/*-
 * #%L
 * HAPI FHIR Storage api
 * %%
 * Copyright (C) 2014 - 2025 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%
 */
package ca.uhn.fhir.jpa.patch;

import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.util.FhirPathUtils;
import ca.uhn.fhir.parser.path.EncodeContextPath;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.IModelVisitor2;
import ca.uhn.fhir.util.ParametersUtil;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
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.IBaseEnumeration;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.Stack;
import java.util.concurrent.atomic.AtomicReference;
import java.util.function.Predicate;

import static java.util.Objects.isNull;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

/**
 * FhirPatch handler.
 * Patch is defined by the spec: https://www.hl7.org/fhir/R4/fhirpatch.html
 */
public class FhirPatch {
        org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirPatch.class);

        public static final String OPERATION_ADD = "add";
        public static final String OPERATION_DELETE = "delete";
        public static final String OPERATION_INSERT = "insert";
        public static final String OPERATION_MOVE = "move";
        public static final String OPERATION_REPLACE = "replace";
        public static final String PARAMETER_DESTINATION = "destination";
        public static final String PARAMETER_INDEX = "index";
        public static final String PARAMETER_NAME = "name";
        public static final String PARAMETER_OPERATION = "operation";
        public static final String PARAMETER_PATH = "path";
        public static final String PARAMETER_SOURCE = "source";
        public static final String PARAMETER_TYPE = "type";
        public static final String PARAMETER_VALUE = "value";

        private final FhirContext myContext;
        private boolean myIncludePreviousValueInDiff;
        private Set<EncodeContextPath> myIgnorePaths = Collections.emptySet();

        public FhirPatch(FhirContext theContext) {
                myContext = theContext;
        }

        /**
         * Adds a path element that will not be included in generated diffs. Values can take the form
         * <code>ResourceName.fieldName.fieldName</code> and wildcards are supported, such
         * as <code>*.meta</code>.
         */
        public void addIgnorePath(String theIgnorePath) {
                Validate.notBlank(theIgnorePath, "theIgnorePath must not be null or empty");

                if (myIgnorePaths.isEmpty()) {
                        myIgnorePaths = new HashSet<>();
                }
                myIgnorePaths.add(new EncodeContextPath(theIgnorePath));
        }

        public void setIncludePreviousValueInDiff(boolean theIncludePreviousValueInDiff) {
                myIncludePreviousValueInDiff = theIncludePreviousValueInDiff;
        }

        public void apply(IBaseResource theResource, IBaseResource thePatch) {

                List<IBase> opParameters = ParametersUtil.getNamedParameters(myContext, thePatch, PARAMETER_OPERATION);
                for (IBase nextOperation : opParameters) {
                        String type = ParametersUtil.getParameterPartValueAsString(myContext, nextOperation, PARAMETER_TYPE);
                        type = defaultString(type);

                        if (OPERATION_DELETE.equals(type)) {
                                handleDeleteOperation(theResource, nextOperation);
                        } else if (OPERATION_ADD.equals(type)) {
                                handleAddOperation(theResource, nextOperation);
                        } else if (OPERATION_REPLACE.equals(type)) {
                                handleReplaceOperation(theResource, nextOperation);
                        } else if (OPERATION_INSERT.equals(type)) {
                                handleInsertOperation(theResource, nextOperation);
                        } else if (OPERATION_MOVE.equals(type)) {
                                handleMoveOperation(theResource, nextOperation);
                        } else {
                                throw new InvalidRequestException(Msg.code(1267) + "Unknown patch operation type: " + type);
                        }
                }
        }

        private void handleAddOperation(IBaseResource theResource, IBase theParameters) {

                String path = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_PATH);
                String elementName = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_NAME);

                String containingPath = defaultString(path);

                List<IBase> containingElements = myContext.newFhirPath().evaluate(theResource, containingPath, IBase.class);
                for (IBase nextElement : containingElements) {
                        ChildDefinition childDefinition = findChildDefinition(nextElement, elementName);

                        IBase newValue = getNewValue(theParameters, childDefinition);

                        childDefinition.getUseableChildDef().getMutator().addValue(nextElement, newValue);
                }
        }

        private void handleInsertOperation(IBaseResource theResource, IBase theParameters) {

                String path = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_PATH);
                path = defaultString(path);

                int lastDot = path.lastIndexOf(".");
                String containingPath = path.substring(0, lastDot);
                String elementName = path.substring(lastDot + 1);
                Integer insertIndex = ParametersUtil.getParameterPartValueAsInteger(myContext, theParameters, PARAMETER_INDEX)
                                .orElseThrow(() -> new InvalidRequestException("No index supplied for insert operation"));

                List<IBase> containingElements = myContext.newFhirPath().evaluate(theResource, containingPath, IBase.class);
                for (IBase nextElement : containingElements) {

                        ChildDefinition childDefinition = findChildDefinition(nextElement, elementName);

                        IBase newValue = getNewValue(theParameters, childDefinition);

                        List<IBase> existingValues = new ArrayList<>(
                                        childDefinition.getUseableChildDef().getAccessor().getValues(nextElement));
                        if (insertIndex == null || insertIndex < 0 || insertIndex > existingValues.size()) {
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(FhirPatch.class, "invalidInsertIndex", insertIndex, path, existingValues.size());
                                throw new InvalidRequestException(Msg.code(1270) + msg);
                        }
                        existingValues.add(insertIndex, newValue);

                        childDefinition.getUseableChildDef().getMutator().setValue(nextElement, null);
                        for (IBase nextNewValue : existingValues) {
                                childDefinition.getUseableChildDef().getMutator().addValue(nextElement, nextNewValue);
                        }
                }
        }

        private void handleDeleteOperation(IBaseResource theResource, IBase theParameters) {
                String path = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_PATH);
                path = defaultString(path);

