package ca.uhn.fhir.util;

import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildDirectResource;
import ca.uhn.fhir.context.RuntimeExtensionDtDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IIdentifiableElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.parser.DataFormatException;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseElement;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.substring;

/*
 * #%L
 * HAPI FHIR - Core Library
 * %%
 * Copyright (C) 2014 - 2021 Smile CDR, Inc.
 * %%
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * #L%
 */

public class FhirTerser {

        private static final Pattern COMPARTMENT_MATCHER_PATH = Pattern.compile("([a-zA-Z.]+)\\.where\\(resolve\\(\\) is ([a-zA-Z]+)\\)");
        private static final EnumSet<OptionsEnum> EMPTY_OPTION_SET = EnumSet.noneOf(OptionsEnum.class);
        private static final String USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED = FhirTerser.class.getName() + "_CONTAIN_RESOURCES_COMPLETED";
        private final FhirContext myContext;

        public FhirTerser(FhirContext theContext) {
                super();
                myContext = theContext;
        }

        private List<String> addNameToList(List<String> theCurrentList, BaseRuntimeChildDefinition theChildDefinition) {
                if (theChildDefinition == null)
                        return null;
                if (theCurrentList == null || theCurrentList.isEmpty())
                        return new ArrayList<>(Collections.singletonList(theChildDefinition.getElementName()));
                List<String> newList = new ArrayList<>(theCurrentList);
                newList.add(theChildDefinition.getElementName());
                return newList;
        }

        private ExtensionDt createEmptyExtensionDt(IBaseExtension theBaseExtension, String theUrl) {
                return createEmptyExtensionDt(theBaseExtension, false, theUrl);
        }

        @SuppressWarnings("unchecked")
        private ExtensionDt createEmptyExtensionDt(IBaseExtension theBaseExtension, boolean theIsModifier, String theUrl) {
                ExtensionDt retVal = new ExtensionDt(theIsModifier, theUrl);
                theBaseExtension.getExtension().add(retVal);
                return retVal;
        }

        private ExtensionDt createEmptyExtensionDt(ISupportsUndeclaredExtensions theSupportsUndeclaredExtensions, String theUrl) {
                return createEmptyExtensionDt(theSupportsUndeclaredExtensions, false, theUrl);
        }

        private ExtensionDt createEmptyExtensionDt(ISupportsUndeclaredExtensions theSupportsUndeclaredExtensions, boolean theIsModifier, String theUrl) {
                return theSupportsUndeclaredExtensions.addUndeclaredExtension(theIsModifier, theUrl);
        }

        private IBaseExtension createEmptyExtension(IBaseHasExtensions theBaseHasExtensions, String theUrl) {
                return (IBaseExtension) theBaseHasExtensions.addExtension().setUrl(theUrl);
        }

        private IBaseExtension createEmptyModifierExtension(IBaseHasModifierExtensions theBaseHasModifierExtensions, String theUrl) {
                return (IBaseExtension) theBaseHasModifierExtensions.addModifierExtension().setUrl(theUrl);
        }

        private ExtensionDt createEmptyModifierExtensionDt(ISupportsUndeclaredExtensions theSupportsUndeclaredExtensions, String theUrl) {
                return createEmptyExtensionDt(theSupportsUndeclaredExtensions, true, theUrl);
        }

        /**
         * Clones all values from a source object into the equivalent fields in a target object
         *
         * @param theSource              The source object (must not be null)
         * @param theTarget              The target object to copy values into (must not be null)
         * @param theIgnoreMissingFields The ignore fields in the target which do not exist (if false, an exception will be thrown if the target is unable to accept a value from the source)
         * @return Returns the target (which will be the same object that was passed into theTarget) for easy chaining
         */
        public IBase cloneInto(IBase theSource, IBase theTarget, boolean theIgnoreMissingFields) {
                Validate.notNull(theSource, "theSource must not be null");
                Validate.notNull(theTarget, "theTarget must not be null");

                // DSTU3+
                if (theSource instanceof IBaseElement) {
                        IBaseElement source = (IBaseElement) theSource;
                        IBaseElement target = (IBaseElement) theTarget;
                        target.setId(source.getId());
                }

                // DSTU2 only
                if (theSource instanceof IIdentifiableElement) {
                        IIdentifiableElement source = (IIdentifiableElement) theSource;
                        IIdentifiableElement target = (IIdentifiableElement) theTarget;
                        target.setElementSpecificId(source.getElementSpecificId());
                }

                // DSTU2 only
                if (theSource instanceof IResource) {
                        IResource source = (IResource) theSource;
                        IResource target = (IResource) theTarget;
                        target.setId(source.getId());
                        target.getResourceMetadata().putAll(source.getResourceMetadata());
                }

                if (theSource instanceof IPrimitiveType<?>) {
                        if (theTarget instanceof IPrimitiveType<?>) {
                                String valueAsString = ((IPrimitiveType<?>) theSource).getValueAsString();
                                if (isNotBlank(valueAsString)) {
                                        ((IPrimitiveType<?>) theTarget).setValueAsString(valueAsString);
                                }
                                if (theSource instanceof IBaseHasExtensions && theTarget instanceof IBaseHasExtensions) {
                                        List<? extends IBaseExtension<?, ?>> extensions = ((IBaseHasExtensions) theSource).getExtension();
                                        for (IBaseExtension<?, ?> nextSource : extensions) {
                                                IBaseExtension<?, ?> nextTarget = ((IBaseHasExtensions) theTarget).addExtension();
                                                cloneInto(nextSource, nextTarget, theIgnoreMissingFields);
                                        }
                                }
                                return theSource;
                        }
                        if (theIgnoreMissingFields) {
                                return theSource;
                        }
                        throw new DataFormatException("Can not copy value from primitive of type " + theSource.getClass().getName() + " into type " + theTarget.getClass().getName());
                }

                BaseRuntimeElementCompositeDefinition<?> sourceDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSource.getClass());
                BaseRuntimeElementCompositeDefinition<?> targetDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theTarget.getClass());

                List<BaseRuntimeChildDefinition> children = sourceDef.getChildren();
                if (sourceDef instanceof RuntimeExtensionDtDefinition) {
                        children = ((RuntimeExtensionDtDefinition) sourceDef).getChildrenIncludingUrl();
                }

                for (BaseRuntimeChildDefinition nextChild : children)
                        for (IBase nextValue : nextChild.getAccessor().getValues(theSource)) {
                                String elementName = nextChild.getChildNameByDatatype(nextValue.getClass());
                                BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(elementName);
                                if (targetChild == null) {
                                        if (theIgnoreMissingFields) {
                                                continue;
                                        }
                                        throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + elementName);
                                }

