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Merge branch 'master' into 2566_update_s13n_and_validation_handling

This commit is contained in:
Nick Goupinets 2021-04-28 10:16:27 -04:00
parent 418c1aa2c6 dd61a8aa2c
commit 21d8cdfefc
20 changed files with 1136 additions and 144 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/HapiLocalizer.java
View File

@ -10,6 +10,8 @@ import java.util.concurrent.ConcurrentHashMap;
import static org.apache.commons.lang3.StringUtils.*;
/*
* #%L
* HAPI FHIR - Core Library

64
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
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@ -1420,6 +1420,12 @@ public enum Pointcut implements IPointcut {
* <li>
* ca.uhn.fhir.rest.api.server.storage.TransactionDetails - The outer transaction details object (since 5.0.0)
* </li>
* <li>
* Boolean - Whether this pointcut invocation was deferred or not(since 5.4.0)
* </li>
* <li>
* ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum - The timing at which the invocation of the interceptor took place. Options are ACTIVE and DEFERRED.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
@ -1429,7 +1435,8 @@ public enum Pointcut implements IPointcut {
"org.hl7.fhir.instance.model.api.IBaseResource",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails"
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails",
"ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum"
),
/**
@ -1446,7 +1453,7 @@ public enum Pointcut implements IPointcut {
* Hooks may accept the following parameters:
* <ul>
* <li>org.hl7.fhir.instance.model.api.IBaseResource - The previous contents of the resource</li>
* <li>org.hl7.fhir.instance.model.api.IBaseResource - The proposed new new contents of the resource</li>
* <li>org.hl7.fhir.instance.model.api.IBaseResource - The proposed new contents of the resource</li>
* <li>
* ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
@ -1463,6 +1470,9 @@ public enum Pointcut implements IPointcut {
* <li>
* ca.uhn.fhir.rest.api.server.storage.TransactionDetails - The outer transaction details object (since 5.0.0)
* </li>
* <li>
* ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum - The timing at which the invocation of the interceptor took place. Options are ACTIVE and DEFERRED.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
@ -1473,7 +1483,8 @@ public enum Pointcut implements IPointcut {
"org.hl7.fhir.instance.model.api.IBaseResource",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails"
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails",
"ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum"
),
@ -1503,6 +1514,9 @@ public enum Pointcut implements IPointcut {
* <li>
* ca.uhn.fhir.rest.api.server.storage.TransactionDetails - The outer transaction details object (since 5.0.0)
* </li>
* <li>
* ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum - The timing at which the invocation of the interceptor took place. Options are ACTIVE and DEFERRED.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
@ -1512,9 +1526,53 @@ public enum Pointcut implements IPointcut {
"org.hl7.fhir.instance.model.api.IBaseResource",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails",
"ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum"
),
/**
* <b>Storage Hook:</b>
* Invoked after all entries in a transaction bundle have been executed
* <p>
* Hooks will have access to the original bundle, as well as all the deferred interceptor broadcasts related to the
* processing of the transaction bundle
* </p>
* Hooks may accept the following parameters:
* <ul>
* <li>org.hl7.fhir.instance.model.api.IBaseResource - The resource being deleted</li>
* <li>
* ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. Note that the bean
* properties are not all guaranteed to be populated, depending on how early during processing the
* exception occurred.
* </li>
* <li>
* ca.uhn.fhir.rest.server.servlet.ServletRequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* ca.uhn.fhir.rest.api.server.storage.TransactionDetails - The outer transaction details object (since 5.0.0)
* </li>
* <li>
* ca.uhn.fhir.rest.api.server.storage.DeferredInterceptorBroadcasts- A collection of pointcut invocations and their parameters which were deferred.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
STORAGE_TRANSACTION_PROCESSED(void.class,
"org.hl7.fhir.instance.model.api.IBaseBundle",
"ca.uhn.fhir.rest.api.server.storage.DeferredInterceptorBroadcasts",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails"
),
/**
* <b>Storage Hook:</b>
* Invoked when a resource delete operation is about to fail due to referential integrity checks. Intended for use with {@literal ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor}.

30
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/InterceptorInvocationTimingEnum.java Normal file
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@ -0,0 +1,30 @@
package ca.uhn.fhir.rest.api;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/**
* during invocation of certain pointcuts, it is important to know whether they are being executed in
* active or deferred fashion. This enum allows the pointcuts to see how they were invoked.
*/
public enum InterceptorInvocationTimingEnum {
ACTIVE,
DEFERRED
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleBuilder.java
View File

@ -403,7 +403,6 @@ public class BundleBuilder {
public void conditional(String theConditionalUrl) {
myUrl.setValueAsString(theConditionalUrl);
}
}
public class CreateBuilder {