                ParsedPath parsedPath = ParsedPath.parse(path);
                List<IBase> containingElements = myContext
                                .newFhirPath()
                                .evaluate(
                                                theResource,
                                                parsedPath.getEndsWithAFilterOrIndex() ? parsedPath.getContainingPath() : path,
                                                IBase.class);

                for (IBase nextElement : containingElements) {
                        if (parsedPath.getEndsWithAFilterOrIndex()) {
                                // if the path ends with a filter or index, we must be dealing with a list
                                deleteFromList(theResource, nextElement, parsedPath.getLastElementName(), path);
                        } else {
                                deleteSingleElement(nextElement);
                        }
                }
        }

        private void deleteFromList(
                        IBaseResource theResource,
                        IBase theContainingElement,
                        String theListElementName,
                        String theElementToDeletePath) {
                ChildDefinition childDefinition = findChildDefinition(theContainingElement, theListElementName);

                List<IBase> existingValues = new ArrayList<>(
                                childDefinition.getUseableChildDef().getAccessor().getValues(theContainingElement));
                List<IBase> elementsToRemove =
                                myContext.newFhirPath().evaluate(theResource, theElementToDeletePath, IBase.class);
                existingValues.removeAll(elementsToRemove);

                childDefinition.getUseableChildDef().getMutator().setValue(theContainingElement, null);
                for (IBase nextNewValue : existingValues) {
                        childDefinition.getUseableChildDef().getMutator().addValue(theContainingElement, nextNewValue);
                }
        }

        private void handleReplaceOperation(IBaseResource theResource, IBase theParameters) {
                String path = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_PATH);
                path = defaultString(path);

                ParsedFhirPath parsedFhirPath = ParsedFhirPath.parse(path);
                IFhirPath fhirPath = myContext.newFhirPath();

                FhirPathChildDefinition parentDef = new FhirPathChildDefinition();

                List<ParsedFhirPath.FhirPathNode> pathNodes = new ArrayList<>();
                parsedFhirPath.getAllNodesWithPred(pathNodes, ParsedFhirPath.FhirPathNode::isNormalPathNode);
                List<String> parts = new ArrayList<>();
                for (ParsedFhirPath.FhirPathNode node : pathNodes) {
                        parts.add(node.getValue());
                }

                // fetch all runtime definitions along fhirpath
                FhirPathChildDefinition cd = childDefinition(parentDef, parts, theResource, fhirPath, parsedFhirPath, path);

                // replace the value
                replaceValuesByPath(cd, theParameters, fhirPath, parsedFhirPath);
        }

        private void replaceValuesByPath(
                        FhirPathChildDefinition theChildDefinition,
                        IBase theParameters,
                        IFhirPath theFhirPath,
                        ParsedFhirPath theParsedFhirPath) {
                Optional<IBase> singleValuePart =
                                ParametersUtil.getParameterPartValue(myContext, theParameters, PARAMETER_VALUE);
                if (singleValuePart.isPresent()) {
                        IBase replacementValue = singleValuePart.get();

                        FhirPathChildDefinition childDefinitionToUse =
                                        findChildDefinitionByReplacementType(theChildDefinition, replacementValue);

                        // only a single replacement value (ie, not a replacement CompositeValue or anything)
                        replaceSingleValue(theFhirPath, theParsedFhirPath, childDefinitionToUse, replacementValue);
                        return; // guard
                }

                Optional<IBase> valueParts = ParametersUtil.getParameterPart(myContext, theParameters, PARAMETER_VALUE);
                if (valueParts.isPresent()) {
                        // multiple replacement values provided via parts
                        List<IBase> partParts = valueParts.map(this::extractPartsFromPart).orElse(Collections.emptyList());

                        for (IBase nextValuePartPart : partParts) {
                                String name = myContext
                                                .newTerser()
                                                .getSingleValue(nextValuePartPart, PARAMETER_NAME, IPrimitiveType.class)
                                                .map(IPrimitiveType::getValueAsString)
                                                .orElse(null);

                                if (StringUtils.isBlank(name)) {
                                        continue;
                                }

                                Optional<IBase> optionalValue =
                                                myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);
                                if (optionalValue.isPresent()) {
                                        FhirPathChildDefinition childDefinitionToUse =
                                                        findChildDefinitionAtEndOfPath(theChildDefinition, nextValuePartPart);

                                        BaseRuntimeChildDefinition subChild =
                                                        childDefinitionToUse.getElementDefinition().getChildByName(name);

                                        subChild.getMutator().setValue(childDefinitionToUse.getBase(), optionalValue.get());
                                }
                        }

                        return; // guard
                }

                // fall through to error state
                throw new InvalidRequestException(Msg.code(2720) + " No valid replacement value for patch operation.");
        }

        private FhirPathChildDefinition findChildDefinitionByReplacementType(
                        FhirPathChildDefinition theChildDefinition, IBase replacementValue) {
                boolean isPrimitive = replacementValue instanceof IPrimitiveType<?>;
                Predicate<FhirPathChildDefinition> predicate = def -> {
                        if (isPrimitive) {
                                // primitives will be at the very bottom (ie, no children underneath)
                                return def.getBase() instanceof IPrimitiveType<?>;
                        } else if (def.getBase().fhirType().equalsIgnoreCase(replacementValue.fhirType())) {
                                return true;
                        }
                        return false;
                };

