ca.uhn.fhir.util.BundleUtil Maven / Gradle / Ivy
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2024 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.
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*/
package ca.uhn.fhir.util;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.bundle.BundleEntryMutator;
import ca.uhn.fhir.util.bundle.BundleEntryParts;
import ca.uhn.fhir.util.bundle.EntryListAccumulator;
import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
import ca.uhn.fhir.util.bundle.SearchBundleEntryParts;
import com.google.common.collect.Sets;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_PREV;
/**
* Fetch resources from a bundle
*/
public class BundleUtil {
/** Non instantiable */
private BundleUtil() {
// nothing
}
private static final Logger ourLog = LoggerFactory.getLogger(BundleUtil.class);
private static final String PREVIOUS = LINK_PREV;
private static final String PREV = "prev";
private static final Set previousOrPrev = Sets.newHashSet(PREVIOUS, PREV);
public static final String DIFFERENT_LINK_ERROR_MSG =
"Mismatching 'previous' and 'prev' links exist. 'previous' " + "is: '$PREVIOUS' and 'prev' is: '$PREV'.";
/**
* @return Returns null if the link isn't found or has no value
*/
public static String getLinkUrlOfType(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation) {
return getLinkUrlOfType(theContext, theBundle, theLinkRelation, true);
}
private static String getLinkUrlOfType(
FhirContext theContext, IBaseBundle theBundle, String theLinkRelation, boolean isPreviousCheck) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("link");
List links = entryChild.getAccessor().getValues(theBundle);
for (IBase nextLink : links) {
boolean isRightRel = false;
BaseRuntimeElementCompositeDefinition relDef =
(BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
BaseRuntimeChildDefinition relChild = relDef.getChildByName("relation");
List relValues = relChild.getAccessor().getValues(nextLink);
for (IBase next : relValues) {
IPrimitiveType nextValue = (IPrimitiveType) next;
if (isRelationMatch(
theContext, theBundle, theLinkRelation, nextValue.getValueAsString(), isPreviousCheck)) {
isRightRel = true;
}
}
if (!isRightRel) {
continue;
}
BaseRuntimeElementCompositeDefinition linkDef =
(BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
BaseRuntimeChildDefinition urlChild = linkDef.getChildByName("url");
List values = urlChild.getAccessor().getValues(nextLink);
for (IBase nextUrl : values) {
IPrimitiveType nextValue = (IPrimitiveType) nextUrl;
if (isNotBlank(nextValue.getValueAsString())) {
return nextValue.getValueAsString();
}
}
}
return null;
}
private static boolean isRelationMatch(
FhirContext theContext, IBaseBundle theBundle, String value, String matching, boolean theIsPreviousCheck) {
if (!theIsPreviousCheck) {
return value.equals(matching);
}
if (previousOrPrev.contains(value)) {
validateUniqueOrMatchingPreviousValues(theContext, theBundle);
if (previousOrPrev.contains(matching)) {
return true;
}
}
return (value.equals(matching));
}
private static void validateUniqueOrMatchingPreviousValues(FhirContext theContext, IBaseBundle theBundle) {
String previousLink = getLinkNoCheck(theContext, theBundle, PREVIOUS);
String prevLink = getLinkNoCheck(theContext, theBundle, PREV);
if (prevLink != null && previousLink != null) {
if (!previousLink.equals(prevLink)) {
String msg = DIFFERENT_LINK_ERROR_MSG
.replace("$PREVIOUS", previousLink)
.replace("$PREV", prevLink);
throw new InternalErrorException(Msg.code(2368) + msg);
}
}
}
private static String getLinkNoCheck(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation) {
return getLinkUrlOfType(theContext, theBundle, theLinkRelation, false);
}
/**
* Returns a collection of Pairs, one for each entry in the bundle. Each pair will contain
* the values of Bundle.entry.fullUrl, and Bundle.entry.resource respectively. Nulls
* are possible in either or both values in the Pair.
