  }
+  private void produceType(StructureDefinition sd, ElementDefinition ed, String typeName, QName typeParent, String lang) throws IOException, FHIRException {
+    if (processed.contains(ed))
+      return;
+    processed.add(ed);
+    
+    // ok 
+    ln("  <xs:complexType name=\""+typeName+"\">");
+    if (annotations) {
+      ln("    <xs:annotation>");
+      ln("      <xs:documentation xml:lang=\""+lang+"\">"+Utilities.escapeXml(ed.getDefinition())+"</xs:documentation>");
+      ln("    </xs:annotation>");
+    }
+    ln("    <xs:complexContent>");
+    ln("      <xs:extension base=\""+typeParent.toString()+"\">");
+    ln("        <xs:sequence>");
+    
+    // hack....
+    for (ElementDefinition edc : ProfileUtilities.getChildList(sd,  ed)) {
+      if (!(edc.hasRepresentation(PropertyRepresentation.XMLATTR) || edc.hasRepresentation(PropertyRepresentation.XMLTEXT)) && !inheritedElement(edc))
+        produceElement(sd, ed, edc, lang);
+    }
+    ln("        </xs:sequence>");
+    for (ElementDefinition edc : ProfileUtilities.getChildList(sd,  ed)) {
+      if ((edc.hasRepresentation(PropertyRepresentation.XMLATTR) || edc.hasRepresentation(PropertyRepresentation.XMLTEXT)) && !inheritedElement(edc))
+        produceAttribute(sd, ed, edc, lang);
+    }
+    ln("      </xs:extension>");
+    ln("    </xs:complexContent>");
+    ln("  </xs:complexType>");    
+  }
+
+
+  private boolean inheritedElement(ElementDefinition edc) {
+    return !edc.getPath().equals(edc.getBase().getPath());
+  }
+
+  private void produceElement(StructureDefinition sd, ElementDefinition ed, ElementDefinition edc, String lang) throws IOException, FHIRException {
+    if (edc.getType().size() == 0) 
+      throw new Error("No type at "+edc.getPath());
+    
+    if (edc.getType().size() > 1 && edc.hasRepresentation(PropertyRepresentation.TYPEATTR)) {
+      // first, find the common base type
+      StructureDefinition lib = getCommonAncestor(edc.getType());
+      if (lib == null)
+        throw new Error("Common ancester not found at "+edc.getPath());
+      CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+      for (TypeRefComponent t : edc.getType()) {
+        b.append(getQN(sd, edc, t.getCode(), true).toString());
+      }
+      
+      String name = tailDot(edc.getPath());
+      String min = String.valueOf(edc.getMin());
+      String max = edc.getMax();
+      if ("*".equals(max))
+        max = "unbounded";
+
+      QName qn = getQN(sd, edc, lib.getUrl(), true);
+
+      ln("        <xs:element name=\""+name+"\" minOccurs=\""+min+"\" maxOccurs=\""+max+"\" type=\""+qn.typeNs+":"+qn.type+"\">");
+      ln("          <xs:annotation>");
+      ln("          <xs:appinfo xml:lang=\"en\">Possible types: "+b.toString()+"</xs:appinfo>");
+      if (annotations && edc.hasDefinition()) 
+        ln("            <xs:documentation xml:lang=\""+lang+"\">"+Utilities.escapeXml(edc.getDefinition())+"</xs:documentation>");
+      ln("          </xs:annotation>");
+      ln("        </xs:element>");
+    } else for (TypeRefComponent t : edc.getType()) {
+      String name = tailDot(edc.getPath());
+      if (edc.getType().size() > 1)
+        name = name + Utilities.capitalize(t.getCode());
+      QName qn = getQN(sd, edc, t.getCode(), true);
+      String min = String.valueOf(edc.getMin());
+      String max = edc.getMax();
+      if ("*".equals(max))
+        max = "unbounded";
+
+
+      w("        <xs:element name=\""+name+"\" minOccurs=\""+min+"\" maxOccurs=\""+max+"\" type=\""+qn.typeNs+":"+qn.type+"\"");
+      if (annotations && edc.hasDefinition()) {
+        ln(">");
+        ln("          <xs:annotation>");
+        ln("            <xs:documentation xml:lang=\""+lang+"\">"+Utilities.escapeXml(edc.getDefinition())+"</xs:documentation>");
+        ln("          </xs:annotation>");
+        ln("        </xs:element>");
+      } else
+        ln("/>");
+    }
+  }
+
+  public QName getQN(StructureDefinition sd, String type) throws FHIRException {
+    return getQN(sd, sd.getSnapshot().getElementFirstRep(), type, false);
+  }
+  
+  public QName getQN(StructureDefinition sd, ElementDefinition edc, String t, boolean chase) throws FHIRException {
+    QName qn = new QName();
+    qn.type = Utilities.isAbsoluteUrl(t) ? tail(t) : t;
+    if (Utilities.isAbsoluteUrl(t)) {
+      String ns = root(t);
+      if (ns.equals(root(sd.getUrl())))
+        ns = getNs(sd);
+      if (ns.equals("http://hl7.org/fhir/StructureDefinition"))
+        ns = "http://hl7.org/fhir";
+      if (!namespaces.containsKey(ns))
+        throw new FHIRException("Unknown type namespace "+ns+" for "+edc.getPath());
+      qn.typeNs = namespaces.get(ns);
+      StructureDefinition lib = library.get(t);
+      if (lib == null && !Utilities.existsInList(t, "http://hl7.org/fhir/cda/StructureDefinition/StrucDoc.Text", "http://hl7.org/fhir/StructureDefinition/Element"))
+        throw new FHIRException("Unable to resolve "+t+" for "+edc.getPath());
+      if (lib != null) 
+        queueLib.add(lib);
+    } else
+      qn.typeNs = namespaces.get("http://hl7.org/fhir");
+
+    if (chase && qn.type.equals("Element")) {
+      String tname = typeNameFromPath(edc);
+      if (typeNames.contains(tname)) {
+        int i = 1;
+        while (typeNames.contains(tname+i)) 
+          i++;
+        tname = tname+i;
+      }
+      queue.add(new ElementToGenerate(tname, sd, edc));
+      qn.typeNs = "lm";
+      qn.type = tname;
+    }
+    return qn;
+  }
+  
+  private StructureDefinition getCommonAncestor(List<TypeRefComponent> type) throws FHIRException {
+    StructureDefinition sd = library.get(type.get(0).getCode());
+    if (sd == null)
+      throw new FHIRException("Unable to find definition for "+type.get(0).getCode()); 
+    for (int i = 1; i < type.size(); i++) {
+      StructureDefinition t = library.get(type.get(i).getCode());
+      if (t == null)
+        throw new FHIRException("Unable to find definition for "+type.get(i).getCode()); 
+      sd = getCommonAncestor(sd, t);
+    }
+    return sd;
+  }
+
+  private StructureDefinition getCommonAncestor(StructureDefinition sd1, StructureDefinition sd2) throws FHIRException {
+    // this will always return something because everything comes from Element
+    List<StructureDefinition> chain1 = new ArrayList<>();
+    List<StructureDefinition> chain2 = new ArrayList<>();
+    chain1.add(sd1);
+    chain2.add(sd2);
+    StructureDefinition root = library.get("Element");
+    StructureDefinition common = findIntersection(chain1, chain2);
+    boolean chain1Done = false;
+    boolean chain2Done = false;
+    while (common == null) {
+       chain1Done = checkChain(chain1, root, chain1Done);
+       chain2Done = checkChain(chain2, root, chain2Done);
+       if (chain1Done && chain2Done)
+         return null;
+       common = findIntersection(chain1, chain2);
+    }
+    return common;
+  }
+
+  
+  private StructureDefinition findIntersection(List<StructureDefinition> chain1, List<StructureDefinition> chain2) {
+    for (StructureDefinition sd1 : chain1)
+      for (StructureDefinition sd2 : chain2)
+        if (sd1 == sd2)
+          return sd1;
+    return null;
+  }
+
+  public boolean checkChain(List<StructureDefinition> chain1, StructureDefinition root, boolean chain1Done) throws FHIRException {
+    if (!chain1Done) {
+       StructureDefinition sd = chain1.get(chain1.size()-1);
+      String bu = sd.getBaseDefinition();
+       if (bu == null)
+         throw new FHIRException("No base definition for "+sd.getUrl());
+       StructureDefinition t = library.get(bu);
+       if (t == null)
+         chain1Done = true;
+       else
+         chain1.add(t);
+     }
+    return chain1Done;
+  }
+
+  private StructureDefinition getBase(StructureDefinition structureDefinition) {
+    return null;
+  }
+
+  private String typeNameFromPath(ElementDefinition edc) {
+    StringBuilder b = new StringBuilder();
+    boolean up = true;
+    for (char ch : edc.getPath().toCharArray()) {
+      if (ch == '.')
+        up = true;
+      else if (up) {
+        b.append(Character.toUpperCase(ch));
+        up = false;
+      } else
+        b.append(ch);
+    }
+    return b.toString();
+  }
+
+  private void produceAttribute(StructureDefinition sd, ElementDefinition ed, ElementDefinition edc, String lang) throws IOException, FHIRException {
+    TypeRefComponent t = edc.getTypeFirstRep();
+    String name = tailDot(edc.getPath());
+    String min = String.valueOf(edc.getMin());
+    String max = edc.getMax();
+    // todo: check it's a code...
+//    if (!max.equals("1"))
+//      throw new FHIRException("Illegal cardinality \""+max+"\" for attribute "+edc.getPath());
+    
+    if (Utilities.isAbsoluteUrl(t.getCode())) 
+      throw new FHIRException("Only FHIR primitive types are supported for attributes ("+t.getCode()+")");
+    String typeNs = namespaces.get("http://hl7.org/fhir");
+    String type = t.getCode(); 
+    
+    w("        <xs:attribute name=\""+name+"\" use=\""+(min.equals("0") || edc.hasFixed() || edc.hasDefaultValue() ? "optional" : "required")+"\" type=\""+typeNs+":"+type+(typeNs.equals("fhir") ? "-primitive" : "")+"\""+
+    (edc.hasFixed() ? " fixed=\""+edc.getFixed().primitiveValue()+"\"" : "")+(edc.hasDefaultValue() && !edc.hasFixed() ? " default=\""+edc.getDefaultValue().primitiveValue()+"\"" : "")+"");
+    if (annotations && edc.hasDefinition()) {
+      ln(">");
+      ln("          <xs:annotation>");
+      ln("            <xs:documentation xml:lang=\""+lang+"\">"+Utilities.escapeXml(edc.getDefinition())+"</xs:documentation>");
+      ln("          </xs:annotation>");
+      ln("        </xs:attribute>");
+    } else
+      ln("/>");
+  }
+
+	
+}