                return findChildDefinition(theChildDefinition, predicate);
        }

        private FhirPathChildDefinition findChildDefinitionAtEndOfPath(
                        FhirPathChildDefinition theChildDefinition, IBase replacementValue) {
                return findChildDefinition(theChildDefinition, childDefinition -> {
                        return childDefinition.getChild() == null;
                });
        }

        private FhirPathChildDefinition findChildDefinition(
                        FhirPathChildDefinition theChildDefinition, Predicate<FhirPathChildDefinition> thePredicate) {
                FhirPathChildDefinition childDefinitionToUse = theChildDefinition;
                while (childDefinitionToUse != null) {
                        if (thePredicate.test(childDefinitionToUse)) {
                                return childDefinitionToUse;
                        }
                        childDefinitionToUse = childDefinitionToUse.getChild();
                }

                throw new InvalidRequestException(Msg.code(2719) + " No runtime definition found for patch operation.");
        }

        private void replaceSingleValue(
                        IFhirPath theFhirPath,
                        ParsedFhirPath theParsedFhirPath,
                        FhirPathChildDefinition theTargetChildDefinition,
                        IBase theReplacementValue) {
                if (theTargetChildDefinition.getElementDefinition().getChildType()
                                == BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE) {
                        if (theTargetChildDefinition.getBase() instanceof IPrimitiveType<?> target
                                        && theReplacementValue instanceof IPrimitiveType<?> source) {
                                if (target.fhirType().equalsIgnoreCase(source.fhirType())) {
                                        if (theTargetChildDefinition
                                                                        .getParent()
                                                                        .getBase()
                                                                        .fhirType()
                                                                        .equalsIgnoreCase("narrative")
                                                        && theTargetChildDefinition.getFhirPath().equalsIgnoreCase("div")) {
                                                /*
                                                 * Special case handling for Narrative elements
                                                 * because xhtml is a primitive type, but it's fhirtype is recorded as "string"
                                                 * (which means we cannot actually assign it as a primitive type).
                                                 *
                                                 * Instead, we have to get the parent's type and set it's child as a new
                                                 * XHTML child.
                                                 */
                                                FhirPathChildDefinition narrativeDefinition = theTargetChildDefinition.getParent();
                                                BaseRuntimeElementDefinition<?> narrativeElement = narrativeDefinition.getElementDefinition();

                                                BaseRuntimeElementDefinition<?> newXhtmlEl = myContext.getElementDefinition("xhtml");

                                                IPrimitiveType<?> xhtmlType;
                                                if (theTargetChildDefinition.getBaseRuntimeDefinition().getInstanceConstructorArguments()
                                                                != null) {
                                                        xhtmlType = (IPrimitiveType<?>) newXhtmlEl.newInstance(theTargetChildDefinition
                                                                        .getBaseRuntimeDefinition()
                                                                        .getInstanceConstructorArguments());
                                                } else {
                                                        xhtmlType = (IPrimitiveType<?>) newXhtmlEl.newInstance();
                                                }

                                                xhtmlType.setValueAsString(source.getValueAsString());
                                                narrativeElement
                                                                .getChildByName(theTargetChildDefinition.getFhirPath())
                                                                .getMutator()
                                                                .setValue(narrativeDefinition.getBase(), xhtmlType);
                                        } else {
                                                target.setValueAsString(source.getValueAsString());
                                        }
                                } else if (theTargetChildDefinition.getChild() != null) {
                                        // there's subchildren (possibly we're setting an 'extension' value
                                        FhirPathChildDefinition ct =
                                                        findChildDefinitionAtEndOfPath(theTargetChildDefinition, theReplacementValue);
                                        replaceSingleValue(theFhirPath, theParsedFhirPath, ct, theReplacementValue);
                                } else {
                                        if (theTargetChildDefinition.getBaseRuntimeDefinition() != null
                                                        && !theTargetChildDefinition
                                                                        .getBaseRuntimeDefinition()
                                                                        .isMultipleCardinality()) {
                                                // basic primitive type assignment
                                                target.setValueAsString(source.getValueAsString());
                                                return;
                                        }

                                        // the primitive can have multiple value types
                                        BaseRuntimeElementDefinition<?> parentEl =
                                                        theTargetChildDefinition.getParent().getElementDefinition();
                                        String childFhirPath = theTargetChildDefinition.getFhirPath();

                                        BaseRuntimeChildDefinition choiceTarget = parentEl.getChildByName(childFhirPath);
                                        if (choiceTarget == null) {
                                                // possibly a choice type
                                                choiceTarget = parentEl.getChildByName(childFhirPath + "[x]");
                                        }
                                        choiceTarget
                                                        .getMutator()
                                                        .setValue(theTargetChildDefinition.getParent().getBase(), theReplacementValue);
                                }
                        }
                        return;
                }

                IBase containingElement = theTargetChildDefinition.getParent().getBase();
                BaseRuntimeChildDefinition runtimeDef = theTargetChildDefinition.getBaseRuntimeDefinition();
                if (runtimeDef == null) {
                        runtimeDef = theTargetChildDefinition.getParent().getBaseRuntimeDefinition();
                }

                if (runtimeDef.isMultipleCardinality()) {
                        // a list
                        List<IBase> existing = new ArrayList<>(runtimeDef.getAccessor().getValues(containingElement));
                        if (existing.isEmpty()) {
                                // no elements to replace - we shouldn't see this here though
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(FhirPatch.class, "noMatchingElementForPath", theParsedFhirPath.getRawPath());
                                throw new InvalidRequestException(Msg.code(2617) + msg);
                        }