313
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
View File

@ -1,6 +1,10 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.context.*;
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.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -9,15 +13,23 @@ import ca.uhn.fhir.util.bundle.BundleEntryParts;
import ca.uhn.fhir.util.bundle.EntryListAccumulator;
import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.*;
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.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
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.isNotBlank;
/*
* #%L
* HAPI FHIR - Core Library
@ -42,6 +54,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* Fetch resources from a bundle
*/
public class BundleUtil {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BundleUtil.class);
/**
* @return Returns <code>null</code> if the link isn't found or has no value
@ -170,16 +184,200 @@ public class BundleUtil {
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<BundleEntryParts, IBase> partsToIBaseMap = getPartsToIBaseMap(theContext, theBundle);
LinkedHashSet<IBase> retVal = new LinkedHashSet<>();
//Get all deletions.
LinkedHashSet<IBase> deleteParts = sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.DELETE, partsToIBaseMap);
validatePartsNotNull(deleteParts);
retVal.addAll(deleteParts);
//Get all Creations
LinkedHashSet<IBase> createParts= sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.POST, partsToIBaseMap);
validatePartsNotNull(createParts);
retVal.addAll(createParts);
// Get all Updates
LinkedHashSet<IBase> 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, "entry", theBundle);
TerserUtil.setField(theContext, "entry", theBundle, retVal.toArray(new IBase[0]));
}
private static void validatePartsNotNull(LinkedHashSet<IBase> theDeleteParts) {
if (theDeleteParts == null) {
throw new IllegalStateException("This transaction contains a cycle, so it cannot be sorted.");
}
}
private static LinkedHashSet<IBase> sortEntriesOfTypeIntoProcessingOrder(FhirContext theContext, RequestTypeEnum theRequestTypeEnum, Map<BundleEntryParts, IBase> thePartsToIBaseMap) {
SortLegality legality = new SortLegality();
HashMap<String, Integer> color = new HashMap<>();
HashMap<String, List<String>> adjList = new HashMap<>();
List<String> topologicalOrder = new ArrayList<>();
Set<BundleEntryParts> bundleEntryParts = thePartsToIBaseMap.keySet().stream().filter(part -> part.getRequestType().equals(theRequestTypeEnum)).collect(Collectors.toSet());
HashMap<String, BundleEntryParts> 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<ResourceReferenceInfo> 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<String, Integer> 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<IBase> 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<String, Integer> theResourceIdToColor, HashMap<String, List<String>> theAdjList, List<String> 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<BundleEntryParts, IBase> getPartsToIBaseMap(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List<IBase> 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<BundleEntryParts, IBase> 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;
}
/**
* 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<ModifiableBundleEntry> theProcessor) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List<IBase> 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");
@ -188,57 +386,62 @@ public class BundleUtil {
BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
for (IBase nextEntry : entries) {
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:
conditionalUrl = url != null && url.contains("?") ? url : null;
break;
case POST:
List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
if (ifNoneExistReps.size() > 0) {
IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
conditionalUrl = ifNoneExist.getValueAsString();
}
break;
}
}
}
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(new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl), mutator);
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:
conditionalUrl = url != null && url.contains("?") ? url : null;
break;
case POST:
List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
if (ifNoneExistReps.size() > 0) {
IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
conditionalUrl = ifNoneExist.getValueAsString();
}
break;
}
}
}
BundleEntryParts parts = new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl);
return parts;
}
/**
* Extract all of the resources from a given bundle
*/
@ -290,4 +493,20 @@ public class BundleUtil {
}
return isPatch;
}
private static class SortLegality {
private boolean myIsLegal;
SortLegality() {
this.myIsLegal = true;
}
private void setLegal(boolean theLegal) {
myIsLegal = theLegal;
}
public boolean isLegal() {
return myIsLegal;
}
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/bundle/BundleEntryParts.java
View File

@ -58,5 +58,4 @@ public class BundleEntryParts {
public String getUrl() {
return myUrl;
}
}

4
hapi-fhir-base/src/test/java/ca/uhn/fhir/interceptor/executor/InterceptorServiceTest.java
View File

@ -455,11 +455,12 @@ public class InterceptorServiceTest {
params.add(String.class, "D");
params.add(String.class, "E");
params.add(String.class, "F");
params.add(String.class, "G");
try {
svc.haveAppropriateParams(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, params);
fail();
} catch (IllegalArgumentException e) {
assertEquals("Wrong number of params for pointcut STORAGE_PRECOMMIT_RESOURCE_UPDATED - Wanted ca.uhn.fhir.rest.api.server.RequestDetails,ca.uhn.fhir.rest.api.server.storage.TransactionDetails,ca.uhn.fhir.rest.server.servlet.ServletRequestDetails,org.hl7.fhir.instance.model.api.IBaseResource,org.hl7.fhir.instance.model.api.IBaseResource but found [String, String, String, String, String, String]", e.getMessage());
assertEquals("Wrong number of params for pointcut STORAGE_PRECOMMIT_RESOURCE_UPDATED - Wanted ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum,ca.uhn.fhir.rest.api.server.RequestDetails,ca.uhn.fhir.rest.api.server.storage.TransactionDetails,ca.uhn.fhir.rest.server.servlet.ServletRequestDetails,org.hl7.fhir.instance.model.api.IBaseResource,org.hl7.fhir.instance.model.api.IBaseResource but found [String, String, String, String, String, String, String]", e.getMessage());
}
}
@ -474,6 +475,7 @@ public class InterceptorServiceTest {
params.add((Class) String.class, 3);
params.add((Class) String.class, 4);
params.add((Class) String.class, 5);
params.add((Class) String.class, 6);
try {
svc.haveAppropriateParams(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, params);
fail();

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2526-add-operation-section-to-conformance-statement.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2526
title: "Added Operation section to Conformance Statement."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2534-new-pointcut.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
issue: 2534
title: "Add new pointcut `STORAGE_TRANSACTION_PROCESSED`, which fires after all operations in a transaction have executed."