                                BaseRuntimeElementDefinition<?> element = myContext.getElementDefinition(nextValue.getClass());
                                Object instanceConstructorArg = targetChild.getInstanceConstructorArguments();
                                IBase target;
                                if (instanceConstructorArg != null) {
                                        target = element.newInstance(instanceConstructorArg);
                                } else {
                                        target = element.newInstance();
                                }

                                targetChild.getMutator().addValue(theTarget, target);
                                cloneInto(nextValue, target, theIgnoreMissingFields);
                        }

                return theTarget;
        }

        /**
         * Returns a list containing all child elements (including the resource itself) which are <b>non-empty</b> and are either of the exact type specified, or are a subclass of that type.
         * <p>
         * For example, specifying a type of {@link StringDt} would return all non-empty string instances within the message. Specifying a type of {@link IResource} would return the resource itself, as
         * well as any contained resources.
         * </p>
         * <p>
         * Note on scope: This method will descend into any contained resources ({@link IResource#getContained()}) as well, but will not descend into linked resources (e.g.
         * {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
         * </p>
         *
         * @param theResource The resource instance to search. Must not be null.
         * @param theType     The type to search for. Must not be null.
         * @return Returns a list of all matching elements
         */
        public <T extends IBase> List<T> getAllPopulatedChildElementsOfType(IBaseResource theResource, final Class<T> theType) {
                final ArrayList<T> retVal = new ArrayList<>();
                BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
                visit(newMap(), theResource, theResource, null, null, def, new IModelVisitor() {
                        @SuppressWarnings("unchecked")
                        @Override
                        public void acceptElement(IBaseResource theOuterResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
                                if (theElement == null || theElement.isEmpty()) {
                                        return;
                                }

                                if (theType.isAssignableFrom(theElement.getClass())) {
                                        retVal.add((T) theElement);
                                }
                        }
                });
                return retVal;
        }

        public List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
                final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<>();
                BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
                visit(newMap(), theResource, theResource, null, null, def, new IModelVisitor() {
                        @Override
                        public void acceptElement(IBaseResource theOuterResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
                                if (theElement == null || theElement.isEmpty()) {
                                        return;
                                }
                                if (IBaseReference.class.isAssignableFrom(theElement.getClass())) {
                                        retVal.add(new ResourceReferenceInfo(myContext, theOuterResource, thePathToElement, (IBaseReference) theElement));
                                }
                        }
                });
                return retVal;
        }

        private BaseRuntimeChildDefinition getDefinition(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
                BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(theSubList.get(0));

                if (theSubList.size() == 1) {
                        return nextDef;
                }
                BaseRuntimeElementCompositeDefinition<?> cmp = (BaseRuntimeElementCompositeDefinition<?>) nextDef.getChildByName(theSubList.get(0));
                return getDefinition(cmp, theSubList.subList(1, theSubList.size()));
        }

        public BaseRuntimeChildDefinition getDefinition(Class<? extends IBaseResource> theResourceType, String thePath) {
                RuntimeResourceDefinition def = myContext.getResourceDefinition(theResourceType);

                List<String> parts = Arrays.asList(thePath.split("\\."));
                List<String> subList = parts.subList(1, parts.size());
                if (subList.size() < 1) {
                        throw new ConfigurationException("Invalid path: " + thePath);
                }
                return getDefinition(def, subList);

        }

        public Object getSingleValueOrNull(IBase theTarget, String thePath) {
                Class<IBase> wantedType = IBase.class;

                return getSingleValueOrNull(theTarget, thePath, wantedType);
        }

        public <T extends IBase> T getSingleValueOrNull(IBase theTarget, String thePath, Class<T> theWantedType) {
                Validate.notNull(theTarget, "theTarget must not be null");
                Validate.notBlank(thePath, "thePath must not be empty");

                BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theTarget.getClass());
                if (!(def instanceof BaseRuntimeElementCompositeDefinition)) {
                        throw new IllegalArgumentException("Target is not a composite type: " + theTarget.getClass().getName());
                }

                BaseRuntimeElementCompositeDefinition<?> currentDef = (BaseRuntimeElementCompositeDefinition<?>) def;

                List<String> parts = parsePath(currentDef, thePath);

                List<T> retVal = getValues(currentDef, theTarget, parts, theWantedType);
                if (retVal.isEmpty()) {
                        return null;
                }
                return retVal.get(0);
        }

        public Optional<String> getSinglePrimitiveValue(IBase theTarget, String thePath) {
                return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t->t.getValueAsString());
        }

        public String getSinglePrimitiveValueOrNull(IBase theTarget, String thePath) {
                return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t->t.getValueAsString()).orElse(null);
        }

        public <T extends IBase> Optional<T> getSingleValue(IBase theTarget, String thePath, Class<T> theWantedType) {
                return Optional.ofNullable(getSingleValueOrNull(theTarget, thePath, theWantedType));
        }

        private <T extends IBase> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, IBase theCurrentObj, List<String> theSubList, Class<T> theWantedClass) {
                return getValues(theCurrentDef, theCurrentObj, theSubList, theWantedClass, false, false);
        }

        @SuppressWarnings("unchecked")
        private <T extends IBase> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, IBase theCurrentObj, List<String> theSubList, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
                String name = theSubList.get(0);
                List<T> retVal = new ArrayList<>();

                if (name.startsWith("extension('")) {
                        String extensionUrl = name.substring("extension('".length());
                        int endIndex = extensionUrl.indexOf('\'');
                        if (endIndex != -1) {
                                extensionUrl = extensionUrl.substring(0, endIndex);
                        }

                        if (myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
                                // DTSU2
                                final String extensionDtUrlForLambda = extensionUrl;
                                List<ExtensionDt> extensionDts = Collections.emptyList();
                                if (theCurrentObj instanceof ISupportsUndeclaredExtensions) {
                                        extensionDts = ((ISupportsUndeclaredExtensions) theCurrentObj).getUndeclaredExtensions()
                                                .stream()
                                                .filter(t -> t.getUrl().equals(extensionDtUrlForLambda))
                                                .collect(Collectors.toList());

                                        if (theAddExtension
                                                && (!(theCurrentObj instanceof IBaseExtension) || (extensionDts.isEmpty() && theSubList.size() == 1))) {
                                                extensionDts.add(createEmptyExtensionDt((ISupportsUndeclaredExtensions) theCurrentObj, extensionUrl));
                                        }

                                        if (extensionDts.isEmpty() && theCreate) {
                                                extensionDts.add(createEmptyExtensionDt((ISupportsUndeclaredExtensions) theCurrentObj, extensionUrl));
                                        }

                                } else if (theCurrentObj instanceof IBaseExtension) {
                                        extensionDts = ((IBaseExtension) theCurrentObj).getExtension();

                                        if (theAddExtension
                                                && (extensionDts.isEmpty() && theSubList.size() == 1)) {
                                                extensionDts.add(createEmptyExtensionDt((IBaseExtension) theCurrentObj, extensionUrl));
                                        }