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/context/IWorkerContext.java

@@ -11,8 +11,8 @@ import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent;
-import org.hl7.fhir.r4.model.ExpansionProfile;
 import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.StructureMap;
@@ -194,8 +194,8 @@ public interface IWorkerContext {
   
   // -- Terminology services ------------------------------------------------------
 
-  public ExpansionProfile getExpansionProfile();
+  public Parameters getExpansionParameters();
-  public void setExpansionProfile(ExpansionProfile expProfile);
+  public void setExpansionProfile(Parameters expParameters);
 
   // these are the terminology services used internally by the tools
   /**
@@ -256,7 +256,7 @@ public interface IWorkerContext {
    * @return
    * @throws FHIRException 
    */
-  public ValueSetExpansionComponent expandVS(ConceptSetComponent inc, boolean heirarchical) throws TerminologyServiceException;
+  public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean heirarchical) throws TerminologyServiceException;
   
   public class ValidationResult {
     private ConceptDefinitionComponent definition;
@@ -286,7 +286,7 @@ public interface IWorkerContext {
     }
 
     public boolean isOk() {
-      return definition != null;
+      return severity == null || severity == IssueSeverity.INFORMATION || severity == IssueSeverity.WARNING;
     }
 
     public String getDisplay() {
@@ -314,6 +314,16 @@ public interface IWorkerContext {
     public TerminologyServiceErrorClass getErrorClass() {
       return errorClass;
     }
+
+    public ValidationResult setSeverity(IssueSeverity severity) {
+      this.severity = severity;
+      return this;
+    }
+
+    public ValidationResult setMessage(String message) {
+      this.message = message;
+      return this;
+    }
     
     
   }
@@ -348,6 +358,7 @@ public interface IWorkerContext {
    * @return
    */
   public ValidationResult validateCode(String system, String code, String display, ValueSet vs);
+  public ValidationResult validateCode(String code, ValueSet vs);
   public ValidationResult validateCode(Coding code, ValueSet vs);
   public ValidationResult validateCode(CodeableConcept code, ValueSet vs);
   
@@ -391,10 +402,16 @@ public interface IWorkerContext {
   }
 
   public void setLogger(ILoggingService logger);
+  public ILoggingService getLogger();
 
   public boolean isNoTerminologyServer();
 
   public TranslationServices translator();
   public List<StructureMap> listTransforms();
   public StructureMap getTransform(String url);
+
+  public String getOverrideVersionNs();
+  public void setOverrideVersionNs(String value);
+
+  public StructureDefinition fetchTypeDefinition(String typeName);
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/context/SimpleWorkerContext.java

@@ -61,6 +61,7 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.OIDUtils;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.cache.NpmPackage;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
@@ -92,12 +93,13 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   private String date;
   private IValidatorFactory validatorFactory;
   private UcumService ucumService;
+  private boolean ignoreProfileErrors;
   
-  public SimpleWorkerContext() {
+  public SimpleWorkerContext() throws FileNotFoundException, IOException, FHIRException {
     super();
   }
   
-  public SimpleWorkerContext(SimpleWorkerContext other) {
+  public SimpleWorkerContext(SimpleWorkerContext other) throws FileNotFoundException, IOException, FHIRException {
     super();
     copy(other);
   }
@@ -130,6 +132,26 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     return res;
   }
 
+  public static SimpleWorkerContext fromPackage(NpmPackage pi, boolean allowDuplicates) throws FileNotFoundException, IOException, FHIRException {
+    SimpleWorkerContext res = new SimpleWorkerContext();
+    res.setAllowLoadingDuplicates(allowDuplicates);
+    res.loadFromPackage(pi, null);
+    return res;
+  }
+
+  public static SimpleWorkerContext fromPackage(NpmPackage pi) throws FileNotFoundException, IOException, FHIRException {
+    SimpleWorkerContext res = new SimpleWorkerContext();
+    res.loadFromPackage(pi, null);
+    return res;
+  }
+
+  public static SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException {
+    SimpleWorkerContext res = new SimpleWorkerContext();
+    res.setAllowLoadingDuplicates(true);
+    res.loadFromPackage(pi, loader);
+    return res;
+  }
+
   public static SimpleWorkerContext fromPack(String path, boolean allowDuplicates) throws FileNotFoundException, IOException, FHIRException {
     SimpleWorkerContext res = new SimpleWorkerContext();
     res.setAllowLoadingDuplicates(allowDuplicates);
@@ -224,29 +246,43 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
 	}
 
   private void loadFromFileJson(InputStream stream, String name, IContextResourceLoader loader) throws IOException, FHIRException {
-    Bundle f;
+    Bundle f = null;
     try {
       if (loader != null)
         f = loader.loadBundle(stream, true);
       else {
         JsonParser json = new JsonParser();
-        f = (Bundle) json.parse(stream);
+        Resource r = json.parse(stream);
+        if (r instanceof Bundle)
+          f = (Bundle) r;
+        else
+          cacheResource(r);
       }
     } catch (FHIRFormatError e1) {
       throw new org.hl7.fhir.exceptions.FHIRFormatError(e1.getMessage(), e1);
     }
-    for (BundleEntryComponent e : f.getEntry()) {
+    if (f != null)
-
+      for (BundleEntryComponent e : f.getEntry()) {
-      if (e.getFullUrl() == null) {
+        cacheResource(e.getResource());
-        logger.logDebugMessage(LogCategory.CONTEXT, "unidentified resource in " + name+" (no fullUrl)");
-      }
-      cacheResource(e.getResource());
     }
   }
 