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -70,6 +70,7 @@ import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
@ -1364,7 +1365,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
.add(IBaseResource.class, theResource)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, hookParams);
}

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -54,6 +54,7 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@ -376,7 +377,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
.add(IBaseResource.class, theResource)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, theTransactionDetails);
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, hookParams);
}
@ -483,13 +485,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED));
if (theTransactionDetails.isAcceptingDeferredInterceptorBroadcasts()) {
theTransactionDetails.addDeferredInterceptorBroadcast(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
} else {
doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, resourceToDelete).setCreated(true);
@ -597,7 +597,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, transactionDetails);
.add(TransactionDetails.class, transactionDetails)
.add(InterceptorInvocationTimingEnum.class, transactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED));
doCallHooks(transactionDetails, theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
});
@ -681,16 +682,24 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
myEntityManager.merge(theEntity);
// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
// Interceptor call: STORAGE_PRESTORAGE_RESOURCE_UPDATED
IBaseResource newVersion = toResource(theEntity, false);
HookParams params = new HookParams()
HookParams preStorageParams = new HookParams()
.add(IBaseResource.class, oldVersion)
.add(IBaseResource.class, newVersion)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, params);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, params);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, preStorageParams);
// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
HookParams preCommitParams = new HookParams()
.add(IBaseResource.class, oldVersion)
.add(IBaseResource.class, newVersion)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED));
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, preCommitParams);
}
@ -720,14 +729,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
IBaseResource newVersion = toResource(theEntity, false);
HookParams params = new HookParams()
HookParams preStorageParams = new HookParams()
.add(IBaseResource.class, oldVersion)
.add(IBaseResource.class, newVersion)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, params);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, params);
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, preStorageParams);
HookParams preCommitParams = new HookParams()
.add(IBaseResource.class, oldVersion)
.add(IBaseResource.class, newVersion)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED));
myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, preCommitParams);
}

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -49,6 +49,7 @@ import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.PreferReturnEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.DeferredInterceptorBroadcasts;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.ParameterUtil;
@ -1005,25 +1006,16 @@ public abstract class BaseTransactionProcessor {
flushSession(theIdToPersistedOutcome);
theTransactionStopWatch.endCurrentTask();
if (conditionalRequestUrls.size() > 0) {
theTransactionStopWatch.startTask("Check for conflicts in conditional resources");
}
/*
* Double check we didn't allow any duplicates we shouldn't have
*/
for (Map.Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
String matchUrl = nextEntry.getKey();
Class<? extends IBaseResource> resType = nextEntry.getValue();
if (isNotBlank(matchUrl)) {
Set<ResourcePersistentId> val = myMatchResourceUrlService.processMatchUrl(matchUrl, resType, theRequest);
if (val.size() > 1) {
throw new InvalidRequestException(
"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
}
}
if (conditionalRequestUrls.size() > 0) {
theTransactionStopWatch.startTask("Check for conflicts in conditional resources");
}
validateNoDuplicates(theRequest, theActionName, conditionalRequestUrls);
theTransactionStopWatch.endCurrentTask();
for (IIdType next : theAllIds) {
@ -1044,6 +1036,19 @@ public abstract class BaseTransactionProcessor {
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, nextPointcut, nextParams);
}
DeferredInterceptorBroadcasts deferredInterceptorBroadcasts = new DeferredInterceptorBroadcasts(deferredBroadcastEvents);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(DeferredInterceptorBroadcasts.class, deferredInterceptorBroadcasts)
.add(TransactionDetails.class, theTransactionDetails)
.add(IBaseBundle.class, theResponse);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_TRANSACTION_PROCESSED, params);
theTransactionDetails.deferredBroadcastProcessingFinished();
//finishedCallingDeferredInterceptorBroadcasts
return entriesToProcess;
} finally {
@ -1053,6 +1058,20 @@ public abstract class BaseTransactionProcessor {
}
}
private void validateNoDuplicates(RequestDetails theRequest, String theActionName, Map<String, Class<? extends IBaseResource>> conditionalRequestUrls) {
for (Map.Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
String matchUrl = nextEntry.getKey();
Class<? extends IBaseResource> resType = nextEntry.getValue();
if (isNotBlank(matchUrl)) {
Set<ResourcePersistentId> val = myMatchResourceUrlService.processMatchUrl(matchUrl, resType, theRequest);
if (val.size() > 1) {
throw new InvalidRequestException(
"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
}
}
}
}
protected abstract void flushSession(Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome);
private void validateResourcePresent(IBaseResource theResource, Integer theOrder, String theVerb) {

257
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/TransactionHookTest.java Normal file
View File