                                        if (extensionDts.isEmpty() && theCreate) {
                                                extensionDts.add(createEmptyExtensionDt((IBaseExtension) theCurrentObj, extensionUrl));
                                        }
                                }

                                for (ExtensionDt next : extensionDts) {
                                        if (theWantedClass.isAssignableFrom(next.getClass())) {
                                                retVal.add((T) next);
                                        }
                                }
                        } else {
                                // DSTU3+
                                final String extensionUrlForLambda = extensionUrl;
                                List<IBaseExtension> extensions = Collections.emptyList();
                                if (theCurrentObj instanceof IBaseHasExtensions) {
                                        extensions = ((IBaseHasExtensions) theCurrentObj).getExtension()
                                                .stream()
                                                .filter(t -> t.getUrl().equals(extensionUrlForLambda))
                                                .collect(Collectors.toList());

                                        if (theAddExtension
                                                && (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
                                                extensions.add(createEmptyExtension((IBaseHasExtensions) theCurrentObj, extensionUrl));
                                        }

                                        if (extensions.isEmpty() && theCreate) {
                                                extensions.add(createEmptyExtension((IBaseHasExtensions) theCurrentObj, extensionUrl));
                                        }
                                }

                                for (IBaseExtension next : extensions) {
                                        if (theWantedClass.isAssignableFrom(next.getClass())) {
                                                retVal.add((T) next);
                                        }
                                }
                        }

                        if (theSubList.size() > 1) {
                                List<T> values = retVal;
                                retVal = new ArrayList<>();
                                for (T nextElement : values) {
                                        BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(nextElement.getClass());
                                        List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension);
                                        retVal.addAll(foundValues);
                                }
                        }

                        return retVal;
                }

                if (name.startsWith("modifierExtension('")) {
                        String extensionUrl = name.substring("modifierExtension('".length());
                        int endIndex = extensionUrl.indexOf('\'');
                        if (endIndex != -1) {
                                extensionUrl = extensionUrl.substring(0, endIndex);
                        }

                        if (myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
                                // DSTU2
                                final String extensionDtUrlForLambda = extensionUrl;
                                List<ExtensionDt> extensionDts = Collections.emptyList();
                                if (theCurrentObj instanceof ISupportsUndeclaredExtensions) {
                                        extensionDts = ((ISupportsUndeclaredExtensions) theCurrentObj).getUndeclaredModifierExtensions()
                                                .stream()
                                                .filter(t -> t.getUrl().equals(extensionDtUrlForLambda))
                                                .collect(Collectors.toList());

                                        if (theAddExtension
                                                && (!(theCurrentObj instanceof IBaseExtension) || (extensionDts.isEmpty() && theSubList.size() == 1))) {
                                                extensionDts.add(createEmptyModifierExtensionDt((ISupportsUndeclaredExtensions) theCurrentObj, extensionUrl));
                                        }

                                        if (extensionDts.isEmpty() && theCreate) {
                                                extensionDts.add(createEmptyModifierExtensionDt((ISupportsUndeclaredExtensions) theCurrentObj, extensionUrl));
                                        }

                                } else if (theCurrentObj instanceof IBaseExtension) {
                                        extensionDts = ((IBaseExtension) theCurrentObj).getExtension();

                                        if (theAddExtension
                                                && (extensionDts.isEmpty() && theSubList.size() == 1)) {
                                                extensionDts.add(createEmptyExtensionDt((IBaseExtension) theCurrentObj, extensionUrl));
                                        }

                                        if (extensionDts.isEmpty() && theCreate) {
                                                extensionDts.add(createEmptyExtensionDt((IBaseExtension) theCurrentObj, extensionUrl));
                                        }
                                }

                                for (ExtensionDt next : extensionDts) {
                                        if (theWantedClass.isAssignableFrom(next.getClass())) {
                                                retVal.add((T) next);
                                        }
                                }
                        } else {
                                // DSTU3+
                                final String extensionUrlForLambda = extensionUrl;
                                List<IBaseExtension> extensions = Collections.emptyList();

                                if (theCurrentObj instanceof IBaseHasModifierExtensions) {
                                        extensions = ((IBaseHasModifierExtensions) theCurrentObj).getModifierExtension()
                                                .stream()
                                                .filter(t -> t.getUrl().equals(extensionUrlForLambda))
                                                .collect(Collectors.toList());

                                        if (theAddExtension
                                                && (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
                                                extensions.add(createEmptyModifierExtension((IBaseHasModifierExtensions) theCurrentObj, extensionUrl));
                                        }

                                        if (extensions.isEmpty() && theCreate) {
                                                extensions.add(createEmptyModifierExtension((IBaseHasModifierExtensions) theCurrentObj, extensionUrl));
                                        }
                                }

                                for (IBaseExtension next : extensions) {
                                        if (theWantedClass.isAssignableFrom(next.getClass())) {
                                                retVal.add((T) next);
                                        }
                                }
                        }

                        if (theSubList.size() > 1) {
                                List<T> values = retVal;
                                retVal = new ArrayList<>();
                                for (T nextElement : values) {
                                        BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(nextElement.getClass());
                                        List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension);
                                        retVal.addAll(foundValues);
                                }
                        }

                        return retVal;
                }

                BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(name);
                List<? extends IBase> values = nextDef.getAccessor().getValues(theCurrentObj);

                if (values.isEmpty() && theCreate) {
                        BaseRuntimeElementDefinition<?> childByName = nextDef.getChildByName(name);
                        Object arg = nextDef.getInstanceConstructorArguments();
                        IBase value;
                        if (arg != null) {
                                value = childByName.newInstance(arg);
                        } else {
                                value = childByName.newInstance();
                        }
                        nextDef.getMutator().addValue(theCurrentObj, value);
                        List<IBase> list = new ArrayList<>();
                        list.add(value);
                        values = list;
                }

                if (theSubList.size() == 1) {
                        if (nextDef instanceof RuntimeChildChoiceDefinition) {
                                for (IBase next : values) {
                                        if (next != null) {
                                                if (name.endsWith("[x]")) {
                                                        if (theWantedClass == null || theWantedClass.isAssignableFrom(next.getClass())) {
                                                                retVal.add((T) next);
                                                        }
                                                } else {
                                                        String childName = nextDef.getChildNameByDatatype(next.getClass());
                                                        if (theSubList.get(0).equals(childName)) {
                                                                if (theWantedClass == null || theWantedClass.isAssignableFrom(next.getClass())) {
                                                                        retVal.add((T) next);
                                                                }
                                                        }
                                                }
                                        }
                                }
                        } else {
                                for (IBase next : values) {
                                        if (next != null) {
                                                if (theWantedClass == null || theWantedClass.isAssignableFrom(next.getClass())) {
                                                        retVal.add((T) next);
                                                }
                                        }
                                }
                        }
                } else {
                        for (IBase nextElement : values) {
                                BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(nextElement.getClass());
                                List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension);
                                retVal.addAll(foundValues);
                        }
                }
                return retVal;
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type {@link Object}.
         *
         * @param theElement The element to be accessed. Must not be null.
         * @param thePath    The path for the element to be accessed.@param theElement The resource instance to be accessed. Must not be null.
         * @return A list of values of type {@link Object}.
         */
        public List<IBase> getValues(IBase theElement, String thePath) {
                Class<IBase> wantedClass = IBase.class;