 	private void loadFromPack(String path, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException {
 		loadFromStream(new CSFileInputStream(path), loader);
 	}
+  
+	public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
+	  if (types.length == 0)
+	    types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire","ConceptMap","StructureMap", "NamingSystem"};
+	  for (String s : pi.list("package")) {
+	    if (s.contains("-") && s.endsWith(".json")) {
+	      String t = s.substring(0, s.indexOf("-"));
+	      if (Utilities.existsInList(t, types)) {
+	        loadDefinitionItem(s, pi.load("package", s), loader);
+	      }
+	    }
+	  }
+	}
 
   public void loadFromFile(String file, IContextResourceLoader loader) throws IOException, FHIRException {
     loadDefinitionItem(file, new CSFileInputStream(file), loader);
@@ -423,6 +459,18 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     return result;
   }
 
+  public void loadBinariesFromFolder(String folder) throws FileNotFoundException, Exception {
+    for (String n : new File(folder).list()) {
+      loadBytes(n, new FileInputStream(Utilities.path(folder, n)));
+    }
+  }
+  
+  public void loadBinariesFromFolder(NpmPackage pi) throws FileNotFoundException, Exception {
+    for (String n : pi.list("other")) {
+      loadBytes(n, pi.load("other", n));
+    }
+  }
+  
   public void loadFromFolder(String folder) throws FileNotFoundException, Exception {
     for (String n : new File(folder).list()) {
       if (n.endsWith(".json")) 
@@ -507,12 +555,13 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
         List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();
         List<String> errors = new ArrayList<String>();
         ProfileUtilities pu = new ProfileUtilities(this, msgs, this);
+        pu.setThrowException(false);
         pu.sortDifferential(sd, p, p.getUrl(), errors);
         for (String err : errors)
           msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: "+err, ValidationMessage.IssueSeverity.ERROR));
         pu.generateSnapshot(sd, p, p.getUrl(), p.getName());
         for (ValidationMessage msg : msgs) {
-          if (msg.getLevel() == ValidationMessage.IssueSeverity.ERROR || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
+          if ((!ignoreProfileErrors && msg.getLevel() == ValidationMessage.IssueSeverity.ERROR) || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
             throw new DefinitionException("Profile "+p.getName()+" ("+p.getUrl()+"). Error generating snapshot: "+msg.getMessage());
         }
         if (!p.hasSnapshot())
@@ -531,6 +580,14 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     this.ucumService = ucumService;
   }
 
+  public boolean isIgnoreProfileErrors() {
+    return ignoreProfileErrors;
+  }
+
+  public void setIgnoreProfileErrors(boolean ignoreProfileErrors) {
+    this.ignoreProfileErrors = ignoreProfileErrors;
+  }
+
 
 
 

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/context/TerminologyCache.java