                        List<IBase> replaceables;
                        if (FhirPathUtils.isSubsettingNode(theParsedFhirPath.getTail())) {
                                replaceables = applySubsettingFilter(theParsedFhirPath, theParsedFhirPath.getTail(), existing);
                        } else if (existing.size() == 1) {
                                replaceables = existing;
                        } else {
                                String raw = theParsedFhirPath.getRawPath();
                                String finalNode = theParsedFhirPath.getLastElementName();
                                String subpath = raw.substring(raw.indexOf(finalNode));
                                if (subpath.startsWith(finalNode) && subpath.length() > finalNode.length()) {
                                        subpath = subpath.substring(finalNode.length() + 1); // + 1 for the "."
                                }

                                AtomicReference<String> subpathRef = new AtomicReference<>();
                                subpathRef.set(subpath);
                                replaceables = existing.stream()
                                                .filter(item -> {
                                                        Optional<IBase> matched = theFhirPath.evaluateFirst(item, subpathRef.get(), IBase.class);
                                                        return matched.isPresent();
                                                })
                                                .toList();
                        }

                        if (replaceables.size() != 1) {
                                throw new InvalidRequestException(
                                                Msg.code(2715) + " Expected to find a single element, but provided FhirPath returned "
                                                                + replaceables.size() + " elements.");
                        }
                        IBase valueToReplace = replaceables.get(0);

                        BaseRuntimeChildDefinition.IMutator listMutator = runtimeDef.getMutator();
                        // clear the whole list first, then reconstruct it in the loop below replacing the values that need to be
                        // replaced
                        listMutator.setValue(containingElement, null);
                        for (IBase existingValue : existing) {
                                if (valueToReplace.equals(existingValue)) {
                                        listMutator.addValue(containingElement, theReplacementValue);
                                } else {
                                        listMutator.addValue(containingElement, existingValue);
                                }
                        }
                } else {
                        // a single element
                        runtimeDef.getMutator().setValue(containingElement, theReplacementValue);
                }
        }

        private List<IBase> applySubsettingFilter(
                        ParsedFhirPath theParsed, ParsedFhirPath.FhirPathNode tail, List<IBase> filtered) {
                if (tail.getListIndex() >= 0) {
                        // specific index
                        if (tail.getListIndex() < filtered.size()) {
                                return List.of(filtered.get(tail.getListIndex()));
                        } else {
                                ourLog.info("Nothing matching index {}; nothing patched.", tail.getListIndex());
                                return List.of();
                        }
                } else {
                        if (filtered.isEmpty()) {
                                // empty lists should match all filters, so we'll return it here
                                ourLog.info("List contains no elements; no patching will occur");
                                return List.of();
                        }

                        switch (tail.getValue()) {
                                case "first" -> {
                                        return List.of(filtered.get(0));
                                }
                                case "last" -> {
                                        return List.of(filtered.get(filtered.size() - 1));
                                }
                                case "tail" -> {
                                        if (filtered.size() == 1) {
                                                ourLog.info("List contains only a single element - no patching will occur");
                                                return List.of();
                                        }
                                        return filtered.subList(1, filtered.size());
                                }
                                case "single" -> {
                                        if (filtered.size() != 1) {
                                                throw new InvalidRequestException(
                                                                Msg.code(2710) + " List contains more than a single element.");
                                        }
                                        // only one element
                                        return filtered;
                                }
                                case "skip", "take" -> {
                                        if (tail instanceof ParsedFhirPath.FhirPathFunction fn) {
                                                String containedNum = fn.getContainedExp().getHead().getValue();
                                                try {
                                                        int num = Integer.parseInt(containedNum);

                                                        if (tail.getValue().equals("skip")) {
                                                                if (num < filtered.size()) {
                                                                        return filtered.subList(num, filtered.size());
                                                                }
                                                        } else if (tail.getValue().equals("take")) {
                                                                if (num < filtered.size()) {
                                                                        return filtered.subList(0, num);
                                                                } else {
                                                                        // otherwise, return everything
                                                                        return filtered;
                                                                }
                                                        }

                                                        return List.of();
                                                } catch (NumberFormatException ex) {
                                                        ourLog.error("{} is not a number", containedNum, ex);
                                                }
                                        }
                                        throw new InvalidRequestException(
                                                        Msg.code(2712) + " Invalid fhir path element encountered: " + theParsed.getRawPath());
                                }
                                default -> {
                                        // we shouldn't see this; it means we have not handled a filtering case
                                        throw new InvalidRequestException(
                                                        Msg.code(2711) + " Unrecognized filter of type " + tail.getValue());
                                }
                        }
                }
        }

        private void throwNoElementsError(String theFullReplacePath) {
                String msg =
                                myContext.getLocalizer().getMessage(FhirPatch.class, "noMatchingElementForPath", theFullReplacePath);
                throw new InvalidRequestException(Msg.code(2617) + msg);
        }

        private void handleMoveOperation(IBaseResource theResource, IBase theParameters) {
                String path = ParametersUtil.getParameterPartValueAsString(myContext, theParameters, PARAMETER_PATH);
                path = defaultString(path);

                int lastDot = path.lastIndexOf(".");
                String containingPath = path.substring(0, lastDot);
                String elementName = path.substring(lastDot + 1);
                Integer insertIndex = ParametersUtil.getParameterPartValueAsInteger(
                                                myContext, theParameters, PARAMETER_DESTINATION)
                                .orElseThrow(() -> new InvalidRequestException("No index supplied for move operation"));
                Integer removeIndex = ParametersUtil.getParameterPartValueAsInteger(myContext, theParameters, PARAMETER_SOURCE)
                                .orElseThrow(() -> new InvalidRequestException("No index supplied for move operation"));

                List<IBase> containingElements = myContext.newFhirPath().evaluate(theResource, containingPath, IBase.class);
                for (IBase nextElement : containingElements) {