                return getValues(theElement, thePath, wantedClass);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type {@link Object}.
         *
         * @param theElement The element to be accessed. Must not be null.
         * @param thePath    The path for the element to be accessed.
         * @param theCreate  When set to <code>true</code>, the terser will create a null-valued element where none exists.
         * @return A list of values of type {@link Object}.
         */
        public List<IBase> getValues(IBase theElement, String thePath, boolean theCreate) {
                Class<IBase> wantedClass = IBase.class;

                return getValues(theElement, thePath, wantedClass, theCreate);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type {@link Object}.
         *
         * @param theElement      The element to be accessed. Must not be null.
         * @param thePath         The path for the element to be accessed.
         * @param theCreate       When set to <code>true</code>, the terser will create a null-valued element where none exists.
         * @param theAddExtension When set to <code>true</code>, the terser will add a null-valued extension where one or more such extensions already exist.
         * @return A list of values of type {@link Object}.
         */
        public List<IBase> getValues(IBase theElement, String thePath, boolean theCreate, boolean theAddExtension) {
                Class<IBase> wantedClass = IBase.class;

                return getValues(theElement, thePath, wantedClass, theCreate, theAddExtension);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type <code>theWantedClass</code>.
         *
         * @param theElement     The element to be accessed. Must not be null.
         * @param thePath        The path for the element to be accessed.
         * @param theWantedClass The desired class to be returned in a list.
         * @param <T>            Type declared by <code>theWantedClass</code>
         * @return A list of values of type <code>theWantedClass</code>.
         */
        public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass) {
                BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theElement, parts, theWantedClass);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type <code>theWantedClass</code>.
         *
         * @param theElement     The element to be accessed. Must not be null.
         * @param thePath        The path for the element to be accessed.
         * @param theWantedClass The desired class to be returned in a list.
         * @param theCreate      When set to <code>true</code>, the terser will create a null-valued element where none exists.
         * @param <T>            Type declared by <code>theWantedClass</code>
         * @return A list of values of type <code>theWantedClass</code>.
         */
        public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass, boolean theCreate) {
                BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theElement, parts, theWantedClass, theCreate, false);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type <code>theWantedClass</code>.
         *
         * @param theElement      The element to be accessed. Must not be null.
         * @param thePath         The path for the element to be accessed.
         * @param theWantedClass  The desired class to be returned in a list.
         * @param theCreate       When set to <code>true</code>, the terser will create a null-valued element where none exists.
         * @param theAddExtension When set to <code>true</code>, the terser will add a null-valued extension where one or more such extensions already exist.
         * @param <T>             Type declared by <code>theWantedClass</code>
         * @return A list of values of type <code>theWantedClass</code>.
         */
        public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
                BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theElement, parts, theWantedClass, theCreate, theAddExtension);
        }

        private List<String> parsePath(BaseRuntimeElementCompositeDefinition<?> theElementDef, String thePath) {
                List<String> parts = new ArrayList<>();

                int currentStart = 0;
                boolean inSingleQuote = false;
                for (int i = 0; i < thePath.length(); i++) {
                        switch (thePath.charAt(i)) {
                                case '\'':
                                        inSingleQuote = !inSingleQuote;
                                        break;
                                case '.':
                                        if (!inSingleQuote) {
                                                parts.add(thePath.substring(currentStart, i));
                                                currentStart = i + 1;
                                        }
                                        break;
                        }
                }

                parts.add(thePath.substring(currentStart));

                if (parts.size() > 0 && parts.get(0).equals(theElementDef.getName())) {
                        parts = parts.subList(1, parts.size());
                }

                if (parts.size() < 1) {
                        throw new ConfigurationException("Invalid path: " + thePath);
                }
                return parts;
        }

        /**
         * Returns <code>true</code> if <code>theSource</code> is in the compartment named <code>theCompartmentName</code>
         * belonging to resource <code>theTarget</code>
         *
         * @param theCompartmentName The name of the compartment
         * @param theSource          The potential member of the compartment
         * @param theTarget          The owner of the compartment. Note that both the resource type and ID must be filled in on this IIdType or the method will throw an {@link IllegalArgumentException}
         * @return <code>true</code> if <code>theSource</code> is in the compartment
         * @throws IllegalArgumentException If theTarget does not contain both a resource type and ID
         */
        public boolean isSourceInCompartmentForTarget(String theCompartmentName, IBaseResource theSource, IIdType theTarget) {
                Validate.notBlank(theCompartmentName, "theCompartmentName must not be null or blank");
                Validate.notNull(theSource, "theSource must not be null");
                Validate.notNull(theTarget, "theTarget must not be null");
                Validate.notBlank(defaultString(theTarget.getResourceType()), "theTarget must have a populated resource type (theTarget.getResourceType() does not return a value)");
                Validate.notBlank(defaultString(theTarget.getIdPart()), "theTarget must have a populated ID (theTarget.getIdPart() does not return a value)");

                String wantRef = theTarget.toUnqualifiedVersionless().getValue();

                RuntimeResourceDefinition sourceDef = myContext.getResourceDefinition(theSource);
                if (theSource.getIdElement().hasIdPart()) {
                        if (wantRef.equals(sourceDef.getName() + '/' + theSource.getIdElement().getIdPart())) {
                                return true;
                        }
                }

                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);
                                }

                                List<IBaseReference> values = getValues(theSource, nextPath, IBaseReference.class);
                                for (IBaseReference nextValue : values) {
                                        IIdType nextTargetId = nextValue.getReferenceElement();
                                        String nextRef = nextTargetId.toUnqualifiedVersionless().getValue();

                                        /*
                                         * If the reference isn't an explicit resource ID, but instead is just
                                         * a resource object, we'll calculate its ID and treat the target
                                         * as that.
                                         */
                                        if (isBlank(nextRef) && nextValue.getResource() != null) {
                                                IBaseResource nextTarget = nextValue.getResource();
                                                nextTargetId = nextTarget.getIdElement().toUnqualifiedVersionless();
                                                if (!nextTargetId.hasResourceType()) {
                                                        String resourceType = myContext.getResourceType(nextTarget);
                                                        nextTargetId.setParts(null, resourceType, nextTargetId.getIdPart(), null);
                                                }
                                                nextRef = nextTargetId.getValue();
                                        }