@@ -0,0 +1,426 @@
+package org.hl7.fhir.r4.context;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.codec.Charsets;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4.context.IWorkerContext.ValidationResult;
+import org.hl7.fhir.r4.formats.IParser.OutputStyle;
+import org.hl7.fhir.r4.formats.JsonParser;
+import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.UriType;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
+import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
+
+import com.google.gson.JsonElement;
+import com.google.gson.JsonNull;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonPrimitive;
+
+/**
+ * This implements a two level cache. 
+ *  - a temporary cache for remmbering previous local operations
+ *  - a persistent cache for rembering tx server operations
+ *  
+ * the cache is a series of pairs: a map, and a list. the map is the loaded cache, the list is the persiistent cache, carefully maintained in order for version control consistency
+ * 
+ * @author graha
+ *
+ */
+public class TerminologyCache {
+  public static final boolean TRANSIENT = false;
+  public static final boolean PERMANENT = true;
+  private static final String NAME_FOR_NO_SYSTEM = "all-systems";
+  private static final String ENTRY_MARKER = "-------------------------------------------------------------------------------------";
+  private static final String BREAK = "####";
+
+  public class CacheToken {
+    private String name;
+    private String key;
+    private String request;
+    public void setName(String n) {
+      if (name == null)
+        name = n;
+      else if (!n.equals(name))
+        name = NAME_FOR_NO_SYSTEM;
+    }
+  }
+
+  private class CacheEntry {
+    private String request;
+    private boolean persistent;
+    private ValidationResult v;
+    private ValueSetExpansionOutcome e;
+  }
+  
+  private class NamedCache {
+    private String name; 
+    private List<CacheEntry> list = new ArrayList<CacheEntry>(); // persistent entries
+    private Map<String, CacheEntry> map = new HashMap<String, CacheEntry>();
+  }
+  
+
+  private Object lock;
+  private String folder;
+  private Map<String, NamedCache> caches = new HashMap<String, NamedCache>();
+  
+  // use lock from the context
+  public TerminologyCache(Object lock, String folder) throws FileNotFoundException, IOException, FHIRException {
+    super();
+    this.lock = lock;
+    this.folder = folder;
+    if (folder != null)
+      load();
+  }
+  
+  public CacheToken generateValidationToken(Coding code, ValueSet vs) {
+    CacheToken ct = new CacheToken();
+    if (code.hasSystem())
+      ct.name = getNameForSystem(code.getSystem());
+    else
+      ct.name = NAME_FOR_NO_SYSTEM;
+    JsonParser json = new JsonParser();
+    json.setOutputStyle(OutputStyle.PRETTY);
+    ValueSet vsc = getVSEssense(vs);
+    try {
+      ct.request = "{\"code\" : "+json.composeString(code, "code")+", \"valueSet\" :"+(vsc == null ? "null" : json.composeString(vsc))+"}";
+    } catch (IOException e) {
+      throw new Error(e);
+    }
+    ct.key = String.valueOf(hashNWS(ct.request));
+    return ct;
+  }
+
+  public CacheToken generateValidationToken(CodeableConcept code, ValueSet vs) {
+    CacheToken ct = new CacheToken();
+    for (Coding c : code.getCoding()) {
+      if (c.hasSystem())
+        ct.setName(getNameForSystem(c.getSystem()));
+    }
+    JsonParser json = new JsonParser();
+    json.setOutputStyle(OutputStyle.PRETTY);
+    ValueSet vsc = getVSEssense(vs);
+    try {
+      ct.request = "{\"code\" : "+json.composeString(code, "codeableConcept")+", \"valueSet\" :"+json.composeString(vsc)+"}";
+    } catch (IOException e) {
+      throw new Error(e);
+    }
+    ct.key = String.valueOf(hashNWS(ct.request));
+    return ct;
+  }
+  
+  public ValueSet getVSEssense(ValueSet vs) {
+    if (vs == null)
+      return null;
+    ValueSet vsc = new ValueSet();
+    vsc.setCompose(vs.getCompose());
+    if (vs.hasExpansion()) {
+      vsc.getExpansion().getParameter().addAll(vs.getExpansion().getParameter());
+      vsc.getExpansion().getContains().addAll(vs.getExpansion().getContains());
+    }
+    return vsc;
+  }
+
+  public CacheToken generateExpandToken(ValueSet vs, boolean heirarchical) {
+    CacheToken ct = new CacheToken();
+    ValueSet vsc = getVSEssense(vs);
+    for (ConceptSetComponent inc : vs.getCompose().getInclude())
+      if (inc.hasSystem())
+        ct.setName(getNameForSystem(inc.getSystem()));
+    for (ConceptSetComponent inc : vs.getCompose().getExclude())
+      if (inc.hasSystem())
+        ct.setName(getNameForSystem(inc.getSystem()));
+    for (ValueSetExpansionContainsComponent inc : vs.getExpansion().getContains())
+      if (inc.hasSystem())
+        ct.setName(getNameForSystem(inc.getSystem()));
+    JsonParser json = new JsonParser();
+    json.setOutputStyle(OutputStyle.PRETTY);
+    try {
+      ct.request = "{\"hierarchical\" : "+(heirarchical ? "true" : "false")+", \"valueSet\" :"+json.composeString(vsc)+"}\r\n";
+    } catch (IOException e) {
+      throw new Error(e);
+    }
+    ct.key = String.valueOf(hashNWS(ct.request));
+    return ct;
+  }
+
+  private String getNameForSystem(String system) {
+    if (system.equals("http://snomed.info/sct"))
+      return "snomed";
+    if (system.equals("http://www.nlm.nih.gov/research/umls/rxnorm"))
+      return "rxnorm";
+    if (system.equals("http://loinc.org"))
+      return "loinc";
+    if (system.equals("http://unitsofmeasure.org"))
+      return "ucum";
+    if (system.startsWith("http://hl7.org/fhir/sid/"))
+      return system.substring(24).replace("/", "");
+    if (system.startsWith("urn:iso:std:iso:"))
+      return "iso"+system.substring(16).replace(":", "");
+    if (system.startsWith("http://terminology.hl7.org/CodeSystem/"))
+      return system.substring(38).replace("/", "");
+    if (system.startsWith("http://hl7.org/fhir/"))
+      return system.substring(20).replace("/", "");
+    if (system.equals("urn:ietf:bcp:47"))
+      return "lang";
+    if (system.equals("urn:ietf:bcp:13"))
+      return "mimetypes";
+    if (system.equals("urn:iso:std:iso:11073:10101"))
+      return "11073";
+    if (system.equals("http://dicom.nema.org/resources/ontology/DCM"))
+      return "dicom";
+    return system.replace("/", "_").replace(":", "_");
+  }
+
+  public NamedCache getNamedCache(CacheToken cacheToken) {
+    NamedCache nc = caches.get(cacheToken.name);
+    if (nc == null) {
+      nc = new NamedCache();
+      nc.name = cacheToken.name;
+      caches.put(nc.name, nc);
+    }
+    return nc;
+  }
+  
+  public ValueSetExpansionOutcome getExpansion(CacheToken cacheToken) {
+    synchronized (lock) {
+      NamedCache nc = getNamedCache(cacheToken);
+      CacheEntry e = nc.map.get(cacheToken.key);
+      if (e == null)
+        return null;
+      else
+        return e.e;
+    }
+  }
+
+  public void cacheExpansion(CacheToken cacheToken, ValueSetExpansionOutcome res, boolean persistent) {
+    synchronized (lock) {      
+      NamedCache nc = getNamedCache(cacheToken);
+      CacheEntry e = new CacheEntry();
+      e.request = cacheToken.request;
+      e.persistent = persistent;
+      e.e = res;
+      store(cacheToken, persistent, nc, e);
+    }    
+  }
+
+  public void store(CacheToken cacheToken, boolean persistent, NamedCache nc, CacheEntry e) {
+    boolean n = nc.map.containsKey(cacheToken.key);
+    nc.map.put(cacheToken.key, e);
+    if (persistent) {
+      if (n) {
+        for (int i = nc.list.size()- 1; i>= 0; i--) {
+          if (nc.list.get(i).request.equals(e.request)) {
+            nc.list.remove(i);
+          }
+        }
+      }
+      nc.list.add(e);
+      save(nc);  
+    }
+  }
+
+  public ValidationResult getValidation(CacheToken cacheToken) {
+    synchronized (lock) {
+      NamedCache nc = getNamedCache(cacheToken);
+      CacheEntry e = nc.map.get(cacheToken.key);
+      if (e == null)
+        return null;
+      else
+        return e.v;
+    }
+  }
+
+  public void cacheValidation(CacheToken cacheToken, ValidationResult res, boolean persistent) {
+    synchronized (lock) {      
+      NamedCache nc = getNamedCache(cacheToken);
+      CacheEntry e = new CacheEntry();
+      e.request = cacheToken.request;
+      e.persistent = persistent;
+      e.v = res;
+      store(cacheToken, persistent, nc, e);
+    }    
+  }
+
+  
+  // persistence
+  
+  public void save() {
+    
+  }
+  
+  private void save(NamedCache nc) {
+    if (folder == null)
+      return;
+    
+    try {
+      FileWriter sw = new FileWriter(new File(Utilities.path(folder, nc.name+".cache")));
+      sw.write(ENTRY_MARKER+"\r\n");
+      JsonParser json = new JsonParser();
+      json.setOutputStyle(OutputStyle.PRETTY);
+      for (CacheEntry ce : nc.list) {
+        sw.write(ce.request);
+        sw.write(BREAK+"\r\n");
+        if (ce.e != null) {
+          sw.write("e: {\r\n");
+          if (ce.e.getValueset() != null)
+            sw.write("  \"valueSet\" : "+json.composeString(ce.e.getValueset())+",\r\n");
+          sw.write("  \"error\" : \""+Utilities.escapeJson(ce.e.getError())+"\"\r\n}\r\n");
+        } else {
+          sw.write("v: {\r\n");
+          sw.write("  \"display\" : \""+Utilities.escapeJson(ce.v.getDisplay())+"\",\r\n");
+          sw.write("  \"severity\" : "+(ce.v.getSeverity() == null ? "null" : "\""+ce.v.getSeverity().toCode()+"\"")+",\r\n");
+          sw.write("  \"error\" : \""+Utilities.escapeJson(ce.v.getMessage())+"\"\r\n}\r\n");
+        }
+        sw.write(ENTRY_MARKER+"\r\n");
+      }      
+      sw.close();
+    } catch (Exception e) {
+      System.out.println("error saving "+nc.name+": "+e.getMessage());
+    }
+  }
+
+  private void load() throws FHIRException {
+    for (String fn : new File(folder).list()) {
+      if (fn.endsWith(".cache") && !fn.equals("validation.cache")) {
+        try {
+          //  System.out.println("Load "+fn);
+          String title = fn.substring(0, fn.lastIndexOf("."));
+          NamedCache nc = new NamedCache();
+          nc.name = title;
+          caches.put(title, nc);
+          String src = TextFile.fileToString(Utilities.path(folder, fn));
+          int i = src.indexOf(ENTRY_MARKER); 
+          while (i > -1) {
+            String s = src.substring(0, i);
+            src = src.substring(i+ENTRY_MARKER.length()+1);
+            i = src.indexOf(ENTRY_MARKER);
+            if (!Utilities.noString(s)) {
+              int j = s.indexOf(BREAK);
+              String q = s.substring(0, j);
+              String p = s.substring(j+BREAK.length()+1).trim();
+              CacheEntry ce = new CacheEntry();
+              ce.persistent = true;
+              ce.request = q;
+              boolean e = p.charAt(0) == 'e';
+              p = p.substring(3);
+              JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p);
+              String error = loadJS(o.get("error"));
+              if (e) {
+                if (o.has("valueSet"))
+                  ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
+                else
+                  ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
+              } else {
+                IssueSeverity severity = o.get("severity") instanceof JsonNull ? null :  IssueSeverity.fromCode(o.get("severity").getAsString());
+                String display = loadJS(o.get("display"));
+                ce.v = new ValidationResult(severity, error, new ConceptDefinitionComponent().setDisplay(display));
+              }
+              nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
+              nc.list.add(ce);
+            }
+          }        
+        } catch (Exception e) {
+          throw new FHIRException("Error loading "+fn+": "+e.getMessage(), e);
+        }
+      }
+    }
+  }
+  
+  private String loadJS(JsonElement e) {
+    if (e == null)
+      return null;
+    if (!(e instanceof JsonPrimitive))
+      return null;
+    String s = e.getAsString();
+    if ("".equals(s))
+      return null;
+    return s;
+  }
+
+  private String hashNWS(String s) {
+    return String.valueOf(s.replace("\r", "").replace("\n", "").replace(" ", "").hashCode());
+  }
+
+  // management
+  
+  public TerminologyCache copy() {
+    // TODO Auto-generated method stub
+    return null;
+  }
+  
+  public String summary(ValueSet vs) {
+    if (vs == null)
+      return "null";
+    
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+    for (ConceptSetComponent cc : vs.getCompose().getInclude())
+      b.append("Include "+getIncSummary(cc));
+    for (ConceptSetComponent cc : vs.getCompose().getExclude())
+      b.append("Exclude "+getIncSummary(cc));
+    return b.toString();
+  }
+
+  private String getIncSummary(ConceptSetComponent cc) {
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+    for (UriType vs : cc.getValueSet())
+      b.append(vs.asStringValue());
+    String vsd = b.length() > 0 ? " where the codes are in the value sets ("+b.toString()+")" : "";
+    String system = cc.getSystem();
+    if (cc.hasConcept())
+      return Integer.toString(cc.getConcept().size())+" codes from "+system+vsd;
+    if (cc.hasFilter()) {
+      String s = "";
+      for (ConceptSetFilterComponent f : cc.getFilter()) {
+        if (!Utilities.noString(s))
+          s = s + " & ";
+        s = s + f.getProperty()+" "+f.getOp().toCode()+" "+f.getValue();
+      }
+      return "from "+system+" where "+s+vsd;
+    }
+    return "All codes from "+system+vsd;
+  }
+
+  public String summary(Coding code) {
+    return code.getSystem()+"#"+code.getCode()+": \""+code.getDisplay()+"\"";
+  }
+
+
+  public String summary(CodeableConcept code) {
+    StringBuilder b = new StringBuilder();
+    b.append("{");
+    boolean first = true;
+    for (Coding c : code.getCoding()) {
+      if (first) first = false; else b.append(",");
+      b.append(summary(c));
+    }
+    b.append("}: \"");
+    b.append(code.getText());
+    b.append("\"");
+    return b.toString();
+  }
+  
+}

