package ca.uhn.fhir.util;

import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
import ca.uhn.fhir.model.api.ExtensionDt;
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.StringDt;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.*;

import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import static org.apache.commons.lang3.StringUtils.*;

/*
 * #%L
 * HAPI FHIR - Core Library
 * %%
 * Copyright (C) 2014 - 2019 University Health Network
 * %%
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * #L%
 */

public class FhirTerser {

        private static final Pattern COMPARTMENT_MATCHER_PATH = Pattern.compile("([a-zA-Z.]+)\\.where\\(resolve\\(\\) is ([a-zA-Z]+)\\)");
        private 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");

                if (theSource instanceof IPrimitiveType<?>) {
                        if (theTarget instanceof IPrimitiveType<?>) {
                                ((IPrimitiveType<?>) theTarget).setValueAsString(((IPrimitiveType<?>) theSource).getValueAsString());
                                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());
                                IBase 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(new IdentityHashMap<>(), 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(new IdentityHashMap<>(), 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<Object> wantedType = Object.class;

                return getSingleValueOrNull(theTarget, thePath, wantedType);
        }

        public <T> 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);
        }

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

        @SuppressWarnings("unchecked")
        private <T> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, Object 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((Class<? extends IBase>) 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((Class<? extends IBase>) 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) {
                        IBase value = nextDef.getChildByName(name).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 theResource The resource instance to be accessed. Must not be null.
         * @param thePath     The path for the element to be accessed.
         * @return A list of values of type {@link Object}.
         */
        public List<Object> getValues(IBaseResource theResource, String thePath) {
                Class<Object> wantedClass = Object.class;

                return getValues(theResource, thePath, wantedClass);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type {@link Object}.
         *
         * @param theResource The resource instance 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<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate) {
                Class<Object> wantedClass = Object.class;

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

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type {@link Object}.
         *
         * @param theResource     The resource instance 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<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate, boolean theAddExtension) {
                Class<Object> wantedClass = Object.class;

                return getValues(theResource, 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 theResource    The resource instance 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> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass) {
                RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theResource, parts, theWantedClass);
        }

        /**
         * Returns values stored in an element identified by its path. The list of values is of
         * type <code>theWantedClass</code>.
         *
         * @param theResource    The resource instance 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> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate) {
                RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theResource, 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 theResource     The resource instance 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> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
                RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
                List<String> parts = parsePath(def, thePath);
                return getValues(def, theResource, 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 (theElementDef instanceof RuntimeResourceDefinition) {
                        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.getResourceDefinition(nextTarget).getName();
                                                        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;
                                                                childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());

                                                                if (childElementDef == null) {
                                                                        StringBuilder b = new StringBuilder();
                                                                        b.append("Found value of type[");
                                                                        b.append(nextValue.getClass().getSimpleName());
                                                                        b.append("] which is not valid for field[");
                                                                        b.append(nextChild.getElementName());
                                                                        b.append("] in ");
                                                                        b.append(childDef.getName());
                                                                        b.append(" - Valid types: ");
                                                                        for (Iterator<String> iter = new TreeSet<>(nextChild.getValidChildNames()).iterator(); iter.hasNext(); ) {
                                                                                BaseRuntimeElementDefinition<?> childByName = nextChild.getChildByName(iter.next());
                                                                                b.append(childByName.getImplementingClass().getSimpleName());
                                                                                if (iter.hasNext()) {
                                                                                        b.append(", ");
                                                                                }
                                                                        }
                                                                        throw new DataFormatException(b.toString());
                                                                }

                                                                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(new IdentityHashMap<>(), theResource, theResource, null, null, def, theVisitor);
        }

        /**
         * Visit all elements in a given resource
         * <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 theResource The resource to visit
         * @param theVisitor  The visitor
         */
        public void visit(IBaseResource theResource, IModelVisitor2 theVisitor) {
                BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
                visit(theResource, null, def, theVisitor, new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
        }

        private void visit(IdentityHashMap<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;
                        }

                });
        }
}