*
* @since 7.0.0
*/
@SuppressWarnings("unchecked")
public static List> getBundleEntryFullUrlsAndResources(
FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
List entries = entryChild.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildElem =
(BaseRuntimeElementCompositeDefinition) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
BaseRuntimeChildDefinition urlChild = entryChildElem.getChildByName("fullUrl");
List> retVal = new ArrayList<>(entries.size());
for (IBase nextEntry : entries) {
String fullUrl = urlChild.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t -> (((IPrimitiveType) t).getValueAsString()))
.orElse(null);
IBaseResource resource = (IBaseResource)
resourceChild.getAccessor().getFirstValueOrNull(nextEntry).orElse(null);
retVal.add(Pair.of(fullUrl, resource));
}
return retVal;
}
public static List> getBundleEntryUrlsAndResources(
FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
List entries = entryChild.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildElem =
(BaseRuntimeElementCompositeDefinition) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
BaseRuntimeElementCompositeDefinition requestDef =
(BaseRuntimeElementCompositeDefinition) requestChild.getChildByName("request");
BaseRuntimeChildDefinition urlChild = requestDef.getChildByName("url");
List> retVal = new ArrayList<>(entries.size());
for (IBase nextEntry : entries) {
String url = requestChild
.getAccessor()
.getFirstValueOrNull(nextEntry)
.flatMap(e -> urlChild.getAccessor().getFirstValueOrNull(e))
.map(t -> ((IPrimitiveType) t).getValueAsString())
.orElse(null);
IBaseResource resource = (IBaseResource)
resourceChild.getAccessor().getFirstValueOrNull(nextEntry).orElse(null);
retVal.add(Pair.of(url, resource));
}
return retVal;
}
public static String getBundleType(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("type");
List entries = entryChild.getAccessor().getValues(theBundle);
if (entries.size() > 0) {
IPrimitiveType typeElement = (IPrimitiveType) entries.get(0);
return typeElement.getValueAsString();
}
return null;
}
public static BundleTypeEnum getBundleTypeEnum(FhirContext theContext, IBaseBundle theBundle) {
String bundleTypeCode = BundleUtil.getBundleType(theContext, theBundle);
if (isBlank(bundleTypeCode)) {
return null;
}
return BundleTypeEnum.forCode(bundleTypeCode);
}
public static void setBundleType(FhirContext theContext, IBaseBundle theBundle, String theType) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("type");
BaseRuntimeElementDefinition element = entryChild.getChildByName("type");
IPrimitiveType typeInstance =
(IPrimitiveType) element.newInstance(entryChild.getInstanceConstructorArguments());
typeInstance.setValueAsString(theType);
entryChild.getMutator().setValue(theBundle, typeInstance);
}
public static Integer getTotal(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("total");
List entries = entryChild.getAccessor().getValues(theBundle);
if (entries.size() > 0) {
@SuppressWarnings("unchecked")
IPrimitiveType typeElement = (IPrimitiveType) entries.get(0);
if (typeElement != null && typeElement.getValue() != null) {
return typeElement.getValue().intValue();
}
}
return null;
}
public static void setTotal(FhirContext theContext, IBaseBundle theBundle, Integer theTotal) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("total");
@SuppressWarnings("unchecked")
IPrimitiveType value =
(IPrimitiveType) entryChild.getChildByName("total").newInstance();
value.setValue(theTotal);
entryChild.getMutator().setValue(theBundle, value);
}
/**
* Extract all of the resources from a given bundle
*/
public static List toListOfEntries(FhirContext theContext, IBaseBundle theBundle) {
EntryListAccumulator entryListAccumulator = new EntryListAccumulator();
processEntries(theContext, theBundle, entryListAccumulator);
return entryListAccumulator.getList();
}
static int WHITE = 1;
static int GRAY = 2;
static int BLACK = 3;
/**
* Function which will do an in-place sort of a bundles' entries, to the correct processing order, which is:
* 1. Deletes
* 2. Creates
* 3. Updates
*
* Furthermore, within these operation types, the entries will be sorted based on the order in which they should be processed
* e.g. if you have 2 CREATEs, one for a Patient, and one for an Observation which has this Patient as its Subject,
* the patient will come first, then the observation.