                                        if (isNotBlank(wantType)) {
                                                String nextTargetIdResourceType = nextTargetId.getResourceType();
                                                if (nextTargetIdResourceType == null || !nextTargetIdResourceType.equals(wantType)) {
                                                        continue;
                                                }
                                        }

                                        if (wantRef.equals(nextRef)) {
                                                return true;
                                        }
                                }
                        }
                }

                return false;
        }

        private void visit(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor2 theCallback, List<IBase> theContainingElementPath,
                                                         List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
                if (theChildDefinition != null) {
                        theChildDefinitionPath.add(theChildDefinition);
                }
                theContainingElementPath.add(theElement);
                theElementDefinitionPath.add(theDefinition);

                boolean recurse = theCallback.acceptElement(theElement, Collections.unmodifiableList(theContainingElementPath), Collections.unmodifiableList(theChildDefinitionPath),
                        Collections.unmodifiableList(theElementDefinitionPath));
                if (recurse) {

                        /*
                         * Visit undeclared extensions
                         */
                        if (theElement instanceof ISupportsUndeclaredExtensions) {
                                ISupportsUndeclaredExtensions containingElement = (ISupportsUndeclaredExtensions) theElement;
                                for (ExtensionDt nextExt : containingElement.getUndeclaredExtensions()) {
                                        theContainingElementPath.add(nextExt);
                                        theCallback.acceptUndeclaredExtension(nextExt, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
                                        theContainingElementPath.remove(theContainingElementPath.size() - 1);
                                }
                        }

                        /*
                         * Now visit the children of the given element
                         */
                        switch (theDefinition.getChildType()) {
                                case ID_DATATYPE:
                                case PRIMITIVE_XHTML_HL7ORG:
                                case PRIMITIVE_XHTML:
                                case PRIMITIVE_DATATYPE:
                                        // These are primitive types, so we don't need to visit their children
                                        break;
                                case RESOURCE:
                                case RESOURCE_BLOCK:
                                case COMPOSITE_DATATYPE: {
                                        BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) theDefinition;
                                        for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
                                                List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
                                                if (values != null) {
                                                        for (IBase nextValue : values) {
                                                                if (nextValue == null) {
                                                                        continue;
                                                                }
                                                                if (nextValue.isEmpty()) {
                                                                        continue;
                                                                }
                                                                BaseRuntimeElementDefinition<?> childElementDef;
                                                                Class<? extends IBase> valueType = nextValue.getClass();
                                                                childElementDef = nextChild.getChildElementDefinitionByDatatype(valueType);
                                                                while (childElementDef == null && IBase.class.isAssignableFrom(valueType)) {
                                                                        childElementDef = nextChild.getChildElementDefinitionByDatatype(valueType);
                                                                        valueType = (Class<? extends IBase>) valueType.getSuperclass();
                                                                }

                                                                Class<? extends IBase> typeClass = nextValue.getClass();
                                                                while (childElementDef == null && IBase.class.isAssignableFrom(typeClass)) {
                                                                        //noinspection unchecked
                                                                        typeClass = (Class<? extends IBase>) typeClass.getSuperclass();
                                                                        childElementDef = nextChild.getChildElementDefinitionByDatatype(typeClass);
                                                                }

                                                                Validate.notNull(childElementDef, "Found value of type[%s] which is not valid for field[%s] in %s", nextValue.getClass(), nextChild.getElementName(), childDef.getName());

                                                                visit(nextValue, nextChild, childElementDef, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
                                                        }
                                                }
                                        }
                                        break;
                                }
                                case CONTAINED_RESOURCES: {
                                        BaseContainedDt value = (BaseContainedDt) theElement;
                                        for (IResource next : value.getContainedResources()) {
                                                BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
                                                visit(next, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
                                        }
                                        break;
                                }
                                case EXTENSION_DECLARED:
                                case UNDECL_EXT: {
                                        throw new IllegalStateException("state should not happen: " + theDefinition.getChildType());
                                }
                                case CONTAINED_RESOURCE_LIST: {
                                        if (theElement != null) {
                                                BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
                                                visit(theElement, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
                                        }
                                        break;
                                }
                        }

                }

                if (theChildDefinition != null) {
                        theChildDefinitionPath.remove(theChildDefinitionPath.size() - 1);
                }
                theContainingElementPath.remove(theContainingElementPath.size() - 1);
                theElementDefinitionPath.remove(theElementDefinitionPath.size() - 1);
        }

        /**
         * Visit all elements in a given resource
         *
         * <p>
         * Note on scope: This method will descend into any contained resources ({@link IResource#getContained()}) as well, but will not descend into linked resources (e.g.
         * {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
         * </p>
         *
         * @param theResource The resource to visit
         * @param theVisitor  The visitor
         */
        public void visit(IBaseResource theResource, IModelVisitor theVisitor) {
                BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
                visit(newMap(), theResource, theResource, null, null, def, theVisitor);
        }

        public Map<Object, Object> newMap() {
                return new IdentityHashMap<>();
        }

        /**
         * Visit all elements in a given resource or element
         * <p>
         * <b>THIS ALTERNATE METHOD IS STILL EXPERIMENTAL! USE WITH CAUTION</b>
         * </p>
         * <p>
         * Note on scope: This method will descend into any contained resources ({@link IResource#getContained()}) as well, but will not descend into linked resources (e.g.
         * {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
         * </p>
         *
         * @param theElement The element to visit
         * @param theVisitor The visitor
         */
        public void visit(IBase theElement, IModelVisitor2 theVisitor) {
                BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
                if (def instanceof BaseRuntimeElementCompositeDefinition) {
                        BaseRuntimeElementCompositeDefinition<?> defComposite = (BaseRuntimeElementCompositeDefinition<?>) def;
                        visit(theElement, null, def, theVisitor, new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
                } else if (theElement instanceof IBaseExtension) {
                        theVisitor.acceptUndeclaredExtension((IBaseExtension<?, ?>) theElement, Collections.emptyList(), Collections.emptyList(), Collections.emptyList());
                } else {
                        theVisitor.acceptElement(theElement, Collections.emptyList(), Collections.emptyList(), Collections.emptyList());
                }
        }

        private void visit(Map<Object, Object> theStack, IBaseResource theResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition,
                                                         BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
                List<String> pathToElement = addNameToList(thePathToElement, theChildDefinition);

                if (theStack.put(theElement, theElement) != null) {
                        return;
                }

                theCallback.acceptElement(theResource, theElement, pathToElement, theChildDefinition, theDefinition);