@ -0,0 +1,257 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.server.storage.DeferredInterceptorBroadcasts;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.test.concurrency.PointcutLatch;
import com.google.common.collect.ListMultimap;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.matchesPattern;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.DELETE;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class TransactionHookTest extends BaseJpaR4SystemTest {
@AfterEach
public void after() {
myDaoConfig.setEnforceReferentialIntegrityOnDelete(true);
}
PointcutLatch myPointcutLatch = new PointcutLatch(Pointcut.STORAGE_TRANSACTION_PROCESSED);
@Autowired
private IInterceptorService myInterceptorService;
@BeforeEach
public void beforeEach() {
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_TRANSACTION_PROCESSED, myPointcutLatch);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, myPointcutLatch);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, myPointcutLatch);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, myPointcutLatch);
}
@Test
public void testHookShouldContainParamsForAllCreateUpdateDeleteInvocations() throws InterruptedException {
String urnReference = "urn:uuid:3bc44de3-069d-442d-829b-f3ef68cae371";
final Observation obsToDelete = new Observation();
obsToDelete.setStatus(Observation.ObservationStatus.FINAL);
DaoMethodOutcome daoMethodOutcome = myObservationDao.create(obsToDelete);
Patient pat1 = new Patient();
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setSubject(new Reference(urnReference));
Bundle b = new Bundle();
Bundle.BundleEntryComponent bundleEntryComponent = b.addEntry();
bundleEntryComponent.setResource(obs1);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
Bundle.BundleEntryComponent patientComponent = b.addEntry();
patientComponent.setFullUrl(urnReference);
patientComponent.setResource(pat1);
patientComponent.getRequest().setMethod(POST).setUrl("Patient");
//Delete an observation
b.addEntry().getRequest().setMethod(DELETE).setUrl(daoMethodOutcome.getId().toUnqualifiedVersionless().getValue());
myPointcutLatch.setExpectedCount(4);
mySystemDao.transaction(mySrd, b);
List<HookParams> hookParams = myPointcutLatch.awaitExpected();
DeferredInterceptorBroadcasts broadcastsParam = hookParams.get(3).get(DeferredInterceptorBroadcasts.class);
ListMultimap<Pointcut, HookParams> deferredInterceptorBroadcasts = broadcastsParam.getDeferredInterceptorBroadcasts();
assertThat(deferredInterceptorBroadcasts.entries(), hasSize(3));
List<HookParams> createPointcutInvocations = deferredInterceptorBroadcasts.get(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED);
assertThat(createPointcutInvocations, hasSize(2));
IBaseResource firstCreatedResource = createPointcutInvocations.get(0).get(IBaseResource.class);
InterceptorInvocationTimingEnum timing = createPointcutInvocations.get(0).get(InterceptorInvocationTimingEnum.class);
assertTrue(firstCreatedResource instanceof Observation);
assertTrue(timing.equals(InterceptorInvocationTimingEnum.DEFERRED));
IBaseResource secondCreatedResource = createPointcutInvocations.get(1).get(IBaseResource.class);
timing = createPointcutInvocations.get(1).get(InterceptorInvocationTimingEnum.class);
assertTrue(secondCreatedResource instanceof Patient);
assertTrue(timing.equals(InterceptorInvocationTimingEnum.DEFERRED));
assertThat(deferredInterceptorBroadcasts.get(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED), hasSize(1));
}
@Test
public void testDeleteInTransactionShouldSucceedWhenReferencesAreAlsoRemoved() {
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs1id = myObservationDao.create(obs1).getId().toUnqualifiedVersionless();
final Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs2id = myObservationDao.create(obs2).getId().toUnqualifiedVersionless();
final DiagnosticReport rpt = new DiagnosticReport();
rpt.addResult(new Reference(obs2id));
IIdType rptId = myDiagnosticReportDao.create(rpt).getId().toUnqualifiedVersionless();
myObservationDao.read(obs1id);
myObservationDao.read(obs2id);
myDiagnosticReportDao.read(rptId);
Bundle b = new Bundle();
b.addEntry().getRequest().setMethod(DELETE).setUrl(rptId.getValue());
b.addEntry().getRequest().setMethod(DELETE).setUrl(obs2id.getValue());
try {
// transaction should succeed because the DiagnosticReport which references obs2 is also deleted
mySystemDao.transaction(mySrd, b);
} catch (ResourceVersionConflictException e) {
fail();
}
}
@Test
public void testDeleteWithHas_SourceModifiedToNoLongerIncludeReference() {
Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs1id = myObservationDao.create(obs1).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs2id = myObservationDao.create(obs2).getId().toUnqualifiedVersionless();
DiagnosticReport rpt = new DiagnosticReport();
rpt.addIdentifier().setSystem("foo").setValue("IDENTIFIER");
rpt.addResult(new Reference(obs2id));
IIdType rptId = myDiagnosticReportDao.create(rpt).getId().toUnqualifiedVersionless();
myObservationDao.read(obs1id);
myObservationDao.read(obs2id);
rpt = new DiagnosticReport();
rpt.addIdentifier().setSystem("foo").setValue("IDENTIFIER");
Bundle b = new Bundle();
b.addEntry().getRequest().setMethod(DELETE).setUrl("Observation?_has:DiagnosticReport:result:identifier=foo|IDENTIFIER");
b.addEntry().setResource(rpt).getRequest().setMethod(PUT).setUrl("DiagnosticReport?identifier=foo|IDENTIFIER");
mySystemDao.transaction(mySrd, b);
myObservationDao.read(obs1id);
try {
myObservationDao.read(obs2id);
fail();
} catch (ResourceGoneException e) {
// good
}
rpt = myDiagnosticReportDao.read(rptId);
assertThat(rpt.getResult(), empty());
}
@Test
public void testDeleteWithId_SourceModifiedToNoLongerIncludeReference() {
Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs1id = myObservationDao.create(obs1).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs2id = myObservationDao.create(obs2).getId().toUnqualifiedVersionless();
DiagnosticReport rpt = new DiagnosticReport();
rpt.addResult(new Reference(obs1id));
IIdType rptId = myDiagnosticReportDao.create(rpt).getId().toUnqualifiedVersionless();
myObservationDao.read(obs1id);
myObservationDao.read(obs2id);
rpt = new DiagnosticReport();
rpt.addResult(new Reference(obs2id));
Bundle b = new Bundle();
b.addEntry().getRequest().setMethod(DELETE).setUrl(obs1id.getValue());
b.addEntry().setResource(rpt).getRequest().setMethod(PUT).setUrl(rptId.getValue());
mySystemDao.transaction(mySrd, b);
myObservationDao.read(obs2id);
myDiagnosticReportDao.read(rptId);
try {
myObservationDao.read(obs1id);
fail();
} catch (ResourceGoneException e) {
// good
}
}
@Test
public void testDeleteWithHas_SourceModifiedToStillIncludeReference() {
Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs1id = myObservationDao.create(obs1).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
IIdType obs2id = myObservationDao.create(obs2).getId().toUnqualifiedVersionless();
DiagnosticReport rpt = new DiagnosticReport();
rpt.addIdentifier().setSystem("foo").setValue("IDENTIFIER");
rpt.addResult(new Reference(obs2id));
IIdType rptId = myDiagnosticReportDao.create(rpt).getId().toUnqualifiedVersionless();
myObservationDao.read(obs1id);
myObservationDao.read(obs2id);
rpt = new DiagnosticReport();
rpt.addIdentifier().setSystem("foo").setValue("IDENTIFIER");
rpt.addResult(new Reference(obs2id));
Bundle b = new Bundle();
b.addEntry().getRequest().setMethod(DELETE).setUrl("Observation?_has:DiagnosticReport:result:identifier=foo|IDENTIFIER");
b.addEntry().setResource(rpt).getRequest().setMethod(PUT).setUrl("DiagnosticReport?identifier=foo|IDENTIFIER");
try {
mySystemDao.transaction(mySrd, b);
fail();
} catch (ResourceVersionConflictException e ) {
assertThat(e.getMessage(), matchesPattern("Unable to delete Observation/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource DiagnosticReport/[0-9]+ in path DiagnosticReport.result"));
}
myObservationDao.read(obs1id);
myObservationDao.read(obs2id);
myDiagnosticReportDao.read(rptId);
}
}