*
* In cases of there being a cyclic dependency (e.g. Organization/1 is partOf Organization/2 and Organization/2 is partOf Organization/1)
* this function will throw an IllegalStateException.
*
* @param theContext The FhirContext.
* @param theBundle The {@link IBaseBundle} which contains the entries you would like sorted into processing order.
*/
public static void sortEntriesIntoProcessingOrder(FhirContext theContext, IBaseBundle theBundle)
throws IllegalStateException {
Map partsToIBaseMap = getPartsToIBaseMap(theContext, theBundle);
// Get all deletions.
LinkedHashSet deleteParts =
sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.DELETE, partsToIBaseMap);
validatePartsNotNull(deleteParts);
LinkedHashSet retVal = new LinkedHashSet<>(deleteParts);
// Get all Creations
LinkedHashSet createParts =
sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.POST, partsToIBaseMap);
validatePartsNotNull(createParts);
retVal.addAll(createParts);
// Get all Updates
LinkedHashSet updateParts =
sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.PUT, partsToIBaseMap);
validatePartsNotNull(updateParts);
retVal.addAll(updateParts);
// Once we are done adding all DELETE, POST, PUT operations, add everything else.
// Since this is a set, it will just fail to add already-added operations.
retVal.addAll(partsToIBaseMap.values());
// Blow away the entries and reset them in the right order.
TerserUtil.clearField(theContext, theBundle, "entry");
TerserUtil.setField(theContext, "entry", theBundle, retVal.toArray(new IBase[0]));
}
/**
* Converts a Bundle containing resources into a FHIR transaction which
* creates/updates the resources. This method does not modify the original
* bundle, but returns a new copy.
*
* This method is mostly intended for test scenarios where you have a Bundle
* containing search results or other sourced resources, and want to upload
* these resources to a server using a single FHIR transaction.
*
*
* The Bundle is converted using the following logic:
*
* - Bundle.type is changed to
transaction
* - Bundle.request.method is changed to
PUT
* - Bundle.request.url is changed to
[resourceType]/[id]
* - Bundle.fullUrl is changed to
[resourceType]/[id]
*
*
*
* @param theContext The FhirContext to use with the bundle
* @param theBundle The Bundle to modify. All resources in the Bundle should have an ID.
* @param thePrefixIdsOrNull If not null, all resource IDs and all references in the Bundle will be
* modified to such that their IDs contain the given prefix. For example, for a value
* of "A", the resource "Patient/123" will be changed to be "Patient/A123". If set to
* null, resource IDs are unchanged.
* @since 7.4.0
*/
public static T convertBundleIntoTransaction(
@Nonnull FhirContext theContext, @Nonnull T theBundle, @Nullable String thePrefixIdsOrNull) {
String prefix = defaultString(thePrefixIdsOrNull);
BundleBuilder bb = new BundleBuilder(theContext);
FhirTerser terser = theContext.newTerser();
List entries = terser.getValues(theBundle, "Bundle.entry");
for (var entry : entries) {
IBaseResource resource = terser.getSingleValueOrNull(entry, "resource", IBaseResource.class);
if (resource != null) {
Validate.isTrue(resource.getIdElement().hasIdPart(), "Resource in bundle has no ID");
String newId = theContext.getResourceType(resource) + "/" + prefix
+ resource.getIdElement().getIdPart();
IBaseResource resourceClone = terser.clone(resource);
resourceClone.setId(newId);
if (isNotBlank(prefix)) {
for (var ref : terser.getAllResourceReferences(resourceClone)) {
var refElement = ref.getResourceReference().getReferenceElement();
ref.getResourceReference()
.setReference(refElement.getResourceType() + "/" + prefix + refElement.getIdPart());
}
}
bb.addTransactionUpdateEntry(resourceClone);
}
}
return bb.getBundleTyped();
}
private static void validatePartsNotNull(LinkedHashSet theDeleteParts) {
if (theDeleteParts == null) {
throw new IllegalStateException(
Msg.code(1745) + "This transaction contains a cycle, so it cannot be sorted.");
}
}
private static LinkedHashSet sortEntriesOfTypeIntoProcessingOrder(
FhirContext theContext,
RequestTypeEnum theRequestTypeEnum,
Map thePartsToIBaseMap) {
SortLegality legality = new SortLegality();
HashMap color = new HashMap<>();
HashMap> adjList = new HashMap<>();