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/Element.java

@@ -21,6 +21,8 @@ import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.ElementDecoration;
+import org.hl7.fhir.utilities.ElementDecoration.DecorationType;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@@ -470,9 +472,30 @@ public class Element extends Base {
 		return this;
 	}
 
-	public void markValidation(StructureDefinition profile, ElementDefinition definition) {
+	public void clearDecorations() {
+	  clearUserData("fhir.decorations");
+	  for (Element e : children)
+	    e.clearDecorations();	  
 	}
 	
+	public void markValidation(StructureDefinition profile, ElementDefinition definition) {
+	  @SuppressWarnings("unchecked")
+    List<ElementDecoration> decorations = (List<ElementDecoration>) getUserData("fhir.decorations");
+	  if (decorations == null) {
+	    decorations = new ArrayList<ElementDecoration>();
+	    setUserData("fhir.decorations", decorations);
+	  }
+	  decorations.add(new ElementDecoration(DecorationType.TYPE, profile.getUserString("path"), definition.getPath()));
+	  if (tail(definition.getId()).contains(":")) {
+	    String[] details = tail(definition.getId()).split("\\:");
+	    decorations.add(new ElementDecoration(DecorationType.SLICE, null, details[1]));
+	  }
+	}
+	
+  private String tail(String id) {
+    return id.contains(".") ? id.substring(id.lastIndexOf(".")+1) : id;
+  }
+
   public Element getNamedChild(String name) {
 	  if (children == null)
   		return null;
@@ -660,7 +683,7 @@ public class Element extends Base {
     private List<ElementDefinition> children;
     public ElementSortComparator(Element e, Property property) {
       String tn = e.getType();
-      StructureDefinition sd = property.getContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(tn));
+      StructureDefinition sd = property.getContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(tn, property.getContext().getOverrideVersionNs()));
       if (sd != null && !sd.getAbstract())
         children = sd.getSnapshot().getElement();
       else

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/JsonParser.java

@@ -80,7 +80,7 @@ public class JsonParser extends ParserBase {
 		  assert (map.containsKey(obj));
 			return parse(obj);	
 		} else {
-			JsonObject obj = (JsonObject) new com.google.gson.JsonParser().parse(source);
+			JsonObject obj = JsonTrackingParser.parse(source, null); // (JsonObject) new com.google.gson.JsonParser().parse(source);
 //			assert (map.containsKey(obj));
 			return parse(obj);	
 		} 
@@ -284,7 +284,7 @@ public class JsonParser extends ParserBase {
 			logError(line(res), col(res), npath, IssueType.INVALID, "Unable to find resourceType property", IssueSeverity.FATAL);
 		} else {
 			String name = rt.getAsString();
-			StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name));
+			StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, context.getOverrideVersionNs()));
 			if (sd == null)
 				throw new FHIRFormatError("Contained resource does not appear to be a FHIR resource (unknown name '"+name+"')");
 			parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
@@ -447,7 +447,11 @@ public class JsonParser extends ParserBase {
 		else if (Utilities.existsInList(type, "integer", "unsignedInt", "positiveInt"))
 			json.value(new Integer(item.getValue()));
 		else if (Utilities.existsInList(type, "decimal"))
-			json.value(new BigDecimal(item.getValue()));
+		  try {
+  			json.value(new BigDecimal(item.getValue()));
+		  } catch (Exception e) {
+		    throw new NumberFormatException("error writing number '"+item.getValue()+"' to JSON");
+		  }
 		else
 			json.value(item.getValue());	
 	}

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/ObjectConverter.java

@@ -42,7 +42,7 @@ public class ObjectConverter  {
     if (base == null)
       return null;
     String tn = base.fhirType();
-    StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(tn));
+    StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(tn, context.getOverrideVersionNs()));
     if (sd == null)
       throw new FHIRException("Unable to find definition for type "+tn);
     Element res = new Element(property.getName(), property);
@@ -86,7 +86,7 @@ public class ObjectConverter  {
     ByteArrayOutputStream bo = new ByteArrayOutputStream();
     try {
       new JsonParser(context).compose(element, bo, OutputStyle.NORMAL, null);
-      TextFile.bytesToFile(bo.toByteArray(), "c:\\temp\\json.json");
+//      TextFile.bytesToFile(bo.toByteArray(), "c:\\temp\\json.json");
       return new org.hl7.fhir.r4.formats.JsonParser().parse(bo.toByteArray());
     } catch (IOException e) {
       // won't happen

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/ParserBase.java

@@ -3,13 +3,16 @@ package org.hl7.fhir.r4.elementmodel;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.hl7.fhir.r4.context.IWorkerContext;
 import org.hl7.fhir.r4.formats.FormatUtilities;
 import org.hl7.fhir.r4.formats.IParser.OutputStyle;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r4.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -33,7 +36,7 @@ public abstract class ParserBase {
   public boolean isPrimitive(String code) {
     return Utilities.existsInList(code, "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", "time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "xhtml", "url", "canonical");
     
-//    StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/"+code);
+//    StructureDefinition sd = context.fetchTypeDefinition(code);
 //    return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
 	}
 
@@ -41,7 +44,8 @@ public abstract class ParserBase {
 	protected ValidationPolicy policy;
   protected List<ValidationMessage> errors;
   protected ILinkResolver linkResolver;
-
+  protected boolean showDecorations;
+  
 	public ParserBase(IWorkerContext context) {
 		super();
 		this.context = context;
@@ -77,7 +81,7 @@ public abstract class ParserBase {
       return null;
   	}
 	  for (StructureDefinition sd : context.allStructures()) {
-	    if (name.equals(sd.getIdElement().getIdPart()) && !sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/de-")) {
+	    if (name.equals(sd.getType()) && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && !sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/de-")) {
 	      if((ns == null || ns.equals(FormatUtilities.FHIR_NS)) && !ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
 	        return sd;
 	      String sns = ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
@@ -101,7 +105,7 @@ public abstract class ParserBase {
 	    }
 	  }
     for (StructureDefinition sd : context.allStructures()) {
-      if (name.equals(sd.getIdElement().getIdPart())) {
+      if (name.equals(sd.getType()) && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
         return sd;
       }
     }
@@ -118,7 +122,13 @@ public abstract class ParserBase {
     return this;
   }
 