38
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/DeferredInterceptorBroadcasts.java Normal file
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@ -0,0 +1,38 @@
package ca.uhn.fhir.rest.api.server.storage;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.Pointcut;
import com.google.common.collect.ListMultimap;
public class DeferredInterceptorBroadcasts {
ListMultimap<Pointcut, HookParams> myDeferredInterceptorBroadcasts;
public DeferredInterceptorBroadcasts(ListMultimap<Pointcut, HookParams> theDeferredInterceptorBroadcasts) {
myDeferredInterceptorBroadcasts = theDeferredInterceptorBroadcasts;
}
public ListMultimap<Pointcut, HookParams> getDeferredInterceptorBroadcasts() {
return myDeferredInterceptorBroadcasts;
}
}

16
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/TransactionDetails.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.rest.api.server.storage;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.commons.lang3.Validate;
@ -32,6 +33,7 @@ import java.util.Collections;
import java.util.Date;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Supplier;
@ -53,6 +55,7 @@ public class TransactionDetails {
private Map<String, Object> myUserData;
private ListMultimap<Pointcut, HookParams> myDeferredInterceptorBroadcasts;
private EnumSet<Pointcut> myDeferredInterceptorBroadcastPointcuts;
private boolean myIsPointcutDeferred;
/**
* Constructor
@ -189,7 +192,20 @@ public class TransactionDetails {
*/
public void addDeferredInterceptorBroadcast(Pointcut thePointcut, HookParams theHookParams) {
Validate.isTrue(isAcceptingDeferredInterceptorBroadcasts(thePointcut));
myIsPointcutDeferred = true;
myDeferredInterceptorBroadcasts.put(thePointcut, theHookParams);
}
public InterceptorInvocationTimingEnum getInvocationTiming(Pointcut thePointcut) {
if (myDeferredInterceptorBroadcasts == null) {
return InterceptorInvocationTimingEnum.ACTIVE;
}
List<HookParams> hookParams = myDeferredInterceptorBroadcasts.get(thePointcut);
return hookParams == null ? InterceptorInvocationTimingEnum.ACTIVE : InterceptorInvocationTimingEnum.DEFERRED;
}
public void deferredBroadcastProcessingFinished() {
myIsPointcutDeferred = false;
}
}

3
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceMessage.java
View File

@ -160,6 +160,7 @@ public abstract class BaseResourceMessage implements IResourceMessage, IModelJso
CREATE,
UPDATE,
DELETE,
MANUALLY_TRIGGERED
MANUALLY_TRIGGERED,
TRANSACTION
}
}

30
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/HashMapResourceProvider.java
View File

@ -39,6 +39,7 @@ import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
@ -387,25 +388,42 @@ public class HashMapResourceProvider<T extends IBaseResource> implements IResour
if (!myIdToHistory.containsKey(theIdPart)) {
// Interceptor call: STORAGE_PRESTORAGE_RESOURCE_CREATED
HookParams params = new HookParams()
HookParams preStorageParams = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(IBaseResource.class, theResource)
.add(TransactionDetails.class, theTransactionDetails);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, params);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, params);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, preStorageParams);
// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_CREATED
HookParams preCommitParams = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(IBaseResource.class, theResource)
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, preCommitParams);
} else {
// Interceptor call: STORAGE_PRESTORAGE_RESOURCE_UPDATED
HookParams params = new HookParams()
HookParams preStorageParams = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(IBaseResource.class, myIdToHistory.get(theIdPart).getFirst())
.add(IBaseResource.class, theResource)
.add(TransactionDetails.class, theTransactionDetails);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, params);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, params);
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, preStorageParams);
// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
HookParams preCommitParams = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(IBaseResource.class, myIdToHistory.get(theIdPart).getFirst())
.add(IBaseResource.class, theResource)
.add(TransactionDetails.class, theTransactionDetails)
.add(InterceptorInvocationTimingEnum.class, theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
interceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, preCommitParams);
}
}

236
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/bundle/BundleUtilTest.java
View File