List topologicalOrder = new ArrayList<>();
Set bundleEntryParts = thePartsToIBaseMap.keySet().stream()
.filter(part -> part.getRequestType().equals(theRequestTypeEnum))
.collect(Collectors.toSet());
HashMap resourceIdToBundleEntryMap = new HashMap<>();
for (BundleEntryParts bundleEntryPart : bundleEntryParts) {
IBaseResource resource = bundleEntryPart.getResource();
if (resource != null) {
String resourceId = resource.getIdElement().toVersionless().toString();
resourceIdToBundleEntryMap.put(resourceId, bundleEntryPart);
if (resourceId == null) {
if (bundleEntryPart.getFullUrl() != null) {
resourceId = bundleEntryPart.getFullUrl();
}
}
color.put(resourceId, WHITE);
}
}
for (BundleEntryParts bundleEntryPart : bundleEntryParts) {
IBaseResource resource = bundleEntryPart.getResource();
if (resource != null) {
String resourceId = resource.getIdElement().toVersionless().toString();
resourceIdToBundleEntryMap.put(resourceId, bundleEntryPart);
if (resourceId == null) {
if (bundleEntryPart.getFullUrl() != null) {
resourceId = bundleEntryPart.getFullUrl();
}
}
List allResourceReferences =
theContext.newTerser().getAllResourceReferences(resource);
String finalResourceId = resourceId;
allResourceReferences.forEach(refInfo -> {
String referencedResourceId = refInfo.getResourceReference()
.getReferenceElement()
.toVersionless()
.getValue();
if (color.containsKey(referencedResourceId)) {
if (!adjList.containsKey(finalResourceId)) {
adjList.put(finalResourceId, new ArrayList<>());
}
adjList.get(finalResourceId).add(referencedResourceId);
}
});
}
}
for (Map.Entry entry : color.entrySet()) {
if (entry.getValue() == WHITE) {
depthFirstSearch(entry.getKey(), color, adjList, topologicalOrder, legality);
}
}
if (legality.isLegal()) {
if (ourLog.isDebugEnabled()) {
ourLog.debug("Topological order is: {}", String.join(",", topologicalOrder));
}
LinkedHashSet orderedEntries = new LinkedHashSet<>();
for (int i = 0; i < topologicalOrder.size(); i++) {
BundleEntryParts bep;
if (theRequestTypeEnum.equals(RequestTypeEnum.DELETE)) {
int index = topologicalOrder.size() - i - 1;
bep = resourceIdToBundleEntryMap.get(topologicalOrder.get(index));
} else {
bep = resourceIdToBundleEntryMap.get(topologicalOrder.get(i));
}
IBase base = thePartsToIBaseMap.get(bep);
orderedEntries.add(base);
}
return orderedEntries;
} else {
return null;
}
}
private static void depthFirstSearch(
String theResourceId,
HashMap theResourceIdToColor,
HashMap> theAdjList,
List theTopologicalOrder,
SortLegality theLegality) {
if (!theLegality.isLegal()) {
ourLog.debug("Found a cycle while trying to sort bundle entries. This bundle is not sortable.");
return;
}
// We are currently recursing over this node (gray)
theResourceIdToColor.put(theResourceId, GRAY);
for (String neighbourResourceId : theAdjList.getOrDefault(theResourceId, new ArrayList<>())) {
if (theResourceIdToColor.get(neighbourResourceId) == WHITE) {
depthFirstSearch(
neighbourResourceId, theResourceIdToColor, theAdjList, theTopologicalOrder, theLegality);
} else if (theResourceIdToColor.get(neighbourResourceId) == GRAY) {
theLegality.setLegal(false);
return;
}
}
// Mark the node as black
theResourceIdToColor.put(theResourceId, BLACK);
theTopologicalOrder.add(theResourceId);
}
private static Map getPartsToIBaseMap(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List entries = entryChildDef.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildContentsDef =
(BaseRuntimeElementCompositeDefinition) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
BaseRuntimeElementCompositeDefinition requestChildContentsDef =
(BaseRuntimeElementCompositeDefinition) requestChildDef.getChildByName("request");
BaseRuntimeChildDefinition requestUrlChildDef = requestChildContentsDef.getChildByName("url");
BaseRuntimeChildDefinition requestIfNoneExistChildDef = requestChildContentsDef.getChildByName("ifNoneExist");
BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
Map map = new HashMap<>();
for (IBase nextEntry : entries) {
BundleEntryParts parts = getBundleEntryParts(
fullUrlChildDef,
resourceChildDef,
requestChildDef,
requestUrlChildDef,
requestIfNoneExistChildDef,
methodChildDef,
nextEntry);
/*
* All 3 might be null - That's ok because we still want to know the
* order in the original bundle.