                        ChildDefinition childDefinition = findChildDefinition(nextElement, elementName);

                        List<IBase> existingValues = new ArrayList<>(
                                        childDefinition.getUseableChildDef().getAccessor().getValues(nextElement));
                        if (removeIndex == null || removeIndex < 0 || removeIndex >= existingValues.size()) {
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(
                                                                FhirPatch.class, "invalidMoveSourceIndex", removeIndex, path, existingValues.size());
                                throw new InvalidRequestException(Msg.code(1268) + msg);
                        }
                        IBase newValue = existingValues.remove(removeIndex.intValue());

                        if (insertIndex == null || insertIndex < 0 || insertIndex > existingValues.size()) {
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(
                                                                FhirPatch.class,
                                                                "invalidMoveDestinationIndex",
                                                                insertIndex,
                                                                path,
                                                                existingValues.size());
                                throw new InvalidRequestException(Msg.code(1269) + msg);
                        }
                        existingValues.add(insertIndex, newValue);

                        childDefinition.getUseableChildDef().getMutator().setValue(nextElement, null);
                        for (IBase nextNewValue : existingValues) {
                                childDefinition.getUseableChildDef().getMutator().addValue(nextElement, nextNewValue);
                        }
                }
        }

        private FhirPathChildDefinition childDefinition(
                        FhirPathChildDefinition theParent,
                        List<String> theFhirPathParts,
                        IBase theBase,
                        IFhirPath theFhirPath,
                        ParsedFhirPath theParsedFhirPath,
                        String theOriginalPath) {
                FhirPathChildDefinition definition = new FhirPathChildDefinition();
                definition.setBase(theBase); // set this IBase value
                BaseRuntimeElementDefinition<?> parentElementDefinition = myContext.getElementDefinition(theBase.getClass());
                definition.setElementDefinition(parentElementDefinition); // set this element

                String head = theParsedFhirPath.getHead().getValue();
                definition.setFhirPath(head);

                if (theParent.getElementDefinition() != null) {
                        definition.setBaseRuntimeDefinition(theParent.getElementDefinition().getChildByName(head));
                }

                String rawPath = theParsedFhirPath.getRawPath();

                if (rawPath.equalsIgnoreCase(head)) {
                        // we're at the bottom
                        // return
                        return definition;
                }

                // detach the head
                String headVal = theFhirPathParts.remove(0);
                String pathBeneathParent = rawPath.substring(headVal.length());
                pathBeneathParent = FhirPathUtils.cleansePath(pathBeneathParent);

                if (isNotBlank(pathBeneathParent) && !theFhirPathParts.isEmpty()) {
                        Stack<ParsedFhirPath.FhirPathNode> filteringNodes = new Stack<>();

                        String childFilteringPath = pathBeneathParent;
                        String nextPath = pathBeneathParent;

                        if (FhirPathUtils.isSubsettingNode(theParsedFhirPath.getTail())) {
                                // the final node in this path is .first() or [0]... etc
                                ParsedFhirPath.FhirPathNode filteringNode = theParsedFhirPath.getTail();
                                filteringNodes.push(filteringNode);
                                /*
                                 * the field filtering path will be the path - tail value.
                                 * This will also be nextPath (the one we recurse on)
                                 */
                                int endInd = pathBeneathParent.indexOf(filteringNode.getValue());
                                if (endInd == -1) {
                                        endInd = pathBeneathParent.length();
                                }
                                childFilteringPath = pathBeneathParent.substring(0, endInd);
                                childFilteringPath = FhirPathUtils.cleansePath(childFilteringPath);
                                nextPath = childFilteringPath;
                        }

                        String directChildName = theFhirPathParts.get(0);

                        ParsedFhirPath newPath = ParsedFhirPath.parse(nextPath);

                        if (newPath.getHead() instanceof ParsedFhirPath.FhirPathFunction fn && fn.hasContainedExp()) {
                                newPath = fn.getContainedExp();

                                childFilteringPath = newPath.getRawPath();
                        }

                        // get all direct children
                        ParsedFhirPath.FhirPathNode newHead = newPath.getHead();
                        List<IBase> allChildren = theFhirPath.evaluate(theBase, directChildName, IBase.class);

                        // go through the children and take only the ones that match the path we have
                        String filterPath = childFilteringPath;

                        List<IBase> childs;
                        if (filterPath.startsWith(newHead.getValue()) && !filterPath.equalsIgnoreCase(newHead.getValue())) {
                                filterPath = filterPath.substring(newHead.getValue().length());
                                filterPath = FhirPathUtils.cleansePath(filterPath);

                                if (newPath.getHead().getNext() != null
                                                && FhirPathUtils.isSubsettingNode(newPath.getHead().getNext())) {
                                        // yet another filter node
                                        ParsedFhirPath.FhirPathNode filterNode = newPath.getHead().getNext();
                                        filteringNodes.push(filterNode);

                                        String newRaw = newPath.getRawPath();
                                        String updated = "";
                                        if (filterNode.hasNext()) {
                                                updated = newRaw.substring(
                                                                newRaw.indexOf(filterNode.getNext().getValue()));
                                                updated = FhirPathUtils.cleansePath(updated);
                                        }
                                        filterPath = updated;
                                        updated = newPath.getHead().getValue() + "." + updated;
                                        newPath = ParsedFhirPath.parse(updated);
                                }
                        }