                BaseRuntimeElementDefinition<?> def = theDefinition;
                if (def.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST) {
                        def = myContext.getElementDefinition(theElement.getClass());
                }

                if (theElement instanceof IBaseReference) {
                        IBaseResource target = ((IBaseReference) theElement).getResource();
                        if (target != null) {
                                if (target.getIdElement().hasIdPart() == false || target.getIdElement().isLocal()) {
                                        RuntimeResourceDefinition targetDef = myContext.getResourceDefinition(target);
                                        visit(theStack, target, target, pathToElement, null, targetDef, theCallback);
                                }
                        }
                }

                switch (def.getChildType()) {
                        case ID_DATATYPE:
                        case PRIMITIVE_XHTML_HL7ORG:
                        case PRIMITIVE_XHTML:
                        case PRIMITIVE_DATATYPE:
                                // These are primitive types
                                break;
                        case RESOURCE:
                        case RESOURCE_BLOCK:
                        case COMPOSITE_DATATYPE: {
                                BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) def;
                                for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {

                                        List<?> values = nextChild.getAccessor().getValues(theElement);
                                        if (values != null) {
                                                for (Object nextValueObject : values) {
                                                        IBase nextValue;
                                                        try {
                                                                nextValue = (IBase) nextValueObject;
                                                        } catch (ClassCastException e) {
                                                                String s = "Found instance of " + nextValueObject.getClass() + " - Did you set a field value to the incorrect type? Expected " + IBase.class.getName();
                                                                throw new ClassCastException(s);
                                                        }
                                                        if (nextValue == null) {
                                                                continue;
                                                        }
                                                        if (nextValue.isEmpty()) {
                                                                continue;
                                                        }
                                                        BaseRuntimeElementDefinition<?> childElementDef;
                                                        childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());

                                                        if (childElementDef == null) {
                                                                childElementDef = myContext.getElementDefinition(nextValue.getClass());
                                                        }

                                                        if (nextChild instanceof RuntimeChildDirectResource) {
                                                                // Don't descend into embedded resources
                                                                theCallback.acceptElement(theResource, nextValue, null, nextChild, childElementDef);
                                                        } else {
                                                                visit(theStack, theResource, nextValue, pathToElement, nextChild, childElementDef, theCallback);
                                                        }
                                                }
                                        }
                                }
                                break;
                        }
                        case CONTAINED_RESOURCES: {
                                BaseContainedDt value = (BaseContainedDt) theElement;
                                for (IResource next : value.getContainedResources()) {
                                        def = myContext.getResourceDefinition(next);
                                        visit(theStack, next, next, pathToElement, null, def, theCallback);
                                }
                                break;
                        }
                        case CONTAINED_RESOURCE_LIST:
                        case EXTENSION_DECLARED:
                        case UNDECL_EXT: {
                                throw new IllegalStateException("state should not happen: " + def.getChildType());
                        }
                }

                theStack.remove(theElement);

        }

        /**
         * Returns all embedded resources that are found embedded within <code>theResource</code>.
         * An embedded resource is a resource that can be found as a direct child within a resource,
         * as opposed to being referenced by the resource.
         * <p>
         * Examples include resources found within <code>Bundle.entry.resource</code>
         * and <code>Parameters.parameter.resource</code>, as well as contained resources
         * found within <code>Resource.contained</code>
         * </p>
         *
         * @param theRecurse Should embedded resources be recursively scanned for further embedded
         *                   resources
         * @return A collection containing the embedded resources. Order is arbitrary.
         */
        public Collection<IBaseResource> getAllEmbeddedResources(IBaseResource theResource, boolean theRecurse) {
                Validate.notNull(theResource, "theResource must not be null");
                ArrayList<IBaseResource> retVal = new ArrayList<>();

                visit(theResource, new IModelVisitor2() {
                        @Override
                        public boolean acceptElement(IBase theElement, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
                                if (theElement == theResource) {
                                        return true;
                                }
                                if (theElement instanceof IBaseResource) {
                                        retVal.add((IBaseResource) theElement);
                                        return theRecurse;
                                }
                                return true;
                        }

                        @Override
                        public boolean acceptUndeclaredExtension(IBaseExtension<?, ?> theNextExt, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
                                return true;
                        }
                });

                return retVal;
        }

        /**
         * Clear all content on a resource
         */
        public void clear(IBaseResource theInput) {
                visit(theInput, new IModelVisitor2() {
                        @Override
                        public boolean acceptElement(IBase theElement, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
                                if (theElement instanceof IPrimitiveType) {
                                        ((IPrimitiveType) theElement).setValueAsString(null);
                                }
                                return true;
                        }

                        @Override
                        public boolean acceptUndeclaredExtension(IBaseExtension<?, ?> theNextExt, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
                                theNextExt.setUrl(null);
                                theNextExt.setValue(null);
                                return true;
                        }

                });
        }

        private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, EnumSet<OptionsEnum> theOptions) {
                List<IBaseReference> allReferences = getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
                for (IBaseReference next : allReferences) {
                        IBaseResource resource = next.getResource();
                        if (resource == null && next.getReferenceElement().isLocal()) {
                                if (theContained.hasExistingIdToContainedResource()) {
                                        IBaseResource potentialTarget = theContained.getExistingIdToContainedResource().remove(next.getReferenceElement().getValue());
                                        if (potentialTarget != null) {
                                                theContained.addContained(next.getReferenceElement(), potentialTarget);
                                                containResourcesForEncoding(theContained, potentialTarget, theOptions);
                                        }
                                }
                        }
                }

                for (IBaseReference next : allReferences) {
                        IBaseResource resource = next.getResource();
                        if (resource != null) {
                                if (resource.getIdElement().isEmpty() || resource.getIdElement().isLocal()) {
                                        if (theContained.getResourceId(resource) != null) {
                                                // Prevent infinite recursion if there are circular loops in the contained resources
                                                continue;
                                        }
                                        IIdType id = theContained.addContained(resource);
                                        if (theOptions.contains(OptionsEnum.MODIFY_RESOURCE)) {
                                                getContainedResourceList(theResource).add(resource);
                                                next.setReference(id.getValue());
                                        }
                                        if (resource.getIdElement().isLocal() && theContained.hasExistingIdToContainedResource()) {
                                                theContained.getExistingIdToContainedResource().remove(resource.getIdElement().getValue());
                                        }
                                } else {
                                        continue;
                                }

                        }

                }

        }

        /**
         * Iterate through the whole resource and identify any contained resources. Optionally this method
         * can also assign IDs and modify references where the resource link has been specified but not the
         * reference text.
         *
         * @since 5.4.0
         */
        public ContainedResources containResources(IBaseResource theResource, OptionsEnum... theOptions) {
                EnumSet<OptionsEnum> options = toOptionSet(theOptions);

                if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
                        Object cachedValue = theResource.getUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED);
                        if (cachedValue != null) {
                                return (ContainedResources) cachedValue;
                        }
                }

                ContainedResources contained = new ContainedResources();