*/
map.put(parts, nextEntry);
}
return map;
}
public static List getSearchBundleEntryParts(
FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List entries = entryChildDef.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildContentsDef =
(BaseRuntimeElementCompositeDefinition) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition searchChildDef = entryChildContentsDef.getChildByName("search");
BaseRuntimeElementCompositeDefinition searchChildContentsDef =
(BaseRuntimeElementCompositeDefinition) searchChildDef.getChildByName("search");
BaseRuntimeChildDefinition searchModeChildDef = searchChildContentsDef.getChildByName("mode");
BaseRuntimeChildDefinition searchScoreChildDef = searchChildContentsDef.getChildByName("score");
List retVal = new ArrayList<>();
for (IBase nextEntry : entries) {
SearchBundleEntryParts parts = getSearchBundleEntryParts(
fullUrlChildDef,
resourceChildDef,
searchChildDef,
searchModeChildDef,
searchScoreChildDef,
nextEntry);
retVal.add(parts);
}
return retVal;
}
private static SearchBundleEntryParts getSearchBundleEntryParts(
BaseRuntimeChildDefinition theFullUrlChildDef,
BaseRuntimeChildDefinition theResourceChildDef,
BaseRuntimeChildDefinition theSearchChildDef,
BaseRuntimeChildDefinition theSearchModeChildDef,
BaseRuntimeChildDefinition theSearchScoreChildDef,
IBase entry) {
IBaseResource resource = null;
String matchMode = null;
BigDecimal searchScore = null;
String fullUrl = theFullUrlChildDef
.getAccessor()
.getFirstValueOrNull(entry)
.map(t -> ((IPrimitiveType) t).getValueAsString())
.orElse(null);
for (IBase nextResource : theResourceChildDef.getAccessor().getValues(entry)) {
resource = (IBaseResource) nextResource;
}
for (IBase nextSearch : theSearchChildDef.getAccessor().getValues(entry)) {
for (IBase nextUrl : theSearchModeChildDef.getAccessor().getValues(nextSearch)) {
matchMode = ((IPrimitiveType) nextUrl).getValueAsString();
}
for (IBase nextUrl : theSearchScoreChildDef.getAccessor().getValues(nextSearch)) {
searchScore = (BigDecimal) ((IPrimitiveType) nextUrl).getValue();
}
}
return new SearchBundleEntryParts(fullUrl, resource, matchMode, searchScore);
}
/**
* Given a bundle, and a consumer, apply the consumer to each entry in the bundle.
* @param theContext The FHIR Context
* @param theBundle The bundle to have its entries processed.
* @param theProcessor a {@link Consumer} which will operate on all the entries of a bundle.