                        if (isNotBlank(filterPath)) {
                                if (theFhirPathParts.contains(filterPath)) {
                                        /*
                                         * We're filtering on just a fhirpath node for some reason (ie, "identifier" or "reference" or "string").
                                         *
                                         * We don't need to apply the filter;
                                         * all children should be the same as this filtered type
                                         * (likely we have a subsetting filter to apply)
                                         */
                                        childs = allChildren;
                                } else {
                                        AtomicReference<String> ref = new AtomicReference<>();
                                        ref.set(filterPath);
                                        if (allChildren.size() > 1) {
                                                childs = allChildren.stream()
                                                                .filter(el -> {
                                                                        Optional<IBase> match = theFhirPath.evaluateFirst(el, ref.get(), IBase.class);
                                                                        return match.isPresent();
                                                                })
                                                                .toList();
                                        } else {
                                                // there is only 1 child (probably a top level element)
                                                // we still filter own because child elements can have different child types (that might match
                                                // multiple childs)
                                                // eg: everything has "extension" on it
                                                childs = allChildren.stream()
                                                                .filter(el -> {
                                                                        Optional<IBase> match = theFhirPath.evaluateFirst(el, ref.get(), IBase.class);
                                                                        return match.isPresent();
                                                                })
                                                                .findFirst()
                                                                .stream()
                                                                .toList();
                                        }
                                }
                        } else {
                                childs = allChildren;
                        }

                        while (!filteringNodes.empty()) {
                                ParsedFhirPath.FhirPathNode filteringNode = filteringNodes.pop();
                                childs = applySubsettingFilter(newPath, filteringNode, childs);
                        }

                        // should only be one
                        if (childs.size() != 1) {
                                if (childs.isEmpty()) {
                                        throwNoElementsError(theOriginalPath);
                                }
                                throw new InvalidRequestException(Msg.code(2704)
                                                + " FhirPath returns more than 1 element. Patch cannot be done. " + theOriginalPath);
                        }
                        IBase child = childs.get(0);

                        definition.setChild(
                                        childDefinition(definition, theFhirPathParts, child, theFhirPath, newPath, theOriginalPath));
                }

                return definition;
        }

        private ChildDefinition findChildDefinition(IBase theContainingElement, String theElementName) {
                BaseRuntimeElementDefinition<?> elementDef = myContext.getElementDefinition(theContainingElement.getClass());

                String childName = theElementName;
                BaseRuntimeChildDefinition childDef = elementDef.getChildByName(childName);
                BaseRuntimeElementDefinition<?> childElement;
                if (childDef == null) {
                        childName = theElementName + "[x]";
                        childDef = elementDef.getChildByName(childName);
                        childElement = childDef.getChildByName(
                                        childDef.getValidChildNames().iterator().next());
                } else {
                        childElement = childDef.getChildByName(childName);
                }

                return new ChildDefinition(childDef, childElement);
        }

        private IBase getNewValue(IBase theParameters, ChildDefinition theChildDefinition) {
                Optional<IBase> valuePart = ParametersUtil.getParameterPart(myContext, theParameters, PARAMETER_VALUE);
                Optional<IBase> valuePartValue =
                                ParametersUtil.getParameterPartValue(myContext, theParameters, PARAMETER_VALUE);

                IBase newValue;
                if (valuePartValue.isPresent()) {
                        newValue = maybeMassageToEnumeration(valuePartValue.get(), theChildDefinition);

                } else {
                        List<IBase> partParts = valuePart.map(this::extractPartsFromPart).orElse(Collections.emptyList());

                        newValue = createAndPopulateNewElement(theChildDefinition, partParts);
                }

                return newValue;
        }

        private IBase maybeMassageToEnumeration(IBase theValue, ChildDefinition theChildDefinition) {
                IBase retVal = theValue;

                if (IBaseEnumeration.class.isAssignableFrom(
                                                theChildDefinition.getChildElement().getImplementingClass())
                                || XhtmlNode.class.isAssignableFrom(
                                                theChildDefinition.getChildElement().getImplementingClass())) {
                        // If the compositeElementDef is an IBaseEnumeration, we will use the actual compositeElementDef definition
                        // to build one, since
                        // it needs the right factory object passed to its constructor
                        IPrimitiveType<?> newValueInstance;
                        if (theChildDefinition.getUseableChildDef().getInstanceConstructorArguments() != null) {
                                newValueInstance = (IPrimitiveType<?>) theChildDefinition
                                                .getChildElement()
                                                .newInstance(theChildDefinition.getUseableChildDef().getInstanceConstructorArguments());
                        } else {
                                newValueInstance =
                                                (IPrimitiveType<?>) theChildDefinition.getChildElement().newInstance();
                        }
                        newValueInstance.setValueAsString(((IPrimitiveType<?>) theValue).getValueAsString());
                        retVal = newValueInstance;
                }

                return retVal;
        }

        @Nonnull
        private List<IBase> extractPartsFromPart(IBase theParametersParameterComponent) {
                return myContext.newTerser().getValues(theParametersParameterComponent, "part");
        }

        /**
         * this method will instantiate an element according to the provided Definition and initialize its fields
         * from the values provided in thePartParts.  a part usually represent a datatype as a name/value[X] pair.
         * it may also represent a complex type like an Extension.
         *
         * @param theDefinition wrapper around the runtime definition of the element to be populated
         * @param thePartParts list of Part to populate the element that will be created from theDefinition
         * @return an element that was created from theDefinition and populated with the parts
         */
        private IBase createAndPopulateNewElement(ChildDefinition theDefinition, List<IBase> thePartParts) {
                IBase newElement = theDefinition.getChildElement().newInstance();

                for (IBase nextValuePartPart : thePartParts) {
                        String name = myContext
                                        .newTerser()
                                        .getSingleValue(nextValuePartPart, PARAMETER_NAME, IPrimitiveType.class)
                                        .map(IPrimitiveType::getValueAsString)
                                        .orElse(null);