                List<? extends IBaseResource> containedResources = getContainedResourceList(theResource);
                for (IBaseResource next : containedResources) {
                        String nextId = next.getIdElement().getValue();
                        if (StringUtils.isNotBlank(nextId)) {
                                if (!nextId.startsWith("#")) {
                                        nextId = '#' + nextId;
                                }
                                next.getIdElement().setValue(nextId);
                        }
                        contained.addContained(next);
                }

                containResourcesForEncoding(contained, theResource, options);

                if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
                        theResource.setUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED, contained);
                }

                return contained;
        }

        private EnumSet<OptionsEnum> toOptionSet(OptionsEnum[] theOptions) {
                EnumSet<OptionsEnum> options;
                if (theOptions == null || theOptions.length == 0) {
                        options = EMPTY_OPTION_SET;
                } else {
                        options = EnumSet.of(theOptions[0], theOptions);
                }
                return options;
        }

        @SuppressWarnings("unchecked")
        private <T extends IBaseResource> List<T> getContainedResourceList(T theResource) {
                List<T> containedResources = Collections.emptyList();
                if (theResource instanceof IResource) {
                        containedResources = (List<T>) ((IResource) theResource).getContained().getContainedResources();
                } else if (theResource instanceof IDomainResource) {
                        containedResources = (List<T>) ((IDomainResource) theResource).getContained();
                }
                return containedResources;
        }

        /**
         * Adds and returns a new element at the given path within the given structure. The paths used here
         * are <b>not FHIRPath expressions</b> but instead just simple dot-separated path expressions.
         * <p>
         * Only the last entry in the path is always created, existing repetitions of elements before
         * the final dot are returned if they exists (although they are created if they do not). For example,
         * given the path <code>Patient.name.given</code>, a new repetition of <code>given</code> is always
         * added to the first (index 0) repetition of the name. If an index-0 repetition of <code>name</code>
         * already exists, it is added to. If one does not exist, it if created and then added to.
         * </p>
         * <p>
         * If the last element in the path refers to a non-repeatable element that is already present and
         * is not empty, a {@link DataFormatException} error will be thrown.
         * </p>
         *
         * @param theTarget The element to add to. This will often be a {@link IBaseResource resource}
         *                  instance, but does not need to be.
         * @param thePath   The path.
         * @return The newly added element
         * @throws DataFormatException If the path is invalid or does not end with either a repeatable element, or
         *                             an element that is non-repeatable but not already populated.
         */
        @SuppressWarnings("unchecked")
        @Nonnull
        public <T extends IBase> T addElement(@Nonnull IBase theTarget, @Nonnull String thePath) {
                return (T) doAddElement(theTarget, thePath, 1).get(0);
        }

        @SuppressWarnings("unchecked")
        private <T extends IBase> List<T> doAddElement(IBase theTarget, String thePath, int theElementsToAdd) {
                if (theElementsToAdd == 0) {
                        return Collections.emptyList();
                }

                IBase target = theTarget;
                BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(target.getClass());
                List<String> parts = parsePath(def, thePath);

                for (int i = 0, partsSize = parts.size(); ; i++) {
                        String nextPart = parts.get(i);
                        boolean lastPart = i == partsSize - 1;

                        BaseRuntimeChildDefinition nextChild = def.getChildByName(nextPart);
                        if (nextChild == null) {
                                throw new DataFormatException("Invalid path " + thePath + ": Element of type " + def.getName() + " has no child named " + nextPart + ". Valid names: " + def.getChildrenAndExtension().stream().map(t -> t.getElementName()).sorted().collect(Collectors.joining(", ")));
                        }

                        List<IBase> childValues = nextChild.getAccessor().getValues(target);
                        IBase childValue;
                        if (childValues.size() > 0 && !lastPart) {
                                childValue = childValues.get(0);
                        } else {

                                if (lastPart) {
                                        if (!childValues.isEmpty()) {
                                                if (theElementsToAdd == -1) {
                                                        return (List<T>) Collections.singletonList(childValues.get(0));
                                                } else if (nextChild.getMax() == 1 && !childValues.get(0).isEmpty()) {
                                                        throw new DataFormatException("Element at path " + thePath + " is not repeatable and not empty");
                                                } else if (nextChild.getMax() == 1 && childValues.get(0).isEmpty()) {
                                                        return (List<T>) Collections.singletonList(childValues.get(0));
                                                }
                                        }
                                }

                                BaseRuntimeElementDefinition<?> elementDef = nextChild.getChildByName(nextPart);
                                childValue = elementDef.newInstance(nextChild.getInstanceConstructorArguments());
                                nextChild.getMutator().addValue(target, childValue);

                                if (lastPart) {
                                        if (theElementsToAdd == 1 || theElementsToAdd == -1) {
                                                return (List<T>) Collections.singletonList(childValue);
                                        } else {
                                                if (nextChild.getMax() == 1) {
                                                        throw new DataFormatException("Can not add multiple values at path " + thePath + ": Element does not repeat");
                                                }

                                                List<T> values = (List<T>) Lists.newArrayList(childValue);
                                                for (int j = 1; j < theElementsToAdd; j++) {
                                                        childValue = elementDef.newInstance(nextChild.getInstanceConstructorArguments());
                                                        nextChild.getMutator().addValue(target, childValue);
                                                        values.add((T) childValue);
                                                }

                                                return values;
                                        }
                                }

                        }

                        target = childValue;

                        if (!lastPart) {
                                BaseRuntimeElementDefinition<?> nextDef = myContext.getElementDefinition(target.getClass());
                                if (!(nextDef instanceof BaseRuntimeElementCompositeDefinition)) {
                                        throw new DataFormatException("Invalid path " + thePath + ": Element of type " + def.getName() + " has no child named " + nextPart + " (this is a primitive type)");
                                }
                                def = (BaseRuntimeElementCompositeDefinition<?>) nextDef;
                        }
                }

        }

        /**
         * Adds and returns a new element at the given path within the given structure. The paths used here
         * are <b>not FHIRPath expressions</b> but instead just simple dot-separated path expressions.
         * <p>
         * This method follows all of the same semantics as {@link #addElement(IBase, String)} but it
         * requires the path to point to an element with a primitive datatype and set the value of
         * the datatype to the given value.
         * </p>
         *
         * @param theTarget The element to add to. This will often be a {@link IBaseResource resource}
         *                  instance, but does not need to be.
         * @param thePath   The path.
         * @param theValue  The value to set, or <code>null</code>.
         * @return The newly added element
         * @throws DataFormatException If the path is invalid or does not end with either a repeatable element, or
         *                             an element that is non-repeatable but not already populated.
         */
        @SuppressWarnings("unchecked")
        @Nonnull
        public <T extends IBase> T addElement(@Nonnull IBase theTarget, @Nonnull String thePath, @Nullable String theValue) {
                T value = (T) doAddElement(theTarget, thePath, 1).get(0);
                if (!(value instanceof IPrimitiveType)) {
                        throw new DataFormatException("Element at path " + thePath + " is not a primitive datatype. Found: " + myContext.getElementDefinition(value.getClass()).getName());
                }