*/
public static void processEntries(
FhirContext theContext, IBaseBundle theBundle, Consumer theProcessor) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List entries = entryChildDef.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildContentsDef =
(BaseRuntimeElementCompositeDefinition) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
BaseRuntimeElementCompositeDefinition requestChildContentsDef =
(BaseRuntimeElementCompositeDefinition) requestChildDef.getChildByName("request");
BaseRuntimeChildDefinition requestUrlChildDef = requestChildContentsDef.getChildByName("url");
BaseRuntimeChildDefinition requestIfNoneExistChildDef = requestChildContentsDef.getChildByName("ifNoneExist");
BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
for (IBase nextEntry : entries) {
BundleEntryParts parts = getBundleEntryParts(
fullUrlChildDef,
resourceChildDef,
requestChildDef,
requestUrlChildDef,
requestIfNoneExistChildDef,
methodChildDef,
nextEntry);
/*
* All 3 might be null - That's ok because we still want to know the
* order in the original bundle.
*/
BundleEntryMutator mutator = new BundleEntryMutator(
theContext, nextEntry, requestChildDef, requestChildContentsDef, entryChildContentsDef);
ModifiableBundleEntry entry = new ModifiableBundleEntry(parts, mutator);
theProcessor.accept(entry);
}
}
private static BundleEntryParts getBundleEntryParts(
BaseRuntimeChildDefinition fullUrlChildDef,
BaseRuntimeChildDefinition resourceChildDef,
BaseRuntimeChildDefinition requestChildDef,
BaseRuntimeChildDefinition requestUrlChildDef,
BaseRuntimeChildDefinition requestIfNoneExistChildDef,
BaseRuntimeChildDefinition methodChildDef,
IBase nextEntry) {
IBaseResource resource = null;
String url = null;
RequestTypeEnum requestType = null;
String conditionalUrl = null;
String fullUrl = fullUrlChildDef
.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t -> ((IPrimitiveType) t).getValueAsString())
.orElse(null);
for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextResource;
}
for (IBase nextRequest : requestChildDef.getAccessor().getValues(nextEntry)) {
for (IBase nextUrl : requestUrlChildDef.getAccessor().getValues(nextRequest)) {
url = ((IPrimitiveType) nextUrl).getValueAsString();
}
for (IBase nextMethod : methodChildDef.getAccessor().getValues(nextRequest)) {
String methodString = ((IPrimitiveType) nextMethod).getValueAsString();
if (isNotBlank(methodString)) {
requestType = RequestTypeEnum.valueOf(methodString);
}
}
if (requestType != null) {
//noinspection EnumSwitchStatementWhichMissesCases
switch (requestType) {
case PUT:
case DELETE:
case PATCH:
conditionalUrl = url != null && url.contains("?") ? url : null;
break;
case POST:
List ifNoneExistReps =
requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
if (ifNoneExistReps.size() > 0) {
IPrimitiveType ifNoneExist = (IPrimitiveType) ifNoneExistReps.get(0);
conditionalUrl = ifNoneExist.getValueAsString();
}
break;
}
}
}
return new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl);
}
/**
* Extract all of the resources from a given bundle
*/
public static List toListOfResources(FhirContext theContext, IBaseBundle theBundle) {
return toListOfResourcesOfType(theContext, theBundle, IBaseResource.class);
}
/**
* Extract all of ids of all the resources from a given bundle
*/
public static List toListOfResourceIds(FhirContext theContext, IBaseBundle theBundle) {
return toListOfResourcesOfType(theContext, theBundle, IBaseResource.class).stream()
.map(resource -> resource.getIdElement().getIdPart())
.collect(Collectors.toList());
}
/**
* Extract all of the resources of a given type from a given bundle
*/
@SuppressWarnings("unchecked")
public static List toListOfResourcesOfType(
FhirContext theContext, IBaseBundle theBundle, Class theTypeToInclude) {
Objects.requireNonNull(theTypeToInclude, "ResourceType must not be null");
List retVal = new ArrayList<>();
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
List entries = entryChild.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition entryChildElem =