@ -1,17 +1,35 @@
package ca.uhn.fhir.util.bundle;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import java.util.Collections;
import java.util.List;
import java.util.function.Consumer;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.DELETE;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.GET;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST;
import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class BundleUtilTest {
@ -87,6 +105,224 @@ public class BundleUtilTest {
assertEquals("Observation?foo=bar", bundle.getEntryFirstRep().getRequest().getUrl());
}
@Test
public void testTopologicalTransactionSortForCreates() {
Bundle b = new Bundle();
Bundle.BundleEntryComponent bundleEntryComponent = b.addEntry();
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setSubject(new Reference("Patient/P1"));
obs1.setValue(new Quantity(4));
obs1.setId("Observation/O1");
bundleEntryComponent.setResource(obs1);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
bundleEntryComponent = b.addEntry();
final Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
obs2.setValue(new Quantity(4));
obs2.setId("Observation/O2");
bundleEntryComponent.setResource(obs2);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
Bundle.BundleEntryComponent patientComponent = b.addEntry();
Patient pat1 = new Patient();
pat1.setId("Patient/P1");
pat1.setManagingOrganization(new Reference("Organization/Org1"));
patientComponent.setResource(pat1);
patientComponent.getRequest().setMethod(POST).setUrl("Patient");
Bundle.BundleEntryComponent organizationComponent = b.addEntry();
Organization org1 = new Organization();
org1.setId("Organization/Org1");
organizationComponent.setResource(org1);
organizationComponent.getRequest().setMethod(POST).setUrl("Patient");
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, b);
assertThat(b.getEntry(), hasSize(4));
List<Bundle.BundleEntryComponent> entry = b.getEntry();
int observationIndex = getIndexOfEntryWithId("Observation/O1", b);
int patientIndex = getIndexOfEntryWithId("Patient/P1", b);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", b);
assertTrue(organizationIndex < patientIndex);
assertTrue(patientIndex < observationIndex);
}
@Test
public void testTransactionSorterFailsOnCyclicReference() {
Bundle b = new Bundle();
Bundle.BundleEntryComponent bundleEntryComponent = b.addEntry();
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setSubject(new Reference("Patient/P1"));
obs1.setValue(new Quantity(4));
obs1.setId("Observation/O1/_history/1");
obs1.setHasMember(Collections.singletonList(new Reference("Observation/O2")));
bundleEntryComponent.setResource(obs1);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
bundleEntryComponent = b.addEntry();
final Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
obs2.setValue(new Quantity(4));
obs2.setId("Observation/O2/_history/1");
//We use a random history version here to ensure cycles are counted without versions.
obs2.setHasMember(Collections.singletonList(new Reference("Observation/O1/_history/300")));
bundleEntryComponent.setResource(obs2);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
try {
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, b);
fail();
} catch (IllegalStateException e ) {
}
}
@Test
public void testTransactionSortingReturnsOperationsInCorrectOrder() {
Bundle b = new Bundle();
//UPDATE patient
Bundle.BundleEntryComponent patientUpdateComponent= b.addEntry();
final Patient p2 = new Patient();
p2.setId("Patient/P2");
p2.getNameFirstRep().setFamily("Test!");
patientUpdateComponent.setResource(p2);
patientUpdateComponent.getRequest().setMethod(PUT).setUrl("Patient/P2");
//CREATE observation
Bundle.BundleEntryComponent bundleEntryComponent = b.addEntry();
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setSubject(new Reference("Patient/P1"));
obs1.setValue(new Quantity(4));
obs1.setId("Observation/O1");
bundleEntryComponent.setResource(obs1);
bundleEntryComponent.getRequest().setMethod(POST).setUrl("Observation");
//DELETE medication
Bundle.BundleEntryComponent medicationComponent= b.addEntry();
final Medication med1 = new Medication();
med1.setId("Medication/M1");
medicationComponent.setResource(med1);
medicationComponent.getRequest().setMethod(DELETE).setUrl("Medication");
//GET medication
Bundle.BundleEntryComponent searchComponent = b.addEntry();
searchComponent.getRequest().setMethod(GET).setUrl("Medication?code=123");
//CREATE patient
Bundle.BundleEntryComponent patientComponent = b.addEntry();
Patient pat1 = new Patient();
pat1.setId("Patient/P1");
pat1.setManagingOrganization(new Reference("Organization/Org1"));
patientComponent.setResource(pat1);
patientComponent.getRequest().setMethod(POST).setUrl("Patient");
//CREATE organization
Bundle.BundleEntryComponent organizationComponent = b.addEntry();
Organization org1 = new Organization();
org1.setId("Organization/Org1");
organizationComponent.setResource(org1);
organizationComponent.getRequest().setMethod(POST).setUrl("Organization");
//DELETE ExplanationOfBenefit
Bundle.BundleEntryComponent explanationOfBenefitComponent= b.addEntry();
final ExplanationOfBenefit eob1 = new ExplanationOfBenefit();
eob1.setId("ExplanationOfBenefit/E1");
explanationOfBenefitComponent.setResource(eob1);
explanationOfBenefitComponent.getRequest().setMethod(DELETE).setUrl("ExplanationOfBenefit");
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, b);
assertThat(b.getEntry(), hasSize(7));
List<Bundle.BundleEntryComponent> entry = b.getEntry();
// DELETEs first
assertThat(entry.get(0).getRequest().getMethod(), is(equalTo(DELETE)));
assertThat(entry.get(1).getRequest().getMethod(), is(equalTo(DELETE)));
// Then POSTs
assertThat(entry.get(2).getRequest().getMethod(), is(equalTo(POST)));
assertThat(entry.get(3).getRequest().getMethod(), is(equalTo(POST)));
assertThat(entry.get(4).getRequest().getMethod(), is(equalTo(POST)));
// Then PUTs
assertThat(entry.get(5).getRequest().getMethod(), is(equalTo(PUT)));
// Then GETs
assertThat(entry.get(6).getRequest().getMethod(), is(equalTo(GET)));
}
@Test
public void testBundleSortsCanHandlesDeletesThatContainNoResources() {
Patient p = new Patient();
p.setId("Patient/123");
BundleBuilder builder = new BundleBuilder(ourCtx);
builder.addTransactionDeleteEntry(p);
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, builder.getBundle());
}
@Test
public void testTransactionSorterReturnsDeletesInCorrectProcessingOrder() {
Bundle b = new Bundle();
Bundle.BundleEntryComponent bundleEntryComponent = b.addEntry();
final Observation obs1 = new Observation();
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setSubject(new Reference("Patient/P1"));
obs1.setValue(new Quantity(4));
obs1.setId("Observation/O1");
bundleEntryComponent.setResource(obs1);
bundleEntryComponent.getRequest().setMethod(DELETE).setUrl("Observation");
bundleEntryComponent = b.addEntry();
final Observation obs2 = new Observation();
obs2.setStatus(Observation.ObservationStatus.FINAL);
obs2.setValue(new Quantity(4));
obs2.setId("Observation/O2");
bundleEntryComponent.setResource(obs2);
bundleEntryComponent.getRequest().setMethod(DELETE).setUrl("Observation");
Bundle.BundleEntryComponent patientComponent = b.addEntry();
Patient pat1 = new Patient();
pat1.setId("Patient/P1");
pat1.setManagingOrganization(new Reference("Organization/Org1"));
patientComponent.setResource(pat1);
patientComponent.getRequest().setMethod(DELETE).setUrl("Patient");
Bundle.BundleEntryComponent organizationComponent = b.addEntry();
Organization org1 = new Organization();
org1.setId("Organization/Org1");
organizationComponent.setResource(org1);
organizationComponent.getRequest().setMethod(DELETE).setUrl("Organization");
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, b);
assertThat(b.getEntry(), hasSize(4));
int observationIndex = getIndexOfEntryWithId("Observation/O1", b);
int patientIndex = getIndexOfEntryWithId("Patient/P1", b);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", b);
assertTrue(patientIndex < organizationIndex);
assertTrue(observationIndex < patientIndex);
}
private int getIndexOfEntryWithId(String theResourceId, Bundle theBundle) {
List<Bundle.BundleEntryComponent> entries = theBundle.getEntry();
for (int i = 0; i < entries.size(); i++) {
String id = entries.get(i).getResource().getIdElement().toUnqualifiedVersionless().toString();
if (id.equals(theResourceId)) {
return i;
}
}
fail("Didn't find resource with ID " + theResourceId);
return -1;
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