                        if (StringUtils.isBlank(name)) {
                                continue;
                        }

                        Optional<IBase> optionalValue =
                                        myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);

                        if (optionalValue.isPresent()) {
                                // we have a dataType. let's extract its value and assign it.
                                ChildDefinition childDefinition;
                                childDefinition = findChildDefinition(newElement, name);

                                IBase newValue = maybeMassageToEnumeration(optionalValue.get(), childDefinition);

                                BaseRuntimeChildDefinition partChildDef =
                                                theDefinition.getUsableChildElement().getChildByName(name);

                                if (isNull(partChildDef)) {
                                        name = name + "[x]";
                                        partChildDef = theDefinition.getUsableChildElement().getChildByName(name);
                                }

                                partChildDef.getMutator().setValue(newElement, newValue);

                                // a part represent a datatype or a complexType but not both at the same time.
                                continue;
                        }

                        List<IBase> part = extractPartsFromPart(nextValuePartPart);

                        if (!part.isEmpty()) {
                                // we have a complexType.  let's find its definition and recursively process
                                // them till all complexTypes are processed.
                                ChildDefinition childDefinition = findChildDefinition(newElement, name);

                                IBase childNewValue = createAndPopulateNewElement(childDefinition, part);

                                childDefinition.getUseableChildDef().getMutator().setValue(newElement, childNewValue);
                        }
                }

                return newElement;
        }

        private void deleteSingleElement(IBase theElementToDelete) {
                myContext.newTerser().visit(theElementToDelete, 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;
                        }
                });
        }

        public IBaseParameters diff(@Nullable IBaseResource theOldValue, @Nonnull IBaseResource theNewValue) {
                IBaseParameters retVal = ParametersUtil.newInstance(myContext);
                String newValueTypeName = myContext.getResourceDefinition(theNewValue).getName();

                if (theOldValue == null) {
                        IBase operation = ParametersUtil.addParameterToParameters(myContext, retVal, PARAMETER_OPERATION);
                        ParametersUtil.addPartCode(myContext, operation, PARAMETER_TYPE, OPERATION_INSERT);
                        ParametersUtil.addPartString(myContext, operation, PARAMETER_PATH, newValueTypeName);
                        ParametersUtil.addPart(myContext, operation, PARAMETER_VALUE, theNewValue);
                } else {
                        String oldValueTypeName =
                                        myContext.getResourceDefinition(theOldValue).getName();
                        Validate.isTrue(oldValueTypeName.equalsIgnoreCase(newValueTypeName), "Resources must be of same type");

                        BaseRuntimeElementCompositeDefinition<?> def =
                                        myContext.getResourceDefinition(theOldValue).getBaseDefinition();
                        String path = def.getName();

                        EncodeContextPath contextPath = new EncodeContextPath();
                        contextPath.pushPath(path, true);

                        compare(retVal, contextPath, def, path, path, theOldValue, theNewValue);

                        contextPath.popPath();
                        assert contextPath.getPath().isEmpty();
                }

                return retVal;
        }

        private void compare(
                        IBaseParameters theDiff,
                        EncodeContextPath theSourceEncodeContext,
                        BaseRuntimeElementDefinition<?> theDef,
                        String theSourcePath,
                        String theTargetPath,
                        IBase theOldField,
                        IBase theNewField) {

                boolean pathIsIgnored = pathIsIgnored(theSourceEncodeContext);
                if (pathIsIgnored) {
                        return;
                }

                BaseRuntimeElementDefinition<?> sourceDef = myContext.getElementDefinition(theOldField.getClass());
                BaseRuntimeElementDefinition<?> targetDef = myContext.getElementDefinition(theNewField.getClass());
                if (!sourceDef.getName().equals(targetDef.getName())) {
                        IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, PARAMETER_OPERATION);
                        ParametersUtil.addPartCode(myContext, operation, PARAMETER_TYPE, OPERATION_REPLACE);
                        ParametersUtil.addPartString(myContext, operation, PARAMETER_PATH, theTargetPath);
                        addValueToDiff(operation, theOldField, theNewField);
                } else {
                        if (theOldField instanceof IPrimitiveType) {
                                IPrimitiveType<?> oldPrimitive = (IPrimitiveType<?>) theOldField;
                                IPrimitiveType<?> newPrimitive = (IPrimitiveType<?>) theNewField;
                                String oldValueAsString = toValue(oldPrimitive);
                                String newValueAsString = toValue(newPrimitive);
                                if (!Objects.equals(oldValueAsString, newValueAsString)) {
                                        IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, PARAMETER_OPERATION);
                                        ParametersUtil.addPartCode(myContext, operation, PARAMETER_TYPE, OPERATION_REPLACE);
                                        ParametersUtil.addPartString(myContext, operation, PARAMETER_PATH, theTargetPath);
                                        addValueToDiff(operation, oldPrimitive, newPrimitive);
                                }
                        }

                        List<BaseRuntimeChildDefinition> children = theDef.getChildren();
                        for (BaseRuntimeChildDefinition nextChild : children) {
                                compareField(
                                                theDiff,
                                                theSourceEncodeContext,
                                                theSourcePath,
                                                theTargetPath,
                                                theOldField,
                                                theNewField,
                                                nextChild);
                        }
                }
        }

        private void compareField(
                        IBaseParameters theDiff,
                        EncodeContextPath theSourceEncodePath,
                        String theSourcePath,
                        String theTargetPath,
                        IBase theOldField,
                        IBase theNewField,
                        BaseRuntimeChildDefinition theChildDef) {
                String elementName = theChildDef.getElementName();
                boolean repeatable = theChildDef.getMax() != 1;
                theSourceEncodePath.pushPath(elementName, false);
                if (pathIsIgnored(theSourceEncodePath)) {
                        theSourceEncodePath.popPath();
                        return;
                }