(BaseRuntimeElementCompositeDefinition) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
for (IBase nextEntry : entries) {
for (IBase next : resourceChild.getAccessor().getValues(nextEntry)) {
if (theTypeToInclude.isAssignableFrom(next.getClass())) {
retVal.add((T) next);
}
}
}
return retVal;
}
public static IBase getReferenceInBundle(
@Nonnull FhirContext theFhirContext, @Nonnull String theUrl, @Nullable Object theAppContext) {
if (!(theAppContext instanceof IBaseBundle) || isBlank(theUrl) || theUrl.startsWith("#")) {
return null;
}
/*
* If this is a reference that is a UUID, we must be looking for local references within a Bundle
*/
IBaseBundle bundle = (IBaseBundle) theAppContext;
final boolean isPlaceholderReference = theUrl.startsWith("urn:");
final String unqualifiedVersionlessReference =
new IdDt(theUrl).toUnqualifiedVersionless().getValue();
for (BundleEntryParts next : BundleUtil.toListOfEntries(theFhirContext, bundle)) {
IBaseResource nextResource = next.getResource();
if (nextResource == null) {
continue;
}
if (isPlaceholderReference) {
if (theUrl.equals(next.getFullUrl())
|| theUrl.equals(nextResource.getIdElement().getValue())) {
return nextResource;
}
} else {
if (unqualifiedVersionlessReference.equals(
nextResource.getIdElement().toUnqualifiedVersionless().getValue())) {
return nextResource;
}
}
}
return null;
}
/**
* DSTU3 did not allow the PATCH verb for transaction bundles- so instead we infer that a bundle
* is a patch if the payload is a binary resource containing a patch. This method
* tests whether a resource (which should have come from
* Bundle.entry.resource is a Binary resource with a patch
* payload type.
*/
public static boolean isDstu3TransactionPatch(FhirContext theContext, IBaseResource thePayloadResource) {
boolean isPatch = false;
if (thePayloadResource instanceof IBaseBinary) {
String contentType = ((IBaseBinary) thePayloadResource).getContentType();
try {
PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(theContext, contentType);
isPatch = true;
} catch (InvalidRequestException e) {
// ignore
}
}
return isPatch;
}
/**
* create a new bundle entry and set a value for a single field
* @param theContext Context holding resource definition
* @param theFieldName Child field name of the bundle entry to set
* @param theValues The values to set on the bundle entry child field name
* @return the new bundle entry
*/
public static IBase createNewBundleEntryWithSingleField(
FhirContext theContext, String theFieldName, IBase... theValues) {
IBaseBundle newBundle = TerserUtil.newResource(theContext, "Bundle");
BaseRuntimeChildDefinition entryChildDef =
theContext.getResourceDefinition(newBundle).getChildByName("entry");
BaseRuntimeElementCompositeDefinition entryChildElem =
(BaseRuntimeElementCompositeDefinition) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName(theFieldName);
IBase bundleEntry = entryChildElem.newInstance();
for (IBase value : theValues) {
try {
resourceChild.getMutator().addValue(bundleEntry, value);
} catch (UnsupportedOperationException e) {
ourLog.warn(
"Resource {} does not support multiple values, but an attempt to set {} was made. Setting the first item only",
bundleEntry,
theValues);
resourceChild.getMutator().setValue(bundleEntry, value);
break;
}
}
return bundleEntry;
}
/**
* Get resource from bundle by resource type and reference
* @param theContext FhirContext
* @param theBundle IBaseBundle
* @param theReference IBaseReference
* @return IBaseResource if found and null if not found.
*/
@Nonnull
public static IBaseResource getResourceByReferenceAndResourceType(
@Nonnull FhirContext theContext, @Nonnull IBaseBundle theBundle, @Nonnull IBaseReference theReference) {
return toListOfResources(theContext, theBundle).stream()
.filter(theResource -> theReference
.getReferenceElement()
.getIdPart()
.equals(theResource.getIdElement().getIdPart()))
.findFirst()
.orElse(null);
}
private static class SortLegality {
private boolean myIsLegal;
SortLegality() {
this.myIsLegal = true;
}
private void setLegal(boolean theLegal) {
myIsLegal = theLegal;
}
public boolean isLegal() {
return myIsLegal;
}
}
}