7
hapi-fhir-validation/pom.xml
View File

@ -284,7 +284,6 @@
<artifactId>spring-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
@ -295,6 +294,12 @@
<artifactId>jena-arq</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<version>5.4.0-PRE8-SNAPSHOT</version>
<scope>test</scope>
</dependency>
</dependencies>

171
hapi-fhir-validation/src/test/java/ca/uhn/fhir/rest/server/ServerCapabilityStatementProviderR4Test.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
@ -46,7 +47,6 @@ import ca.uhn.fhir.rest.server.provider.HashMapResourceProvider;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.rest.server.provider.ServerCapabilityStatementProvider;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.server.MockServletUtil;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
@ -71,6 +71,7 @@ import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.OperationDefinition;
@ -85,14 +86,17 @@ import org.junit.jupiter.api.Test;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.test.utilities.server.MockServletUtil.createServletConfig;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
@ -118,6 +122,19 @@ public class ServerCapabilityStatementProviderR4Test {
private final FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
private FhirValidator myValidator;
private static Set<String> toStrings(Collection<? extends IPrimitiveType> theType) {
HashSet<String> retVal = new HashSet<String>();
for (IPrimitiveType next : theType) {
retVal.add(next.getValueAsString());
}
return retVal;
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeEach
public void before() {
myValidator = myCtx.newValidator();
@ -154,7 +171,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement cs = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
List<String> formats = cs
@ -172,7 +189,6 @@ public class ServerCapabilityStatementProviderR4Test {
));
}
@Test
public void testConditionalOperations() throws Exception {
@ -182,7 +198,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = myCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
@ -214,7 +230,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -243,7 +259,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
OperationDefinition opDef = (OperationDefinition) sc.readOperationDefinition(new IdType("OperationDefinition/Patient-i-everything"), createRequestDetails(rs));
validate(opDef);
@ -264,7 +280,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = validate(conformance);
@ -282,7 +298,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
boolean found = false;
Collection<ResourceBinding> resourceBindings = rs.getResourceBindings();
@ -314,7 +330,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -327,7 +343,6 @@ public class ServerCapabilityStatementProviderR4Test {
assertNull(res.getConditionalUpdateElement().getValue());
}
@Test
public void testOperationParameterDocumentation() throws Exception {
RestfulServer rs = new RestfulServer(myCtx);
@ -337,7 +352,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -362,7 +377,6 @@ public class ServerCapabilityStatementProviderR4Test {
assertEquals("2002", exampleExtensions.get(1).getValueAsPrimitive().getValueAsString());
}
/**
* See #379
*/
@ -375,7 +389,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -431,7 +445,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -451,7 +465,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -480,7 +494,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = validate(conformance);
@ -498,7 +512,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = myCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
@ -518,7 +532,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
boolean found = false;
Collection<ResourceBinding> resourceBindings = rs.getResourceBindings();
@ -545,7 +559,6 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Test
public void testFormatIncludesSpecialNonMediaTypeFormats() throws ServletException {
RestfulServer rs = new RestfulServer(myCtx);
@ -554,7 +567,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement serverConformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
List<String> formatCodes = serverConformance.getFormat().stream().map(c -> c.getCode()).collect(Collectors.toList());
@ -577,7 +590,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
boolean found = false;
Collection<ResourceBinding> resourceBindings = rs.getResourceBindings();
@ -609,7 +622,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
boolean found = false;
Collection<ResourceBinding> resourceBindings = rs.getResourceBindings();
@ -649,7 +662,7 @@ public class ServerCapabilityStatementProviderR4Test {
rsNoType.registerProvider(new SearchProviderWithListNoType());
ServerCapabilityStatementProvider scNoType = new ServerCapabilityStatementProvider(rsNoType);
rsNoType.setServerConformanceProvider(scNoType);
rsNoType.init(MockServletUtil.createServletConfig());
rsNoType.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) scNoType.getServerConformance(createHttpServletRequest(), createRequestDetails(rsNoType));
conformance.setId("");
@ -666,7 +679,7 @@ public class ServerCapabilityStatementProviderR4Test {
rsWithType.registerProvider(new SearchProviderWithListWithType());
ServerCapabilityStatementProvider scWithType = new ServerCapabilityStatementProvider(rsWithType);
rsWithType.setServerConformanceProvider(scWithType);
rsWithType.init(MockServletUtil.createServletConfig());
rsWithType.init(createServletConfig());
CapabilityStatement conformanceWithType = (CapabilityStatement) scWithType.getServerConformance(createHttpServletRequest(), createRequestDetails(rsWithType));
conformanceWithType.setId("");
@ -685,7 +698,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = validate(conformance);
@ -702,7 +715,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = validate(conformance);