+  public boolean isShowDecorations() {
+    return showDecorations;
+  }
+
+  public void setShowDecorations(boolean showDecorations) {
+    this.showDecorations = showDecorations;
+  }
 
 
-  
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/Property.java

@@ -13,6 +13,7 @@ import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r4.model.TypeDetails;
 import org.hl7.fhir.r4.utils.ToolingExtensions;
+import org.hl7.fhir.r4.utils.TypesUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.exceptions.DefinitionException;
@@ -88,7 +89,10 @@ public class Property {
 			} else
         throw new Error("logic error, gettype when types > 1, name mismatch for "+elementName+" on at "+ed.getPath());
     } else if (ed.getType().get(0).getCode() == null) {
-      return structure.getId();
+      if (Utilities.existsInList(ed.getId(), "Element.id", "Extension.url"))
+        return "string";
+      else
+        return structure.getId();
 		} else
       return ed.getType().get(0).getCode();
 	}
@@ -135,8 +139,10 @@ public class Property {
 	 * @param E.g. "integer"
 	 */
 	public boolean isPrimitive(String code) {
-		StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/"+code);
+	  return TypesUtilities.isPrimitive(code);
-      return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
+	 // was this... but this can be very inefficient compared to hard coding the list
+//		StructureDefinition sd = context.fetchTypeDefinition(code);
+//      return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
 	}
 
 	private String lowFirst(String t) {
@@ -191,7 +197,7 @@ public class Property {
   		return false;
   	StructureDefinition sd = context.fetchResource(StructureDefinition.class, structure.getUrl().substring(0, structure.getUrl().lastIndexOf("/")+1)+getType(name));
   	if (sd == null)
-  	  sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(getType(name)));
+  	  sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(getType(name), context.getOverrideVersionNs()));
     if (sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
       return true;
   	if (sd == null || sd.getKind() != StructureDefinitionKind.LOGICAL)
@@ -274,7 +280,7 @@ public class Property {
               assert aType.getProfile().size() == 1; 
               url = aType.getProfile().get(0).getValue();
             } else {
-              url = ProfileUtilities.sdNs(t);
+              url = ProfileUtilities.sdNs(t, context.getOverrideVersionNs());
             }
             break;
           }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/elementmodel/XmlParser.java

@@ -1,5 +1,6 @@
 package org.hl7.fhir.r4.elementmodel;
 
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -7,8 +8,10 @@ import java.io.UnsupportedEncodingException;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
+import java.util.Map;
 import java.util.ArrayList;
 
+import javax.sql.rowset.spi.XmlWriter;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.SAXParser;
@@ -33,9 +36,12 @@ import org.hl7.fhir.r4.utils.formats.XmlLocationData;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.ElementDecoration;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
+import org.hl7.fhir.utilities.xhtml.CDANarrativeFormat;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xhtml.XhtmlParser;
@@ -47,6 +53,8 @@ import org.w3c.dom.Node;
 import org.xml.sax.InputSource;
 import org.xml.sax.XMLReader;
 
+import com.sun.webkit.ContextMenu.ShowContext;
+
 public class XmlParser extends ParserBase {
   private boolean allowXsiLocation;
 
@@ -63,7 +71,6 @@ public class XmlParser extends ParserBase {
     this.allowXsiLocation = allowXsiLocation;
   }
 
-
   public Element parse(InputStream stream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
 		Document doc = null;
   	try {
@@ -115,7 +122,7 @@ public class XmlParser extends ParserBase {
   }
 
   private void checkForProcessingInstruction(Document document) throws FHIRFormatError {
-    if (policy == ValidationPolicy.EVERYTHING) {
+    if (policy == ValidationPolicy.EVERYTHING && FormatUtilities.FHIR_NS.equals(document.getDocumentElement().getNamespaceURI())) {
       Node node = document.getFirstChild();
       while (node != null) {
         if (node.getNodeType() == Node.PROCESSING_INSTRUCTION_NODE)
@@ -192,7 +199,7 @@ public class XmlParser extends ParserBase {
   
   private void checkElement(org.w3c.dom.Element element, String path, Property prop) throws FHIRFormatError {
     if (policy == ValidationPolicy.EVERYTHING) {
-      if (empty(element))
+      if (empty(element) && FormatUtilities.FHIR_NS.equals(element.getNamespaceURI())) // this rule only applies to FHIR Content
         logError(line(element), col(element), path, IssueType.INVALID, "Element must have some content", IssueSeverity.ERROR);
       String ns = FormatUtilities.FHIR_NS;
       if (ToolingExtensions.hasExtension(prop.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
@@ -237,13 +244,22 @@ public class XmlParser extends ParserBase {
       	if (property != null) {
 	    	  String av = attr.getNodeValue();
 	    	  if (ToolingExtensions.hasExtension(property.getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"))
-	    	  	av = convertForDateFormat(ToolingExtensions.readStringExtension(property.getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"), av);
+	    	  	av = convertForDateFormatFromExternal(ToolingExtensions.readStringExtension(property.getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"), av);
 	    		if (property.getName().equals("value") && context.isPrimitive())
 	    			context.setValue(av);
 	    		else
 	    	    context.getChildren().add(new Element(property.getName(), property, property.getType(), av).markLocation(line(node), col(node)));
-        } else if (!allowXsiLocation || !attr.getNodeName().endsWith(":schemaLocation") ) {
+        } else {
-          logError(line(node), col(node), path, IssueType.STRUCTURE, "Undefined attribute '@"+attr.getNodeName()+"' on "+node.getNodeName()+" for type "+context.fhirType()+" (properties = "+properties+")", IssueSeverity.ERROR);      		
+          boolean ok = false;
+          if (FormatUtilities.FHIR_NS.equals(node.getNamespaceURI())) {
+            if (attr.getLocalName().equals("schemaLocation") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())) {
+              ok = ok || allowXsiLocation; 
+            }
+          } else
+            ok = ok || (attr.getLocalName().equals("schemaLocation")); // xsi:schemalocation allowed for non FHIR content
+          ok = ok || (hasTypeAttr(context) && attr.getLocalName().equals("type") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())); // xsi:type allowed if element says so
+          if (!ok)  
+            logError(line(node), col(node), path, IssueType.STRUCTURE, "Undefined attribute '@"+attr.getNodeName()+"' on "+node.getNodeName()+" for type "+context.fhirType()+" (properties = "+properties+")", IssueSeverity.ERROR);         
       	}
     	}
     }
@@ -254,8 +270,12 @@ public class XmlParser extends ParserBase {
     		Property property = getElementProp(properties, child.getLocalName());
     		if (property != null) {
     			if (!property.isChoice() && "xhtml".equals(property.getType())) {
-          	XhtmlNode xhtml = new XhtmlParser().setValidatorMode(true).parseHtmlNode((org.w3c.dom.Element) child);
+    			  XhtmlNode xhtml;
-						context.getChildren().add(new Element("div", property, "xhtml", new XhtmlComposer(XhtmlComposer.XML, false).compose(xhtml)).setXhtml(xhtml).markLocation(line(child), col(child)));
+    			  if (property.getDefinition().hasRepresentation(PropertyRepresentation.CDATEXT)) 
+    			    xhtml = new CDANarrativeFormat().convert((org.w3c.dom.Element) child);
+          	else 
+              xhtml = new XhtmlParser().setValidatorMode(true).parseHtmlNode((org.w3c.dom.Element) child);
+						context.getChildren().add(new Element(property.getName(), property, "xhtml", new XhtmlComposer(XhtmlComposer.XML, false).compose(xhtml)).setXhtml(xhtml).markLocation(line(child), col(child)));
     			} else {
     			  String npath = path+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
     				Element n = new Element(child.getLocalName(), property).markLocation(line(child), col(child));
@@ -328,7 +348,7 @@ public class XmlParser extends ParserBase {
   	return null;
 	}
 