                ((IPrimitiveType<?>) value).setValueAsString(theValue);

                return value;
        }


        /**
         * Adds and returns a new element at the given path within the given structure. The paths used here
         * are <b>not FHIRPath expressions</b> but instead just simple dot-separated path expressions.
         * <p>
         * This method follows all of the same semantics as {@link #addElement(IBase, String)} but it
         * requires the path to point to an element with a primitive datatype and set the value of
         * the datatype to the given value.
         * </p>
         *
         * @param theTarget The element to add to. This will often be a {@link IBaseResource resource}
         *                  instance, but does not need to be.
         * @param thePath   The path.
         * @param theValue  The value to set, or <code>null</code>.
         * @return The newly added element
         * @throws DataFormatException If the path is invalid or does not end with either a repeatable element, or
         *                             an element that is non-repeatable but not already populated.
         */
        @SuppressWarnings("unchecked")
        @Nonnull
        public <T extends IBase> T setElement(@Nonnull IBase theTarget, @Nonnull String thePath, @Nullable String theValue) {
                T value = (T) doAddElement(theTarget, thePath, -1).get(0);
                if (!(value instanceof IPrimitiveType)) {
                        throw new DataFormatException("Element at path " + thePath + " is not a primitive datatype. Found: " + myContext.getElementDefinition(value.getClass()).getName());
                }

                ((IPrimitiveType<?>) value).setValueAsString(theValue);

                return value;
        }


        /**
         * This method has the same semantics as {@link #addElement(IBase, String, String)} but adds
         * a collection of primitives instead of a single one.
         *
         * @param theTarget The element to add to. This will often be a {@link IBaseResource resource}
         *                  instance, but does not need to be.
         * @param thePath   The path.
         * @param theValues The values to set, or <code>null</code>.
         */
        public void addElements(IBase theTarget, String thePath, Collection<String> theValues) {
                List<IBase> targets = doAddElement(theTarget, thePath, theValues.size());
                Iterator<String> valuesIter = theValues.iterator();
                for (IBase target : targets) {

                        if (!(target instanceof IPrimitiveType)) {
                                throw new DataFormatException("Element at path " + thePath + " is not a primitive datatype. Found: " + myContext.getElementDefinition(target.getClass()).getName());
                        }

                        ((IPrimitiveType<?>) target).setValueAsString(valuesIter.next());
                }

        }


        public enum OptionsEnum {

                /**
                 * Should we modify the resource in the case that contained resource IDs are assigned
                 * during a {@link #containResources(IBaseResource, OptionsEnum...)} pass.
                 */
                MODIFY_RESOURCE,

                /**
                 * Store the results of the operation in the resource metadata and reuse them if
                 * subsequent calls are made.
                 */
                STORE_AND_REUSE_RESULTS
        }

        public static class ContainedResources {
                private long myNextContainedId = 1;

                private List<IBaseResource> myResourceList;
                private IdentityHashMap<IBaseResource, IIdType> myResourceToIdMap;
                private Map<String, IBaseResource> myExistingIdToContainedResourceMap;

                public Map<String, IBaseResource> getExistingIdToContainedResource() {
                        if (myExistingIdToContainedResourceMap == null) {
                                myExistingIdToContainedResourceMap = new HashMap<>();
                        }
                        return myExistingIdToContainedResourceMap;
                }

                public IIdType addContained(IBaseResource theResource) {
                        IIdType existing = getResourceToIdMap().get(theResource);
                        if (existing != null) {
                                return existing;
                        }

                        IIdType newId = theResource.getIdElement();
                        if (isBlank(newId.getValue())) {
                                newId.setValue("#" + myNextContainedId++);
                        } else {
                                // Avoid auto-assigned contained IDs colliding with pre-existing ones
                                String idPart = newId.getValue();
                                if (substring(idPart, 0, 1).equals("#")) {
                                        idPart = idPart.substring(1);
                                        if (StringUtils.isNumeric(idPart)) {
                                                myNextContainedId = Long.parseLong(idPart) + 1;
                                        }
                                }
                        }

                        getResourceToIdMap().put(theResource, newId);
                        getOrCreateResourceList().add(theResource);
                        return newId;
                }

                public void addContained(IIdType theId, IBaseResource theResource) {
                        if (!getResourceToIdMap().containsKey(theResource)) {
                                getResourceToIdMap().put(theResource, theId);
                                getOrCreateResourceList().add(theResource);
                        }
                }

                public List<IBaseResource> getContainedResources() {
                        if (getResourceToIdMap() == null) {
                                return Collections.emptyList();
                        }
                        return getOrCreateResourceList();
                }

                public IIdType getResourceId(IBaseResource theNext) {
                        if (getResourceToIdMap() == null) {
                                return null;
                        }
                        return getResourceToIdMap().get(theNext);
                }

                private List<IBaseResource> getOrCreateResourceList() {
                        if (myResourceList == null) {
                                myResourceList = new ArrayList<>();
                        }
                        return myResourceList;
                }

                private IdentityHashMap<IBaseResource, IIdType> getResourceToIdMap() {
                        if (myResourceToIdMap == null) {
                                myResourceToIdMap = new IdentityHashMap<>();
                        }
                        return myResourceToIdMap;
                }

                public boolean isEmpty() {
                        if (myResourceToIdMap == null) {
                                return true;
                        }
                        return myResourceToIdMap.isEmpty();
                }

                public boolean hasExistingIdToContainedResource() {
                        return myExistingIdToContainedResourceMap != null;
                }

                public void assignIdsToContainedResources() {

                        if (!getContainedResources().isEmpty()) {

                                /*
                                 * The idea with the code block below:
                                 *
                                 * We want to preserve any IDs that were user-assigned, so that if it's really
                                 * important to someone that their contained resource have the ID of #FOO
                                 * or #1 we will keep that.
                                 *
                                 * For any contained resources where no ID was assigned by the user, we
                                 * want to manually create an ID but make sure we don't reuse an existing ID.
                                 */

                                Set<String> ids = new HashSet<>();

                                // Gather any user assigned IDs
                                for (IBaseResource nextResource : getContainedResources()) {
                                        if (getResourceToIdMap().get(nextResource) != null) {
                                                ids.add(getResourceToIdMap().get(nextResource).getValue());
                                        }
                                }

                                // Automatically assign IDs to the rest
                                for (IBaseResource nextResource : getContainedResources()) {

                                        while (getResourceToIdMap().get(nextResource) == null) {
                                                String nextCandidate = "#" + myNextContainedId;
                                                myNextContainedId++;
                                                if (!ids.add(nextCandidate)) {
                                                        continue;
                                                }

                                                getResourceToIdMap().put(nextResource, new IdDt(nextCandidate));
                                        }

                                }

                        }

                }
        }

}