@ -737,7 +750,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement opDef = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -778,7 +791,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement opDef = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -818,7 +831,6 @@ public class ServerCapabilityStatementProviderR4Test {
assertTrue(operationDefinition.getInstance());
}
@Test
public void testPlainProviderGlobalSystemAndInstanceOperations() throws Exception {
@ -871,7 +883,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement opDef = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -949,7 +961,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement opDef = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -1013,7 +1025,7 @@ public class ServerCapabilityStatementProviderR4Test {
};
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement opDef = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -1034,7 +1046,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -1079,7 +1091,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
validate(conformance);
@ -1121,7 +1133,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
@ -1148,7 +1160,7 @@ public class ServerCapabilityStatementProviderR4Test {
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(myCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
@ -1198,7 +1210,7 @@ public class ServerCapabilityStatementProviderR4Test {
sc.setRestResourceRevIncludesEnabled(true);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(myCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
@ -1235,7 +1247,7 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Search
public List<Observation> search(@OptionalParam(name = "subject") ReferenceParam theSubject) {
public List<Observation> search(@OptionalParam(name = "subject") ReferenceParam theSubject) {
return Collections.emptyList();
}
@ -1248,7 +1260,7 @@ public class ServerCapabilityStatementProviderR4Test {
sc.setRestResourceRevIncludesEnabled(true);
rs.setServerConformanceProvider(sc);
rs.init(MockServletUtil.createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(myCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
@ -1260,6 +1272,27 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(toStrings(patientResource.getSearchRevInclude()), containsInAnyOrder("Observation:subject"));
}
@Test
public void testBulkDataExport() throws ServletException {
RestfulServer rs = new RestfulServer(myCtx);
rs.setResourceProviders(new BulkDataExportProvider());
rs.setServerAddressStrategy(new HardcodedServerAddressStrategy("http://localhost/baseR4"));
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider(rs);
rs.setServerConformanceProvider(sc);
rs.init(createServletConfig());
CapabilityStatement conformance = (CapabilityStatement) sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conformance));
List<CapabilityStatementRestResourceComponent> resources = conformance.getRestFirstRep().getResource();
CapabilityStatementRestResourceComponent groupResource = resources.stream()
.filter(resource -> "Group".equals(resource.getType()))
.findFirst().get();
assertThat(toOperationNames(groupResource.getOperation()),containsInAnyOrder("export", "export-poll-status"));
}
private List<String> toOperationIdParts(List<CapabilityStatementRestResourceOperationComponent> theOperation) {
ArrayList<String> retVal = Lists.newArrayList();
for (CapabilityStatementRestResourceOperationComponent next : theOperation) {
@ -1304,6 +1337,52 @@ public class ServerCapabilityStatementProviderR4Test {
return myCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(theResource);
}
public static class BulkDataExportProvider implements IResourceProvider {
@Operation(name = JpaConstants.OPERATION_EXPORT, global = false /* set to true once we can handle this */, manualResponse = true, idempotent = true)
public void export(
@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
ServletRequestDetails theRequestDetails
) {
}
@Operation(name = JpaConstants.OPERATION_EXPORT, manualResponse = true, idempotent = true, typeName = "Group")
public void groupExport(
@IdParam IIdType theIdParam,
@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
@OperationParam(name = JpaConstants.PARAM_EXPORT_MDM, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theMdm,
ServletRequestDetails theRequestDetails
) {
}
@Operation(name = JpaConstants.OPERATION_EXPORT, manualResponse = true, idempotent = true, typeName = "Patient")
public void patientExport(
@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
ServletRequestDetails theRequestDetails
) {
}
@Operation(name = JpaConstants.OPERATION_EXPORT_POLL_STATUS, manualResponse = true, idempotent = true)
public void exportPollStatus(
@OperationParam(name = JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID, typeName = "string", min = 0, max = 1) IPrimitiveType<String> theJobId,
ServletRequestDetails theRequestDetails
) throws IOException {
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return Group.class;
}
}
@SuppressWarnings("unused")
public static class ConditionalProvider implements IResourceProvider {
@ -1400,7 +1479,6 @@ public class ServerCapabilityStatementProviderR4Test {
public IBundleProvider validate(HttpServletRequest theServletRequest, @IdParam IdType theId, @ResourceParam Patient thePatient) {
return null;
}
}
@SuppressWarnings("unused")
@ -1658,17 +1736,4 @@ public class ServerCapabilityStatementProviderR4Test {
public static class PatientTripleSub extends PatientSubSub {
}
private static Set<String> toStrings(Collection<? extends IPrimitiveType> theType) {
HashSet<String> retVal = new HashSet<String>();
for (IPrimitiveType next : theType) {
retVal.add(next.getValueAsString());
}
return retVal;
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}