                List<? extends IBase> sourceValues = theChildDef.getAccessor().getValues(theOldField);
                List<? extends IBase> targetValues = theChildDef.getAccessor().getValues(theNewField);

                int sourceIndex = 0;
                int targetIndex = 0;
                while (sourceIndex < sourceValues.size() && targetIndex < targetValues.size()) {

                        IBase sourceChildField = sourceValues.get(sourceIndex);
                        Validate.notNull(sourceChildField); // not expected to happen, but just in case
                        BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(sourceChildField.getClass());
                        IBase targetChildField = targetValues.get(targetIndex);
                        Validate.notNull(targetChildField); // not expected to happen, but just in case
                        String sourcePath = theSourcePath + "." + elementName + (repeatable ? "[" + sourceIndex + "]" : "");
                        String targetPath = theSourcePath + "." + elementName + (repeatable ? "[" + targetIndex + "]" : "");

                        compare(theDiff, theSourceEncodePath, def, sourcePath, targetPath, sourceChildField, targetChildField);

                        sourceIndex++;
                        targetIndex++;
                }

                // Find newly inserted items
                while (targetIndex < targetValues.size()) {
                        String path = theTargetPath + "." + elementName;
                        addInsertItems(theDiff, targetValues, targetIndex, path, theChildDef);
                        targetIndex++;
                }

                // Find deleted items
                while (sourceIndex < sourceValues.size()) {
                        IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, PARAMETER_OPERATION);
                        ParametersUtil.addPartCode(myContext, operation, PARAMETER_TYPE, OPERATION_DELETE);
                        ParametersUtil.addPartString(
                                        myContext,
                                        operation,
                                        PARAMETER_PATH,
                                        theTargetPath + "." + elementName + (repeatable ? "[" + targetIndex + "]" : ""));

                        sourceIndex++;
                        targetIndex++;
                }

                theSourceEncodePath.popPath();
        }

        private void addInsertItems(
                        IBaseParameters theDiff,
                        List<? extends IBase> theTargetValues,
                        int theTargetIndex,
                        String thePath,
                        BaseRuntimeChildDefinition theChildDefinition) {
                IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, PARAMETER_OPERATION);
                ParametersUtil.addPartCode(myContext, operation, PARAMETER_TYPE, OPERATION_INSERT);
                ParametersUtil.addPartString(myContext, operation, PARAMETER_PATH, thePath);
                ParametersUtil.addPartInteger(myContext, operation, PARAMETER_INDEX, theTargetIndex);

                IBase value = theTargetValues.get(theTargetIndex);
                BaseRuntimeElementDefinition<?> valueDef = myContext.getElementDefinition(value.getClass());

                /*
                 * If the value is a Resource or a datatype, we can put it into the part.value and that will cover
                 * all of its children. If it's an infrastructure element though, such as Patient.contact we can't
                 * just put it into part.value because it isn't an actual type. So we have to put all of its
                 * children in instead.
                 */
                if (valueDef.isStandardType()) {
                        ParametersUtil.addPart(myContext, operation, PARAMETER_VALUE, value);
                } else {
                        for (BaseRuntimeChildDefinition nextChild : valueDef.getChildren()) {
                                List<IBase> childValues = nextChild.getAccessor().getValues(value);
                                for (int index = 0; index < childValues.size(); index++) {
                                        boolean childRepeatable = theChildDefinition.getMax() != 1;
                                        String elementName = nextChild.getChildNameByDatatype(
                                                        childValues.get(index).getClass());
                                        String targetPath = thePath + (childRepeatable ? "[" + index + "]" : "") + "." + elementName;
                                        addInsertItems(theDiff, childValues, index, targetPath, nextChild);
                                }
                        }
                }
        }

        private void addValueToDiff(IBase theOperationPart, IBase theOldValue, IBase theNewValue) {

                if (myIncludePreviousValueInDiff) {
                        IBase oldValue = massageValueForDiff(theOldValue);
                        ParametersUtil.addPart(myContext, theOperationPart, "previousValue", oldValue);
                }

                IBase newValue = massageValueForDiff(theNewValue);
                ParametersUtil.addPart(myContext, theOperationPart, PARAMETER_VALUE, newValue);
        }

        private boolean pathIsIgnored(EncodeContextPath theSourceEncodeContext) {
                boolean pathIsIgnored = false;
                for (EncodeContextPath next : myIgnorePaths) {
                        if (theSourceEncodeContext.startsWith(next, false)) {
                                pathIsIgnored = true;
                                break;
                        }
                }
                return pathIsIgnored;
        }

        private IBase massageValueForDiff(IBase theNewValue) {
                IBase massagedValue = theNewValue;

                // XHTML content is dealt with by putting it in a string
                if (theNewValue instanceof XhtmlNode) {
                        String xhtmlString = ((XhtmlNode) theNewValue).getValueAsString();
                        massagedValue = myContext.getElementDefinition("string").newInstance(xhtmlString);
                }

                // IIdType can hold a fully qualified ID, but we just want the ID part to show up in diffs
                if (theNewValue instanceof IIdType) {
                        String idPart = ((IIdType) theNewValue).getIdPart();
                        massagedValue = myContext.getElementDefinition("id").newInstance(idPart);
                }

                return massagedValue;
        }

        private String toValue(IPrimitiveType<?> theOldPrimitive) {
                if (theOldPrimitive instanceof IIdType) {
                        return ((IIdType) theOldPrimitive).getIdPart();
                }
                return theOldPrimitive.getValueAsString();
        }
}