-	private String convertForDateFormat(String fmt, String av) throws FHIRException {
+	private String convertForDateFormatFromExternal(String fmt, String av) throws FHIRException {
   	if ("v3".equals(fmt)) {
   		DateTimeType d = DateTimeType.parseV3(av);
   		return d.asStringValue();
@@ -336,10 +356,18 @@ public class XmlParser extends ParserBase {
   		throw new FHIRException("Unknown Data format '"+fmt+"'");
 	}
 
+  private String convertForDateFormatToExternal(String fmt, String av) throws FHIRException {
+    if ("v3".equals(fmt)) {
+      DateTimeType d = new DateTimeType(av);
+      return d.getAsV3();
+    } else
+      throw new FHIRException("Unknown Data format '"+fmt+"'");
+  }
+
   private void parseResource(String string, org.w3c.dom.Element container, Element parent, Property elementProperty) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
   	org.w3c.dom.Element res = XMLUtil.getFirstChild(container);
     String name = res.getLocalName();
-    StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name));
+    StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, context.getOverrideVersionNs()));
     if (sd == null)
       throw new FHIRFormatError("Contained resource does not appear to be a FHIR resource (unknown name '"+res.getLocalName()+"')");
     parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
@@ -365,14 +393,32 @@ public class XmlParser extends ParserBase {
 		}
 	}
 
-	private boolean isAttr(Property property) {
+  private boolean isAttr(Property property) {
-		for (Enumeration<PropertyRepresentation> r : property.getDefinition().getRepresentation()) {
+    for (Enumeration<PropertyRepresentation> r : property.getDefinition().getRepresentation()) {
-			if (r.getValue() == PropertyRepresentation.XMLATTR) {
+      if (r.getValue() == PropertyRepresentation.XMLATTR) {
-				return true;
+        return true;
-			}
+      }
-		}
+    }
-		return false;
+    return false;
-	}
+  }
+
+  private boolean isCdaText(Property property) {
+    for (Enumeration<PropertyRepresentation> r : property.getDefinition().getRepresentation()) {
+      if (r.getValue() == PropertyRepresentation.CDATEXT) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private boolean isTypeAttr(Property property) {
+    for (Enumeration<PropertyRepresentation> r : property.getDefinition().getRepresentation()) {
+      if (r.getValue() == PropertyRepresentation.TYPEATTR) {
+        return true;
+      }
+    }
+    return false;
+  }
 
   private boolean isText(Property property) {
 		for (Enumeration<PropertyRepresentation> r : property.getDefinition().getRepresentation()) {
@@ -384,16 +430,30 @@ public class XmlParser extends ParserBase {
   }
 
 	@Override
-  public void compose(Element e, OutputStream stream, OutputStyle style, String base) throws IOException {
+  public void compose(Element e, OutputStream stream, OutputStyle style, String base) throws IOException, FHIRException {
-    XMLWriter xml = new XMLWriter(stream, "UTF-8");
+	  XMLWriter xml = new XMLWriter(stream, "UTF-8");
+    xml.setSortAttributes(false);
     xml.setPretty(style == OutputStyle.PRETTY);
     xml.start();
     xml.setDefaultNamespace(e.getProperty().getNamespace());
+    if (hasTypeAttr(e))
+      xml.namespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
     composeElement(xml, e, e.getType(), true);
     xml.end();
 
   }
 
+  private boolean hasTypeAttr(Element e) {
+    if (isTypeAttr(e.getProperty()))
+      return true;
+    for (Element c : e.getChildren()) {
+      if (hasTypeAttr(c))
+        return true;
+    }
+    return false;
+  }
+
+
   public void compose(Element e, IXMLWriter xml) throws Exception {
     xml.start();
     xml.setDefaultNamespace(e.getProperty().getNamespace());
@@ -401,7 +461,14 @@ public class XmlParser extends ParserBase {
     xml.end();
   }
 
-  private void composeElement(IXMLWriter xml, Element element, String elementName, boolean root) throws IOException {
+  private void composeElement(IXMLWriter xml, Element element, String elementName, boolean root) throws IOException, FHIRException {
+    if (showDecorations) {
+      @SuppressWarnings("unchecked")
+      List<ElementDecoration> decorations = (List<ElementDecoration>) element.getUserData("fhir.decorations");
+      if (decorations != null)
+        for (ElementDecoration d : decorations)
+          xml.decorate(d);
+    }
     for (String s : element.getComments()) {
       xml.comment(s, true);
     }
@@ -413,12 +480,19 @@ public class XmlParser extends ParserBase {
       xml.exit(elementName);      
     } else if (element.isPrimitive() || (element.hasType() && isPrimitive(element.getType()))) {
       if (element.getType().equals("xhtml")) {
-        xml.escapedText(element.getValue());
+        String rawXhtml = element.getValue();
+        if (isCdaText(element.getProperty())) {
+          new CDANarrativeFormat().convert(xml, element.getXhtml());
+        } else
+          xml.escapedText(rawXhtml);
       } else if (isText(element.getProperty())) {
         if (linkResolver != null)
           xml.link(linkResolver.resolveProperty(element.getProperty()));
         xml.text(element.getValue());
       } else {
+        if (isTypeAttr(element.getProperty()) && !Utilities.noString(element.getType())) {
+          xml.attribute("xsi:type", element.getType());
+        }
         if (element.hasValue()) {
           if (linkResolver != null)
             xml.link(linkResolver.resolveType(element.getType()));
@@ -432,14 +506,20 @@ public class XmlParser extends ParserBase {
 						composeElement(xml, child, child.getName(), false);
 					xml.exit(elementName);
 				} else
-        xml.element(elementName);
+          xml.element(elementName);
       }
     } else {
+      if (isTypeAttr(element.getProperty()) && !Utilities.noString(element.getType())) {
+        xml.attribute("xsi:type", element.getType());
+      }
       for (Element child : element.getChildren()) {
         if (isAttr(child.getProperty())) {
           if (linkResolver != null)
             xml.link(linkResolver.resolveType(child.getType()));
-          xml.attribute(child.getName(), child.getValue());
+          String av = child.getValue();
+          if (ToolingExtensions.hasExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"))
+            av = convertForDateFormatToExternal(ToolingExtensions.readStringExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"), av);
+          xml.attribute(child.getName(), av);
       }
       }
       if (linkResolver != null)

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/formats/JsonCreator.java

@@ -26,6 +26,7 @@ public interface JsonCreator {
   void value(Boolean value) throws IOException;
 
   void value(BigDecimal value) throws IOException;
+  void valueNum(String value) throws IOException; // allow full control of representation
 
   void value(Integer value) throws IOException;
 

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/formats/JsonCreatorCanonical.java

@@ -8,8 +8,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Stack;
 
-import com.google.gson.stream.JsonWriter;
-
 public class JsonCreatorCanonical implements JsonCreator {
 
   public class JsonCanValue {
@@ -27,6 +25,14 @@ public class JsonCreatorCanonical implements JsonCreator {
     }
   }
 
+  private class JsonCanPresentedNumberValue extends JsonCanValue {
+    private String value;
+    private JsonCanPresentedNumberValue(String name, String value) {
+      super(name);
+      this.value = value;  
+    }
+  }
+
   private class JsonCanIntegerValue extends JsonCanValue {
     private Integer value;
     private JsonCanIntegerValue(String name, Integer value) {
@@ -74,12 +80,12 @@ public class JsonCreatorCanonical implements JsonCreator {
 
   Stack<JsonCanObject> stack;
   JsonCanObject root; 
-  JsonWriter gson;
+  JsonCreatorDirect jj;
   String name;
   
   public JsonCreatorCanonical(OutputStreamWriter osw) {
     stack = new Stack<JsonCreatorCanonical.JsonCanObject>();
-    gson = new JsonWriter(osw);
+    jj = new JsonCreatorDirect(osw);
     name = null;
   }
 
@@ -93,7 +99,7 @@ public class JsonCreatorCanonical implements JsonCreator {
   public void setIndent(String indent) {
     if (!indent.equals(""))
       throw new Error("do not use pretty when canonical is set");
-    gson.setIndent(indent);
+    jj.setIndent(indent);
   }
 
   @Override
@@ -135,6 +141,11 @@ public class JsonCreatorCanonical implements JsonCreator {
   public void value(BigDecimal value) throws IOException {
     stack.peek().addProp(new JsonCanNumberValue(takeName(), value));    
   }
+  @Override
+  public void valueNum(String value) throws IOException {
+    stack.peek().addProp(new JsonCanPresentedNumberValue(takeName(), value));    
+  }
+
 
   @Override
   public void value(Integer value) throws IOException {
@@ -161,24 +172,26 @@ public class JsonCreatorCanonical implements JsonCreator {
   }
 
   private void writeObject(JsonCanObject obj) throws IOException {
-    gson.beginObject();
+    jj.beginObject();
     List<String> names = new ArrayList<String>();
     for (JsonCanValue v : obj.children) 
       names.add(v.name);
     Collections.sort(names);
     for (String n : names) {
-      gson.name(n);
+      jj.name(n);
       JsonCanValue v = getPropForName(n, obj.children);
       if (v instanceof JsonCanNumberValue)
-        gson.value(((JsonCanNumberValue) v).value);
+        jj.value(((JsonCanNumberValue) v).value);
+      else if (v instanceof JsonCanPresentedNumberValue)
+        jj.valueNum(((JsonCanPresentedNumberValue) v).value);
       else if (v instanceof JsonCanIntegerValue)
-          gson.value(((JsonCanIntegerValue) v).value);
+        jj.value(((JsonCanIntegerValue) v).value);
       else if (v instanceof JsonCanBooleanValue)
-        gson.value(((JsonCanBooleanValue) v).value);
+        jj.value(((JsonCanBooleanValue) v).value);
       else if (v instanceof JsonCanStringValue)
-        gson.value(((JsonCanStringValue) v).value);
+        jj.value(((JsonCanStringValue) v).value);
       else if (v instanceof JsonCanNullValue)
-        gson.nullValue();
+        jj.nullValue();
       else if (v instanceof JsonCanObject) {
         JsonCanObject o = (JsonCanObject) v;
         if (o.array) 
@@ -188,7 +201,7 @@ public class JsonCreatorCanonical implements JsonCreator {
       } else
         throw new Error("not possible");
     }
-    gson.endObject();
+    jj.endObject();
   }
 
   private JsonCanValue getPropForName(String name, List<JsonCanValue> children) {
@@ -199,18 +212,18 @@ public class JsonCreatorCanonical implements JsonCreator {
   }
 
   private void writeArray(JsonCanObject arr) throws IOException {
-    gson.beginArray();
+    jj.beginArray();
     for (JsonCanValue v : arr.children) { 
       if (v instanceof JsonCanNumberValue)
-        gson.value(((JsonCanNumberValue) v).value);
+        jj.value(((JsonCanNumberValue) v).value);
       else if (v instanceof JsonCanIntegerValue)
-          gson.value(((JsonCanIntegerValue) v).value);
+          jj.value(((JsonCanIntegerValue) v).value);
       else if (v instanceof JsonCanBooleanValue)
-        gson.value(((JsonCanBooleanValue) v).value);
+        jj.value(((JsonCanBooleanValue) v).value);
       else if (v instanceof JsonCanStringValue)
-        gson.value(((JsonCanStringValue) v).value);
+        jj.value(((JsonCanStringValue) v).value);
       else if (v instanceof JsonCanNullValue)
-        gson.nullValue();
+        jj.nullValue();
       else if (v instanceof JsonCanObject) {
         JsonCanObject o = (JsonCanObject) v;
         if (o.array) 
@@ -220,7 +233,7 @@ public class JsonCreatorCanonical implements JsonCreator {
       } else
         throw new Error("not possible");
     }
-    gson.endArray();    
+    jj.endArray();    
   }
 
   @Override

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/formats/JsonCreatorDirect.java

@@ -0,0 +1,172 @@
+package org.hl7.fhir.r4.formats;
+
+import java.io.IOException;
+import java.io.Writer;
+import java.math.BigDecimal;
+import java.util.Stack;
+
+import org.hl7.fhir.utilities.Utilities;
+
+/**
+ * A little implementation of a json write to replace Gson .... because Gson screws up decimal values, and *we care*
+ * 
+ * @author Grahame Grieve
+ *
+ */
+public class JsonCreatorDirect implements JsonCreator {
+
+  private Writer writer;
+  private boolean pretty;
+  private boolean named;
+  private boolean valued;
+  private int indent;
+  
+  public JsonCreatorDirect(Writer writer) {
+    super();
+    this.writer = writer;
+  }
+
+  @Override
+  public void setIndent(String indent) {
+    this.pretty = !Utilities.noString(indent);
+  }
+
+  @Override
+  public void beginObject() throws IOException {
+    checkState();
+    writer.write("{");
+    stepIn();
+  }
+
+  public void stepIn() throws IOException {
+    if (pretty) {
+      indent++;
+      writer.write("\r\n");
+      for (int i = 0; i < indent; i++) {
+        writer.write("  ");
+      }
+    }
+  }
+
+  public void stepOut() throws IOException {
+    if (pretty) {
+      indent--;
+      writer.write("\r\n");
+      for (int i = 0; i < indent; i++) {
+        writer.write("  ");
+      }
+    }
+  }
+
+  private void checkState() throws IOException {
+    if (named) {
+      if (pretty)
+        writer.write(" : ");
+      else
+        writer.write(":");
+      named = false;
+    }
+    if (valued) {
+      writer.write(",");
+      if (pretty) {
+        writer.write("\r\n");
+        for (int i = 0; i < indent; i++) {
+          writer.write("  ");
+        }        
+      }
+      valued = false;
+    }
+  }
+
+  @Override
+  public void endObject() throws IOException {
+    stepOut();
+    writer.write("}");    
+  }
+
+  @Override
+  public void nullValue() throws IOException {
+    checkState();
+    writer.write("null");
+    valued = true;
+  }
+
+  @Override
+  public void name(String name) throws IOException {
+    checkState();
+    writer.write("\""+name+"\"");
+    named = true;
+  }
+
+  @Override
+  public void value(String value) throws IOException {
+    checkState();
+    writer.write("\""+Utilities.escapeJson(value)+"\"");    
+    valued = true;
+  }
+
+  @Override
+  public void value(Boolean value) throws IOException {
+    checkState();
+    if (value == null)
+      writer.write("null");
+    else if (value.booleanValue())
+      writer.write("true");
+    else
+      writer.write("false");
+    valued = true;
+  }
+
+  @Override
+  public void value(BigDecimal value) throws IOException {
+    checkState();
+    if (value == null)
+      writer.write("null");
+    else 
+      writer.write(value.toString());    
+    valued = true;
+  }
+
+  @Override
+  public void valueNum(String value) throws IOException {
+    checkState();
+    if (value == null)
+      writer.write("null");
+    else 
+      writer.write(value);    
+    valued = true;
+  }
+
+  @Override
+  public void value(Integer value) throws IOException {
+    checkState();
+    if (value == null)
+      writer.write("null");
+    else 
+      writer.write(value.toString());    
+    valued = true;
+  }
+
+  @Override
+  public void beginArray() throws IOException {
+    checkState();
+    writer.write("[");    
+  }
+
+  @Override
+  public void endArray() throws IOException {
+    writer.write("]");        
+  }
+
+  @Override
+  public void finish() throws IOException {
+    // nothing
+  }
+
+  @Override
+  public void link(String href) {
+    // not used
+    
+  }
+
+}

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/formats/JsonCreatorGson.java

@@ -80,4 +80,9 @@ public class JsonCreatorGson implements JsonCreator {
     // not used
   }
 
+  @Override
+  public void valueNum(String value) throws IOException {
+    value(new BigDecimal(value));    
+  }
+
 }